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/package.json b/package.json
index 0730fe89e05d7348caff149e6e23345cfb3194c2..34f59326c9d625d3b5eb83ea8e5da411d337b021 100644
--- a/package.json
+++ b/package.json
@@ -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/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
+}