diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 0000000000000000000000000000000000000000..1a52bf384c81e38a291f36a0ad13191c99357ccb
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,18 @@
+on:
+ push:
+ pull_request:
+
+jobs:
+ eslint:
+ name: eslint
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v1
+ - name: install node v12
+ uses: actions/setup-node@v1
+ with:
+ node-version: 12
+ - name: yarn install
+ run: yarn install
+ - name: eslint
+ uses: icrawl/action-eslint@v1
\ No newline at end of file
diff --git a/README.md b/README.md
index 81160af21366484a03a8b104294ed8adcaf497b7..5b5ead33d2cf3cd0239daa67e14d2cc5833bc64d 100644
--- a/README.md
+++ b/README.md
@@ -89,12 +89,11 @@ and navigate to `build/viewer`
### Code generation
**CIF schemas**
-Install CIFTools `npm install ciftools -g`
- cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
- cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
- cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
- cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
+ node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
+ node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
+ node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
+ node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
**GraphQL schemas**
@@ -103,7 +102,7 @@ Install CIFTools `npm install ciftools -g`
### Other scripts
**Create chem comp bond table**
- export NODE_PATH="lib"; node --max-old-space-size=4096 lib/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
+ node --max-old-space-size=4096 lib/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
**Test model server**
@@ -119,6 +118,10 @@ Install CIFTools `npm install ciftools -g`
To see all available commands, use ``node build/model-server/preprocess -h``.
+Or
+
+ node ./lib/apps/cif2bcif
+
## Development
### Installation
diff --git a/data/cif-field-names/bird-field-names.csv b/data/cif-field-names/bird-field-names.csv
new file mode 100644
index 0000000000000000000000000000000000000000..c214ad3694cf0ce92eb573244b5a33985c576e3d
--- /dev/null
+++ b/data/cif-field-names/bird-field-names.csv
@@ -0,0 +1,88 @@
+pdbx_reference_molecule.prd_id
+pdbx_reference_molecule.name
+pdbx_reference_molecule.represent_as
+pdbx_reference_molecule.type
+pdbx_reference_molecule.type_evidence_code
+pdbx_reference_molecule.class
+pdbx_reference_molecule.class_evidence_code
+pdbx_reference_molecule.formula
+pdbx_reference_molecule.chem_comp_id
+pdbx_reference_molecule.formula_weight
+pdbx_reference_molecule.release_status
+pdbx_reference_molecule.replaces
+pdbx_reference_molecule.replaced_by
+pdbx_reference_molecule.compound_details
+pdbx_reference_molecule.description
+pdbx_reference_molecule.representative_PDB_id_code
+
+pdbx_reference_entity_list.prd_id
+pdbx_reference_entity_list.ref_entity_id
+pdbx_reference_entity_list.component_id
+pdbx_reference_entity_list.type
+pdbx_reference_entity_list.details
+
+pdbx_reference_entity_nonpoly.prd_id
+pdbx_reference_entity_nonpoly.ref_entity_id
+pdbx_reference_entity_nonpoly.name
+pdbx_reference_entity_nonpoly.chem_comp_id
+
+pdbx_reference_entity_link.prd_id
+pdbx_reference_entity_link.link_id
+pdbx_reference_entity_link.link_class
+pdbx_reference_entity_link.ref_entity_id_1
+pdbx_reference_entity_link.entity_seq_num_1
+pdbx_reference_entity_link.comp_id_1
+pdbx_reference_entity_link.atom_id_1
+pdbx_reference_entity_link.ref_entity_id_2
+pdbx_reference_entity_link.entity_seq_num_2
+pdbx_reference_entity_link.comp_id_2
+pdbx_reference_entity_link.atom_id_2
+pdbx_reference_entity_link.value_order
+pdbx_reference_entity_link.component_1
+pdbx_reference_entity_link.component_2
+pdbx_reference_entity_link.details
+
+pdbx_reference_entity_poly_link.prd_id
+pdbx_reference_entity_poly_link.ref_entity_id
+pdbx_reference_entity_poly_link.link_id
+pdbx_reference_entity_poly_link.atom_id_1
+pdbx_reference_entity_poly_link.comp_id_1
+pdbx_reference_entity_poly_link.entity_seq_num_1
+pdbx_reference_entity_poly_link.atom_id_2
+pdbx_reference_entity_poly_link.comp_id_2
+pdbx_reference_entity_poly_link.entity_seq_num_2
+pdbx_reference_entity_poly_link.value_order
+pdbx_reference_entity_poly_link.component_id
+
+pdbx_reference_entity_poly.prd_id
+pdbx_reference_entity_poly.ref_entity_id
+pdbx_reference_entity_poly.db_code
+pdbx_reference_entity_poly.db_name
+pdbx_reference_entity_poly.type
+
+pdbx_reference_entity_sequence.prd_id
+pdbx_reference_entity_sequence.ref_entity_id
+pdbx_reference_entity_sequence.type
+pdbx_reference_entity_sequence.NRP_flag
+pdbx_reference_entity_sequence.one_letter_codes
+
+pdbx_reference_entity_poly_seq.prd_id
+pdbx_reference_entity_poly_seq.ref_entity_id
+pdbx_reference_entity_poly_seq.num
+pdbx_reference_entity_poly_seq.mon_id
+pdbx_reference_entity_poly_seq.parent_mon_id
+pdbx_reference_entity_poly_seq.hetero
+pdbx_reference_entity_poly_seq.observed
+
+pdbx_reference_entity_src_nat.prd_id
+pdbx_reference_entity_src_nat.ref_entity_id
+pdbx_reference_entity_src_nat.ordinal
+pdbx_reference_entity_src_nat.taxid
+pdbx_reference_entity_src_nat.organism_scientific
+pdbx_reference_entity_src_nat.db_code
+pdbx_reference_entity_src_nat.db_name
+
+pdbx_prd_audit.prd_id
+pdbx_prd_audit.date
+pdbx_prd_audit.processing_site
+pdbx_prd_audit.action_type
\ No newline at end of file
diff --git a/data/cif-field-names/ccd-field-names.csv b/data/cif-field-names/ccd-field-names.csv
new file mode 100644
index 0000000000000000000000000000000000000000..811f7bdc5aa5865b60c24b30f86ee95d3695c66c
--- /dev/null
+++ b/data/cif-field-names/ccd-field-names.csv
@@ -0,0 +1,60 @@
+chem_comp.id
+chem_comp.name
+chem_comp.type
+chem_comp.pdbx_type
+chem_comp.formula
+chem_comp.mon_nstd_parent_comp_id
+chem_comp.pdbx_synonyms
+chem_comp.pdbx_formal_charge
+chem_comp.pdbx_initial_date
+chem_comp.pdbx_modified_date
+chem_comp.pdbx_ambiguous_flag
+chem_comp.pdbx_release_status
+chem_comp.pdbx_replaced_by
+chem_comp.pdbx_replaces
+chem_comp.formula_weight
+chem_comp.one_letter_code
+chem_comp.three_letter_code
+chem_comp.pdbx_model_coordinates_details
+chem_comp.pdbx_model_coordinates_missing_flag
+chem_comp.pdbx_ideal_coordinates_details
+chem_comp.pdbx_ideal_coordinates_missing_flag
+chem_comp.pdbx_model_coordinates_db_code
+chem_comp.pdbx_processing_site
+
+chem_comp_atom.comp_id
+chem_comp_atom.atom_id
+chem_comp_atom.alt_atom_id
+chem_comp_atom.type_symbol
+chem_comp_atom.charge
+chem_comp_atom.pdbx_align
+chem_comp_atom.pdbx_aromatic_flag
+chem_comp_atom.pdbx_leaving_atom_flag
+chem_comp_atom.pdbx_stereo_config
+chem_comp_atom.model_Cartn_x
+chem_comp_atom.model_Cartn_y
+chem_comp_atom.model_Cartn_z
+chem_comp_atom.pdbx_model_Cartn_x_ideal
+chem_comp_atom.pdbx_model_Cartn_y_ideal
+chem_comp_atom.pdbx_model_Cartn_z_ideal
+chem_comp_atom.pdbx_ordinal
+
+chem_comp_bond.comp_id
+chem_comp_bond.atom_id_1
+chem_comp_bond.atom_id_2
+chem_comp_bond.value_order
+chem_comp_bond.pdbx_aromatic_flag
+chem_comp_bond.pdbx_stereo_config
+chem_comp_bond.pdbx_ordinal
+
+pdbx_chem_comp_descriptor.comp_id
+pdbx_chem_comp_descriptor.type
+pdbx_chem_comp_descriptor.program
+pdbx_chem_comp_descriptor.program_version
+pdbx_chem_comp_descriptor.descriptor
+
+pdbx_chem_comp_identifier.comp_id
+pdbx_chem_comp_identifier.type
+pdbx_chem_comp_identifier.program
+pdbx_chem_comp_identifier.program_version
+pdbx_chem_comp_identifier.identifier
\ No newline at end of file
diff --git a/data/cif-field-names/cif-core-field-names.csv b/data/cif-field-names/cif-core-field-names.csv
new file mode 100644
index 0000000000000000000000000000000000000000..25ce0320c9e0e7c60a833309094d6a27814b7a4c
--- /dev/null
+++ b/data/cif-field-names/cif-core-field-names.csv
@@ -0,0 +1,60 @@
+audit.block_doi
+
+database_code.depnum_ccdc_archive
+
+chemical.name_systematic
+chemical.name_common
+chemical.melting_point
+
+chemical_formula.moiety
+chemical_formula.sum
+chemical_formula.weight
+
+atom_type.symbol
+atom_type.description
+
+atom_type_scat.dispersion_real
+atom_type_scat.dispersion_imag
+atom_type_scat.source
+
+space_group.crystal_system
+space_group.name_H-M_full
+space_group_symop.operation_xyz
+
+cell.length_a
+cell.length_b
+cell.length_c
+cell.angle_alpha
+cell.angle_beta
+cell.angle_gamma
+cell.volume
+cell.formula_units_Z
+
+atom_site.label
+atom_site.type_symbol
+atom_site.fract_x
+atom_site.fract_y
+atom_site.fract_z
+atom_site.U_iso_or_equiv
+atom_site.adp_type
+atom_site.occupancy
+atom_site.calc_flag
+atom_site.refinement_flags
+atom_site.disorder_assembly
+atom_site.disorder_group
+
+atom_site.site_symmetry_multiplicity
+
+atom_site_aniso.label
+atom_site_aniso.U_11
+atom_site_aniso.U_22
+atom_site_aniso.U_33
+atom_site_aniso.U_23
+atom_site_aniso.U_13
+atom_site_aniso.U_12
+
+geom_bond.atom_site_label_1
+geom_bond.atom_site_label_2
+geom_bond.distance
+geom_bond.site_symmetry_2
+geom_bond.publ_flag
\ No newline at end of file
diff --git a/data/cif-field-names/mmcif-field-names.csv b/data/cif-field-names/mmcif-field-names.csv
new file mode 100644
index 0000000000000000000000000000000000000000..825f2b931474b08d233bd113c7c5854f65b58d20
--- /dev/null
+++ b/data/cif-field-names/mmcif-field-names.csv
@@ -0,0 +1,805 @@
+atom_sites.entry_id
+atom_sites.fract_transf_matrix
+atom_sites.fract_transf_vector
+
+atom_site.group_PDB
+atom_site.id
+atom_site.type_symbol
+atom_site.label_atom_id
+atom_site.label_alt_id
+atom_site.label_comp_id
+atom_site.label_asym_id
+atom_site.label_entity_id
+atom_site.label_seq_id
+atom_site.pdbx_PDB_ins_code
+atom_site.pdbx_formal_charge
+atom_site.Cartn_x
+atom_site.Cartn_y
+atom_site.Cartn_z
+atom_site.occupancy
+atom_site.B_iso_or_equiv
+atom_site.auth_atom_id
+atom_site.auth_comp_id
+atom_site.auth_asym_id
+atom_site.auth_seq_id
+atom_site.pdbx_PDB_model_num
+atom_site.ihm_model_id
+
+atom_site_anisotrop.id
+atom_site_anisotrop.U
+atom_site_anisotrop.U_esd
+atom_site_anisotrop.pdbx_PDB_ins_code
+atom_site_anisotrop.pdbx_auth_asym_id
+atom_site_anisotrop.pdbx_auth_atom_id
+atom_site_anisotrop.pdbx_auth_comp_id
+atom_site_anisotrop.pdbx_auth_seq_id
+atom_site_anisotrop.pdbx_label_alt_id
+atom_site_anisotrop.pdbx_label_asym_id
+atom_site_anisotrop.pdbx_label_atom_id
+atom_site_anisotrop.pdbx_label_comp_id
+atom_site_anisotrop.pdbx_label_seq_id
+atom_site_anisotrop.type_symbol
+
+chem_comp.id
+chem_comp.type
+chem_comp.mon_nstd_flag
+chem_comp.name
+chem_comp.pdbx_synonyms
+chem_comp.formula
+chem_comp.formula_weight
+
+chem_comp_bond.comp_id
+chem_comp_bond.pdbx_stereo_config
+chem_comp_bond.pdbx_ordinal
+chem_comp_bond.pdbx_aromatic_flag
+chem_comp_bond.atom_id_1
+chem_comp_bond.atom_id_2
+chem_comp_bond.value_order
+
+pdbx_chem_comp_identifier.comp_id
+pdbx_chem_comp_identifier.type
+pdbx_chem_comp_identifier.program
+pdbx_chem_comp_identifier.program_version
+pdbx_chem_comp_identifier.identifier
+
+pdbx_chem_comp_related.comp_id
+pdbx_chem_comp_related.related_comp_id
+pdbx_chem_comp_related.relationship_type
+pdbx_chem_comp_related.details
+
+pdbx_chem_comp_synonyms.comp_id
+pdbx_chem_comp_synonyms.name
+pdbx_chem_comp_synonyms.provenance
+
+cell.entry_id
+cell.length_a
+cell.length_b
+cell.length_c
+cell.angle_alpha
+cell.angle_beta
+cell.angle_gamma
+cell.Z_PDB
+cell.pdbx_unique_axis
+
+pdbx_database_related.db_name
+pdbx_database_related.details
+pdbx_database_related.db_id
+pdbx_database_related.content_type
+
+pdbx_database_status.status_code
+pdbx_database_status.status_code_sf
+pdbx_database_status.status_code_mr
+pdbx_database_status.entry_id
+pdbx_database_status.recvd_initial_deposition_date
+pdbx_database_status.SG_entry
+pdbx_database_status.deposit_site
+pdbx_database_status.process_site
+pdbx_database_status.status_code_cs
+pdbx_database_status.methods_development_category
+pdbx_database_status.pdb_format_compatible
+
+entity.id
+entity.type
+entity.src_method
+entity.pdbx_description
+entity.formula_weight
+entity.pdbx_number_of_molecules
+entity.details
+entity.pdbx_mutation
+entity.pdbx_fragment
+entity.pdbx_ec
+
+entity_poly.entity_id
+entity_poly.type
+entity_poly.nstd_linkage
+entity_poly.nstd_monomer
+entity_poly.pdbx_seq_one_letter_code
+entity_poly.pdbx_seq_one_letter_code_can
+entity_poly.pdbx_strand_id
+entity_poly.pdbx_target_identifier
+
+entity_poly_seq.entity_id
+entity_poly_seq.num
+entity_poly_seq.mon_id
+entity_poly_seq.hetero
+
+entity_src_gen.entity_id
+entity_src_gen.pdbx_src_id
+entity_src_gen.pdbx_beg_seq_num
+entity_src_gen.pdbx_end_seq_num
+entity_src_gen.pdbx_gene_src_gene
+entity_src_gen.pdbx_gene_src_scientific_name
+entity_src_gen.plasmid_name
+
+entity_src_nat.entity_id
+entity_src_nat.pdbx_src_id
+entity_src_nat.pdbx_beg_seq_num
+entity_src_nat.pdbx_end_seq_num
+entity_src_nat.pdbx_organism_scientific
+entity_src_nat.pdbx_plasmid_name
+
+pdbx_entity_instance_feature.ordinal
+pdbx_entity_instance_feature.feature_type
+pdbx_entity_instance_feature.details
+pdbx_entity_instance_feature.asym_id
+pdbx_entity_instance_feature.comp_id
+pdbx_entity_instance_feature.seq_num
+pdbx_entity_instance_feature.auth_asym_id
+pdbx_entity_instance_feature.auth_comp_id
+pdbx_entity_instance_feature.auth_seq_num
+
+pdbx_entity_src_syn.entity_id
+pdbx_entity_src_syn.pdbx_src_id
+pdbx_entity_src_syn.pdbx_beg_seq_num
+pdbx_entity_src_syn.pdbx_end_seq_num
+pdbx_entity_src_syn.organism_scientific
+
+pdbx_entity_branch.entity_id
+pdbx_entity_branch.type
+
+pdbx_entity_branch_list.entity_id
+pdbx_entity_branch_list.comp_id
+pdbx_entity_branch_list.num
+pdbx_entity_branch_list.hetero
+
+pdbx_entity_branch_link.link_id
+pdbx_entity_branch_link.entity_id
+pdbx_entity_branch_link.entity_branch_list_num_1
+pdbx_entity_branch_link.comp_id_1
+pdbx_entity_branch_link.atom_id_1
+pdbx_entity_branch_link.leaving_atom_id_1
+pdbx_entity_branch_link.atom_stereo_config_1
+pdbx_entity_branch_link.entity_branch_list_num_2
+pdbx_entity_branch_link.comp_id_2
+pdbx_entity_branch_link.atom_id_2
+pdbx_entity_branch_link.leaving_atom_id_2
+pdbx_entity_branch_link.atom_stereo_config_2
+pdbx_entity_branch_link.value_order
+pdbx_entity_branch_link.details
+
+pdbx_branch_scheme.asym_id
+pdbx_branch_scheme.entity_id
+pdbx_branch_scheme.mon_id
+pdbx_branch_scheme.num
+pdbx_branch_scheme.auth_asym_id
+pdbx_branch_scheme.auth_mon_id
+pdbx_branch_scheme.auth_seq_num
+pdbx_branch_scheme.hetero
+pdbx_branch_scheme.pdb_mon_id
+pdbx_branch_scheme.pdb_asym_id
+pdbx_branch_scheme.pdb_seq_num
+
+pdbx_entity_branch_descriptor.ordinal
+pdbx_entity_branch_descriptor.entity_id
+pdbx_entity_branch_descriptor.descriptor
+pdbx_entity_branch_descriptor.type
+pdbx_entity_branch_descriptor.program
+pdbx_entity_branch_descriptor.program_version
+
+pdbx_entity_nonpoly.entity_id
+pdbx_entity_nonpoly.name
+pdbx_entity_nonpoly.comp_id
+
+pdbx_nonpoly_scheme.asym_id
+pdbx_nonpoly_scheme.entity_id
+pdbx_nonpoly_scheme.mon_id
+pdbx_nonpoly_scheme.ndb_seq_num
+pdbx_nonpoly_scheme.pdb_seq_num
+pdbx_nonpoly_scheme.auth_seq_num
+pdbx_nonpoly_scheme.pdb_mon_id
+pdbx_nonpoly_scheme.auth_mon_id
+pdbx_nonpoly_scheme.pdb_strand_id
+pdbx_nonpoly_scheme.pdb_ins_code
+
+entry.id
+
+audit_conform.dict_name
+audit_conform.dict_version
+audit_conform.dict_location
+
+database_2.database_id
+database_2.database_code
+
+audit_author.name
+audit_author.pdbx_ordinal
+audit_author.identifier_ORCID
+
+citation.id
+citation.title
+citation.journal_abbrev
+citation.journal_volume
+citation.page_first
+citation.page_last
+citation.year
+citation.journal_id_ASTM
+citation.country
+citation.journal_id_ISSN
+citation.journal_id_CSD
+citation.book_publisher
+citation.pdbx_database_id_PubMed
+citation.pdbx_database_id_DOI
+
+citation_author.citation_id
+citation_author.name
+citation_author.ordinal
+
+exptl.entry_id
+exptl.method
+
+struct.entry_id
+struct.title
+struct.pdbx_descriptor
+
+struct_asym.id
+struct_asym.pdbx_blank_PDB_chainid_flag
+struct_asym.pdbx_modified
+struct_asym.entity_id
+struct_asym.details
+
+struct_conf.conf_type_id
+struct_conf.id
+struct_conf.pdbx_PDB_helix_id
+struct_conf.beg_label_comp_id
+struct_conf.beg_label_asym_id
+struct_conf.beg_label_seq_id
+struct_conf.pdbx_beg_PDB_ins_code
+struct_conf.end_label_comp_id
+struct_conf.end_label_asym_id
+struct_conf.end_label_seq_id
+struct_conf.pdbx_end_PDB_ins_code
+struct_conf.beg_auth_comp_id
+struct_conf.beg_auth_asym_id
+struct_conf.beg_auth_seq_id
+struct_conf.end_auth_comp_id
+struct_conf.end_auth_asym_id
+struct_conf.end_auth_seq_id
+struct_conf.pdbx_PDB_helix_class
+struct_conf.details
+struct_conf.pdbx_PDB_helix_length
+
+struct_conn.id
+struct_conn.conn_type_id
+struct_conn.pdbx_PDB_id
+struct_conn.ptnr1_label_asym_id
+struct_conn.ptnr1_label_comp_id
+struct_conn.ptnr1_label_seq_id
+struct_conn.ptnr1_label_atom_id
+struct_conn.pdbx_ptnr1_label_alt_id
+struct_conn.pdbx_ptnr1_PDB_ins_code
+struct_conn.pdbx_ptnr1_standard_comp_id
+struct_conn.ptnr1_symmetry
+struct_conn.ptnr2_label_asym_id
+struct_conn.ptnr2_label_comp_id
+struct_conn.ptnr2_label_seq_id
+struct_conn.ptnr2_label_atom_id
+struct_conn.pdbx_ptnr2_label_alt_id
+struct_conn.pdbx_ptnr2_PDB_ins_code
+struct_conn.ptnr1_auth_asym_id
+struct_conn.ptnr1_auth_comp_id
+struct_conn.ptnr1_auth_seq_id
+struct_conn.ptnr2_auth_asym_id
+struct_conn.ptnr2_auth_comp_id
+struct_conn.ptnr2_auth_seq_id
+struct_conn.ptnr2_symmetry
+struct_conn.pdbx_ptnr3_label_atom_id
+struct_conn.pdbx_ptnr3_label_seq_id
+struct_conn.pdbx_ptnr3_label_comp_id
+struct_conn.pdbx_ptnr3_label_asym_id
+struct_conn.pdbx_ptnr3_label_alt_id
+struct_conn.pdbx_ptnr3_PDB_ins_code
+struct_conn.details
+struct_conn.pdbx_dist_value
+struct_conn.pdbx_value_order
+
+struct_conn_type.id
+struct_conn_type.criteria
+struct_conn_type.reference
+
+struct_keywords.entry_id
+struct_keywords.pdbx_keywords
+struct_keywords.text
+
+struct_ncs_oper.id
+struct_ncs_oper.code
+struct_ncs_oper.matrix
+struct_ncs_oper.vector
+struct_ncs_oper.details
+
+struct_sheet_range.sheet_id
+struct_sheet_range.id
+struct_sheet_range.beg_label_comp_id
+struct_sheet_range.beg_label_asym_id
+struct_sheet_range.beg_label_seq_id
+struct_sheet_range.pdbx_beg_PDB_ins_code
+struct_sheet_range.end_label_comp_id
+struct_sheet_range.end_label_asym_id
+struct_sheet_range.end_label_seq_id
+struct_sheet_range.pdbx_end_PDB_ins_code
+struct_sheet_range.beg_auth_comp_id
+struct_sheet_range.beg_auth_asym_id
+struct_sheet_range.beg_auth_seq_id
+struct_sheet_range.end_auth_comp_id
+struct_sheet_range.end_auth_asym_id
+struct_sheet_range.end_auth_seq_id
+
+struct_site.id
+struct_site.pdbx_evidence_code
+struct_site.pdbx_auth_asym_id
+struct_site.pdbx_auth_comp_id
+struct_site.pdbx_auth_seq_id
+struct_site.pdbx_auth_ins_code
+struct_site.pdbx_num_residues
+struct_site.details
+
+struct_site_gen.id
+struct_site_gen.site_id
+struct_site_gen.pdbx_num_res
+struct_site_gen.label_comp_id
+struct_site_gen.label_asym_id
+struct_site_gen.label_seq_id
+struct_site_gen.pdbx_auth_ins_code
+struct_site_gen.auth_comp_id
+struct_site_gen.auth_asym_id
+struct_site_gen.auth_seq_id
+struct_site_gen.label_atom_id
+struct_site_gen.label_alt_id
+struct_site_gen.symmetry
+struct_site_gen.details
+
+symmetry.entry_id
+symmetry.cell_setting
+symmetry.Int_Tables_number
+symmetry.space_group_name_Hall
+symmetry.space_group_name_H-M
+
+pdbx_molecule.instance_id
+pdbx_molecule.prd_id
+pdbx_molecule.asym_id
+
+pdbx_molecule_features.prd_id
+pdbx_molecule_features.name
+pdbx_molecule_features.type
+pdbx_molecule_features.class
+pdbx_molecule_features.details
+
+pdbx_reference_entity_link.prd_id
+pdbx_reference_entity_link.link_id
+pdbx_reference_entity_link.link_class
+pdbx_reference_entity_link.ref_entity_id_1
+pdbx_reference_entity_link.entity_seq_num_1
+pdbx_reference_entity_link.comp_id_1
+pdbx_reference_entity_link.atom_id_1
+pdbx_reference_entity_link.ref_entity_id_2
+pdbx_reference_entity_link.entity_seq_num_2
+pdbx_reference_entity_link.comp_id_2
+pdbx_reference_entity_link.atom_id_2
+pdbx_reference_entity_link.value_order
+pdbx_reference_entity_link.component_1
+pdbx_reference_entity_link.component_2
+pdbx_reference_entity_link.details
+
+pdbx_reference_entity_list.prd_id
+pdbx_reference_entity_list.ref_entity_id
+pdbx_reference_entity_list.component_id
+pdbx_reference_entity_list.type
+pdbx_reference_entity_list.details
+
+pdbx_reference_entity_poly_link.prd_id
+pdbx_reference_entity_poly_link.ref_entity_id
+pdbx_reference_entity_poly_link.link_id
+pdbx_reference_entity_poly_link.atom_id_1
+pdbx_reference_entity_poly_link.comp_id_1
+pdbx_reference_entity_poly_link.entity_seq_num_1
+pdbx_reference_entity_poly_link.atom_id_2
+pdbx_reference_entity_poly_link.comp_id_2
+pdbx_reference_entity_poly_link.entity_seq_num_2
+pdbx_reference_entity_poly_link.value_order
+pdbx_reference_entity_poly_link.component_id
+
+pdbx_struct_assembly.id
+pdbx_struct_assembly.details
+pdbx_struct_assembly.method_details
+pdbx_struct_assembly.oligomeric_details
+pdbx_struct_assembly.oligomeric_count
+
+pdbx_struct_assembly_gen.assembly_id
+pdbx_struct_assembly_gen.oper_expression
+pdbx_struct_assembly_gen.asym_id_list
+
+pdbx_struct_oper_list.id
+pdbx_struct_oper_list.type
+pdbx_struct_oper_list.name
+pdbx_struct_oper_list.symmetry_operation
+pdbx_struct_oper_list.matrix
+pdbx_struct_oper_list.vector
+
+pdbx_struct_mod_residue.id
+pdbx_struct_mod_residue.label_asym_id
+pdbx_struct_mod_residue.label_seq_id
+pdbx_struct_mod_residue.label_comp_id
+pdbx_struct_mod_residue.auth_asym_id
+pdbx_struct_mod_residue.auth_seq_id
+pdbx_struct_mod_residue.auth_comp_id
+pdbx_struct_mod_residue.PDB_ins_code
+pdbx_struct_mod_residue.parent_comp_id
+pdbx_struct_mod_residue.details
+
+pdbx_unobs_or_zero_occ_residues.id
+pdbx_unobs_or_zero_occ_residues.PDB_model_num
+pdbx_unobs_or_zero_occ_residues.polymer_flag
+pdbx_unobs_or_zero_occ_residues.occupancy_flag
+pdbx_unobs_or_zero_occ_residues.auth_asym_id
+pdbx_unobs_or_zero_occ_residues.auth_comp_id
+pdbx_unobs_or_zero_occ_residues.auth_seq_id
+pdbx_unobs_or_zero_occ_residues.PDB_ins_code
+pdbx_unobs_or_zero_occ_residues.label_asym_id
+pdbx_unobs_or_zero_occ_residues.label_comp_id
+pdbx_unobs_or_zero_occ_residues.label_seq_id
+
+ihm_struct_assembly.id
+ihm_struct_assembly.name
+ihm_struct_assembly.description
+
+ihm_struct_assembly_details.id
+ihm_struct_assembly_details.assembly_id
+ihm_struct_assembly_details.parent_assembly_id
+ihm_struct_assembly_details.entity_description
+ihm_struct_assembly_details.entity_id
+ihm_struct_assembly_details.asym_id
+ihm_struct_assembly_details.entity_poly_segment_id
+
+ihm_model_representation.id
+ihm_model_representation.name
+ihm_model_representation.details
+
+ihm_model_representation_details.id
+ihm_model_representation_details.representation_id
+ihm_model_representation_details.entity_id
+ihm_model_representation_details.entity_description
+ihm_model_representation_details.entity_asym_id
+ihm_model_representation_details.entity_poly_segment_id
+ihm_model_representation_details.model_object_primitive
+ihm_model_representation_details.starting_model_id
+ihm_model_representation_details.model_mode
+ihm_model_representation_details.model_granularity
+ihm_model_representation_details.model_object_count
+
+ihm_external_reference_info.reference_id
+ihm_external_reference_info.reference_provider
+ihm_external_reference_info.reference_type
+ihm_external_reference_info.reference
+ihm_external_reference_info.refers_to
+ihm_external_reference_info.associated_url
+
+ihm_external_files.id
+ihm_external_files.reference_id
+ihm_external_files.file_path
+ihm_external_files.content_type
+ihm_external_files.file_size_bytes
+ihm_external_files.details
+
+ihm_dataset_list.id
+ihm_dataset_list.data_type
+ihm_dataset_list.database_hosted
+
+ihm_dataset_group.id
+ihm_dataset_group.name
+ihm_dataset_group.application
+ihm_dataset_group.details
+
+ihm_dataset_group_link.group_id
+ihm_dataset_group_link.dataset_list_id
+
+ihm_dataset_external_reference.id
+ihm_dataset_external_reference.dataset_list_id
+ihm_dataset_external_reference.file_id
+
+ihm_dataset_related_db_reference.id
+ihm_dataset_related_db_reference.dataset_list_id
+ihm_dataset_related_db_reference.db_name
+ihm_dataset_related_db_reference.accession_code
+ihm_dataset_related_db_reference.version
+ihm_dataset_related_db_reference.details
+
+ihm_related_datasets.dataset_list_id_derived
+ihm_related_datasets.dataset_list_id_primary
+
+ihm_poly_residue_feature.ordinal_id
+ihm_poly_residue_feature.feature_id
+ihm_poly_residue_feature.entity_id
+ihm_poly_residue_feature.asym_id
+ihm_poly_residue_feature.seq_id_begin
+ihm_poly_residue_feature.comp_id_begin
+ihm_poly_residue_feature.seq_id_end
+ihm_poly_residue_feature.comp_id_end
+
+ihm_feature_list.feature_id
+ihm_feature_list.feature_type
+ihm_feature_list.entity_type
+
+ihm_cross_link_list.id
+ihm_cross_link_list.group_id
+ihm_cross_link_list.entity_description_1
+ihm_cross_link_list.entity_id_1
+ihm_cross_link_list.seq_id_1
+ihm_cross_link_list.comp_id_1
+ihm_cross_link_list.entity_description_2
+ihm_cross_link_list.entity_id_2
+ihm_cross_link_list.seq_id_2
+ihm_cross_link_list.comp_id_2
+ihm_cross_link_list.linker_type
+ihm_cross_link_list.dataset_list_id
+
+ihm_cross_link_restraint.id
+ihm_cross_link_restraint.group_id
+ihm_cross_link_restraint.entity_id_1
+ihm_cross_link_restraint.asym_id_1
+ihm_cross_link_restraint.seq_id_1
+ihm_cross_link_restraint.atom_id_1
+ihm_cross_link_restraint.comp_id_1
+ihm_cross_link_restraint.entity_id_2
+ihm_cross_link_restraint.asym_id_2
+ihm_cross_link_restraint.seq_id_2
+ihm_cross_link_restraint.atom_id_2
+ihm_cross_link_restraint.comp_id_2
+ihm_cross_link_restraint.restraint_type
+ihm_cross_link_restraint.conditional_crosslink_flag
+ihm_cross_link_restraint.model_granularity
+ihm_cross_link_restraint.distance_threshold
+ihm_cross_link_restraint.psi
+ihm_cross_link_restraint.sigma_1
+ihm_cross_link_restraint.sigma_2
+
+ihm_cross_link_result_parameters.id
+ihm_cross_link_result_parameters.restraint_id
+ihm_cross_link_result_parameters.model_id
+ihm_cross_link_result_parameters.psi
+ihm_cross_link_result_parameters.sigma_1
+ihm_cross_link_result_parameters.sigma_2
+
+ihm_sas_restraint.id
+ihm_sas_restraint.dataset_list_id
+ihm_sas_restraint.model_id
+ihm_sas_restraint.struct_assembly_id
+ihm_sas_restraint.profile_segment_flag
+ihm_sas_restraint.fitting_atom_type
+ihm_sas_restraint.fitting_method
+ihm_sas_restraint.fitting_state
+ihm_sas_restraint.radius_of_gyration
+ihm_sas_restraint.chi_value
+ihm_sas_restraint.details
+
+ihm_derived_distance_restraint.id
+ihm_derived_distance_restraint.group_id
+ihm_derived_distance_restraint.feature_id_1
+ihm_derived_distance_restraint.feature_id_2
+ihm_derived_distance_restraint.group_conditionality
+ihm_derived_distance_restraint.restraint_type
+ihm_derived_distance_restraint.distance_upper_limit
+ihm_derived_distance_restraint.random_exclusion_fraction
+ihm_derived_distance_restraint.dataset_list_id
+
+ihm_2dem_class_average_restraint.id
+ihm_2dem_class_average_restraint.dataset_list_id
+ihm_2dem_class_average_restraint.number_raw_micrographs
+ihm_2dem_class_average_restraint.pixel_size_width
+ihm_2dem_class_average_restraint.pixel_size_height
+ihm_2dem_class_average_restraint.image_resolution
+ihm_2dem_class_average_restraint.image_segment_flag
+ihm_2dem_class_average_restraint.number_of_projections
+ihm_2dem_class_average_restraint.struct_assembly_id
+ihm_2dem_class_average_restraint.details
+
+ihm_2dem_class_average_fitting.id
+ihm_2dem_class_average_fitting.restraint_id
+ihm_2dem_class_average_fitting.model_id
+ihm_2dem_class_average_fitting.cross_correlation_coefficient
+ihm_2dem_class_average_fitting.rot_matrix
+ihm_2dem_class_average_fitting.tr_vector
+
+ihm_3dem_restraint.id
+ihm_3dem_restraint.dataset_list_id
+ihm_3dem_restraint.fitting_method
+ihm_3dem_restraint.struct_assembly_id
+ihm_3dem_restraint.number_of_gaussians
+ihm_3dem_restraint.model_id
+ihm_3dem_restraint.cross_correlation_coefficient
+
+ihm_predicted_contact_restraint.id
+ihm_predicted_contact_restraint.group_id
+ihm_predicted_contact_restraint.entity_id_1
+ihm_predicted_contact_restraint.asym_id_1
+ihm_predicted_contact_restraint.seq_id_1
+ihm_predicted_contact_restraint.comp_id_1
+ihm_predicted_contact_restraint.rep_atom_1
+ihm_predicted_contact_restraint.entity_id_2
+ihm_predicted_contact_restraint.asym_id_2
+ihm_predicted_contact_restraint.seq_id_2
+ihm_predicted_contact_restraint.comp_id_2
+ihm_predicted_contact_restraint.rep_atom_2
+ihm_predicted_contact_restraint.restraint_type
+ihm_predicted_contact_restraint.distance_lower_limit
+ihm_predicted_contact_restraint.distance_upper_limit
+ihm_predicted_contact_restraint.probability
+ihm_predicted_contact_restraint.model_granularity
+ihm_predicted_contact_restraint.dataset_list_id
+ihm_predicted_contact_restraint.software_id
+
+ihm_starting_model_details.starting_model_id
+ihm_starting_model_details.entity_id
+ihm_starting_model_details.entity_description
+ihm_starting_model_details.asym_id
+ihm_starting_model_details.entity_poly_segment_id
+ihm_starting_model_details.starting_model_source
+ihm_starting_model_details.starting_model_auth_asym_id
+ihm_starting_model_details.starting_model_sequence_offset
+ihm_starting_model_details.dataset_list_id
+
+ihm_starting_comparative_models.id
+ihm_starting_comparative_models.starting_model_id
+ihm_starting_comparative_models.starting_model_auth_asym_id
+ihm_starting_comparative_models.starting_model_seq_id_begin
+ihm_starting_comparative_models.starting_model_seq_id_end
+ihm_starting_comparative_models.template_auth_asym_id
+ihm_starting_comparative_models.template_seq_id_begin
+ihm_starting_comparative_models.template_seq_id_end
+ihm_starting_comparative_models.template_sequence_identity
+ihm_starting_comparative_models.template_sequence_identity_denominator
+ihm_starting_comparative_models.template_dataset_list_id
+ihm_starting_comparative_models.alignment_file_id
+
+ihm_starting_model_coord.starting_model_id
+ihm_starting_model_coord.group_PDB
+ihm_starting_model_coord.id
+ihm_starting_model_coord.type_symbol
+ihm_starting_model_coord.atom_id
+ihm_starting_model_coord.comp_id
+ihm_starting_model_coord.entity_id
+ihm_starting_model_coord.asym_id
+ihm_starting_model_coord.seq_id
+ihm_starting_model_coord.Cartn_x
+ihm_starting_model_coord.Cartn_y
+ihm_starting_model_coord.Cartn_z
+ihm_starting_model_coord.B_iso_or_equiv
+ihm_starting_model_coord.ordinal_id
+
+ihm_starting_model_seq_dif.id
+ihm_starting_model_seq_dif.entity_id
+ihm_starting_model_seq_dif.asym_id
+ihm_starting_model_seq_dif.seq_id
+ihm_starting_model_seq_dif.comp_id
+ihm_starting_model_seq_dif.starting_model_id
+ihm_starting_model_seq_dif.db_asym_id
+ihm_starting_model_seq_dif.db_seq_id
+ihm_starting_model_seq_dif.db_comp_id
+ihm_starting_model_seq_dif.details
+
+ihm_modeling_protocol.id
+ihm_modeling_protocol.protocol_name
+ihm_modeling_protocol.num_steps
+
+ihm_modeling_protocol_details.id
+ihm_modeling_protocol_details.protocol_id
+ihm_modeling_protocol_details.step_id
+ihm_modeling_protocol_details.struct_assembly_id
+ihm_modeling_protocol_details.dataset_group_id
+ihm_modeling_protocol_details.struct_assembly_description
+ihm_modeling_protocol_details.step_name
+ihm_modeling_protocol_details.step_method
+ihm_modeling_protocol_details.num_models_begin
+ihm_modeling_protocol_details.num_models_end
+ihm_modeling_protocol_details.multi_scale_flag
+ihm_modeling_protocol_details.multi_state_flag
+ihm_modeling_protocol_details.ordered_flag
+ihm_modeling_protocol_details.software_id
+ihm_modeling_protocol_details.script_file_id
+
+ihm_modeling_post_process.id
+ihm_modeling_post_process.protocol_id
+ihm_modeling_post_process.analysis_id
+ihm_modeling_post_process.step_id
+ihm_modeling_post_process.type
+ihm_modeling_post_process.feature
+ihm_modeling_post_process.num_models_begin
+ihm_modeling_post_process.num_models_end
+
+ihm_ensemble_info.ensemble_id
+ihm_ensemble_info.ensemble_name
+ihm_ensemble_info.post_process_id
+ihm_ensemble_info.model_group_id
+ihm_ensemble_info.ensemble_clustering_method
+ihm_ensemble_info.ensemble_clustering_feature
+ihm_ensemble_info.num_ensemble_models
+ihm_ensemble_info.num_ensemble_models_deposited
+ihm_ensemble_info.ensemble_precision_value
+ihm_ensemble_info.ensemble_file_id
+
+ihm_localization_density_files.id
+ihm_localization_density_files.file_id
+ihm_localization_density_files.ensemble_id
+ihm_localization_density_files.entity_id
+ihm_localization_density_files.asym_id
+ihm_localization_density_files.entity_poly_segment_id
+
+ihm_model_list.model_id
+ihm_model_list.model_name
+ihm_model_list.assembly_id
+ihm_model_list.protocol_id
+ihm_model_list.representation_id
+
+ihm_model_group.id
+ihm_model_group.name
+ihm_model_group.details
+
+ihm_model_group_link.group_id
+ihm_model_group_link.model_id
+
+ihm_model_representative.id
+ihm_model_representative.model_group_id
+ihm_model_representative.model_id
+ihm_model_representative.selection_criteria
+
+ihm_sphere_obj_site.id
+ihm_sphere_obj_site.entity_id
+ihm_sphere_obj_site.seq_id_begin
+ihm_sphere_obj_site.seq_id_end
+ihm_sphere_obj_site.asym_id
+ihm_sphere_obj_site.Cartn_x
+ihm_sphere_obj_site.Cartn_y
+ihm_sphere_obj_site.Cartn_z
+ihm_sphere_obj_site.object_radius
+ihm_sphere_obj_site.rmsf
+ihm_sphere_obj_site.model_id
+
+ihm_gaussian_obj_site.id
+ihm_gaussian_obj_site.entity_id
+ihm_gaussian_obj_site.seq_id_begin
+ihm_gaussian_obj_site.seq_id_end
+ihm_gaussian_obj_site.asym_id
+ihm_gaussian_obj_site.mean_Cartn_x
+ihm_gaussian_obj_site.mean_Cartn_y
+ihm_gaussian_obj_site.mean_Cartn_z
+ihm_gaussian_obj_site.weight
+ihm_gaussian_obj_site.covariance_matrix
+ihm_gaussian_obj_site.model_id
+
+ihm_gaussian_obj_ensemble.id
+ihm_gaussian_obj_ensemble.entity_id
+ihm_gaussian_obj_ensemble.seq_id_begin
+ihm_gaussian_obj_ensemble.seq_id_end
+ihm_gaussian_obj_ensemble.asym_id
+ihm_gaussian_obj_ensemble.mean_Cartn_x
+ihm_gaussian_obj_ensemble.mean_Cartn_y
+ihm_gaussian_obj_ensemble.mean_Cartn_z
+ihm_gaussian_obj_ensemble.weight
+ihm_gaussian_obj_ensemble.covariance_matrix
+ihm_gaussian_obj_ensemble.ensemble_id
+
+ihm_multi_state_modeling.state_id
+ihm_multi_state_modeling.state_group_id
+ihm_multi_state_modeling.population_fraction
+ihm_multi_state_modeling.population_fraction_sd
+ihm_multi_state_modeling.state_type
+ihm_multi_state_modeling.state_name
+ihm_multi_state_modeling.experiment_type
+ihm_multi_state_modeling.details
\ No newline at end of file
diff --git a/data/cif-field-names/mmtf-filter.csv b/data/cif-field-names/mmtf-filter.csv
new file mode 100644
index 0000000000000000000000000000000000000000..5a9b2bf0f7d216debfe761f89513d0a2d7d09074
--- /dev/null
+++ b/data/cif-field-names/mmtf-filter.csv
@@ -0,0 +1,76 @@
+cell.length_a
+cell.length_b
+cell.length_c
+cell.angle_alpha
+cell.angle_beta
+cell.angle_gamma
+
+symmetry.space_group_name_H-M
+
+entry.id
+
+struct.title
+
+pdbx_database_status.recvd_initial_deposition_date
+
+pdbx_audit_revision_history.revision_date
+
+struct_ncs_oper
+
+pdbx_struct_assembly_gen
+
+pdbx_struct_oper_list
+
+entity.id
+entity.type
+entity.pdbx_description
+
+entity_poly.entity_id
+entity_poly.pdbx_seq_one_letter_code
+entity_poly.pdbx_strand_id
+
+exptl.method
+
+refine.ls_d_res_low
+refine.ls_R_factor_R_free
+refine.ls_R_factor_R_work
+
+atom_site.pdbx_formal_charge
+atom_site.label_atom_id
+atom_site.type_symbol
+
+chem_comp.id
+chem_comp.type
+chem_comp.name
+
+chem_comp_bond
+
+atom_site.Cartn_x
+atom_site.Cartn_y
+atom_site.Cartn_z
+atom_site.B_iso_or_equiv
+atom_site.id
+atom_site.label_alt_id
+atom_site.occupancy
+atom_site.label_seq_id
+atom_site.label_comp_id
+
+struct_sheet_range.id
+struct_sheet_range.beg_label_asym_id
+struct_sheet_range.beg_label_seq_id
+struct_sheet_range.pdbx_beg_PDB_ins_code
+struct_sheet_range.end_label_asym_id
+struct_sheet_range.end_label_seq_id
+struct_sheet_range.pdbx_end_PDB_ins_code
+struct_conf.conf_type_id
+struct_conf.id
+struct_conf.beg_label_asym_id
+struct_conf.beg_label_seq_id
+struct_conf.pdbx_beg_PDB_ins_code
+struct_conf.end_label_asym_id
+struct_conf.end_label_seq_id
+struct_conf.pdbx_end_PDB_ins_code
+
+atom_site.pdbx_PDB_ins_code
+atom_site.label_asym_id
+atom_site.auth_asym_id
\ No newline at end of file
diff --git a/data/rcsb-graphql/codegen.yml b/data/rcsb-graphql/codegen.yml
index 726a47193be3b15ac8085a40842d210863f722c0..d42a711fef623fe14bc2189a9f92466b65b219a9 100644
--- a/data/rcsb-graphql/codegen.yml
+++ b/data/rcsb-graphql/codegen.yml
@@ -1,4 +1,4 @@
-schema: https://data-beta.rcsb.org/graphql
+schema: https://data.rcsb.org/graphql
documents: './src/mol-model-props/rcsb/graphql/symmetry.gql.ts'
generates:
'./src/mol-model-props/rcsb/graphql/types.ts':
diff --git a/package-lock.json b/package-lock.json
index 215f72bdf42f6a34bba0cb24a63b1b4e8117e302..d6547d6854e46f89bd92643e8e040a937b282ca6 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index 0ca273aad9eae9b9afcdbd83cc4a4aea56777cd5..34f59326c9d625d3b5eb83ea8e5da411d337b021 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "molstar",
- "version": "0.6.4",
+ "version": "0.6.7",
"description": "A comprehensive macromolecular library.",
"homepage": "https://github.com/molstar/molstar#readme",
"repository": {
@@ -38,6 +38,8 @@
"lib/"
],
"bin": {
+ "cif2bcif": "lib/apps/cif2bcif/index.js",
+ "cifschema": "lib/apps/cifschema/index.js",
"model-server": "lib/servers/model/server.js",
"model-server-query": "lib/servers/model/local.js",
"model-server-preprocess": "lib/servers/model/preprocess.js",
diff --git a/src/apps/basic-wrapper/controls.tsx b/src/apps/basic-wrapper/controls.tsx
deleted file mode 100644
index c45a76010edd1bc18d52f4635fd482ae1b9ee7cd..0000000000000000000000000000000000000000
--- a/src/apps/basic-wrapper/controls.tsx
+++ /dev/null
@@ -1,30 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { PluginUIComponent } from '../../mol-plugin-ui/base';
-import * as React from 'react';
-import { TransformUpdaterControl } from '../../mol-plugin-ui/state/update-transform';
-
-export class BasicWrapperControls extends PluginUIComponent {
-
- render() {
- return <div style={{ overflowY: 'auto', display: 'block', height: '100%' }}>
- <TransformUpdaterControl nodeRef='asm' />
- <TransformUpdaterControl nodeRef='seq-visual' header={{ name: 'Sequence Visual' }} />
- <TransformUpdaterControl nodeRef='het-visual' header={{ name: 'HET Visual' }} />
- <TransformUpdaterControl nodeRef='water-visual' header={{ name: 'Water Visual' }} initiallyCollapsed={true} />
- <TransformUpdaterControl nodeRef='ihm-visual' header={{ name: 'I/HM Visual' }} initiallyCollapsed={true} />
- </div>;
- }
-}
-
-export class CustomToastMessage extends PluginUIComponent {
- render() {
- return <>
- Custom <i>Toast</i> content. No timeout.
- </>;
- }
-}
\ No newline at end of file
diff --git a/src/apps/basic-wrapper/helpers.ts b/src/apps/basic-wrapper/helpers.ts
deleted file mode 100644
index b0b364e73b432527d018844dc5befd194a64e252..0000000000000000000000000000000000000000
--- a/src/apps/basic-wrapper/helpers.ts
+++ /dev/null
@@ -1,99 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
-import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import { StateBuilder } from '../../mol-state';
-import Expression from '../../mol-script/language/expression';
-import { ColorTheme } from '../../mol-theme/color';
-import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
-type SupportedFormats = 'cif' | 'pdb'
-
-export namespace StateHelper {
- export function download(b: StateBuilder.To<PSO.Root>, url: string, ref?: string) {
- return b.apply(StateTransforms.Data.Download, { url, isBinary: false }, { ref });
- }
-
- export function getModel(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats, modelIndex = 0) {
- const parsed = format === 'cif'
- ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
- : b.apply(StateTransforms.Model.TrajectoryFromPDB);
-
- return parsed.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex });
- }
-
- export function structure(b: StateBuilder.To<PSO.Molecule.Model>) {
- return b.apply(StateTransforms.Model.StructureFromModel, void 0, { tags: 'structure' })
- };
-
- export function selectChain(b: StateBuilder.To<PSO.Molecule.Structure>, auth_asym_id: string) {
- const expression = MS.struct.generator.atomGroups({
- 'chain-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.auth_asym_id(), auth_asym_id])
- })
- return b.apply(StateTransforms.Model.StructureSelectionFromExpression, { expression, label: `Chain ${auth_asym_id}` });
- }
-
- export function select(b: StateBuilder.To<PSO.Molecule.Structure>, expression: Expression) {
- return b.apply(StateTransforms.Model.StructureSelectionFromExpression, { expression });
- }
-
- export function selectSurroundingsOfFirstResidue(b: StateBuilder.To<PSO.Molecule.Structure>, comp_id: string, radius: number) {
- const expression = MS.struct.modifier.includeSurroundings({
- 0: MS.struct.filter.first([
- MS.struct.generator.atomGroups({
- 'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), comp_id]),
- 'group-by': MS.struct.atomProperty.macromolecular.residueKey()
- })
- ]),
- radius
- })
- return b.apply(StateTransforms.Model.StructureSelectionFromExpression, { expression, label: `Surr. ${comp_id} (${radius} ang)` });
- }
-
- export function identityTransform(b: StateBuilder.To<PSO.Molecule.Structure>, m: Mat4) {
- return b.apply(StateTransforms.Model.TransformStructureConformation,
- { transform: { name: 'components', params: { axis: Vec3.create(1, 0, 0), angle: 0, translation: Vec3.zero() } } },
- { tags: 'transform' });
- }
-
- export function transform(b: StateBuilder.To<PSO.Molecule.Structure>, matrix: Mat4) {
- return b.apply(StateTransforms.Model.TransformStructureConformation, {
- transform: { name: 'matrix', params: matrix }
- }, { tags: 'transform' });
- }
-
- export function assemble(b: StateBuilder.To<PSO.Molecule.Model>, id?: string) {
- const props = {
- type: {
- name: 'assembly' as const,
- params: { id: id || 'deposited' }
- }
- }
- return b.apply(StateTransforms.Model.StructureFromModel, props, { tags: 'asm' })
- }
-
- export function visual(ctx: PluginContext, visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
- visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- createStructureRepresentationParams(ctx, void 0, { type: 'cartoon' }), { tags: 'seq-visual' });
- visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- createStructureRepresentationParams(ctx, void 0, { type: 'ball-and-stick' }), { tags: 'het-visual' });
- return visualRoot;
- }
-
- export function ballsAndSticks(ctx: PluginContext, visualRoot: StateBuilder.To<PSO.Molecule.Structure>, expression: Expression, color?: ColorTheme.BuiltIn) {
- visualRoot
- .apply(StateTransforms.Model.StructureSelectionFromExpression, { expression })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- createStructureRepresentationParams(ctx, void 0, { type: 'ball-and-stick', color }), { tags: 'het-visual' });
- return visualRoot;
- }
-
-}
\ No newline at end of file
diff --git a/src/apps/basic-wrapper/index.ts b/src/apps/basic-wrapper/index.ts
deleted file mode 100644
index 1d30fbf1e5db8bf5a3937dddfa02375fada5c119..0000000000000000000000000000000000000000
--- a/src/apps/basic-wrapper/index.ts
+++ /dev/null
@@ -1,219 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import './index.html'
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { Color } from '../../mol-util/color';
-import { PluginStateObject as PSO, PluginStateObject } from '../../mol-plugin-state/objects';
-import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
-import { StateBuilder, StateTransform } from '../../mol-state';
-import { StripedResidues } from './coloring';
-import { StaticSuperpositionTestData, buildStaticSuperposition, dynamicSuperpositionTest } from './superposition';
-import { PDBeStructureQualityReport } from '../../mol-plugin/behavior/dynamic/custom-props';
-import { CustomToastMessage } from './controls';
-import { EmptyLoci } from '../../mol-model/loci';
-import { StructureSelection } from '../../mol-model/structure';
-import { Script } from '../../mol-script/script';
-import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
-require('mol-plugin-ui/skin/light.scss')
-
-type SupportedFormats = 'cif' | 'pdb'
-type LoadParams = { url: string, format?: SupportedFormats, assemblyId?: string }
-
-class BasicWrapper {
- plugin: PluginContext;
-
- init(target: string | HTMLElement) {
- this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
- ...DefaultPluginSpec,
- layout: {
- initial: {
- isExpanded: false,
- showControls: false
- },
- controls: {
- // left: 'none',
- // right: BasicWrapperControls
- }
- },
- components: {
- remoteState: 'none'
- }
- });
-
- this.plugin.representation.structure.themes.colorThemeRegistry.add(StripedResidues.colorThemeProvider!);
- this.plugin.managers.lociLabels.addProvider(StripedResidues.labelProvider!);
- this.plugin.customModelProperties.register(StripedResidues.propertyProvider, true);
- }
-
- private download(b: StateBuilder.To<PSO.Root>, url: string) {
- return b.apply(StateTransforms.Data.Download, { url, isBinary: false })
- }
-
- private parse(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats, assemblyId: string) {
- const parsed = format === 'cif'
- ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
- : b.apply(StateTransforms.Model.TrajectoryFromPDB);
-
- const props = {
- type: {
- name: 'assembly' as const,
- params: { id: assemblyId || 'deposited' }
- }
- }
- return parsed
- .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
- .apply(StateTransforms.Model.CustomModelProperties, { autoAttach: [StripedResidues.propertyProvider.descriptor.name], properties: {} }, { ref: 'props', state: { isGhost: false } })
- .apply(StateTransforms.Model.StructureFromModel, props, { ref: 'asm' });
- }
-
- private visual(visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
- visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' }, { ref: 'seq' })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- createStructureRepresentationParams(this.plugin, void 0, { type: 'cartoon' }), { ref: 'seq-visual' });
- visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- createStructureRepresentationParams(this.plugin, void 0, { type: 'ball-and-stick' }), { ref: 'het-visual' });
- visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'water' })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- createStructureRepresentationParams(this.plugin, void 0, { type: 'ball-and-stick', typeParams: { alpha: 0.51 } }), { ref: 'water-visual' });
- visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'spheres' })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- createStructureRepresentationParams(this.plugin, void 0, { type: 'spacefill' }), { ref: 'ihm-visual' });
- return visualRoot;
- }
-
- private loadedParams: LoadParams = { url: '', format: 'cif', assemblyId: '' };
- async load({ url, format = 'cif', assemblyId = '' }: LoadParams) {
- let loadType: 'full' | 'update' = 'full';
-
- const state = this.plugin.state.data;
-
- if (this.loadedParams.url !== url || this.loadedParams.format !== format) {
- loadType = 'full';
- } else if (this.loadedParams.url === url) {
- if (state.select('asm').length > 0) loadType = 'update';
- }
-
- let tree: StateBuilder.Root;
- if (loadType === 'full') {
- await PluginCommands.State.RemoveObject(this.plugin, { state, ref: state.tree.root.ref });
- tree = state.build();
- this.visual(this.parse(this.download(tree.toRoot(), url), format, assemblyId));
- } else {
- const props = {
- type: {
- name: 'assembly' as const,
- params: { id: assemblyId || 'deposited' }
- }
- }
-
- tree = state.build();
- tree.to('asm').update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
- }
-
- await PluginCommands.State.Update(this.plugin, { state: this.plugin.state.data, tree });
- this.loadedParams = { url, format, assemblyId };
- PluginCommands.Camera.Reset(this.plugin, { });
- }
-
- setBackground(color: number) {
- const renderer = this.plugin.canvas3d!.props.renderer;
- PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: Color(color) } } });
- }
-
- toggleSpin() {
- if (!this.plugin.canvas3d) return;
-
- const trackball = this.plugin.canvas3d.props.trackball;
- const spinning = trackball.spin;
- PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
- if (!spinning) PluginCommands.Camera.Reset(this.plugin, { });
- }
-
- animate = {
- modelIndex: {
- maxFPS: 8,
- onceForward: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }) },
- onceBackward: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }) },
- palindrome: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }) },
- loop: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }) },
- stop: () => this.plugin.state.animation.stop()
- }
- }
-
- coloring = {
- applyStripes: async () => {
- const state = this.plugin.state.data;
-
- const visuals = state.selectQ(q => q.ofTransformer(StateTransforms.Representation.StructureRepresentation3D));
- const tree = state.build();
- const colorTheme = { name: StripedResidues.propertyProvider.descriptor.name, params: this.plugin.representation.structure.themes.colorThemeRegistry.get(StripedResidues.propertyProvider.descriptor.name).defaultValues };
-
- for (const v of visuals) {
- tree.to(v).update(old => ({ ...old, colorTheme }));
- }
-
- await PluginCommands.State.Update(this.plugin, { state, tree });
- }
- }
-
- interactivity = {
- highlightOn: () => {
- const seq_id = 7;
- const data = (this.plugin.state.data.select('asm')[0].obj as PluginStateObject.Molecule.Structure).data;
- const sel = Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
- 'residue-test': Q.core.rel.eq([Q.struct.atomProperty.macromolecular.label_seq_id(), seq_id]),
- 'group-by': Q.struct.atomProperty.macromolecular.residueKey()
- }), data);
- const loci = StructureSelection.toLociWithSourceUnits(sel);
- this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci });
- },
- clearHighlight: () => {
- this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci: EmptyLoci });
- }
- }
-
- tests = {
- staticSuperposition: async () => {
- const state = this.plugin.state.data;
- const tree = buildStaticSuperposition(this.plugin, StaticSuperpositionTestData);
- await PluginCommands.State.RemoveObject(this.plugin, { state, ref: StateTransform.RootRef });
- await PluginCommands.State.Update(this.plugin, { state, tree });
- },
- dynamicSuperposition: async () => {
- await PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.data, ref: StateTransform.RootRef });
- await dynamicSuperpositionTest(this.plugin, ['1tqn', '2hhb', '4hhb'], 'HEM');
- },
- toggleValidationTooltip: async () => {
- const state = this.plugin.state.behaviors;
- const tree = state.build().to(PDBeStructureQualityReport.id).update(PDBeStructureQualityReport, p => ({ ...p, showTooltip: !p.showTooltip }));
- await PluginCommands.State.Update(this.plugin, { state, tree });
- },
- showToasts: () => {
- PluginCommands.Toast.Show(this.plugin, {
- title: 'Toast 1',
- message: 'This is an example text, timeout 3s',
- key: 'toast-1',
- timeoutMs: 3000
- });
- PluginCommands.Toast.Show(this.plugin, {
- title: 'Toast 2',
- message: CustomToastMessage,
- key: 'toast-2'
- });
- },
- hideToasts: () => {
- PluginCommands.Toast.Hide(this.plugin, { key: 'toast-1' });
- PluginCommands.Toast.Hide(this.plugin, { key: 'toast-2' });
- }
- }
-}
-
-(window as any).BasicMolStarWrapper = new BasicWrapper();
\ No newline at end of file
diff --git a/src/apps/basic-wrapper/superposition.ts b/src/apps/basic-wrapper/superposition.ts
deleted file mode 100644
index 2fd361526afeff62872aae0a5831fc36f3765419..0000000000000000000000000000000000000000
--- a/src/apps/basic-wrapper/superposition.ts
+++ /dev/null
@@ -1,108 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-// TODO: move to an "example"
-
-import { PluginContext } from '../../mol-plugin/context';
-import { Mat4 } from '../../mol-math/linear-algebra';
-import { StateHelper } from './helpers';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { StateSelection, StateBuilder } from '../../mol-state';
-import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import { compile } from '../../mol-script/runtime/query/compiler';
-import { StructureSelection, QueryContext } from '../../mol-model/structure';
-import { superposeStructures } from '../../mol-model/structure/structure/util/superposition';
-import Expression from '../../mol-script/language/expression';
-
-export type SuperpositionTestInput = {
- pdbId: string,
- auth_asym_id: string,
- matrix: Mat4
-}[];
-
-// function getAxisAngleTranslation(m: Mat4) {
-// const translation = Mat4.getTranslation(Vec3.zero(), m);
-// const axis = Vec3.zero();
-// const angle = 180 / Math.PI * Quat.getAxisAngle(axis, Mat4.getRotation(Quat.zero(), m));
-// return { translation, axis, angle };
-// }
-
-export function buildStaticSuperposition(ctx: PluginContext, src: SuperpositionTestInput) {
- const b = ctx.state.data.build().toRoot();
- for (const s of src) {
- StateHelper.visual(ctx,
- StateHelper.transform(
- StateHelper.selectChain(
- StateHelper.structure(
- StateHelper.getModel(StateHelper.download(b, `https://www.ebi.ac.uk/pdbe/static/entry/${s.pdbId}_updated.cif`), 'cif')),
- s.auth_asym_id
- ),
- s.matrix
- )
- );
- }
- return b;
-}
-
-export const StaticSuperpositionTestData: SuperpositionTestInput = [
- { pdbId: '1aj5', auth_asym_id: 'A', matrix: Mat4.identity() },
- { pdbId: '1df0', auth_asym_id: 'B', matrix: Mat4.ofRows([
- [0.406, 0.879, 0.248, -200.633],
- [0.693, -0.473, 0.544, 73.403],
- [0.596, -0.049, -0.802, -14.209],
- [0, 0, 0, 1]] )},
- { pdbId: '1dvi', auth_asym_id: 'A', matrix: Mat4.ofRows([
- [-0.053, -0.077, 0.996, -45.633],
- [-0.312, 0.949, 0.057, -12.255],
- [-0.949, -0.307, -0.074, 53.562],
- [0, 0, 0, 1]] )}
-];
-
-export async function dynamicSuperpositionTest(ctx: PluginContext, src: string[], comp_id: string) {
- const state = ctx.state.data;
-
- const structures = state.build().toRoot();
- for (const s of src) {
- StateHelper.structure(
- StateHelper.getModel(StateHelper.download(structures, `https://www.ebi.ac.uk/pdbe/static/entry/${s}_updated.cif`), 'cif'));
- }
-
- await PluginCommands.State.Update(ctx, { state, tree: structures });
-
- const pivot = MS.struct.filter.first([
- MS.struct.generator.atomGroups({
- 'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), comp_id]),
- 'group-by': MS.struct.atomProperty.macromolecular.residueKey()
- })
- ]);
- const rest = MS.struct.modifier.exceptBy({
- 0: MS.struct.generator.all(),
- by: pivot
- });
-
- const query = compile<StructureSelection>(pivot);
- const xs = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure));
- const selections = xs.map(s => StructureSelection.toLociWithCurrentUnits(query(new QueryContext(s.obj!.data))));
-
- const transforms = superposeStructures(selections);
- const visuals = state.build();
-
- siteVisual(ctx, StateHelper.selectSurroundingsOfFirstResidue(visuals.to(xs[0].transform.ref), 'HEM', 7), pivot, rest);
- for (let i = 1; i < selections.length; i++) {
- const root = visuals.to(xs[i].transform.ref);
- siteVisual(ctx,
- StateHelper.transform(StateHelper.selectSurroundingsOfFirstResidue(root, 'HEM', 7), transforms[i - 1].bTransform),
- pivot, rest);
- }
-
- await PluginCommands.State.Update(ctx, { state, tree: visuals });
-}
-
-function siteVisual(ctx: PluginContext, b: StateBuilder.To<PSO.Molecule.Structure>, pivot: Expression, rest: Expression) {
- StateHelper.ballsAndSticks(ctx, b, pivot, 'residue-name');
- StateHelper.ballsAndSticks(ctx, b, rest, 'uniform');
-}
\ No newline at end of file
diff --git a/src/apps/cif2bcif/converter.ts b/src/apps/cif2bcif/converter.ts
new file mode 100644
index 0000000000000000000000000000000000000000..b1cf3308971ad3fdf41782e923933df6d515d605
--- /dev/null
+++ b/src/apps/cif2bcif/converter.ts
@@ -0,0 +1,119 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ */
+
+import { CIF, CifCategory, getCifFieldType, CifField, CifFile } from '../../mol-io/reader/cif'
+import { CifWriter, EncodingStrategyHint } from '../../mol-io/writer/cif'
+import * as util from 'util'
+import * as fs from 'fs'
+import * as zlib from 'zlib'
+import { Progress, Task, RuntimeContext } from '../../mol-task';
+import { classifyFloatArray, classifyIntArray } from '../../mol-io/common/binary-cif';
+import { BinaryEncodingProvider } from '../../mol-io/writer/cif/encoder/binary';
+import { Category } from '../../mol-io/writer/cif/encoder';
+import { ReaderResult } from '../../mol-io/reader/result';
+
+function showProgress(p: Progress) {
+ process.stdout.write(`\r${new Array(80).join(' ')}`);
+ process.stdout.write(`\r${Progress.format(p)}`);
+}
+
+const readFileAsync = util.promisify(fs.readFile);
+const unzipAsync = util.promisify<zlib.InputType, Buffer>(zlib.unzip);
+
+async function readFile(ctx: RuntimeContext, filename: string): Promise<ReaderResult<CifFile>> {
+ const isGz = /\.gz$/i.test(filename);
+ if (filename.match(/\.bcif/)) {
+ let input = await readFileAsync(filename)
+ if (isGz) input = await unzipAsync(input);
+ return await CIF.parseBinary(new Uint8Array(input)).runInContext(ctx);
+ } else {
+ let str: string;
+ if (isGz) {
+ const data = await unzipAsync(await readFileAsync(filename));
+ str = data.toString('utf8');
+ } else {
+ str = await readFileAsync(filename, 'utf8');
+ }
+ return await CIF.parseText(str).runInContext(ctx);
+ }
+}
+
+async function getCIF(ctx: RuntimeContext, filename: string) {
+ const parsed = await readFile(ctx, filename);
+ if (parsed.isError) {
+ throw new Error(parsed.toString());
+ }
+ return parsed.result;
+}
+
+function getCategoryInstanceProvider(cat: CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
+ return {
+ name: cat.name,
+ instance: () => CifWriter.categoryInstance(fields, { data: cat, rowCount: cat.rowCount })
+ };
+}
+
+function classify(name: string, field: CifField): CifWriter.Field {
+ const type = getCifFieldType(field);
+ if (type['@type'] === 'str') {
+ return { name, type: CifWriter.Field.Type.Str, value: field.str, valueKind: field.valueKind };
+ } else if (type['@type'] === 'float') {
+ const encoder = classifyFloatArray(field.toFloatArray({ array: Float64Array }));
+ return CifWriter.Field.float(name, field.float, { valueKind: field.valueKind, encoder, typedArray: Float64Array });
+ } else {
+ const encoder = classifyIntArray(field.toIntArray({ array: Int32Array }));
+ return CifWriter.Field.int(name, field.int, { valueKind: field.valueKind, encoder, typedArray: Int32Array });
+ }
+}
+
+export default function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
+ return Task.create<Uint8Array>('BinaryCIF', async ctx => {
+ const encodingProvider: BinaryEncodingProvider = hints
+ ? CifWriter.createEncodingProviderFromJsonConfig(hints)
+ : { get: (c, f) => void 0 };
+ const cif = await getCIF(ctx, path);
+
+ const encoder = CifWriter.createEncoder({
+ binary: !asText,
+ encoderName: 'mol*/ciftools cif2bcif',
+ binaryAutoClassifyEncoding: true,
+ binaryEncodingPovider: encodingProvider
+ });
+
+ if (filter) {
+ encoder.setFilter(Category.filterOf(filter));
+ }
+
+ let maxProgress = 0;
+ for (const b of cif.blocks) {
+ maxProgress += b.categoryNames.length;
+ for (const c of b.categoryNames) maxProgress += b.categories[c].fieldNames.length;
+ }
+
+ let current = 0;
+ for (const b of cif.blocks) {
+ encoder.startDataBlock(b.header);
+ for (const c of b.categoryNames) {
+ const cat = b.categories[c];
+ const fields: CifWriter.Field[] = [];
+ for (const f of cat.fieldNames) {
+ fields.push(classify(f, cat.getField(f)!))
+ current++;
+ if (ctx.shouldUpdate) await ctx.update({ message: 'Encoding...', current, max: maxProgress });
+ }
+
+ encoder.writeCategory(getCategoryInstanceProvider(b.categories[c], fields));
+ current++;
+ if (ctx.shouldUpdate) await ctx.update({ message: 'Encoding...', current, max: maxProgress });
+ }
+ }
+ await ctx.update('Exporting...');
+ const ret = encoder.getData() as Uint8Array;
+ await ctx.update('Done.\n');
+ return ret;
+ }).run(showProgress, 250);
+}
\ No newline at end of file
diff --git a/src/apps/cif2bcif/index.ts b/src/apps/cif2bcif/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e6987c9cf51da9e1839b1f7d6f0d6fefd42176ce
--- /dev/null
+++ b/src/apps/cif2bcif/index.ts
@@ -0,0 +1,67 @@
+/**
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as argparse from 'argparse'
+import * as util from 'util'
+import * as fs from 'fs'
+import * as zlib from 'zlib'
+import convert from './converter'
+
+require('util.promisify').shim();
+
+async function process(srcPath: string, outPath: string, configPath?: string, filterPath?: string) {
+ const config = configPath ? JSON.parse(fs.readFileSync(configPath, 'utf8')) : void 0;
+ const filter = filterPath ? fs.readFileSync(filterPath, 'utf8') : void 0;
+
+ const res = await convert(srcPath, false, config, filter);
+ await write(outPath, res);
+}
+
+const zipAsync = util.promisify<zlib.InputType, Buffer>(zlib.gzip);
+
+async function write(outPath: string, res: Uint8Array) {
+ const isGz = /\.gz$/i.test(outPath);
+ if (isGz) {
+ res = await zipAsync(res);
+ }
+ fs.writeFileSync(outPath, res);
+}
+
+function run(args: Args) {
+ process(args.src, args.out, args.config, args.filter)
+}
+
+const parser = new argparse.ArgumentParser({
+ addHelp: true,
+ description: 'Convert any CIF file to a BCIF file'
+});
+parser.addArgument([ 'src' ], {
+ help: 'Source CIF path'
+});
+parser.addArgument([ 'out' ], {
+ help: 'Output BCIF path'
+});
+parser.addArgument([ '-c', '--config' ], {
+ help: 'Optional encoding strategy/precision config path',
+ required: false
+});
+parser.addArgument([ '-f', '--filter' ], {
+ help: 'Optional filter whitelist/blacklist path',
+ required: false
+});
+
+interface Args {
+ src: string
+ out: string
+ config?: string
+ filter?: string
+}
+const args: Args = parser.parseArgs();
+
+if (args) {
+ run(args)
+}
\ No newline at end of file
diff --git a/src/apps/cifschema/index.ts b/src/apps/cifschema/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..38602d919e917f21b660a37f6171afc65008f6e4
--- /dev/null
+++ b/src/apps/cifschema/index.ts
@@ -0,0 +1,274 @@
+/**
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as argparse from 'argparse'
+import * as fs from 'fs'
+import * as path from 'path'
+import fetch from 'node-fetch'
+
+import { parseCsv } from '../../mol-io/reader/csv/parser'
+import { CifFrame, CifBlock } from '../../mol-io/reader/cif'
+import parseText from '../../mol-io/reader/cif/text/parser'
+import { generateSchema } from './util/cif-dic'
+import { generate } from './util/generate'
+import { Filter, Database } from './util/schema'
+import { parseImportGet } from './util/helper'
+
+function getDicVersion(block: CifBlock) {
+ return block.categories.dictionary.getField('version')!.str(0)
+}
+
+function getDicNamespace(block: CifBlock) {
+ return block.categories.dictionary.getField('namespace')!.str(0)
+}
+
+async function runGenerateSchemaMmcif(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
+ await ensureMmcifDicAvailable()
+ const mmcifDic = await parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
+ if (mmcifDic.isError) throw mmcifDic
+
+ await ensureIhmDicAvailable()
+ const ihmDic = await parseText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
+ if (ihmDic.isError) throw ihmDic
+
+ await ensureCarbBranchDicAvailable()
+ const carbBranchDic = await parseText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
+ if (carbBranchDic.isError) throw carbBranchDic
+
+ await ensureCarbCompDicAvailable()
+ const carbCompDic = await parseText(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run();
+ if (carbCompDic.isError) throw carbCompDic
+
+ const mmcifDicVersion = getDicVersion(mmcifDic.result.blocks[0])
+ const ihmDicVersion = getDicVersion(ihmDic.result.blocks[0])
+ const carbDicVersion = 'draft'
+ const version = `Dictionary versions: mmCIF ${mmcifDicVersion}, IHM ${ihmDicVersion}, CARB ${carbDicVersion}.`
+
+ const frames: CifFrame[] = [...mmcifDic.result.blocks[0].saveFrames, ...ihmDic.result.blocks[0].saveFrames, ...carbBranchDic.result.blocks[0].saveFrames, ...carbCompDic.result.blocks[0].saveFrames]
+ const schema = generateSchema(frames)
+
+ await runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases)
+}
+
+async function runGenerateSchemaCifCore(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
+ await ensureCifCoreDicAvailable()
+ const cifCoreDic = await parseText(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run();
+ if (cifCoreDic.isError) throw cifCoreDic
+
+ const cifCoreDicVersion = getDicVersion(cifCoreDic.result.blocks[0])
+ const version = `Dictionary versions: CifCore ${cifCoreDicVersion}.`
+
+ const frames: CifFrame[] = [...cifCoreDic.result.blocks[0].saveFrames]
+ const imports = await resolveImports(frames, DIC_DIR)
+ const schema = generateSchema(frames, imports)
+
+ await runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases)
+}
+
+async function resolveImports(frames: CifFrame[], baseDir: string): Promise<Map<string, CifFrame[]>> {
+ const imports = new Map<string, CifFrame[]>()
+
+ for (const d of frames) {
+ if ('import' in d.categories) {
+ const importGet = parseImportGet(d.categories['import'].getField('get')!.str(0))
+ for (const g of importGet) {
+ const { file } = g
+ if (!file) continue
+ if (imports.has(file)) continue
+
+ const dic = await parseText(fs.readFileSync(path.join(baseDir, file), 'utf8')).run();
+ if (dic.isError) throw dic
+
+ imports.set(file, [...dic.result.blocks[0].saveFrames])
+ }
+ }
+ }
+
+ return imports
+}
+
+async function runGenerateSchemaDic(name: string, dicPath: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
+ const dic = await parseText(fs.readFileSync(dicPath, 'utf8')).run();
+ if (dic.isError) throw dic
+
+ const dicVersion = getDicVersion(dic.result.blocks[0])
+ const dicName = getDicNamespace(dic.result.blocks[0])
+ const version = `Dictionary versions: ${dicName} ${dicVersion}.`
+
+ const frames: CifFrame[] = [...dic.result.blocks[0].saveFrames]
+ const imports = await resolveImports(frames, path.dirname(dicPath))
+ const schema = generateSchema(frames, imports)
+
+ await runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases)
+}
+
+async function runGenerateSchema(name: string, version: string, schema: Database, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
+ const filter = fieldNamesPath ? await getFieldNamesFilter(fieldNamesPath) : undefined
+ const output = typescript ? generate(name, version, schema, filter, moldbImportPath, addAliases) : JSON.stringify(schema, undefined, 4)
+
+ if (out) {
+ fs.writeFileSync(out, output)
+ } else {
+ console.log(output)
+ }
+}
+
+async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
+ const fieldNamesStr = fs.readFileSync(fieldNamesPath, 'utf8')
+ const parsed = await parseCsv(fieldNamesStr, { noColumnNames: true }).run();
+ if (parsed.isError) throw parser.error
+ const csvFile = parsed.result;
+
+ const fieldNamesCol = csvFile.table.getColumn('0')
+ if (!fieldNamesCol) throw 'error getting fields columns'
+ const fieldNames = fieldNamesCol.toStringArray()
+
+ const filter: Filter = {}
+ fieldNames.forEach((name, i) => {
+ const [ category, field ] = name.split('.')
+ // console.log(category, field)
+ if (!filter[ category ]) filter[ category ] = {}
+ filter[ category ][ field ] = true
+ })
+ return filter
+}
+
+async function ensureMmcifDicAvailable() { await ensureDicAvailable(MMCIF_DIC_PATH, MMCIF_DIC_URL) }
+async function ensureIhmDicAvailable() { await ensureDicAvailable(IHM_DIC_PATH, IHM_DIC_URL) }
+async function ensureCarbBranchDicAvailable() { await ensureDicAvailable(CARB_BRANCH_DIC_PATH, CARB_BRANCH_DIC_URL) }
+async function ensureCarbCompDicAvailable() { await ensureDicAvailable(CARB_COMP_DIC_PATH, CARB_COMP_DIC_URL) }
+async function ensureCifCoreDicAvailable() {
+ await ensureDicAvailable(CIF_CORE_DIC_PATH, CIF_CORE_DIC_URL)
+ await ensureDicAvailable(CIF_CORE_ENUM_PATH, CIF_CORE_ENUM_URL)
+ await ensureDicAvailable(CIF_CORE_ATTR_PATH, CIF_CORE_ATTR_URL)
+}
+
+async function ensureDicAvailable(dicPath: string, dicUrl: string) {
+ if (FORCE_DIC_DOWNLOAD || !fs.existsSync(dicPath)) {
+ const name = dicUrl.substr(dicUrl.lastIndexOf('/') + 1)
+ console.log(`downloading ${name}...`)
+ const data = await fetch(dicUrl)
+ if (!fs.existsSync(DIC_DIR)) {
+ fs.mkdirSync(DIC_DIR);
+ }
+ fs.writeFileSync(dicPath, await data.text())
+ console.log(`done downloading ${name}`)
+ }
+}
+
+const DIC_DIR = path.resolve(__dirname, '../dics/')
+const MMCIF_DIC_PATH = `${DIC_DIR}/mmcif_pdbx_v50.dic`
+const MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic'
+const IHM_DIC_PATH = `${DIC_DIR}/ihm-extension.dic`
+const IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/master/ihm-extension.dic'
+const CARB_BRANCH_DIC_PATH = `${DIC_DIR}/entity_branch-extension.dic`
+const CARB_BRANCH_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/entity_branch-extension.dic'
+const CARB_COMP_DIC_PATH = `${DIC_DIR}/chem_comp-extension.dic`
+const CARB_COMP_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/chem_comp-extension.dic'
+
+const CIF_CORE_DIC_PATH = `${DIC_DIR}/cif_core.dic`
+const CIF_CORE_DIC_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic'
+const CIF_CORE_ENUM_PATH = `${DIC_DIR}/templ_enum.cif`
+const CIF_CORE_ENUM_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_enum.cif'
+const CIF_CORE_ATTR_PATH = `${DIC_DIR}/templ_attr.cif`
+const CIF_CORE_ATTR_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_attr.cif'
+
+const parser = new argparse.ArgumentParser({
+ addHelp: true,
+ description: 'Create schema from mmcif dictionary (v50 plus IHM and entity_branch extensions, downloaded from wwPDB)'
+});
+parser.addArgument([ '--preset', '-p' ], {
+ defaultValue: '',
+ choices: ['', 'mmCIF', 'CCD', 'BIRD', 'CifCore'],
+ help: 'Preset name'
+});
+parser.addArgument([ '--name', '-n' ], {
+ defaultValue: '',
+ help: 'Schema name'
+});
+parser.addArgument([ '--out', '-o' ], {
+ help: 'Generated schema output path, if not given printed to stdout'
+});
+parser.addArgument([ '--targetFormat', '-tf' ], {
+ defaultValue: 'typescript-molstar',
+ choices: ['typescript-molstar', 'json-internal'],
+ help: 'Target format'
+});
+parser.addArgument([ '--dicPath', '-d' ], {
+ defaultValue: '',
+ help: 'Path to dictionary'
+});
+parser.addArgument([ '--fieldNamesPath', '-fn' ], {
+ defaultValue: '',
+ help: 'Field names to include'
+});
+parser.addArgument([ '--forceDicDownload', '-f' ], {
+ action: 'storeTrue',
+ help: 'Force download of dictionaries'
+});
+parser.addArgument([ '--moldataImportPath', '-mip' ], {
+ defaultValue: 'molstar/lib/mol-data',
+ help: 'mol-data import path (for typescript target only)'
+});
+parser.addArgument([ '--addAliases', '-aa' ], {
+ action: 'storeTrue',
+ help: 'Add field name/path aliases'
+});
+interface Args {
+ name: string
+ preset: '' | 'mmCIF' | 'CCD' | 'BIRD' | 'CifCore'
+ forceDicDownload: boolean
+ dic: '' | 'mmCIF' | 'CifCore'
+ dicPath: string,
+ fieldNamesPath: string
+ targetFormat: 'typescript-molstar' | 'json-internal'
+ out: string,
+ moldataImportPath: string
+ addAliases: boolean
+}
+const args: Args = parser.parseArgs();
+
+const FORCE_DIC_DOWNLOAD = args.forceDicDownload
+
+switch (args.preset) {
+ case 'mmCIF':
+ args.name = 'mmCIF'
+ args.dic = 'mmCIF'
+ args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/mmcif-field-names.csv')
+ break
+ case 'CCD':
+ args.name = 'CCD'
+ args.dic = 'mmCIF'
+ args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/ccd-field-names.csv')
+ break
+ case 'BIRD':
+ args.name = 'BIRD'
+ args.dic = 'mmCIF'
+ args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/bird-field-names.csv')
+ break
+ case 'CifCore':
+ args.name = 'CifCore'
+ args.dic = 'CifCore'
+ args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/cif-core-field-names.csv')
+ break
+}
+
+if (args.name) {
+ const typescript = args.targetFormat === 'typescript-molstar'
+ if (args.dicPath) {
+ runGenerateSchemaDic(args.name, args.dicPath, args.fieldNamesPath, typescript, args.out, args.moldataImportPath, args.addAliases).catch(e => {
+ console.error(e)
+ })
+ } else if (args.dic === 'mmCIF') {
+ runGenerateSchemaMmcif(args.name, args.fieldNamesPath, typescript, args.out, args.moldataImportPath, args.addAliases).catch(e => {
+ console.error(e)
+ })
+ } else if (args.dic === 'CifCore') {
+ runGenerateSchemaCifCore(args.name, args.fieldNamesPath, typescript, args.out, args.moldataImportPath, args.addAliases).catch(e => {
+ console.error(e)
+ })
+ }
+}
diff --git a/src/apps/cifschema/util/cif-dic.ts b/src/apps/cifschema/util/cif-dic.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2f43e75a00009ae4a2ab604c52c1fd401e6112db
--- /dev/null
+++ b/src/apps/cifschema/util/cif-dic.ts
@@ -0,0 +1,446 @@
+/**
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Database, Column, EnumCol, StrCol, IntCol, ListCol, FloatCol, CoordCol, MatrixCol, VectorCol } from './schema'
+import { parseImportGet } from './helper'
+import * as Data from '../../../mol-io/reader/cif/data-model'
+import { CifFrame } from '../../../mol-io/reader/cif/data-model';
+
+export function getFieldType(type: string, description: string, values?: string[], container?: string): Column {
+ switch (type) {
+ // mmCIF
+ case 'code':
+ case 'ucode':
+ case 'line':
+ case 'uline':
+ case 'text':
+ case 'char':
+ case 'uchar3':
+ case 'uchar1':
+ case 'boolean':
+ return values && values.length ? EnumCol(values, 'str', description) : StrCol(description)
+ case 'aliasname':
+ case 'name':
+ case 'idname':
+ case 'any':
+ case 'atcode':
+ case 'fax':
+ case 'phone':
+ case 'email':
+ case 'code30':
+ case 'seq-one-letter-code':
+ case 'author':
+ case 'orcid_id':
+ case 'sequence_dep':
+ case 'pdb_id':
+ case 'emd_id':
+ // todo, consider adding specialised fields
+ case 'yyyy-mm-dd':
+ case 'yyyy-mm-dd:hh:mm':
+ case 'yyyy-mm-dd:hh:mm-flex':
+ case 'int-range':
+ case 'float-range':
+ case 'binary':
+ case 'operation_expression':
+ case 'point_symmetry':
+ case '4x3_matrix':
+ case '3x4_matrices':
+ case 'point_group':
+ case 'point_group_helical':
+ case 'symmetry_operation':
+ case 'date_dep':
+ case 'url':
+ case 'symop':
+ case 'exp_data_doi':
+ case 'asym_id':
+ return StrCol(description)
+ case 'int':
+ case 'non_negative_int':
+ case 'positive_int':
+ return values && values.length ? EnumCol(values, 'int', description) : IntCol(description)
+ case 'float':
+ return FloatCol(description)
+ case 'ec-type':
+ case 'ucode-alphanum-csv':
+ case 'id_list':
+ return ListCol('str', ',', description)
+ case 'id_list_spc':
+ return ListCol('str', ' ', description)
+
+ // cif
+ case 'Text':
+ case 'Code':
+ case 'Complex':
+ case 'Symop':
+ case 'List':
+ case 'List(Real,Real)':
+ case 'List(Real,Real,Real,Real)':
+ case 'Date':
+ case 'Datetime':
+ case 'Tag':
+ case 'Implied':
+ return wrapContainer('str', ',', description, container)
+ case 'Real':
+ return wrapContainer('float', ',', description, container)
+ case 'Integer':
+ return wrapContainer('int', ',', description, container)
+
+ }
+ console.log(`unknown type '${type}'`)
+ return StrCol(description)
+}
+
+function ColFromType(type: 'int' | 'str' | 'float' | 'coord', description: string): Column {
+ switch (type) {
+ case 'int': return IntCol(description)
+ case 'str': return StrCol(description)
+ case 'float': return FloatCol(description)
+ case 'coord': return CoordCol(description)
+ }
+}
+
+function wrapContainer(type: 'int' | 'str' | 'float' | 'coord', separator: string, description: string, container?: string) {
+ return container && container === 'List' ? ListCol(type, separator, description) : ColFromType(type, description)
+}
+
+type FrameCategories = { [category: string]: Data.CifFrame }
+type FrameLinks = { [k: string]: string }
+
+interface FrameData {
+ categories: FrameCategories
+ links: FrameLinks
+}
+
+type Imports = Map<string, CifFrame[]>
+
+function getImportFrames(d: Data.CifFrame, imports: Imports) {
+ const frames: Data.CifFrame[] = []
+ if (!('import' in d.categories)) return frames
+
+ const importGet = parseImportGet(d.categories['import'].getField('get')!.str(0))
+ for (const g of importGet) {
+ const { file, save } = g
+ if (!file || !save) {
+ console.warn(`missing 'save' or 'file' for import in '${d.header}'`)
+ continue
+ }
+ const importFrames = imports.get(file)
+ if (!importFrames) {
+ console.warn(`missing '${file}' entry in imports`)
+ continue
+ }
+ const importSave = importFrames.find(id => id.header.toLowerCase() === save.toLowerCase())
+ if (!importSave) {
+ console.warn(`missing '${save}' save frame in '${file}'`)
+ continue
+ }
+
+ frames.push(importSave)
+ }
+
+ return frames
+}
+
+/** get field from given or linked category */
+function getField(category: string, field: string, d: Data.CifFrame, imports: Imports, ctx: FrameData): Data.CifField|undefined {
+ const { categories, links } = ctx
+ const cat = d.categories[category]
+ if (cat) {
+ return cat.getField(field)
+ } else if (d.header in links) {
+ const linkName = links[d.header]
+ if (linkName in categories) {
+ return getField(category, field, categories[linkName], imports, ctx)
+ } else {
+ // console.log(`link '${linkName}' not found`)
+ }
+ } else {
+ const importFrames = getImportFrames(d, imports)
+ for (const idf of importFrames) {
+ return getField(category, field, idf, imports, ctx)
+ }
+ }
+}
+
+function getEnums(d: Data.CifFrame, imports: Imports, ctx: FrameData) {
+ const value = getField('item_enumeration', 'value', d, imports, ctx)
+ const enums: string[] = []
+ if (value) {
+ for (let i = 0; i < value.rowCount; ++i) {
+ enums.push(value.str(i))
+ // console.log(value.str(i))
+ }
+ return enums
+ } else {
+ // console.log(`item_enumeration.value not found for '${d.header}'`)
+ }
+}
+
+function getContainer(d: Data.CifFrame, imports: Imports, ctx: FrameData) {
+ const value = getField('type', 'container', d, imports, ctx)
+ return value ? value.str(0) : undefined
+}
+
+function getCode(d: Data.CifFrame, imports: Imports, ctx: FrameData): [string, string[] | undefined, string | undefined ] | undefined {
+ const code = getField('item_type', 'code', d, imports, ctx) || getField('type', 'contents', d, imports, ctx)
+ if (code) {
+ return [ code.str(0), getEnums(d, imports, ctx), getContainer(d, imports, ctx) ]
+ } else {
+ console.log(`item_type.code or type.contents not found for '${d.header}'`)
+ }
+}
+
+function getSubCategory(d: Data.CifFrame, imports: Imports, ctx: FrameData): string | undefined {
+ const value = getField('item_sub_category', 'id', d, imports, ctx)
+ if (value) {
+ return value.str(0)
+ }
+}
+
+function getDescription(d: Data.CifFrame, imports: Imports, ctx: FrameData): string | undefined {
+ const value = getField('item_description', 'description', d, imports, ctx) || getField('description', 'text', d, imports, ctx)
+ if (value) {
+ // trim (after newlines) and remove references to square brackets
+ return value.str(0).trim()
+ .replace(/(\r\n|\r|\n)([ \t]+)/g, '\n')
+ .replace(/(\[[1-3]\])+ element/, 'elements')
+ .replace(/(\[[1-3]\])+/, '')
+ }
+}
+
+function getAliases(d: Data.CifFrame, imports: Imports, ctx: FrameData): string[] | undefined {
+ const value = getField('item_aliases', 'alias_name', d, imports, ctx) || getField('alias', 'definition_id', d, imports, ctx)
+ return value ? value.toStringArray().map(v => v.substr(1)) : undefined
+}
+
+const reMatrixField = /\[[1-3]\]\[[1-3]\]/
+const reVectorField = /\[[1-3]\]/
+
+const FORCE_INT_FIELDS = [
+ '_atom_site.id',
+ '_atom_site.auth_seq_id',
+ '_atom_site_anisotrop.id',
+ '_pdbx_struct_mod_residue.auth_seq_id',
+ '_struct_conf.beg_auth_seq_id',
+ '_struct_conf.end_auth_seq_id',
+ '_struct_conn.ptnr1_auth_seq_id',
+ '_struct_conn.ptnr2_auth_seq_id',
+ '_struct_sheet_range.beg_auth_seq_id',
+ '_struct_sheet_range.end_auth_seq_id',
+];
+
+const COMMA_SEPARATED_LIST_FIELDS = [
+ '_atom_site.pdbx_struct_group_id',
+ '_chem_comp.mon_nstd_parent_comp_id',
+ '_diffrn_radiation.pdbx_wavelength_list',
+ '_diffrn_source.pdbx_wavelength_list',
+ '_em_diffraction.tilt_angle_list', // 20,40,50,55
+ '_em_entity_assembly.entity_id_list',
+ '_entity.pdbx_description', // Endolysin,Beta-2 adrenergic receptor
+ '_entity.pdbx_ec',
+ '_entity_poly.pdbx_strand_id', // A,B
+ '_entity_src_gen.pdbx_gene_src_gene', // ADRB2, ADRB2R, B2AR
+ '_pdbx_depui_entry_details.experimental_methods',
+ '_pdbx_depui_entry_details.requested_accession_types',
+ '_pdbx_soln_scatter_model.software_list', // INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI
+ '_pdbx_soln_scatter_model.software_author_list', // MSI
+ '_pdbx_soln_scatter_model.entry_fitting_list', // Odd example: 'PDB CODE 1HFI, 1HCC, 1HFH, 1VCC'
+ '_pdbx_struct_assembly_gen.entity_inst_id',
+ '_pdbx_struct_assembly_gen.asym_id_list',
+ '_pdbx_struct_assembly_gen.auth_asym_id_list',
+ '_pdbx_struct_assembly_gen_depositor_info.asym_id_list',
+ '_pdbx_struct_assembly_gen_depositor_info.chain_id_list',
+ '_pdbx_struct_group_list.group_enumeration_type',
+ '_reflns.pdbx_diffrn_id',
+ '_refine.pdbx_diffrn_id',
+ '_reflns_shell.pdbx_diffrn_id',
+ '_struct_keywords.text',
+];
+
+const SPACE_SEPARATED_LIST_FIELDS = [
+ '_chem_comp.pdbx_subcomponent_list', // TSM DPH HIS CHF EMR
+ '_pdbx_soln_scatter.data_reduction_software_list', // OTOKO
+ '_pdbx_soln_scatter.data_analysis_software_list', // SCTPL5 GNOM
+];
+
+const SEMICOLON_SEPARATED_LIST_FIELDS = [
+ '_chem_comp.pdbx_synonyms' // GLYCERIN; PROPANE-1,2,3-TRIOL
+]
+
+/**
+ * Useful when a dictionary extension will add enum values to an existing dictionary.
+ * By adding them here, the dictionary extension can be tested before the added enum
+ * values are available in the existing dictionary.
+ */
+const EXTRA_ENUM_VALUES: { [k: string]: string[] } = {
+
+}
+
+export function generateSchema(frames: CifFrame[], imports: Imports = new Map()): Database {
+
+ const tables: Database['tables'] = {}
+ const aliases: Database['aliases'] = {}
+
+ const categories: FrameCategories = {}
+ const links: FrameLinks = {}
+ const ctx = { categories, links }
+
+ // get category metadata
+ frames.forEach(d => {
+ // category definitions in mmCIF start with '_' and don't include a '.'
+ // category definitions in cif don't include a '.'
+ if (d.header[0] === '_' || d.header.includes('.')) return
+ const categoryName = d.header.toLowerCase()
+ // console.log(d.header, d.categoryNames, d.categories)
+ let descriptionField: Data.CifField | undefined
+ const categoryKeyNames = new Set<string>()
+
+ if ('category' in d.categories && 'category_key' in d.categories) {
+ const category = d.categories['category']
+ const categoryKey = d.categories['category_key']
+ if (categoryKey) {
+ const categoryKey_names = categoryKey.getField('name')
+ if (categoryKey_names) {
+ for (let i = 0, il = categoryKey_names.rowCount; i < il; ++i) {
+ categoryKeyNames.add(categoryKey_names.str(i))
+ }
+ }
+ }
+
+ descriptionField = category.getField('description')
+
+ if (categoryKeyNames.size === 0) {
+ console.log(`no key given for category '${categoryName}'`)
+ }
+ }
+
+ if ('description' in d.categories) {
+ descriptionField = d.categories['description'].getField('text')
+ }
+
+ let description = ''
+ if (descriptionField) {
+ description = descriptionField.str(0).trim()
+ .replace(/(\r\n|\r|\n)([ \t]+)/g, '\n') // remove padding after newlines
+ } else {
+ console.log(`no description given for category '${categoryName}'`)
+ }
+
+ tables[categoryName] = { description, key: categoryKeyNames, columns: {} }
+
+ // console.log('++++++++++++++++++++++++++++++++++++++++++')
+ // console.log('name', categoryName)
+ // console.log('desc', description)
+ // console.log('key', categoryKeyNames)
+ })
+
+ // build list of links between categories
+ frames.forEach(d => {
+ if (d.header[0] !== '_' && !d.header.includes('.')) return
+ categories[d.header] = d
+ const item_linked = d.categories['item_linked']
+ if (item_linked) {
+ const child_name = item_linked.getField('child_name')
+ const parent_name = item_linked.getField('parent_name')
+ if (child_name && parent_name) {
+ for (let i = 0; i < item_linked.rowCount; ++i) {
+ const childName = child_name.str(i)
+ const parentName = parent_name.str(i)
+ if (childName in links && links[childName] !== parentName) {
+ console.log(`${childName} linked to ${links[childName]}, ignoring link to ${parentName}`)
+ }
+ links[childName] = parentName
+ }
+ }
+ }
+ })
+
+ // get field data
+ Object.keys(categories).forEach(fullName => {
+ const d = categories[fullName]
+ if (!d) {
+ console.log(`'${fullName}' not found, moving on`)
+ return
+ }
+
+ const categoryName = d.header.substring(d.header[0] === '_' ? 1 : 0, d.header.indexOf('.'))
+ const itemName = d.header.substring(d.header.indexOf('.') + 1)
+ let fields: { [k: string]: Column }
+ if (categoryName in tables) {
+ fields = tables[categoryName].columns
+ tables[categoryName].key.add(itemName)
+ } else if (categoryName.toLowerCase() in tables) {
+ // take case from category name in 'field' data as it is better if data is from cif dictionaries
+ tables[categoryName] = tables[categoryName.toLowerCase()]
+ fields = tables[categoryName].columns
+ } else {
+ console.log(`category '${categoryName}' has no metadata`)
+ fields = {}
+ tables[categoryName] = {
+ description: '',
+ key: new Set(),
+ columns: fields
+ }
+ }
+
+ const itemAliases = getAliases(d, imports, ctx)
+ if (itemAliases) aliases[`${categoryName}.${itemName}`] = itemAliases
+
+ const description = getDescription(d, imports, ctx) || ''
+
+ // need to use regex to check for matrix or vector items
+ // as sub_category assignment is missing for some entries
+ const subCategory = getSubCategory(d, imports, ctx)
+ if (subCategory === 'cartesian_coordinate' || subCategory === 'fractional_coordinate') {
+ fields[itemName] = CoordCol(description)
+ } else if (FORCE_INT_FIELDS.includes(d.header)) {
+ fields[itemName] = IntCol(description)
+ console.log(`forcing int: ${d.header}`)
+ } else if (subCategory === 'matrix') {
+ fields[itemName.replace(reMatrixField, '')] = MatrixCol(3, 3, description)
+ } else if (subCategory === 'vector') {
+ fields[itemName.replace(reVectorField, '')] = VectorCol(3, description)
+ } else {
+ if (itemName.match(reMatrixField)) {
+ fields[itemName.replace(reMatrixField, '')] = MatrixCol(3, 3, description)
+ console.log(`${d.header} should have 'matrix' _item_sub_category.id`)
+ } else if (itemName.match(reVectorField)) {
+ fields[itemName.replace(reVectorField, '')] = VectorCol(3, description)
+ console.log(`${d.header} should have 'vector' _item_sub_category.id`)
+ } else {
+ const code = getCode(d, imports, ctx)
+ if (code) {
+ let fieldType = getFieldType(code[0], description, code[1], code[2]);
+ if (fieldType.type === 'str') {
+ if (COMMA_SEPARATED_LIST_FIELDS.includes(d.header)) {
+ fieldType = ListCol('str', ',', description)
+ console.log(`forcing comma separated: ${d.header}`)
+ } else if (SPACE_SEPARATED_LIST_FIELDS.includes(d.header)) {
+ fieldType = ListCol('str', ' ', description)
+ console.log(`forcing space separated: ${d.header}`)
+ } else if (SEMICOLON_SEPARATED_LIST_FIELDS.includes(d.header)) {
+ fieldType = ListCol('str', ';', description)
+ console.log(`forcing space separated: ${d.header}`)
+ }
+ }
+ if (d.header in EXTRA_ENUM_VALUES) {
+ if (fieldType.type === 'enum') {
+ fieldType.values.push(...EXTRA_ENUM_VALUES[d.header])
+ } else {
+ console.warn(`expected enum: ${d.header}`)
+ }
+ }
+ fields[itemName] = fieldType
+ } else {
+ fields[itemName] = StrCol(description)
+ // console.log(`could not determine code for '${d.header}'`)
+ }
+ }
+ }
+ })
+
+ return { tables, aliases }
+}
diff --git a/src/apps/cifschema/util/generate.ts b/src/apps/cifschema/util/generate.ts
new file mode 100644
index 0000000000000000000000000000000000000000..5024811cd9ab0bfc05f359388a745d886f8f02ee
--- /dev/null
+++ b/src/apps/cifschema/util/generate.ts
@@ -0,0 +1,151 @@
+/**
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Database, Filter, Column } from './schema'
+import { indentString } from '../../../mol-util/string'
+import { FieldPath } from '../../../mol-io/reader/cif/schema';
+
+function header (name: string, info: string, moldataImportPath: string) {
+ return `/**
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated '${name}' schema file. ${info}
+ *
+ * @author molstar/ciftools package
+ */
+
+import { Database, Column } from '${moldataImportPath}/db'
+
+import Schema = Column.Schema`
+}
+
+function footer (name: string) {
+ return `
+export type ${name}_Schema = typeof ${name}_Schema;
+export interface ${name}_Database extends Database<${name}_Schema> {}`
+}
+
+function getTypeShorthands(schema: Database, fields?: Filter) {
+ const types = new Set<string>()
+ Object.keys(schema.tables).forEach(table => {
+ if (fields && !fields[table]) return
+ const { columns } = schema.tables[table]
+ Object.keys(columns).forEach(columnName => {
+ if (fields && !fields[table][columnName]) return
+ types.add(schema.tables[table].columns[columnName].type)
+ })
+ })
+ const shorthands: string[] = []
+ types.forEach(type => {
+ switch (type) {
+ case 'str': shorthands.push('const str = Schema.str;'); break
+ case 'int': shorthands.push('const int = Schema.int;'); break
+ case 'float': shorthands.push('const float = Schema.float;'); break
+ case 'coord': shorthands.push('const coord = Schema.coord;'); break
+ case 'enum': shorthands.push('const Aliased = Schema.Aliased;'); break
+ case 'matrix': shorthands.push('const Matrix = Schema.Matrix;'); break
+ case 'vector': shorthands.push('const Vector = Schema.Vector;'); break
+ case 'list': shorthands.push('const List = Schema.List;'); break
+ }
+ })
+ return shorthands.join('\n')
+}
+
+function getTypeDef(c: Column): string {
+ switch (c.type) {
+ case 'str': return 'str'
+ case 'int': return 'int'
+ case 'float': return 'float'
+ case 'coord': return 'coord'
+ case 'enum':
+ return `Aliased<'${c.values.map(v => v.replace(/'/g, '\\\'')).join(`' | '`)}'>(${c.subType})`
+ case 'matrix':
+ return `Matrix(${c.rows}, ${c.columns})`
+ case 'vector':
+ return `Vector(${c.length})`
+ case 'list':
+ if (c.subType === 'int') {
+ return `List('${c.separator}', x => parseInt(x, 10))`
+ } else if (c.subType === 'float' || c.subType === 'coord') {
+ return `List('${c.separator}', x => parseFloat(x))`
+ } else {
+ return `List('${c.separator}', x => x)`
+ }
+ }
+}
+
+const reSafePropertyName = /^[a-zA-Z_$][0-9a-zA-Z_$]*$/
+function safePropertyString(name: string) { return name.match(reSafePropertyName) ? name : `'${name}'` }
+
+function doc(description: string, spacesCount: number) {
+ const spaces = ' '.repeat(spacesCount)
+ return [
+ `${spaces}/**`,
+ `${indentString(description, 1, `${spaces} * `)}`.replace(/ +\n/g, '\n'),
+ `${spaces} */`
+ ].join('\n')
+}
+
+export function generate (name: string, info: string, schema: Database, fields: Filter | undefined, moldataImportPath: string, addAliases: boolean) {
+ const codeLines: string[] = []
+
+ if (fields) {
+ Object.keys(fields).forEach(table => {
+ if (table in schema.tables) {
+ const schemaTable = schema.tables[table]
+ Object.keys(fields[table]).forEach(column => {
+ if (!(column in schemaTable.columns)) {
+ console.log(`filter field '${table}.${column}' not found in schema`)
+ }
+ })
+ } else {
+ console.log(`filter category '${table}' not found in schema`)
+ }
+ })
+ }
+
+ codeLines.push(`export const ${name}_Schema = {`)
+ Object.keys(schema.tables).forEach(table => {
+ if (fields && !fields[table]) return
+ const { description, columns } = schema.tables[table]
+ if (description) codeLines.push(doc(description, 4))
+ codeLines.push(` ${safePropertyString(table)}: {`)
+ Object.keys(columns).forEach(columnName => {
+ if (fields && !fields[table][columnName]) return
+ const c = columns[columnName]
+ const typeDef = getTypeDef(c)
+ if (c.description) codeLines.push(doc(c.description, 8))
+ codeLines.push(` ${safePropertyString(columnName)}: ${typeDef},`)
+ })
+ codeLines.push(' },')
+ })
+ codeLines.push('}')
+
+ if (addAliases) {
+ codeLines.push('')
+ codeLines.push(`export const ${name}_Aliases = {`)
+ Object.keys(schema.aliases).forEach(path => {
+ const [ table, columnName ] = path.split('.')
+ if (fields && !fields[table]) return
+ if (fields && !fields[table][columnName]) return
+
+ const filteredAliases = new Set<string>()
+ schema.aliases[path].forEach(p => {
+ if (!FieldPath.equal(p, path)) filteredAliases.add(FieldPath.canonical(p))
+ })
+
+ if (filteredAliases.size === 0) return
+ codeLines.push(` ${safePropertyString(path)}: [`)
+ filteredAliases.forEach(alias => {
+ codeLines.push(` '${alias}',`)
+ })
+ codeLines.push(' ],')
+ })
+ codeLines.push('}')
+ }
+
+ return `${header(name, info, moldataImportPath)}\n\n${getTypeShorthands(schema, fields)}\n\n${codeLines.join('\n')}\n${footer(name)}`
+}
\ No newline at end of file
diff --git a/src/apps/cifschema/util/helper.ts b/src/apps/cifschema/util/helper.ts
new file mode 100644
index 0000000000000000000000000000000000000000..b1bb36bb2b22b2f89dd032fe9c6872f3648b4d55
--- /dev/null
+++ b/src/apps/cifschema/util/helper.ts
@@ -0,0 +1,20 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export type Import = { save?: string, file?: string }
+
+export function parseImportGet(s: string): Import[] {
+ // [{'save':hi_ang_Fox_coeffs 'file':templ_attr.cif} {'save':hi_ang_Fox_c0 'file':templ_enum.cif}]
+ // [{"file":'templ_enum.cif' "save":'H_M_ref'}]
+ return s.trim().substring(2, s.length - 2).split(/}[ \n\t]*{/g).map(s => {
+ const save = s.match(/('save'|"save"):([^ \t\n]+)/)
+ const file = s.match(/('file'|"file"):([^ \t\n]+)/)
+ return {
+ save: save ? save[0].substr(7).replace(/['"]/g, '') : undefined,
+ file: file ? file[0].substr(7).replace(/['"]/g, '') : undefined
+ }
+ })
+}
\ No newline at end of file
diff --git a/src/apps/cifschema/util/schema.ts b/src/apps/cifschema/util/schema.ts
new file mode 100644
index 0000000000000000000000000000000000000000..0647c4f82d5d261c53de3846a88950db7b751a4f
--- /dev/null
+++ b/src/apps/cifschema/util/schema.ts
@@ -0,0 +1,77 @@
+/**
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export interface Database {
+ tables: { [ tableName: string ]: Table }
+ aliases: { [ path: string ]: string[] }
+}
+export interface Table {
+ description: string
+ key: Set<string>
+ columns: { [ columnName: string ]: Column }
+}
+export type Column = IntCol | StrCol | FloatCol | CoordCol | EnumCol | VectorCol | MatrixCol | ListCol
+
+type BaseCol = { description: string }
+
+export type IntCol = { type: 'int' } & BaseCol
+export function IntCol(description: string): IntCol { return { type: 'int', description } }
+
+export type StrCol = { type: 'str' } & BaseCol
+export function StrCol(description: string): StrCol { return { type: 'str', description } }
+
+export type FloatCol = { type: 'float' } & BaseCol
+export function FloatCol(description: string): FloatCol { return { type: 'float', description } }
+
+export type CoordCol = { type: 'coord' } & BaseCol
+export function CoordCol(description: string): CoordCol { return { type: 'coord', description } }
+
+export type EnumCol = { type: 'enum', subType: 'int' | 'str', values: string[] } & BaseCol
+export function EnumCol(values: string[], subType: 'int' | 'str', description: string): EnumCol {
+ return { type: 'enum', description, values, subType }
+}
+
+export type VectorCol = { type: 'vector', length: number } & BaseCol
+export function VectorCol(length: number, description: string): VectorCol {
+ return { type: 'vector', description, length }
+}
+
+export type MatrixCol = { type: 'matrix', rows: number, columns: number } & BaseCol
+export function MatrixCol(columns: number, rows: number, description: string): MatrixCol {
+ return { type: 'matrix', description, columns, rows }
+}
+
+export type ListCol = { type: 'list', subType: 'int' | 'str' | 'float' | 'coord', separator: string } & BaseCol
+export function ListCol(subType: 'int' | 'str' | 'float' | 'coord', separator: string, description: string): ListCol {
+ return { type: 'list', description, separator, subType }
+}
+
+export type Filter = { [ table: string ]: { [ column: string ]: true } }
+
+export function mergeFilters (...filters: Filter[]) {
+ const n = filters.length
+ const mergedFilter: Filter = {}
+ const fields: Map<string, number> = new Map()
+ filters.forEach(filter => {
+ Object.keys(filter).forEach(category => {
+ Object.keys(filter[ category ]).forEach(field => {
+ const key = `${category}.${field}`
+ const value = fields.get(key) || 0
+ fields.set(key, value + 1)
+ })
+ })
+ })
+ fields.forEach((v, k) => {
+ if (v !== n) return
+ const [categoryName, fieldName] = k.split('.')
+ if (categoryName in mergedFilter) {
+ mergedFilter[categoryName][fieldName] = true
+ } else {
+ mergedFilter[categoryName] = { fieldName: true }
+ }
+ })
+ return mergedFilter
+}
diff --git a/src/apps/demos/lighting/index.ts b/src/apps/demos/lighting/index.ts
deleted file mode 100644
index 1a50d7f640f5dc2030defa653d21bfe2f3d54097..0000000000000000000000000000000000000000
--- a/src/apps/demos/lighting/index.ts
+++ /dev/null
@@ -1,178 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { createPlugin, DefaultPluginSpec } from '../../../mol-plugin';
-import './index.html'
-import { PluginContext } from '../../../mol-plugin/context';
-import { PluginCommands } from '../../../mol-plugin/commands';
-import { StateTransforms } from '../../../mol-plugin-state/transforms';
-import { PluginStateObject as PSO } from '../../../mol-plugin-state/objects';
-import { StateBuilder } from '../../../mol-state';
-import { Canvas3DProps } from '../../../mol-canvas3d/canvas3d';
-import { createStructureRepresentationParams } from '../../../mol-plugin-state/helpers/structure-representation-params';
-require('mol-plugin-ui/skin/light.scss')
-
-type SupportedFormats = 'cif' | 'pdb'
-type LoadParams = { url: string, format?: SupportedFormats, assemblyId?: string }
-
-const Canvas3DPresets = {
- illustrative: {
- multiSample: {
- mode: 'temporal' as Canvas3DProps['multiSample']['mode']
- },
- postprocessing: {
- occlusionEnable: true,
- occlusionBias: 0.8,
- occlusionKernelSize: 6,
- outlineEnable: true,
- },
- renderer: {
- ambientIntensity: 1,
- lightIntensity: 0,
- }
- },
- occlusion: {
- multiSample: {
- mode: 'temporal' as Canvas3DProps['multiSample']['mode']
- },
- postprocessing: {
- occlusionEnable: true,
- occlusionBias: 0.8,
- occlusionKernelSize: 6,
- outlineEnable: false,
- },
- renderer: {
- ambientIntensity: 0.4,
- lightIntensity: 0.6,
- }
- },
- standard: {
- multiSample: {
- mode: 'off' as Canvas3DProps['multiSample']['mode']
- },
- postprocessing: {
- occlusionEnable: false,
- outlineEnable: false,
- },
- renderer: {
- ambientIntensity: 0.4,
- lightIntensity: 0.6,
- }
- }
-}
-
-type Canvas3DPreset = keyof typeof Canvas3DPresets
-
-function getPreset(preset: Canvas3DPreset) {
- switch (preset) {
- case 'illustrative': return Canvas3DPresets['illustrative']
- case 'standard': return Canvas3DPresets['standard']
- case 'occlusion': return Canvas3DPresets['occlusion']
- }
-}
-
-class LightingDemo {
- plugin: PluginContext;
-
- init(target: string | HTMLElement) {
- this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
- ...DefaultPluginSpec,
- layout: {
- initial: {
- isExpanded: false,
- showControls: false
- },
- controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' }
- }
- });
-
- this.setPreset('illustrative');
- }
-
- setPreset(preset: Canvas3DPreset) {
- const props = getPreset(preset)
- PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
- ...props,
- multiSample: {
- ...this.plugin.canvas3d!.props.multiSample,
- ...props.multiSample
- },
- renderer: {
- ...this.plugin.canvas3d!.props.renderer,
- ...props.renderer
- },
- postprocessing: {
- ...this.plugin.canvas3d!.props.postprocessing,
- ...props.postprocessing
- },
- }});
- }
-
- private download(b: StateBuilder.To<PSO.Root>, url: string) {
- return b.apply(StateTransforms.Data.Download, { url, isBinary: false })
- }
-
- private parse(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats, assemblyId: string) {
- const parsed = format === 'cif'
- ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
- : b.apply(StateTransforms.Model.TrajectoryFromPDB);
-
- const props = {
- type: {
- name: 'assembly' as const,
- params: { id: assemblyId || 'deposited' }
- }
- }
- return parsed
- .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
- .apply(StateTransforms.Model.StructureFromModel, props, { ref: 'asm' });
- }
-
- private visual(visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
- visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- createStructureRepresentationParams(this.plugin, void 0, { type: 'spacefill', color: 'illustrative' }), { ref: 'seq-visual' });
- visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- createStructureRepresentationParams(this.plugin, void 0, { type: 'ball-and-stick' }), { ref: 'het-visual' });
- return visualRoot;
- }
-
- private loadedParams: LoadParams = { url: '', format: 'cif', assemblyId: '' };
- async load({ url, format = 'cif', assemblyId = '' }: LoadParams) {
- let loadType: 'full' | 'update' = 'full';
-
- const state = this.plugin.state.data;
-
- if (this.loadedParams.url !== url || this.loadedParams.format !== format) {
- loadType = 'full';
- } else if (this.loadedParams.url === url) {
- if (state.select('asm').length > 0) loadType = 'update';
- }
-
- let tree: StateBuilder.Root;
- if (loadType === 'full') {
- await PluginCommands.State.RemoveObject(this.plugin, { state, ref: state.tree.root.ref });
- tree = state.build();
- this.visual(this.parse(this.download(tree.toRoot(), url), format, assemblyId));
- } else {
- const props = {
- type: {
- name: 'assembly' as const,
- params: { id: assemblyId || 'deposited' }
- }
- }
- tree = state.build();
- tree.to('asm').update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
- }
-
- await PluginCommands.State.Update(this.plugin, { state: this.plugin.state.data, tree });
- this.loadedParams = { url, format, assemblyId };
- PluginCommands.Camera.Reset(this.plugin, { });
- }
-}
-
-(window as any).LightingDemo = new LightingDemo();
\ No newline at end of file
diff --git a/src/apps/viewer/extensions/cellpack/model.ts b/src/apps/viewer/extensions/cellpack/model.ts
index 0e9a3d067f999f9b12db02378d5f1224a79eb44d..0c985c078f74bf9d493b8182ac30839aca3ce79e 100644
--- a/src/apps/viewer/extensions/cellpack/model.ts
+++ b/src/apps/viewer/extensions/cellpack/model.ts
@@ -8,9 +8,8 @@ import { StateAction, StateBuilder, StateTransformer, State } from '../../../../
import { PluginContext } from '../../../../mol-plugin/context';
import { PluginStateObject as PSO } from '../../../../mol-plugin-state/objects';
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
-import { Ingredient,IngredientSource, CellPacking } from './data';
-import { getFromPdb, getFromCellPackDB } from './util';
-import { computeStructureBoundary } from '../../../../mol-model/structure/structure/util/boundary';
+import { Ingredient, CellPacking } from './data';
+import { getFromPdb, getFromCellPackDB, IngredientFiles, parseCif, parsePDBfile } from './util';
import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit } from '../../../../mol-model/structure';
import { trajectoryFromMmCIF, MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
import { trajectoryFromPDB } from '../../../../mol-model-formats/structure/pdb';
@@ -35,54 +34,52 @@ function getCellPackModelUrl(fileName: string, baseUrl: string) {
return `${baseUrl}/results/${fileName}`
}
-async function getModel(id: string, source:IngredientSource, baseUrl: string) {
+async function getModel(id: string, baseUrl: string, file?: File) {
let model: Model;
- const mid = source.model? parseInt(source.model) : 0;
- if (id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) {
+ if (file) {
+ const text = await file.text()
+ if (file.name.endsWith('.cif')) {
+ const cif = (await parseCif(text)).blocks[0]
+ model = (await trajectoryFromMmCIF(cif).run())[0]
+ } else if (file.name.endsWith('.pdb')) {
+ const pdb = await parsePDBfile(text, id)
+
+ model = (await trajectoryFromPDB(pdb).run())[0]
+ } else {
+ throw new Error(`unsupported file type '${file.name}'`)
+ }
+ } else if (id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) {
// return
const cif = await getFromPdb(id)
- model = (await trajectoryFromMmCIF(cif).run())[mid]
+ model = (await trajectoryFromMmCIF(cif).run())[0]
} else {
const pdb = await getFromCellPackDB(id, baseUrl)
- model = (await trajectoryFromPDB(pdb).run())[mid]
+ model = (await trajectoryFromPDB(pdb).run())[0]
}
return model
}
-async function getStructure(model: Model, source:IngredientSource, props: { assembly?: string } = {}) {
+async function getStructure(model: Model, props: { assembly?: string } = {}) {
let structure = Structure.ofModel(model)
const { assembly } = props
if (assembly) {
structure = await StructureSymmetry.buildAssembly(structure, assembly).run()
}
- if (source.selection){
- //use NGL selection string or :A or :B etc...
- const asymIds:string[] = source.selection.replace(" :","").split(" or")
- console.log(asymIds)
- const query = MS.struct.modifier.union([
- MS.struct.generator.atomGroups({
- 'chain-test': MS.core.set.has([MS.set(...asymIds), MS.ammp('label_asym_id')])
- })
- ])
- const compiled = compile<StructureSelection>(query)
- const result = compiled(new QueryContext(structure))
- structure = StructureSelection.unionStructure(result)
- }
- else {
- const query = MS.struct.modifier.union([
- MS.struct.generator.atomGroups({
- 'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer'])
- })
- ])
- const compiled = compile<StructureSelection>(query)
- const result = compiled(new QueryContext(structure))
- structure = StructureSelection.unionStructure(result)
- }
+
+ const query = MS.struct.modifier.union([
+ MS.struct.generator.atomGroups({
+ 'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer'])
+ })
+ ])
+ const compiled = compile<StructureSelection>(query)
+ const result = compiled(new QueryContext(structure))
+ structure = StructureSelection.unionStructure(result)
+
return structure
}
-function getTransformLegacy(trans: Vec3, rot: Quat) {
+function getTransform(trans: Vec3, rot: Quat) {
const q: Quat = Quat.create(-rot[3], rot[0], rot[1], rot[2])
const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q)
Mat4.transpose(m, m)
@@ -91,25 +88,13 @@ function getTransformLegacy(trans: Vec3, rot: Quat) {
return m
}
-function getTransform(trans: Vec3, rot: Quat) {
- const q: Quat = Quat.create(rot[0], rot[1], rot[2], rot[3])
- const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q)
- const p: Vec3 = Vec3.create(trans[0],trans[1],trans[2])
- Mat4.setTranslation(m, p)
- return m
-}
-
-function getResultTransforms(results: Ingredient['results'],legacy:boolean) {
- if (legacy) return results.map((r: Ingredient['results'][0]) => getTransformLegacy(r[0], r[1]))
- else return results.map((r: Ingredient['results'][0]) => getTransform(r[0], r[1]))
+function getResultTransforms(results: Ingredient['results']) {
+ return results.map((r: Ingredient['results'][0]) => getTransform(r[0], r[1]))
}
function getCurveTransforms(ingredient: Ingredient) {
const n = ingredient.nbCurve || 0
const instances: Mat4[] = []
- const segmentLength = (ingredient.radii)? ((ingredient.radii[0].radii)?ingredient.radii[0].radii[0]*2.0:3.4):3.4;
- console.log(ingredient.radii);
- console.log(segmentLength);
for (let i = 0; i < n; ++i) {
const cname = `curve${i}`
@@ -124,7 +109,7 @@ function getCurveTransforms(ingredient: Ingredient) {
}
const points = new Float32Array(_points.length * 3)
for (let i = 0, il = _points.length; i < il; ++i) Vec3.toArray(_points[i], points, i * 3)
- const newInstances = getMatFromResamplePoints(points,segmentLength)
+ const newInstances = getMatFromResamplePoints(points)
instances.push(...newInstances)
}
@@ -239,7 +224,7 @@ function getCifCurve(name: string, transforms: Mat4[], model: Model) {
};
}
-async function getCurve(name: string, ingredient:Ingredient, transforms: Mat4[], model: Model) {
+async function getCurve(name: string, transforms: Mat4[], model: Model) {
const cif = getCifCurve(name, transforms, model)
const curveModelTask = Task.create('Curve Model', async ctx => {
@@ -249,78 +234,41 @@ async function getCurve(name: string, ingredient:Ingredient, transforms: Mat4[],
})
const curveModel = await curveModelTask.run()
- return getStructure(curveModel,ingredient.source)
+ return getStructure(curveModel)
}
-async function getIngredientStructure(ingredient: Ingredient, baseUrl: string) {
+async function getIngredientStructure(ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles) {
const { name, source, results, nbCurve } = ingredient
-
- // TODO can these be added to the library?
- if (name === 'HIV1_CAhex_0_1_0') return
- if (name === 'HIV1_CAhexCyclophilA_0_1_0') return
- if (name === 'iLDL') return
- if (name === 'peptides') return
- if (name === 'lypoglycane') return
-
if (source.pdb === 'None') return
- const model = await getModel(source.pdb || name,source, baseUrl)
+ const file = ingredientFiles[source.pdb]
+ if (!file) {
+ // TODO can these be added to the library?
+ if (name === 'HIV1_CAhex_0_1_0') return
+ if (name === 'HIV1_CAhexCyclophilA_0_1_0') return
+ if (name === 'iLDL') return
+ if (name === 'peptides') return
+ if (name === 'lypoglycane') return
+ }
+
+ const model = await getModel(source.pdb || name, baseUrl, file)
if (!model) return
if (nbCurve) {
- return getCurve(name,ingredient, getCurveTransforms(ingredient), model)
+ return getCurve(name, getCurveTransforms(ingredient), model)
} else {
- let bu:string|undefined = source.bu ? source.bu : undefined;
- if (bu){
- if (bu=="AU") {bu = undefined;}
- else {
- bu=bu.slice(2)
- }
- }
- let structure = await getStructure(model,source, { assembly: bu })
- //transform with offset and pcp
- let legacy:boolean = true
- if (ingredient.offset || ingredient.principalAxis)
- //center the structure
- {
- legacy=false
- const boundary = computeStructureBoundary(structure)
- let modelCenter:Vec3 = Vec3.zero()
- Vec3.scale(modelCenter,boundary.sphere.center,-1.0);//Model.getCenter(structure.models[0])
- const m1: Mat4 = Mat4.identity()
- Mat4.setTranslation(m1, modelCenter)
- structure = Structure.transform(structure,m1)
- if (ingredient.offset)
- {
- if (!Vec3.exactEquals(ingredient.offset,Vec3.zero()))
- {
- const m: Mat4 = Mat4.identity();
- Mat4.setTranslation(m, ingredient.offset)
- structure = Structure.transform(structure,m);
- }
- }
- if (ingredient.principalAxis)
- {
- if (!Vec3.exactEquals(ingredient.principalAxis,Vec3.create(0, 0, 1)))
- {
- const q: Quat = Quat.identity();
- Quat.rotationTo(q,ingredient.principalAxis,Vec3.create(0, 0, 1))
- const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q)
- structure = Structure.transform(structure,m);
- }
- }
- }
- return getAssembly(getResultTransforms(results,legacy), structure)
+ const structure = await getStructure(model, { assembly: source.biomt ? '1' : undefined })
+ return getAssembly(getResultTransforms(results), structure)
}
}
-export function createStructureFromCellPack(packing: CellPacking, baseUrl: string) {
+export function createStructureFromCellPack(packing: CellPacking, baseUrl: string, ingredientFiles: IngredientFiles) {
return Task.create('Create Packing Structure', async ctx => {
const { ingredients, name } = packing
const structures: Structure[] = []
for (const iName in ingredients) {
if (ctx.shouldUpdate) await ctx.update(iName)
- const s = await getIngredientStructure(ingredients[iName], baseUrl)
+ const s = await getIngredientStructure(ingredients[iName], baseUrl, ingredientFiles)
if (s) structures.push(s)
}
@@ -411,7 +359,7 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
await handleHivRna({ runtime, fetch: plugin.fetch }, packings, params.baseUrl)
for (let i = 0, il = packings.length; i < il; ++i) {
- const p = { packing: i, baseUrl: params.baseUrl }
+ const p = { packing: i, baseUrl: params.baseUrl, ingredientFiles: params.ingredients.files }
const packing = state.build().to(cellPackBuilder.ref).apply(StructureFromCellpack, p)
await plugin.updateDataState(packing, { revertOnError: true });
@@ -439,12 +387,14 @@ const LoadCellPackModelParams = {
['HIV-1_0.1.6-8_mixed_radii_pdb.cpr', 'HIV-1_0.1.6-8_mixed_radii_pdb'],
['hiv_lipids.bcif', 'hiv_lipids'],
['influenza_model1.json', 'influenza_model1'],
- ['ExosomeModel.json', 'ExosomeModel'],
['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma1.5_mixed_pdb_fixed'],
] as const),
'file': PD.File({ accept: 'id' }),
}, { options: [['id', 'Id'], ['file', 'File']] }),
baseUrl: PD.Text(DefaultCellPackBaseUrl),
+ ingredients : PD.Group({
+ files: PD.FileList({ accept: '.cif,.pdb' })
+ }, { isExpanded: true }),
preset: PD.Group({
traceOnly: PD.Boolean(false),
representation: PD.Select('gaussian-surface', PD.arrayToOptions(['spacefill', 'gaussian-surface', 'point', 'ellipsoid']))
@@ -466,4 +416,4 @@ export const LoadCellPackModel = StateAction.build({
} else {
await loadPackings(ctx, taskCtx, state, params)
}
-}));
+}));
\ No newline at end of file
diff --git a/src/apps/viewer/extensions/cellpack/state.ts b/src/apps/viewer/extensions/cellpack/state.ts
index 1e68b486ec540a8add7b71f84e022f5babe8cbfe..abd983c26808377cda7878eaa28a4c12a889c802 100644
--- a/src/apps/viewer/extensions/cellpack/state.ts
+++ b/src/apps/viewer/extensions/cellpack/state.ts
@@ -9,6 +9,7 @@ import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
import { Task } from '../../../../mol-task';
import { CellPack as _CellPack, Cell, CellPacking } from './data';
import { createStructureFromCellPack } from './model';
+import { IngredientFiles } from './util';
export const DefaultCellPackBaseUrl = 'https://mesoscope.scripps.edu/data/cellPACK_data/cellPACK_database_1.1.0/'
@@ -53,20 +54,27 @@ const StructureFromCellpack = PluginStateTransform.BuiltIn({
if (!a) {
return {
packing: PD.Numeric(0, {}, { description: 'Packing Index' }),
- baseUrl: PD.Text(DefaultCellPackBaseUrl)
+ baseUrl: PD.Text(DefaultCellPackBaseUrl),
+ ingredientFiles: PD.FileList({ accept: '.cif,.pdb' })
};
}
const options = a.data.packings.map((d, i) => [i, d.name] as [number, string])
return {
packing: PD.Select(0, options),
- baseUrl: PD.Text(DefaultCellPackBaseUrl)
+ baseUrl: PD.Text(DefaultCellPackBaseUrl),
+ ingredientFiles: PD.FileList({ accept: '.cif,.pdb' })
}
}
})({
apply({ a, params }) {
return Task.create('Structure from CellPack', async ctx => {
const packing = a.data.packings[params.packing]
- const structure = await createStructureFromCellPack(packing, params.baseUrl).runInContext(ctx)
+ const ingredientFiles: IngredientFiles = {}
+ for (let i = 0, il = params.ingredientFiles.length; i < il; ++i) {
+ const file = params.ingredientFiles.item(i)
+ if (file) ingredientFiles[file.name] = file
+ }
+ const structure = await createStructureFromCellPack(packing, params.baseUrl, ingredientFiles).runInContext(ctx)
return new PSO.Molecule.Structure(structure, { label: packing.name })
});
}
diff --git a/src/apps/viewer/extensions/cellpack/util.ts b/src/apps/viewer/extensions/cellpack/util.ts
index 6e64ed3dff740caea81d450a2d80286e800470a8..4c36a142b6e00ee79cd384e447660a599ab1da61 100644
--- a/src/apps/viewer/extensions/cellpack/util.ts
+++ b/src/apps/viewer/extensions/cellpack/util.ts
@@ -7,14 +7,14 @@
import { CIF } from '../../../../mol-io/reader/cif'
import { parsePDB } from '../../../../mol-io/reader/pdb/parser';
-async function parseCif(data: string|Uint8Array) {
+export async function parseCif(data: string|Uint8Array) {
const comp = CIF.parse(data);
const parsed = await comp.run();
if (parsed.isError) throw parsed;
return parsed.result;
}
-async function parsePDBfile(data: string, id: string) {
+export async function parsePDBfile(data: string, id: string) {
const comp = parsePDB(data, id);
const parsed = await comp.run();
if (parsed.isError) throw parsed;
@@ -45,4 +45,6 @@ export async function getFromCellPackDB(id: string, baseUrl: string) {
const name = id.endsWith('.pdb') ? id.substring(0, id.length - 4) : id
const parsed = await downloadPDB(getCellPackDataUrl(id, baseUrl), name);
return parsed;
-}
\ No newline at end of file
+}
+
+export type IngredientFiles = { [name: string]: File }
\ No newline at end of file
diff --git a/src/apps/basic-wrapper/coloring.ts b/src/examples/basic-wrapper/coloring.ts
similarity index 100%
rename from src/apps/basic-wrapper/coloring.ts
rename to src/examples/basic-wrapper/coloring.ts
diff --git a/src/examples/basic-wrapper/controls.tsx b/src/examples/basic-wrapper/controls.tsx
new file mode 100644
index 0000000000000000000000000000000000000000..59e1bdb7c995918e046b65c5867e5464ae842736
--- /dev/null
+++ b/src/examples/basic-wrapper/controls.tsx
@@ -0,0 +1,16 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginUIComponent } from '../../mol-plugin-ui/base';
+import * as React from 'react';
+
+export class CustomToastMessage extends PluginUIComponent {
+ render() {
+ return <>
+ Custom <i>Toast</i> content. No timeout.
+ </>;
+ }
+}
\ No newline at end of file
diff --git a/src/apps/basic-wrapper/index.html b/src/examples/basic-wrapper/index.html
similarity index 96%
rename from src/apps/basic-wrapper/index.html
rename to src/examples/basic-wrapper/index.html
index 7c9a25da6738203aa084b2851e851c649b1441ba..e803d34244d39482e3fc7c96de5e6e2078312e5d 100644
--- a/src/apps/basic-wrapper/index.html
+++ b/src/examples/basic-wrapper/index.html
@@ -50,7 +50,7 @@
<input type='text' id='url' placeholder='url' />
<input type='text' id='assemblyId' placeholder='assembly id' />
<select id='format'>
- <option value='cif' selected>CIF</option>
+ <option value='mmcif' selected>mmCIF</option>
<option value='pdb'>PDB</option>
</select>
</div>
@@ -60,7 +60,7 @@
var pdbId = '1grm', assemblyId= '1';
var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
- var format = 'cif';
+ var format = 'mmcif';
$('url').value = url;
$('url').onchange = function (e) { url = e.target.value; }
@@ -104,6 +104,7 @@
addHeader('Misc');
addControl('Apply Stripes', () => BasicMolStarWrapper.coloring.applyStripes());
+ addControl('Default Coloring', () => BasicMolStarWrapper.coloring.applyDefault());
addHeader('Interactivity');
addControl('Highlight seq_id=7', () => BasicMolStarWrapper.interactivity.highlightOn());
diff --git a/src/examples/basic-wrapper/index.ts b/src/examples/basic-wrapper/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..4fed9b455644763a68fd4bb11837dafcb85cb3c9
--- /dev/null
+++ b/src/examples/basic-wrapper/index.ts
@@ -0,0 +1,155 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { EmptyLoci } from '../../mol-model/loci';
+import { StructureSelection } from '../../mol-model/structure';
+import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { PDBeStructureQualityReport } from '../../mol-plugin/behavior/dynamic/custom-props';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
+import { Script } from '../../mol-script/script';
+import { Color } from '../../mol-util/color';
+import { StripedResidues } from './coloring';
+import { CustomToastMessage } from './controls';
+import './index.html';
+import { buildStaticSuperposition, dynamicSuperpositionTest, StaticSuperpositionTestData } from './superposition';
+require('mol-plugin-ui/skin/light.scss')
+
+type LoadParams = { url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, assemblyId?: string }
+
+class BasicWrapper {
+ plugin: PluginContext;
+
+ init(target: string | HTMLElement) {
+ this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
+ ...DefaultPluginSpec,
+ layout: {
+ initial: {
+ isExpanded: false,
+ showControls: false
+ },
+ controls: {
+ // left: 'none'
+ }
+ },
+ components: {
+ remoteState: 'none'
+ }
+ });
+
+ this.plugin.representation.structure.themes.colorThemeRegistry.add(StripedResidues.colorThemeProvider!);
+ this.plugin.managers.lociLabels.addProvider(StripedResidues.labelProvider!);
+ this.plugin.customModelProperties.register(StripedResidues.propertyProvider, true);
+ }
+
+ async load({ url, format = 'mmcif', isBinary = false, assemblyId = '' }: LoadParams) {
+ await this.plugin.clear();
+
+ const data = await this.plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+ const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
+
+ await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default', {
+ structure: assemblyId ? { name: 'assembly', params: { id: assemblyId } } : { name: 'deposited', params: { } },
+ showUnitcell: false,
+ representationPreset: 'auto'
+ });
+ }
+
+ setBackground(color: number) {
+ PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: props => { props.renderer.backgroundColor = Color(color) } });
+ }
+
+ toggleSpin() {
+ if (!this.plugin.canvas3d) return;
+
+ PluginCommands.Canvas3D.SetSettings(this.plugin, {
+ settings: props => {
+ props.trackball.spin = !props.trackball.spin;
+ }
+ });
+ if (!this.plugin.canvas3d.props.trackball.spin) PluginCommands.Camera.Reset(this.plugin, {});
+ }
+
+ animate = {
+ modelIndex: {
+ maxFPS: 8,
+ onceForward: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }) },
+ onceBackward: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }) },
+ palindrome: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }) },
+ loop: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }) },
+ stop: () => this.plugin.state.animation.stop()
+ }
+ }
+
+ coloring = {
+ applyStripes: async () => {
+ this.plugin.dataTransaction(async () => {
+ for (const s of this.plugin.managers.structure.hierarchy.current.structures) {
+ await this.plugin.managers.structure.component.updateRepresentationsTheme(s.components, { color: StripedResidues.propertyProvider.descriptor.name as any })
+ }
+ });
+ },
+ applyDefault: async () => {
+ this.plugin.dataTransaction(async () => {
+ for (const s of this.plugin.managers.structure.hierarchy.current.structures) {
+ await this.plugin.managers.structure.component.updateRepresentationsTheme(s.components, { color: 'default' })
+ }
+ });
+ }
+ }
+
+ interactivity = {
+ highlightOn: () => {
+ const seq_id = 7;
+ const data = (this.plugin.state.data.select('asm')[0].obj as PluginStateObject.Molecule.Structure).data;
+ const sel = Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
+ 'residue-test': Q.core.rel.eq([Q.struct.atomProperty.macromolecular.label_seq_id(), seq_id]),
+ 'group-by': Q.struct.atomProperty.macromolecular.residueKey()
+ }), data);
+ const loci = StructureSelection.toLociWithSourceUnits(sel);
+ this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci });
+ },
+ clearHighlight: () => {
+ this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci: EmptyLoci });
+ }
+ }
+
+ tests = {
+ staticSuperposition: async () => {
+ await this.plugin.clear();
+ return buildStaticSuperposition(this.plugin, StaticSuperpositionTestData);
+ },
+ dynamicSuperposition: async () => {
+ await this.plugin.clear();
+ return dynamicSuperpositionTest(this.plugin, ['1tqn', '2hhb', '4hhb'], 'HEM');
+ },
+ toggleValidationTooltip: () => {
+ return this.plugin.state.updateBehavior(PDBeStructureQualityReport, params => { params.showTooltip = !params.showTooltip });
+ },
+ showToasts: () => {
+ PluginCommands.Toast.Show(this.plugin, {
+ title: 'Toast 1',
+ message: 'This is an example text, timeout 3s',
+ key: 'toast-1',
+ timeoutMs: 3000
+ });
+ PluginCommands.Toast.Show(this.plugin, {
+ title: 'Toast 2',
+ message: CustomToastMessage,
+ key: 'toast-2'
+ });
+ },
+ hideToasts: () => {
+ PluginCommands.Toast.Hide(this.plugin, { key: 'toast-1' });
+ PluginCommands.Toast.Hide(this.plugin, { key: 'toast-2' });
+ }
+ }
+}
+
+(window as any).BasicMolStarWrapper = new BasicWrapper();
\ No newline at end of file
diff --git a/src/examples/basic-wrapper/superposition.ts b/src/examples/basic-wrapper/superposition.ts
new file mode 100644
index 0000000000000000000000000000000000000000..9c45bc0391b5bae28bc76d93db28636114c3f5ba
--- /dev/null
+++ b/src/examples/basic-wrapper/superposition.ts
@@ -0,0 +1,118 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Mat4 } from '../../mol-math/linear-algebra';
+import { QueryContext, StructureSelection } from '../../mol-model/structure';
+import { superposeStructures } from '../../mol-model/structure/structure/util/superposition';
+import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
+import { PluginContext } from '../../mol-plugin/context';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import Expression from '../../mol-script/language/expression';
+import { compile } from '../../mol-script/runtime/query/compiler';
+import { StateObjectRef } from '../../mol-state';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+
+export type SuperpositionTestInput = {
+ pdbId: string,
+ auth_asym_id: string,
+ matrix: Mat4
+}[];
+
+export function buildStaticSuperposition(plugin: PluginContext, src: SuperpositionTestInput) {
+ return plugin.dataTransaction(async () => {
+ for (const s of src) {
+ const { structure } = await loadStructure(plugin, `https://www.ebi.ac.uk/pdbe/static/entry/${s.pdbId}_updated.cif`, 'mmcif');
+ await transform(plugin, structure, s.matrix);
+ const chain = await plugin.builders.structure.tryCreateComponentFromExpression(structure, chainSelection(s.auth_asym_id), `Chain ${s.auth_asym_id}`);
+ if (chain) await plugin.builders.structure.representation.addRepresentation(chain, { type: 'cartoon' });
+ }
+ })
+}
+
+export const StaticSuperpositionTestData: SuperpositionTestInput = [
+ {
+ pdbId: '1aj5', auth_asym_id: 'A', matrix: Mat4.identity()
+ },
+ {
+ pdbId: '1df0', auth_asym_id: 'B', matrix: Mat4.ofRows([
+ [0.406, 0.879, 0.248, -200.633],
+ [0.693, -0.473, 0.544, 73.403],
+ [0.596, -0.049, -0.802, -14.209],
+ [0, 0, 0, 1]])
+ },
+ {
+ pdbId: '1dvi', auth_asym_id: 'A', matrix: Mat4.ofRows([
+ [-0.053, -0.077, 0.996, -45.633],
+ [-0.312, 0.949, 0.057, -12.255],
+ [-0.949, -0.307, -0.074, 53.562],
+ [0, 0, 0, 1]])
+ }
+];
+
+export function dynamicSuperpositionTest(plugin: PluginContext, src: string[], comp_id: string) {
+ return plugin.dataTransaction(async () => {
+ for (const s of src) {
+ await loadStructure(plugin, `https://www.ebi.ac.uk/pdbe/static/entry/${s}_updated.cif`, 'mmcif');
+ }
+
+ const pivot = MS.struct.filter.first([
+ MS.struct.generator.atomGroups({
+ 'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), comp_id]),
+ 'group-by': MS.struct.atomProperty.macromolecular.residueKey()
+ })
+ ]);
+
+ const rest = MS.struct.modifier.exceptBy({
+ 0: MS.struct.modifier.includeSurroundings({
+ 0: pivot,
+ radius: 5
+ }),
+ by: pivot
+ });
+
+ const query = compile<StructureSelection>(pivot);
+ const xs = plugin.managers.structure.hierarchy.current.structures;
+ const selections = xs.map(s => StructureSelection.toLociWithCurrentUnits(query(new QueryContext(s.cell.obj!.data))));
+
+ const transforms = superposeStructures(selections);
+
+ await siteVisual(plugin, xs[0].cell, pivot, rest);
+ for (let i = 1; i < selections.length; i++) {
+ await transform(plugin, xs[i].cell, transforms[i - 1].bTransform);
+ await siteVisual(plugin, xs[i].cell, pivot, rest);
+ }
+ });
+}
+
+async function siteVisual(plugin: PluginContext, s: StateObjectRef<PSO.Molecule.Structure>, pivot: Expression, rest: Expression) {
+ const center = await plugin.builders.structure.tryCreateComponentFromExpression(s, pivot, 'pivot');
+ if (center) await plugin.builders.structure.representation.addRepresentation(center, { type: 'ball-and-stick', color: 'residue-name' });
+
+ const surr = await plugin.builders.structure.tryCreateComponentFromExpression(s, rest, 'rest');
+ if (surr) await plugin.builders.structure.representation.addRepresentation(surr, { type: 'ball-and-stick', color: 'uniform', size: 'uniform', sizeParams: { value: 0.33 } });
+}
+
+async function loadStructure(plugin: PluginContext, url: string, format: BuiltInTrajectoryFormat, assemblyId?: string) {
+ const data = await plugin.builders.data.download({ url });
+ const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
+ const model = await plugin.builders.structure.createModel(trajectory);
+ const structure = await plugin.builders.structure.createStructure(model, assemblyId ? { name: 'assembly', params: { id: assemblyId } } : void 0);
+
+ return { data, trajectory, model, structure };
+}
+
+function chainSelection(auth_asym_id: string) {
+ return MS.struct.generator.atomGroups({
+ 'chain-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.auth_asym_id(), auth_asym_id])
+ });
+}
+
+function transform(plugin: PluginContext, s: StateObjectRef<PSO.Molecule.Structure>, matrix: Mat4) {
+ const b = plugin.state.data.build().to(s)
+ .insert(StateTransforms.Model.TransformStructureConformation, { transform: { name: 'matrix', params: matrix } });
+ return plugin.runTask(plugin.state.data.updateTree(b));
+}
\ No newline at end of file
diff --git a/src/apps/domain-annotation-server/mapping.ts b/src/examples/domain-annotation-server/mapping.ts
similarity index 100%
rename from src/apps/domain-annotation-server/mapping.ts
rename to src/examples/domain-annotation-server/mapping.ts
diff --git a/src/apps/domain-annotation-server/schemas.ts b/src/examples/domain-annotation-server/schemas.ts
similarity index 100%
rename from src/apps/domain-annotation-server/schemas.ts
rename to src/examples/domain-annotation-server/schemas.ts
diff --git a/src/apps/domain-annotation-server/server.ts b/src/examples/domain-annotation-server/server.ts
similarity index 97%
rename from src/apps/domain-annotation-server/server.ts
rename to src/examples/domain-annotation-server/server.ts
index 1d4f192cad0713c96b559e427535986532c8dc54..4758a4d07e01da4598117900530aff40722334e8 100644
--- a/src/apps/domain-annotation-server/server.ts
+++ b/src/examples/domain-annotation-server/server.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import * as express from 'express'
+import express from 'express'
import fetch from 'node-fetch'
import createMapping from './mapping'
diff --git a/src/apps/domain-annotation-server/test.ts b/src/examples/domain-annotation-server/test.ts
similarity index 100%
rename from src/apps/domain-annotation-server/test.ts
rename to src/examples/domain-annotation-server/test.ts
diff --git a/src/apps/demos/lighting/index.html b/src/examples/lighting/index.html
similarity index 100%
rename from src/apps/demos/lighting/index.html
rename to src/examples/lighting/index.html
diff --git a/src/examples/lighting/index.ts b/src/examples/lighting/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..3c52b3e5d855907624990ab0f96a990f73e8179a
--- /dev/null
+++ b/src/examples/lighting/index.ts
@@ -0,0 +1,117 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Canvas3DProps } from '../../mol-canvas3d/canvas3d';
+import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
+import './index.html';
+require('mol-plugin-ui/skin/light.scss')
+
+type LoadParams = { url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, assemblyId?: string }
+
+type _Preset = Pick<Canvas3DProps, 'multiSample' | 'postprocessing' | 'renderer'>
+type Preset = { [K in keyof _Preset]: Partial<_Preset[K]> }
+
+const Canvas3DPresets = {
+ illustrative: <Preset> {
+ multiSample: {
+ mode: 'temporal' as Canvas3DProps['multiSample']['mode']
+ },
+ postprocessing: {
+ occlusion: { name: 'on', params: { bias: 0.8, kernelSize: 6, radius: 64 } },
+ outline: { name: 'on', params: { scale: 1, threshold: 0.8 } }
+ },
+ renderer: {
+ ambientIntensity: 1,
+ lightIntensity: 0,
+ }
+ },
+ occlusion: <Preset> {
+ multiSample: {
+ mode: 'temporal' as Canvas3DProps['multiSample']['mode']
+ },
+ postprocessing: {
+ occlusion: { name: 'on', params: { bias: 0.8, kernelSize: 6, radius: 64 } },
+ outline: { name: 'off', params: { } }
+ },
+ renderer: {
+ ambientIntensity: 0.4,
+ lightIntensity: 0.6,
+ }
+ },
+ standard: <Preset> {
+ multiSample: {
+ mode: 'off' as Canvas3DProps['multiSample']['mode']
+ },
+ postprocessing: {
+ occlusion: { name: 'off', params: { } },
+ outline: { name: 'off', params: { } }
+ },
+ renderer: {
+ ambientIntensity: 0.4,
+ lightIntensity: 0.6,
+ }
+ }
+}
+
+type Canvas3DPreset = keyof typeof Canvas3DPresets
+
+class LightingDemo {
+ plugin: PluginContext;
+
+ init(target: string | HTMLElement) {
+ this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
+ ...DefaultPluginSpec,
+ layout: {
+ initial: {
+ isExpanded: false,
+ showControls: false
+ },
+ controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' }
+ }
+ });
+
+ this.setPreset('illustrative');
+ }
+
+ setPreset(preset: Canvas3DPreset) {
+ const props = Canvas3DPresets[preset]
+ PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
+ ...props,
+ multiSample: {
+ ...this.plugin.canvas3d!.props.multiSample,
+ ...props.multiSample
+ },
+ renderer: {
+ ...this.plugin.canvas3d!.props.renderer,
+ ...props.renderer
+ },
+ postprocessing: {
+ ...this.plugin.canvas3d!.props.postprocessing,
+ ...props.postprocessing
+ },
+ }});
+ }
+
+ async load({ url, format = 'mmcif', isBinary = false, assemblyId = '' }: LoadParams) {
+ await this.plugin.clear();
+
+ const data = await this.plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+ const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
+ const model = await this.plugin.builders.structure.createModel(trajectory);
+ const structure = await this.plugin.builders.structure.createStructure(model, assemblyId ? { name: 'assembly', params: { id: assemblyId } } : { name: 'deposited', params: { } });
+
+ const polymer = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'polymer');
+ if (polymer) await this.plugin.builders.structure.representation.addRepresentation(polymer, { type: 'spacefill', color: 'illustrative' });
+
+ const ligand = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'ligand');
+ if (ligand) await this.plugin.builders.structure.representation.addRepresentation(ligand, { type: 'ball-and-stick' });
+ }
+}
+
+(window as any).LightingDemo = new LightingDemo();
\ No newline at end of file
diff --git a/src/mol-canvas3d/canvas3d.ts b/src/mol-canvas3d/canvas3d.ts
index 1b282a4cd4c8952024ab0b096bc8035d76b37836..5046ebb83f7392949e0a9c6368e1fd53fd0b84c6 100644
--- a/src/mol-canvas3d/canvas3d.ts
+++ b/src/mol-canvas3d/canvas3d.ts
@@ -35,6 +35,7 @@ import { ImagePass, ImageProps } from './passes/image';
import { Sphere3D } from '../mol-math/geometry';
import { isDebugMode } from '../mol-util/debug';
import { CameraHelperParams } from './helper/camera-helper';
+import { produce } from 'immer';
export const Canvas3DParams = {
camera: PD.Group({
@@ -93,9 +94,8 @@ interface Canvas3D {
requestCameraReset(options?: { durationMs?: number, snapshot?: Partial<Camera.Snapshot> }): void
readonly camera: Camera
readonly boundingSphere: Readonly<Sphere3D>
- downloadScreenshot(): void
getPixelData(variant: GraphicsRenderVariant): PixelData
- setProps(props: Partial<Canvas3DProps>): void
+ setProps(props: Partial<Canvas3DProps> | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void)): void
getImagePass(props: Partial<ImageProps>): ImagePass
/** Returns a copy of the current Canvas3D instance props */
@@ -197,11 +197,6 @@ namespace Canvas3D {
const postprocessing = new PostprocessingPass(webgl, camera, drawPass, p.postprocessing)
const multiSample = new MultiSamplePass(webgl, camera, drawPass, postprocessing, p.multiSample)
- const contextRestoredSub = contextRestored.subscribe(() => {
- pickPass.pickDirty = true
- draw(true)
- })
-
let drawPending = false
let cameraResetRequested = false
let nextCameraResetDuration: number | undefined = void 0
@@ -412,8 +407,38 @@ namespace Canvas3D {
}
}
+ function getProps(): Canvas3DProps {
+ const radius = scene.boundingSphere.radius > 0
+ ? 100 - Math.round((camera.transition.target.radius / scene.boundingSphere.radius) * 100)
+ : 0
+
+ return {
+ camera: {
+ mode: camera.state.mode,
+ helper: { ...drawPass.props.cameraHelper }
+ },
+ cameraFog: camera.state.fog > 0
+ ? { name: 'on' as const, params: { intensity: camera.state.fog } }
+ : { name: 'off' as const, params: {} },
+ cameraClipping: { far: camera.state.clipFar, radius },
+ cameraResetDurationMs: p.cameraResetDurationMs,
+ transparentBackground: p.transparentBackground,
+
+ postprocessing: { ...postprocessing.props },
+ multiSample: { ...multiSample.props },
+ renderer: { ...renderer.props },
+ trackball: { ...controls.props },
+ debug: { ...debugHelper.props }
+ }
+ }
+
handleResize()
+ const contextRestoredSub = contextRestored.subscribe(() => {
+ pickPass.pickDirty = true
+ draw(true)
+ })
+
return {
webgl,
@@ -463,9 +488,6 @@ namespace Canvas3D {
},
camera,
boundingSphere: scene.boundingSphere,
- downloadScreenshot: () => {
- // TODO
- },
getPixelData: (variant: GraphicsRenderVariant) => {
switch (variant) {
case 'color': return webgl.getDrawingBufferPixelData()
@@ -477,7 +499,11 @@ namespace Canvas3D {
},
didDraw,
reprCount,
- setProps: (props: Partial<Canvas3DProps>) => {
+ setProps: (properties) => {
+ const props: Partial<Canvas3DProps> = typeof properties === 'function'
+ ? produce(getProps(), properties)
+ : properties;
+
const cameraState: Partial<Camera.Snapshot> = Object.create(null)
if (props.camera && props.camera.mode !== undefined && props.camera.mode !== camera.state.mode) {
cameraState.mode = props.camera.mode
diff --git a/src/mol-model-props/computed/interactions/hydrogen-bonds.ts b/src/mol-model-props/computed/interactions/hydrogen-bonds.ts
index 1be7234bc0c5daa92ebc976cdc0d054dfa3b44dc..a47f444e04823e1dfdfd2103cbe7639f9e38a4f3 100644
--- a/src/mol-model-props/computed/interactions/hydrogen-bonds.ts
+++ b/src/mol-model-props/computed/interactions/hydrogen-bonds.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Fred Ludlow <Fred.Ludlow@astx.com>
@@ -32,7 +32,7 @@ type GeometryProps = PD.Values<GeometryParams>
const HydrogenBondsParams = {
...GeometryParams,
- water: PD.Boolean(true, { description: 'Include water-to-water hydrogen bonds' }),
+ water: PD.Boolean(false, { description: 'Include water-to-water hydrogen bonds' }),
sulfurDistanceMax: PD.Numeric(4.1, { min: 1, max: 5, step: 0.1 }),
}
type HydrogenBondsParams = typeof HydrogenBondsParams
@@ -174,9 +174,8 @@ function addUnitHydrogenAcceptors(structure: Structure, unit: Unit.Atomic, build
}
}
-
function isWater(unit: Unit.Atomic, index: StructureElement.UnitIndex) {
- return unit.model.atomicHierarchy.derived.residue.moleculeType[unit.elements[index]] === MoleculeType.Water
+ return unit.model.atomicHierarchy.derived.residue.moleculeType[unit.residueIndex[unit.elements[index]]] === MoleculeType.Water
}
function isBackbone(unit: Unit.Atomic, index: StructureElement.UnitIndex) {
diff --git a/src/mol-model-props/computed/interactions/metal.ts b/src/mol-model-props/computed/interactions/metal.ts
index 93c9a41222da1f7514c7d315a72c7db64cc20a54..80d7881c716e7582d3cdb1474543748dd1f9af05 100644
--- a/src/mol-model-props/computed/interactions/metal.ts
+++ b/src/mol-model-props/computed/interactions/metal.ts
@@ -94,7 +94,7 @@ function addMetalBinding(structure: Structure, unit: Unit.Atomic, builder: Featu
dative = true
ionic = true
}
- } else if (element === Elements.S && 'CYS' === resname) {
+ } else if (element === Elements.S && (resname === 'CYS' || resname === 'MET')) {
dative = true
ionic = true
} else if (element === Elements.N) {
diff --git a/src/mol-model-props/computed/representations/interactions.ts b/src/mol-model-props/computed/representations/interactions.ts
index 7f8e02df7e11dd35333463d26b5a51590ba55622..a77f08af3024f8f49519110e202569e09dda65ba 100644
--- a/src/mol-model-props/computed/representations/interactions.ts
+++ b/src/mol-model-props/computed/representations/interactions.ts
@@ -8,11 +8,12 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Representation, RepresentationParamsGetter, RepresentationContext } from '../../../mol-repr/representation';
import { ThemeRegistryContext } from '../../../mol-theme/theme';
import { Structure } from '../../../mol-model/structure';
-import { UnitsRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider, ComplexRepresentation, getUnitKindsParam } from '../../../mol-repr/structure/representation';
+import { UnitsRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider, ComplexRepresentation } from '../../../mol-repr/structure/representation';
import { InteractionsIntraUnitParams, InteractionsIntraUnitVisual } from './interactions-intra-unit-cylinder';
import { InteractionsProvider } from '../interactions';
import { InteractionsInterUnitParams, InteractionsInterUnitVisual } from './interactions-inter-unit-cylinder';
import { CustomProperty } from '../../common/custom-property';
+import { getUnitKindsParam } from '../../../mol-repr/structure/params';
const InteractionsVisuals = {
'intra-unit': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, InteractionsIntraUnitParams>) => UnitsRepresentation('Intra-unit interactions cylinder', ctx, getParams, InteractionsIntraUnitVisual),
@@ -23,7 +24,7 @@ export const InteractionsParams = {
...InteractionsIntraUnitParams,
...InteractionsInterUnitParams,
unitKinds: getUnitKindsParam(['atomic']),
- sizeFactor: PD.Numeric(0.15, { min: 0.01, max: 1, step: 0.01 }),
+ sizeFactor: PD.Numeric(0.2, { min: 0.01, max: 1, step: 0.01 }),
visuals: PD.MultiSelect(['intra-unit', 'inter-unit'], PD.objectToOptions(InteractionsVisuals)),
}
export type InteractionsParams = typeof InteractionsParams
diff --git a/src/mol-model-props/rcsb/assembly-symmetry.ts b/src/mol-model-props/rcsb/assembly-symmetry.ts
index a34b12cc7ee38d9c7af7b320f5d90ac10abcd448..cfcabec150049365c2576535cf1f9d15699b1a67 100644
--- a/src/mol-model-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-model-props/rcsb/assembly-symmetry.ts
@@ -47,7 +47,7 @@ export namespace AssemblySymmetry {
Representation = 'rcsb-assembly-symmetry-3d'
}
- export const DefaultServerUrl = 'https://data-beta.rcsb.org/graphql'
+ export const DefaultServerUrl = 'https://data.rcsb.org/graphql'
export function isApplicable(structure?: Structure): boolean {
return (
diff --git a/src/mol-model-props/rcsb/graphql/types.ts b/src/mol-model-props/rcsb/graphql/types.ts
index 591e83afc715d47a0e70955350c9405f700678d2..d62903be282531a1bdf3561de7fc22f1e8ec9612 100644
--- a/src/mol-model-props/rcsb/graphql/types.ts
+++ b/src/mol-model-props/rcsb/graphql/types.ts
@@ -1,7 +1,7 @@
/* eslint-disable */
export type Maybe<T> = T | null;
-// Generated in 2020-03-30T11:30:30-07:00
+// Generated in 2020-04-08T16:22:40-07:00
/** All built-in and custom scalars, mapped to their actual values */
export type Scalars = {
@@ -800,6 +800,8 @@ export type PdbxAuditRevisionCategory = {
export type PdbxAuditRevisionDetails = {
readonly data_content_type: Scalars['String'];
+ readonly description?: Maybe<Scalars['String']>;
+ readonly details?: Maybe<Scalars['String']>;
readonly ordinal: Scalars['Int'];
readonly provider?: Maybe<Scalars['String']>;
readonly revision_ordinal: Scalars['Int'];
diff --git a/src/mol-model-props/rcsb/representations/validation-report-clashes.ts b/src/mol-model-props/rcsb/representations/validation-report-clashes.ts
index f9f05ff4c2977c02b93e301b5dd34c01b7f0ede3..7cc7553b9c07b28cbf014b6346a2f5093dbdd3bc 100644
--- a/src/mol-model-props/rcsb/representations/validation-report-clashes.ts
+++ b/src/mol-model-props/rcsb/representations/validation-report-clashes.ts
@@ -13,7 +13,7 @@ import { PickingId } from '../../../mol-geo/geometry/picking';
import { EmptyLoci, Loci, DataLoci } from '../../../mol-model/loci';
import { Interval } from '../../../mol-data/int';
import { RepresentationContext, RepresentationParamsGetter, Representation } from '../../../mol-repr/representation';
-import { UnitsRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider, ComplexRepresentation, getUnitKindsParam } from '../../../mol-repr/structure/representation';
+import { UnitsRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider, ComplexRepresentation } from '../../../mol-repr/structure/representation';
import { VisualContext } from '../../../mol-repr/visual';
import { createLinkCylinderMesh, LinkCylinderParams, LinkCylinderStyle } from '../../../mol-repr/structure/visual/util/link';
import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, StructureGroup } from '../../../mol-repr/structure/units-visual';
@@ -27,6 +27,7 @@ import { MarkerActions } from '../../../mol-util/marker-action';
import { CentroidHelper } from '../../../mol-math/geometry/centroid-helper';
import { Sphere3D } from '../../../mol-math/geometry';
import { bondLabel } from '../../../mol-theme/label';
+import { getUnitKindsParam } from '../../../mol-repr/structure/params';
//
diff --git a/src/mol-plugin-state/builder/structure.ts b/src/mol-plugin-state/builder/structure.ts
index 0e7301343b287f31920853e626652d9b345cb6ca..82bb1af27c6d479f883a788893e5d16eeb6f0dad 100644
--- a/src/mol-plugin-state/builder/structure.ts
+++ b/src/mol-plugin-state/builder/structure.ts
@@ -149,12 +149,12 @@ export class StructureBuilder {
}, key, params?.tags);
}
- tryCreateComponentStatic(structure: StateObjectRef<SO.Molecule.Structure>, type: StaticStructureComponentType, key: string, params?: { label?: string, tags?: string[] }) {
+ tryCreateComponentStatic(structure: StateObjectRef<SO.Molecule.Structure>, type: StaticStructureComponentType, params?: { label?: string, tags?: string[] }) {
return this.tryCreateComponent(structure, {
type: { name: 'static', params: type },
nullIfEmpty: true,
label: (params?.label || '').trim()
- }, key, params?.tags);
+ }, `static-${type}`, params?.tags);
}
tryCreateComponentFromSelection(structure: StateObjectRef<SO.Molecule.Structure>, selection: StructureSelectionQuery, key: string, params?: { label?: string, tags?: string[] }): Promise<StateObjectSelector<SO.Molecule.Structure> | undefined> {
diff --git a/src/mol-plugin-state/builder/structure/representation-preset.ts b/src/mol-plugin-state/builder/structure/representation-preset.ts
index 9e67d7dc857d22009337e6e2f78bfb3ee6dc351b..a9088281f6afe32730a01f5784ca224b3c539de7 100644
--- a/src/mol-plugin-state/builder/structure/representation-preset.ts
+++ b/src/mol-plugin-state/builder/structure/representation-preset.ts
@@ -245,7 +245,7 @@ const atomicDetail = StructureRepresentationPresetProvider({
});
export function presetStaticComponent(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, type: StaticStructureComponentType, params?: { label?: string, tags?: string[] }) {
- return plugin.builders.structure.tryCreateComponentStatic(structure, type, `static-${type}`, params);
+ return plugin.builders.structure.tryCreateComponentStatic(structure, type, params);
}
export function presetSelectionComponent(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, query: keyof typeof Q, params?: { label?: string, tags?: string[] }) {
diff --git a/src/mol-plugin-state/manager/loci-label.ts b/src/mol-plugin-state/manager/loci-label.ts
index ddcee6ee9f7b3e87626bd2451a6389baca83aaf4..adabbd1c74657094076593b45169b22d24777336 100644
--- a/src/mol-plugin-state/manager/loci-label.ts
+++ b/src/mol-plugin-state/manager/loci-label.ts
@@ -15,6 +15,8 @@ export type LociLabel = JSX.Element | string
export type LociLabelProvider = {
label: (loci: Loci, repr?: Representation<any>) => LociLabel | undefined
group?: (entry: LociLabel) => string
+ /** Labels from providers with higher priority are shown first */
+ priority?: number
}
export class LociLabelManager {
@@ -22,6 +24,7 @@ export class LociLabelManager {
addProvider(provider: LociLabelProvider) {
this.providers.push(provider);
+ this.providers.sort((a, b) => (b.priority || 0) - (a.priority || 0))
this.isDirty = true
this.showLabels()
}
diff --git a/src/mol-plugin-state/manager/structure/hierarchy.ts b/src/mol-plugin-state/manager/structure/hierarchy.ts
index 3c2f4d284b572e974eed63e45dbd33e439a847bd..4eef242c5336979492db34327c679b2f57fff19f 100644
--- a/src/mol-plugin-state/manager/structure/hierarchy.ts
+++ b/src/mol-plugin-state/manager/structure/hierarchy.ts
@@ -82,7 +82,7 @@ export class StructureHierarchyManager extends PluginComponent {
}
private sync(notify: boolean) {
- if (!notify && this.dataState.behaviors.isUpdating.value) return;
+ if (!notify && this.dataState.inUpdate) return;
if (this.state.syncedTree === this.dataState.tree) {
if (notify && !this.state.notified) {
diff --git a/src/mol-plugin-ui/controls.tsx b/src/mol-plugin-ui/controls.tsx
index 9f1b80a33e7f5b44e98ec4233d4b2b5f3e3dc31e..63409ca18b847924a66639e1fadcbf01d42cdff7 100644
--- a/src/mol-plugin-ui/controls.tsx
+++ b/src/mol-plugin-ui/controls.tsx
@@ -251,9 +251,14 @@ export class SelectionViewportControls extends PluginUIComponent {
this.subscribe(this.plugin.behaviors.interaction.selectionMode, () => this.forceUpdate());
}
+ onMouseMove = (e: React.MouseEvent) => {
+ // ignore mouse moves when no button is held
+ if (e.buttons === 0) e.stopPropagation()
+ }
+
render() {
if (!this.plugin.selectionMode) return null;
- return <div className='msp-selection-viewport-controls'>
+ return <div className='msp-selection-viewport-controls' onMouseMove={this.onMouseMove}>
<StructureSelectionActionsControls />
</div>;
}
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
index dfe688f6190a4a2c0744845b9e5f0cd4c9b2804a..3d2cad2628ee2dce12dc17ea9a840b6c5efb7c3b 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
@@ -181,7 +181,8 @@ export const AssemblySymmetryPreset = StructureRepresentationPresetProvider({
}
const assemblySymmetry = await tryCreateAssemblySymmetry(plugin, structureCell);
- const preset = await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: Tag.Cluster as any }, plugin);
+ const globalThemeName = assemblySymmetry.isOk ? Tag.Cluster as any : undefined
+ const preset = await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName }, plugin);
return { components: preset.components, representations: { ...preset.representations, assemblySymmetry } };
}
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/ui/assembly-symmetry.tsx b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/ui/assembly-symmetry.tsx
index bab4c360a346efece4eb70623f3074ca0a7f1f40..df69ba8f7e6fe0d301267ae809cc644716a92775 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/ui/assembly-symmetry.tsx
+++ b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/ui/assembly-symmetry.tsx
@@ -104,15 +104,16 @@ export class AssemblySymmetryControls extends CollapsableControls<{}, AssemblySy
await this.plugin.builders.structure.insertStructureProperties(s.cell, params);
}
- const components = this.plugin.managers.structure.hierarchy.currentComponentGroups[0];
- if (values.symmetryIndex === -1) {
- const name = components[0]?.representations[0]?.cell.transform.params?.colorTheme.name;
- if (name === AssemblySymmetry.Tag.Cluster) {
- await this.plugin.managers.structure.component.updateRepresentationsTheme(components, { color: 'default' })
+ for (const components of this.plugin.managers.structure.hierarchy.currentComponentGroups) {
+ if (values.symmetryIndex === -1) {
+ const name = components[0]?.representations[0]?.cell.transform.params?.colorTheme.name;
+ if (name === AssemblySymmetry.Tag.Cluster) {
+ await this.plugin.managers.structure.component.updateRepresentationsTheme(components, { color: 'default' })
+ }
+ } else {
+ tryCreateAssemblySymmetry(this.plugin, s.cell)
+ await this.plugin.managers.structure.component.updateRepresentationsTheme(components, { color: AssemblySymmetry.Tag.Cluster as any })
}
- } else {
- tryCreateAssemblySymmetry(this.plugin, s.cell)
- await this.plugin.managers.structure.component.updateRepresentationsTheme(components, { color: AssemblySymmetry.Tag.Cluster as any })
}
}
diff --git a/src/mol-plugin/behavior/dynamic/representation.ts b/src/mol-plugin/behavior/dynamic/representation.ts
index a87f63f7396d572d9dfc0c6a360110b9e233288a..41b0ad9abefdb2b2376131fd5a21ed910753f281 100644
--- a/src/mol-plugin/behavior/dynamic/representation.ts
+++ b/src/mol-plugin/behavior/dynamic/representation.ts
@@ -186,7 +186,8 @@ export const DefaultLociLabelProvider = PluginBehavior.create({
label.push(lociLabel(loci))
return label.join('</br>')
},
- group: (label: LociLabel) => label.toString().replace(/Model [0-9]+/g, 'Models')
+ group: (label: LociLabel) => label.toString().replace(/Model [0-9]+/g, 'Models'),
+ priority: 100
};
register() { this.ctx.managers.lociLabels.addProvider(this.f); }
unregister() { this.ctx.managers.lociLabels.removeProvider(this.f); }
diff --git a/src/mol-plugin/behavior/static/misc.ts b/src/mol-plugin/behavior/static/misc.ts
index b9b09330d6c08416c0d0947fbacba4a6d53aef3c..32f568479d7e4743a7e39ef6ab4e000a25d8017e 100644
--- a/src/mol-plugin/behavior/static/misc.ts
+++ b/src/mol-plugin/behavior/static/misc.ts
@@ -7,14 +7,21 @@
import { PluginContext } from '../../../mol-plugin/context';
import { PluginCommands } from '../../commands';
+import { DefaultCanvas3DParams } from '../../../mol-canvas3d/canvas3d';
export function registerDefault(ctx: PluginContext) {
Canvas3DSetSettings(ctx);
}
export function Canvas3DSetSettings(ctx: PluginContext) {
+ PluginCommands.Canvas3D.ResetSettings.subscribe(ctx, () => {
+ ctx.canvas3d?.setProps(DefaultCanvas3DParams);
+ });
+
PluginCommands.Canvas3D.SetSettings.subscribe(ctx, e => {
+ if (!ctx.canvas3d) return;
+
ctx.canvas3d?.setProps(e.settings);
ctx.events.canvas3d.settingsUpdated.next();
- })
+ });
}
diff --git a/src/mol-plugin/commands.ts b/src/mol-plugin/commands.ts
index be2cfa91432b791b7fd159c691705686ee524ce4..be1b855480a69be6d808cf14a05209beb3d543d8 100644
--- a/src/mol-plugin/commands.ts
+++ b/src/mol-plugin/commands.ts
@@ -70,6 +70,7 @@ export const PluginCommands = {
}
},
Canvas3D: {
- SetSettings: PluginCommand<{ settings: Partial<Canvas3DProps> }>()
+ SetSettings: PluginCommand<{ settings: Partial<Canvas3DProps> | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void) }>(),
+ ResetSettings: PluginCommand<{ }>()
}
}
\ No newline at end of file
diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index db6cc468b5dcd9be824bc6819a6cb835ccbad198..1fd0735ec242773a71ea7581e7a7e29e3e4c6375 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -8,7 +8,7 @@
import { setAutoFreeze } from 'immer';
import { List } from 'immutable';
import { merge } from 'rxjs';
-import { Canvas3D } from '../mol-canvas3d/canvas3d';
+import { Canvas3D, DefaultCanvas3DParams } from '../mol-canvas3d/canvas3d';
import { CustomProperty } from '../mol-model-props/common/custom-property';
import { Model, Structure } from '../mol-model/structure';
import { DataFormatRegistry } from '../mol-plugin-state/actions/data-format';
@@ -30,7 +30,7 @@ import { StateTransformParameters } from '../mol-plugin-ui/state/common';
import { Representation } from '../mol-repr/representation';
import { StructureRepresentationRegistry } from '../mol-repr/structure/registry';
import { VolumeRepresentationRegistry } from '../mol-repr/volume/registry';
-import { State, StateBuilder, StateTree } from '../mol-state';
+import { State, StateBuilder, StateTree, StateTransform } from '../mol-state';
import { Progress, Task } from '../mol-task';
import { ColorTheme } from '../mol-theme/color';
import { SizeTheme } from '../mol-theme/size';
@@ -234,6 +234,11 @@ export class PluginContext {
this.tasks.requestAbort(progress, reason);
}
+ clear(resetViewportSettings = false) {
+ if (resetViewportSettings) this.canvas3d?.setProps(DefaultCanvas3DParams);
+ return PluginCommands.State.RemoveObject(this, { state: this.state.data, ref: StateTransform.RootRef });
+ }
+
dispose() {
if (this.disposed) return;
this.commands.dispose();
diff --git a/src/mol-repr/structure/complex-representation.ts b/src/mol-repr/structure/complex-representation.ts
index c1bbe9e13f71da9856381c54433da0542194b6b9..b6cec476c8e2cc406e0d38014d665ffcc904e68f 100644
--- a/src/mol-repr/structure/complex-representation.ts
+++ b/src/mol-repr/structure/complex-representation.ts
@@ -6,7 +6,7 @@
*/
import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { ComplexVisual, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationState, StructureParams } from './representation';
+import { ComplexVisual, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationState } from './representation';
import { RepresentationContext, RepresentationParamsGetter } from '../representation';
import { Structure, StructureElement, Bond } from '../../mol-model/structure';
import { Subject } from 'rxjs';
@@ -17,6 +17,7 @@ import { PickingId } from '../../mol-geo/geometry/picking';
import { EmptyLoci, Loci, isEveryLoci, isDataLoci } from '../../mol-model/loci';
import { MarkerAction, MarkerActions } from '../../mol-util/marker-action';
import { Overpaint } from '../../mol-theme/overpaint';
+import { StructureParams } from './params';
export function ComplexRepresentation<P extends StructureParams>(label: string, ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, P>, visualCtor: (materialId: number) => ComplexVisual<P>): StructureRepresentation<P> {
let version = 0
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index ae0ce47ee8d84116a7fbf273767f7876474c9e5a..18c5a10283ddd0064676f1d49a515f22cc50ee1f 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/src/mol-repr/structure/complex-visual.ts
@@ -5,7 +5,6 @@
*/
import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { StructureMeshParams, StructureDirectVolumeParams, StructureTextParams, StructureParams } from './representation';
import { Visual, VisualContext } from '../visual';
import { Structure, StructureElement } from '../../mol-model/structure';
import { Geometry, GeometryUtils } from '../../mol-geo/geometry/geometry';
@@ -30,6 +29,7 @@ import { Text } from '../../mol-geo/geometry/text/text';
import { SizeTheme } from '../../mol-theme/size';
import { DirectVolume } from '../../mol-geo/geometry/direct-volume/direct-volume';
import { createMarkers } from '../../mol-geo/geometry/marker-data';
+import { StructureParams, StructureMeshParams, StructureTextParams, StructureDirectVolumeParams } from './params';
export interface ComplexVisual<P extends StructureParams> extends Visual<Structure, P> { }
diff --git a/src/mol-repr/structure/params.ts b/src/mol-repr/structure/params.ts
new file mode 100644
index 0000000000000000000000000000000000000000..5f28b6dc5065b642e1a69602cf583cc2d8820a19
--- /dev/null
+++ b/src/mol-repr/structure/params.ts
@@ -0,0 +1,47 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { DirectVolume } from '../../mol-geo/geometry/direct-volume/direct-volume';
+import { Lines } from '../../mol-geo/geometry/lines/lines';
+import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { Points } from '../../mol-geo/geometry/points/points';
+import { Spheres } from '../../mol-geo/geometry/spheres/spheres';
+import { Text } from '../../mol-geo/geometry/text/text';
+import { TextureMesh } from '../../mol-geo/geometry/texture-mesh/texture-mesh';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { UnitKind, UnitKindOptions } from './visual/util/common';
+
+export function getUnitKindsParam(defaultValue: UnitKind[]) {
+ return PD.MultiSelect<UnitKind>(defaultValue, UnitKindOptions, { description: 'For which kinds of units/chains to show the representation visuals.' })
+}
+
+export const StructureParams = {
+ unitKinds: getUnitKindsParam(['atomic', 'spheres']),
+}
+export type StructureParams = typeof StructureParams
+
+export const StructureMeshParams = { ...Mesh.Params }
+export type StructureMeshParams = typeof StructureMeshParams
+
+export const StructureSpheresParams = { ...Spheres.Params }
+export type StructureSpheresParams = typeof StructureSpheresParams
+
+export const StructurePointsParams = { ...Points.Params }
+export type StructurePointsParams = typeof StructurePointsParams
+
+
+export const StructureLinesParams = { ...Lines.Params }
+export type StructureLinesParams = typeof StructureLinesParams
+
+export const StructureTextParams = { ...Text.Params }
+export type StructureTextParams = typeof StructureTextParams
+
+export const StructureDirectVolumeParams = { ...DirectVolume.Params }
+export type StructureDirectVolumeParams = typeof StructureDirectVolumeParams
+
+export const StructureTextureMeshParams = { ...TextureMesh.Params }
+export type StructureTextureMeshParams = typeof StructureTextureMeshParams
\ No newline at end of file
diff --git a/src/mol-repr/structure/representation.ts b/src/mol-repr/structure/representation.ts
index d57f5dfd4bf848bbe56913471ff8f436b3e7ff02..de9c35430415e63e04fbff9ae18c685ba9e7c30e 100644
--- a/src/mol-repr/structure/representation.ts
+++ b/src/mol-repr/structure/representation.ts
@@ -5,27 +5,10 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { DirectVolume } from '../../mol-geo/geometry/direct-volume/direct-volume';
-import { Lines } from '../../mol-geo/geometry/lines/lines';
-import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
-import { Points } from '../../mol-geo/geometry/points/points';
-import { Spheres } from '../../mol-geo/geometry/spheres/spheres';
-import { Text } from '../../mol-geo/geometry/text/text';
-import { TextureMesh } from '../../mol-geo/geometry/texture-mesh/texture-mesh';
import { Structure } from '../../mol-model/structure';
import { StructureUnitTransforms } from '../../mol-model/structure/structure/util/unit-transforms';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Representation, RepresentationProps, RepresentationProvider } from '../representation';
-import { UnitKind, UnitKindOptions } from './visual/util/common';
-
-export function getUnitKindsParam(defaultValue: UnitKind[]) {
- return PD.MultiSelect<UnitKind>(defaultValue, UnitKindOptions, { description: 'For which kinds of units/chains to show the representation visuals.' })
-}
-
-export const StructureParams = {
- unitKinds: getUnitKindsParam(['atomic', 'spheres']),
-}
-export type StructureParams = typeof StructureParams
export interface StructureRepresentationState extends Representation.State {
unitTransforms: StructureUnitTransforms | null,
@@ -50,29 +33,8 @@ export interface StructureRepresentation<P extends RepresentationProps = {}> ext
export type StructureRepresentationProvider<P extends PD.Params, Id extends string = string> = RepresentationProvider<Structure, P, StructureRepresentationState, Id>
export function StructureRepresentationProvider<P extends PD.Params, Id extends string>(p: StructureRepresentationProvider<P, Id>): StructureRepresentationProvider<P, Id> { return p; }
//
-
-export const StructureMeshParams = { ...Mesh.Params }
-export type StructureMeshParams = typeof StructureMeshParams
-
-export const StructureSpheresParams = { ...Spheres.Params }
-export type StructureSpheresParams = typeof StructureSpheresParams
-
-export const StructurePointsParams = { ...Points.Params }
-export type StructurePointsParams = typeof StructurePointsParams
-
-export const StructureLinesParams = { ...Lines.Params }
-export type StructureLinesParams = typeof StructureLinesParams
-
-export const StructureTextParams = { ...Text.Params }
-export type StructureTextParams = typeof StructureTextParams
-
-export const StructureDirectVolumeParams = { ...DirectVolume.Params }
-export type StructureDirectVolumeParams = typeof StructureDirectVolumeParams
-
-export const StructureTextureMeshParams = { ...TextureMesh.Params }
-export type StructureTextureMeshParams = typeof StructureTextureMeshParams
-
export { ComplexRepresentation } from './complex-representation';
export { ComplexVisual } from './complex-visual';
export { UnitsRepresentation } from './units-representation';
export { UnitsVisual } from './units-visual';
+
diff --git a/src/mol-repr/structure/representation/ball-and-stick.ts b/src/mol-repr/structure/representation/ball-and-stick.ts
index e41229dd240d40b8c9d7b3784bf6cbcd1e1e0051..9a9051d9339dcb0e7358652de583a7626d748f97 100644
--- a/src/mol-repr/structure/representation/ball-and-stick.ts
+++ b/src/mol-repr/structure/representation/ball-and-stick.ts
@@ -10,10 +10,11 @@ import { InterUnitBondVisual, InterUnitBondParams } from '../visual/bond-inter-u
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { UnitsRepresentation } from '../units-representation';
import { ComplexRepresentation } from '../complex-representation';
-import { StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder, getUnitKindsParam } from '../representation';
+import { StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../representation';
import { Representation, RepresentationParamsGetter, RepresentationContext } from '../../../mol-repr/representation';
import { ThemeRegistryContext } from '../../../mol-theme/theme';
import { Structure } from '../../../mol-model/structure';
+import { getUnitKindsParam } from '../params';
const BallAndStickVisuals = {
'element-sphere': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, ElementSphereParams>) => UnitsRepresentation('Element sphere mesh', ctx, getParams, getElementSphereVisual(ctx.webgl)),
diff --git a/src/mol-repr/structure/representation/cartoon.ts b/src/mol-repr/structure/representation/cartoon.ts
index 2c7c14369952e5c96f03a16cf71cc0281160e2be..b271675047305b4c2a398b9c8620109fe24b54a3 100644
--- a/src/mol-repr/structure/representation/cartoon.ts
+++ b/src/mol-repr/structure/representation/cartoon.ts
@@ -35,6 +35,7 @@ export const CartoonParams = {
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
visuals: PD.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], PD.objectToOptions(CartoonVisuals)),
}
+
export type CartoonParams = typeof CartoonParams
export function getCartoonParams(ctx: ThemeRegistryContext, structure: Structure) {
const params = PD.clone(CartoonParams)
diff --git a/src/mol-repr/structure/representation/ellipsoid.ts b/src/mol-repr/structure/representation/ellipsoid.ts
index 2ebf4c911c287d92c2853cfc7a12e0aa1f70c897..2ef2eca8a4cc2c9c4de4f98f90a0ce20d36401b0 100644
--- a/src/mol-repr/structure/representation/ellipsoid.ts
+++ b/src/mol-repr/structure/representation/ellipsoid.ts
@@ -8,11 +8,12 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { RepresentationParamsGetter, RepresentationContext, Representation } from '../../../mol-repr/representation';
import { ThemeRegistryContext } from '../../../mol-theme/theme';
import { Structure } from '../../../mol-model/structure';
-import { UnitsRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider, ComplexRepresentation, getUnitKindsParam } from '../../../mol-repr/structure/representation';
+import { UnitsRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider, ComplexRepresentation } from '../../../mol-repr/structure/representation';
import { EllipsoidMeshParams, EllipsoidMeshVisual } from '../visual/ellipsoid-mesh';
import { AtomSiteAnisotrop } from '../../../mol-model-formats/structure/property/anisotropic';
import { IntraUnitBondParams, IntraUnitBondVisual } from '../visual/bond-intra-unit-cylinder';
import { InterUnitBondParams, InterUnitBondVisual } from '../visual/bond-inter-unit-cylinder';
+import { getUnitKindsParam } from '../params';
const EllipsoidVisuals = {
'ellipsoid-mesh': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, EllipsoidMeshParams>) => UnitsRepresentation('Ellipsoid Mesh', ctx, getParams, EllipsoidMeshVisual),
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index b3ccae350d03b4b93040f9793a8a339fe9859686..ce5c31d12b68b28d9b3970c1ef567036675892f7 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -6,7 +6,7 @@
*/
import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationState, StructureParams } from './representation';
+import { StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationState } from './representation';
import { Visual } from '../visual';
import { StructureGroup } from './units-visual';
import { RepresentationContext, RepresentationParamsGetter } from '../representation';
@@ -22,6 +22,7 @@ import { Overpaint } from '../../mol-theme/overpaint';
import { Transparency } from '../../mol-theme/transparency';
import { Mat4, EPSILON } from '../../mol-math/linear-algebra';
import { Interval } from '../../mol-data/int';
+import { StructureParams } from './params';
export interface UnitsVisual<P extends StructureParams> extends Visual<StructureGroup, P> { }
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index 0ac12f20618066790e0997d6d472bc1a3b3aacc9..61ea73795335d4c1fbcb2525caa54039ddf9e211 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -26,7 +26,6 @@ import { createColors } from '../../mol-geo/geometry/color-data';
import { Mat4 } from '../../mol-math/linear-algebra';
import { Overpaint } from '../../mol-theme/overpaint';
import { Transparency } from '../../mol-theme/transparency';
-import { StructureMeshParams, StructureSpheresParams, StructurePointsParams, StructureLinesParams, StructureDirectVolumeParams, StructureTextureMeshParams, StructureTextParams, StructureParams } from './representation';
import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
import { SizeTheme } from '../../mol-theme/size';
import { Spheres } from '../../mol-geo/geometry/spheres/spheres';
@@ -36,6 +35,7 @@ import { Text } from '../../mol-geo/geometry/text/text';
import { DirectVolume } from '../../mol-geo/geometry/direct-volume/direct-volume';
import { TextureMesh } from '../../mol-geo/geometry/texture-mesh/texture-mesh';
import { SizeValues } from '../../mol-gl/renderable/schema';
+import { StructureParams, StructureMeshParams, StructureSpheresParams, StructurePointsParams, StructureLinesParams, StructureTextParams, StructureDirectVolumeParams, StructureTextureMeshParams } from './params';
export type StructureGroup = { structure: Structure, group: Unit.SymmetryGroup }
diff --git a/src/mol-script/runtime/query/base.ts b/src/mol-script/runtime/query/base.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a64c3a6af0bd2ab6bd453742eedda3eb028de0f7
--- /dev/null
+++ b/src/mol-script/runtime/query/base.ts
@@ -0,0 +1,173 @@
+/**
+ * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Expression from '../../language/expression';
+import { QueryContext, QueryFn, Structure, CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { MSymbol } from '../../language/symbol';
+
+export class QueryRuntimeTable {
+ private map = new Map<string, QuerySymbolRuntime>();
+
+ addSymbol(runtime: QuerySymbolRuntime) {
+ if (this.map.has(runtime.symbol.id)) {
+ throw new Error(`Symbol '${runtime.symbol.id}' already added.`);
+ }
+ this.map.set(runtime.symbol.id, runtime);
+ }
+
+ addCustomProp(desc: CustomPropertyDescriptor<any>) {
+ if (!desc.symbols) return;
+
+ for (const k of Object.keys(desc.symbols)) {
+ this.addSymbol((desc.symbols as any)[k]);
+ }
+ }
+
+ getRuntime(id: string) {
+ return this.map.get(id);
+ }
+}
+
+export const DefaultQueryRuntimeTable = new QueryRuntimeTable();
+
+export class QueryCompilerCtx {
+ constQueryContext: QueryContext = new QueryContext(Structure.Empty);
+
+ constructor(public table: QueryRuntimeTable) {
+
+ }
+}
+
+export type ConstQuerySymbolFn<S extends MSymbol = MSymbol> = (ctx: QueryContext, args: QueryRuntimeArguments<S>) => any
+export type QuerySymbolFn<S extends MSymbol = MSymbol> = (ctx: QueryContext, args: QueryRuntimeArguments<S>) => any
+
+
+export type QueryCompiledSymbolRuntime = { kind: 'const', value: any } | { kind: 'dynamic', runtime: QuerySymbolFn }
+
+export type CompiledQueryFn<T = any> = { isConst: boolean, fn: QueryFn }
+
+export namespace QueryCompiledSymbol {
+ export function Const(value: any): QueryCompiledSymbolRuntime {
+ return { kind: 'const', value }
+ }
+
+ export function Dynamic(runtime: QuerySymbolFn): QueryCompiledSymbolRuntime {
+ return { kind: 'dynamic', runtime };
+ }
+}
+
+export namespace CompiledQueryFn {
+ export function Const(value: any): CompiledQueryFn {
+ return { isConst: true, fn: function CompiledQueryFn_Const(ctx) { return value } };
+ }
+
+ export function Dynamic(fn: QueryFn): CompiledQueryFn {
+ return { isConst: false, fn };
+ }
+}
+
+export interface QuerySymbolRuntime {
+ symbol: MSymbol,
+ compile(ctx: QueryCompilerCtx, args?: Expression.Arguments): CompiledQueryFn
+}
+
+export type QueryRuntimeArguments<S extends MSymbol> =
+ { length?: number } & { [P in keyof S['args']['@type']]: QueryFn<S['args']['@type'][P]> }
+
+export namespace QueryRuntimeArguments {
+ export function forEachEval<S extends MSymbol, Ctx>(xs: QueryRuntimeArguments<S>, queryCtx: QueryContext, f: (arg: any, i: number, ctx: Ctx) => void, ctx: Ctx): Ctx {
+ if (typeof xs.length === 'number') {
+ for (let i = 0, _i = xs.length; i < _i; i++) f((xs as any)[i](queryCtx), i, ctx);
+ } else {
+ let i = 0;
+ for (const k of Object.keys(xs)) f((xs as any)[k](queryCtx), i++, ctx);
+ }
+ return ctx;
+ }
+}
+
+export namespace QuerySymbolRuntime {
+ export function Const<S extends MSymbol<any>>(symbol: S, fn: ConstQuerySymbolFn<S>): QuerySymbolRuntime {
+ return new SymbolRuntimeImpl(symbol, fn, true);
+ }
+
+ export function Dynamic<S extends MSymbol<any>>(symbol: S, fn: QuerySymbolFn<S>): QuerySymbolRuntime {
+ return new SymbolRuntimeImpl(symbol, fn, false);
+ }
+}
+
+class SymbolRuntimeImpl<S extends MSymbol> implements QuerySymbolRuntime {
+ compile(ctx: QueryCompilerCtx, inputArgs?: Expression.Arguments): CompiledQueryFn {
+ let args: any, constArgs = false;
+ if (!inputArgs) {
+ args = void 0;
+ constArgs = true;
+ } else if (Expression.isArgumentsArray(inputArgs)) {
+ args = [];
+ constArgs = false;
+ for (const arg of inputArgs) {
+ const compiled = _compile(ctx, arg);
+ constArgs = constArgs && compiled.isConst;
+ args.push(compiled.fn);
+ }
+ } else {
+ args = Object.create(null);
+ constArgs = false;
+ for (const key of Object.keys(inputArgs)) {
+ const compiled = _compile(ctx, inputArgs[key]);
+ constArgs = constArgs && compiled.isConst;
+ args[key] = compiled.fn;
+ }
+ }
+
+ if (this.isConst) {
+ if (this.isConst && constArgs) {
+ return CompiledQueryFn.Const(this.fn(ctx.constQueryContext, args))
+ }
+
+ return CompiledQueryFn.Dynamic(createDynamicFn(this.fn, args));
+ }
+
+ return CompiledQueryFn.Dynamic(createDynamicFn(this.fn, args));
+ }
+
+ constructor(public symbol: S, private fn: QuerySymbolFn<S>, private isConst: boolean) {
+
+ }
+}
+
+function createDynamicFn<S extends MSymbol>(fn: QuerySymbolFn<S>, args: any): QueryFn {
+ return function DynamicFn(ctx) { return fn(ctx, args) };
+}
+
+function _compile(ctx: QueryCompilerCtx, expression: Expression): CompiledQueryFn {
+ if (Expression.isLiteral(expression)) {
+ return CompiledQueryFn.Const(expression);
+ }
+
+ if (Expression.isSymbol(expression)) {
+ const runtime = ctx.table.getRuntime(expression.name);
+ if (!runtime) return CompiledQueryFn.Const(expression.name);
+
+ return runtime.compile(ctx);
+ }
+
+ if (!Expression.isSymbol(expression.head)) {
+ throw new Error('Can only apply symbols.');
+ }
+
+ const compiler = ctx.table.getRuntime(expression.head.name);
+ if (!compiler) {
+ throw new Error(`Symbol '${expression.head.name}' is not implemented.`);
+ }
+
+ return compiler.compile(ctx, expression.args);
+}
+
+export function compile<T = any>(expression: Expression): QueryFn<T> {
+ const ctx = new QueryCompilerCtx(DefaultQueryRuntimeTable);
+ return _compile(ctx, expression).fn;
+}
\ No newline at end of file
diff --git a/src/mol-script/runtime/query/compiler.ts b/src/mol-script/runtime/query/compiler.ts
index e84880e703e7024f3e28ce298b656516349f9b91..2c799c3efd8dad115d33112cc78ed326f012271b 100644
--- a/src/mol-script/runtime/query/compiler.ts
+++ b/src/mol-script/runtime/query/compiler.ts
@@ -4,172 +4,5 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Expression from '../../language/expression';
-import { QueryContext, QueryFn, Structure, CustomPropertyDescriptor } from '../../../mol-model/structure';
-import { MSymbol } from '../../language/symbol';
-
-export class QueryRuntimeTable {
- private map = new Map<string, QuerySymbolRuntime>();
-
- addSymbol(runtime: QuerySymbolRuntime) {
- if (this.map.has(runtime.symbol.id)) {
- throw new Error(`Symbol '${runtime.symbol.id}' already added.`);
- }
- this.map.set(runtime.symbol.id, runtime);
- }
-
- addCustomProp(desc: CustomPropertyDescriptor<any>) {
- if (!desc.symbols) return;
-
- for (const k of Object.keys(desc.symbols)) {
- this.addSymbol((desc.symbols as any)[k]);
- }
- }
-
- getRuntime(id: string) {
- return this.map.get(id);
- }
-}
-
-export const DefaultQueryRuntimeTable = new QueryRuntimeTable();
-
-export class QueryCompilerCtx {
- constQueryContext: QueryContext = new QueryContext(Structure.Empty);
-
- constructor(public table: QueryRuntimeTable) {
-
- }
-}
-
-export type ConstQuerySymbolFn<S extends MSymbol = MSymbol> = (ctx: QueryContext, args: QueryRuntimeArguments<S>) => any
-export type QuerySymbolFn<S extends MSymbol = MSymbol> = (ctx: QueryContext, args: QueryRuntimeArguments<S>) => any
-
-
-export type QueryCompiledSymbolRuntime = { kind: 'const', value: any } | { kind: 'dynamic', runtime: QuerySymbolFn }
-
-export type CompiledQueryFn<T = any> = { isConst: boolean, fn: QueryFn }
-
-export namespace QueryCompiledSymbol {
- export function Const(value: any): QueryCompiledSymbolRuntime {
- return { kind: 'const', value }
- }
-
- export function Dynamic(runtime: QuerySymbolFn): QueryCompiledSymbolRuntime {
- return { kind: 'dynamic', runtime };
- }
-}
-
-export namespace CompiledQueryFn {
- export function Const(value: any): CompiledQueryFn {
- return { isConst: true, fn: function CompiledQueryFn_Const(ctx) { return value } };
- }
-
- export function Dynamic(fn: QueryFn): CompiledQueryFn {
- return { isConst: false, fn };
- }
-}
-
-export interface QuerySymbolRuntime {
- symbol: MSymbol,
- compile(ctx: QueryCompilerCtx, args?: Expression.Arguments): CompiledQueryFn
-}
-
-export type QueryRuntimeArguments<S extends MSymbol> =
- { length?: number } & { [P in keyof S['args']['@type']]: QueryFn<S['args']['@type'][P]> }
-
-export namespace QueryRuntimeArguments {
- export function forEachEval<S extends MSymbol, Ctx>(xs: QueryRuntimeArguments<S>, queryCtx: QueryContext, f: (arg: any, i: number, ctx: Ctx) => void, ctx: Ctx): Ctx {
- if (typeof xs.length === 'number') {
- for (let i = 0, _i = xs.length; i < _i; i++) f((xs as any)[i](queryCtx), i, ctx);
- } else {
- let i = 0;
- for (const k of Object.keys(xs)) f((xs as any)[k](queryCtx), i++, ctx);
- }
- return ctx;
- }
-}
-
-export namespace QuerySymbolRuntime {
- export function Const<S extends MSymbol<any>>(symbol: S, fn: ConstQuerySymbolFn<S>): QuerySymbolRuntime {
- return new SymbolRuntimeImpl(symbol, fn, true);
- }
-
- export function Dynamic<S extends MSymbol<any>>(symbol: S, fn: QuerySymbolFn<S>): QuerySymbolRuntime {
- return new SymbolRuntimeImpl(symbol, fn, false);
- }
-}
-
-class SymbolRuntimeImpl<S extends MSymbol> implements QuerySymbolRuntime {
- compile(ctx: QueryCompilerCtx, inputArgs?: Expression.Arguments): CompiledQueryFn {
- let args: any, constArgs = false;
- if (!inputArgs) {
- args = void 0;
- constArgs = true;
- } else if (Expression.isArgumentsArray(inputArgs)) {
- args = [];
- constArgs = false;
- for (const arg of inputArgs) {
- const compiled = _compile(ctx, arg);
- constArgs = constArgs && compiled.isConst;
- args.push(compiled.fn);
- }
- } else {
- args = Object.create(null);
- constArgs = false;
- for (const key of Object.keys(inputArgs)) {
- const compiled = _compile(ctx, inputArgs[key]);
- constArgs = constArgs && compiled.isConst;
- args[key] = compiled.fn;
- }
- }
-
- if (this.isConst) {
- if (this.isConst && constArgs) {
- return CompiledQueryFn.Const(this.fn(ctx.constQueryContext, args))
- }
-
- return CompiledQueryFn.Dynamic(createDynamicFn(this.fn, args));
- }
-
- return CompiledQueryFn.Dynamic(createDynamicFn(this.fn, args));
- }
-
- constructor(public symbol: S, private fn: QuerySymbolFn<S>, private isConst: boolean) {
-
- }
-}
-
-function createDynamicFn<S extends MSymbol>(fn: QuerySymbolFn<S>, args: any): QueryFn {
- return function DynamicFn(ctx) { return fn(ctx, args) };
-}
-
-function _compile(ctx: QueryCompilerCtx, expression: Expression): CompiledQueryFn {
- if (Expression.isLiteral(expression)) {
- return CompiledQueryFn.Const(expression);
- }
-
- if (Expression.isSymbol(expression)) {
- const runtime = ctx.table.getRuntime(expression.name);
- if (!runtime) return CompiledQueryFn.Const(expression.name);
-
- return runtime.compile(ctx);
- }
-
- if (!Expression.isSymbol(expression.head)) {
- throw new Error('Can only apply symbols.');
- }
-
- const compiler = ctx.table.getRuntime(expression.head.name);
- if (!compiler) {
- throw new Error(`Symbol '${expression.head.name}' is not implemented.`);
- }
-
- return compiler.compile(ctx, expression.args);
-}
-
-export function compile<T = any>(expression: Expression): QueryFn<T> {
- const ctx = new QueryCompilerCtx(DefaultQueryRuntimeTable);
- return _compile(ctx, expression).fn;
-}
-
+export * from './base'
import './table'
\ No newline at end of file
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index 2046a6bb472b1066350284515affb13749057b21..dbd42f193e2027b5ebe389c7ca7272f0d3e6a90e 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -6,17 +6,18 @@
*/
import { MolScriptSymbolTable as MolScript } from '../../language/symbol-table';
-import { DefaultQueryRuntimeTable, QuerySymbolRuntime, QueryRuntimeArguments } from './compiler';
+import { DefaultQueryRuntimeTable, QuerySymbolRuntime, QueryRuntimeArguments } from './base';
import { Queries, StructureProperties, StructureElement, QueryContext, UnitRing } from '../../../mol-model/structure';
import { ElementSymbol, BondType, SecondaryStructureType } from '../../../mol-model/structure/model/types';
import { SetUtils } from '../../../mol-util/set';
import { upperCaseAny } from '../../../mol-util/string';
import { VdwRadius, AtomWeight, AtomNumber } from '../../../mol-model/structure/model/properties/atomic';
import { cantorPairing } from '../../../mol-data/util';
-import C = QuerySymbolRuntime.Const
-import D = QuerySymbolRuntime.Dynamic
import { bundleElementImpl, bundleGenerator } from '../../../mol-model/structure/query/queries/internal';
+const C = QuerySymbolRuntime.Const
+const D = QuerySymbolRuntime.Dynamic
+
const symbols = [
// ============= TYPES =============
diff --git a/src/mol-state/state.ts b/src/mol-state/state.ts
index 42554a7d7dc837ca2bb72609c03e3b3b3eb8c6d1..4383be5045aed5093b9775dc80391210ccf26c56 100644
--- a/src/mol-state/state.ts
+++ b/src/mol-state/state.ts
@@ -218,6 +218,13 @@ class State {
});
}
+ private _inUpdate = false;
+ /**
+ * Determines whether the state is currently "inside" updateTree function.
+ * This is different from "isUpdating" which wraps entire transactions.
+ */
+ get inUpdate() { return this._inUpdate; }
+
/**
* Queues up a reconciliation of the existing state tree.
*
@@ -233,6 +240,8 @@ class State {
const removed = await this.updateQueue.enqueue(params);
if (!removed) return;
+ this._inUpdate = true;
+
const snapshot = options?.canUndo ? this._tree.asImmutable() : void 0;
let reverted = false;
@@ -248,6 +257,7 @@ class State {
return ret.cell;
} finally {
+ this._inUpdate = false;
this.updateQueue.handled(params);
if (!this.inTransaction) {
this.behaviors.isUpdating.next(false);
diff --git a/src/servers/model/server.ts b/src/servers/model/server.ts
index 2a09960b3e6a87c731fd19fc8f11a8330761f49e..1844c8ae2365a25572e4771822a017094fcf7b12 100644
--- a/src/servers/model/server.ts
+++ b/src/servers/model/server.ts
@@ -5,8 +5,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import * as compression from 'compression'
-import * as express from 'express'
+import compression from 'compression'
+import express from 'express'
import { ConsoleLogger } from '../../mol-util/console-logger'
import { PerformanceMonitor } from '../../mol-util/performance-monitor'
import { configureServer, ModelServerConfig as ServerConfig } from './config'
diff --git a/src/servers/plugin-state/index.ts b/src/servers/plugin-state/index.ts
index f8cd83631679504d0e2b8a55626665d53099858d..afe11ac06c4d9f095599a72f4a9b050baf7f6171 100644
--- a/src/servers/plugin-state/index.ts
+++ b/src/servers/plugin-state/index.ts
@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import * as express from 'express'
-import * as compression from 'compression'
-import * as cors from 'cors'
+import express from 'express'
+import compression from 'compression'
+import cors from 'cors'
import * as bodyParser from 'body-parser'
import * as fs from 'fs'
import * as path from 'path'
diff --git a/src/servers/volume/server.ts b/src/servers/volume/server.ts
index 43983633b519a8f04da63c6f764afd3b97e60d2f..e9420b2589907073892a14407bc2570a5fe1b58d 100644
--- a/src/servers/volume/server.ts
+++ b/src/servers/volume/server.ts
@@ -8,8 +8,8 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import * as compression from 'compression'
-import * as express from 'express'
+import compression from 'compression'
+import express from 'express'
import { ConsoleLogger } from '../../mol-util/console-logger'
import { configureServer, ServerConfig } from './config'
import { State } from './server/state'
diff --git a/tsconfig.json b/tsconfig.json
index 81c072d12efdca006ad1da8167446e7091a1f36f..1d5ba9d043c61d30f86675d4ebe56fd187078f00 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -9,7 +9,9 @@
"noUnusedLocals": true,
"strictNullChecks": true,
"strictFunctionTypes": true,
- // "downlevelIteration": true,
+ "module": "commonjs",
+ "esModuleInterop": true,
+ "moduleResolution": "node",
"importHelpers": true,
"noEmitHelpers": true,
"jsx": "react",
diff --git a/webpack.config.common.js b/webpack.config.common.js
index e3c610c72b04cd52fa46ff710c085bdc52579e38..3834422caa0127e29daf99b4ebb98c38dfec0871 100644
--- a/webpack.config.common.js
+++ b/webpack.config.common.js
@@ -91,12 +91,14 @@ function createNodeEntryPoint(name, dir, out) {
}
function createApp(name) { return createEntryPoint('index', `apps/${name}`, name) }
+function createExample(name) { return createEntry(`examples/${name}/index`, `examples/${name}`, 'index') }
function createBrowserTest(name) { return createEntryPoint(name, 'tests/browser', 'tests') }
function createNodeApp(name) { return createNodeEntryPoint('index', `apps/${name}`, name) }
module.exports = {
createApp,
createEntry,
+ createExample,
createBrowserTest,
createNodeEntryPoint,
createNodeApp
diff --git a/webpack.config.js b/webpack.config.js
index 349c8dd6e3831b434d6f4bf87a3895792df9912e..5412a363045d9c12fdf61d240e1a47832c122ebf 100644
--- a/webpack.config.js
+++ b/webpack.config.js
@@ -1,20 +1,15 @@
-const common = require('./webpack.config.common.js');
-const createApp = common.createApp;
-const createEntry = common.createEntry;
-const createBrowserTest = common.createBrowserTest;
+const { createApp, createExample, createBrowserTest } = require('./webpack.config.common.js');
-module.exports = [
- createApp('viewer'),
- createApp('basic-wrapper'),
- createEntry('examples/proteopedia-wrapper/index', 'examples/proteopedia-wrapper', 'index'),
- createEntry('apps/demos/lighting/index', 'demos/lighting', 'index'),
+const apps = ['viewer'];
+const examples = ['proteopedia-wrapper', 'basic-wrapper', 'lighting'];
+const tests = [
+ 'font-atlas',
+ 'marching-cubes',
+ 'render-lines', 'render-mesh', 'render-shape', 'render-spheres', 'render-structure', 'render-text'
+];
- createBrowserTest('font-atlas'),
- createBrowserTest('marching-cubes'),
- createBrowserTest('render-lines'),
- createBrowserTest('render-mesh'),
- createBrowserTest('render-shape'),
- createBrowserTest('render-spheres'),
- createBrowserTest('render-structure'),
- createBrowserTest('render-text'),
+module.exports = [
+ ...apps.map(createApp),
+ ...examples.map(createExample),
+ ...tests.map(createBrowserTest)
]
\ No newline at end of file