diff --git a/src/mol-io/reader/cif/schema/bird.ts b/src/mol-io/reader/cif/schema/bird.ts
new file mode 100644
index 0000000000000000000000000000000000000000..80329868d023d523388c1da16075b0c4d1adcb7b
--- /dev/null
+++ b/src/mol-io/reader/cif/schema/bird.ts
@@ -0,0 +1,125 @@
+/**
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated 'BIRD' schema file
+ *
+ * @author mol-star package (src/apps/schema-generator/generate)
+ */
+
+import { Database, Column } from 'mol-data/db'
+
+import Schema = Column.Schema
+
+const str = Schema.str;
+const int = Schema.int;
+const float = Schema.float;
+// const coord = Schema.coord;
+
+const Aliased = Schema.Aliased;
+// const Matrix = Schema.Matrix;
+// const Vector = Schema.Vector;
+// const List = Schema.List;
+
+export const BIRD_Schema = {
+ pdbx_reference_molecule: {
+ prd_id: str,
+ formula_weight: float,
+ formula: str,
+ type: Aliased<'Amino acid' | 'Aminoglycoside' | 'Anthracycline' | 'Anthraquinone' | 'Ansamycin' | 'Chalkophore' | 'Chromophore' | 'Glycopeptide' | 'Cyclic depsipeptide' | 'Cyclic lipopeptide' | 'Cyclic peptide' | 'Heterocyclic' | 'Imino sugar' | 'Keto acid' | 'Lipoglycopeptide' | 'Lipopeptide' | 'Macrolide' | 'Non-polymer' | 'Nucleoside' | 'Oligopeptide' | 'Oligosaccharide' | 'Peptaibol' | 'Peptide-like' | 'Polycyclic' | 'Polypeptide' | 'Polysaccharide' | 'Quinolone' | 'Thiolactone' | 'Thiopeptide' | 'Siderophore' | 'Unknown' | 'Chalkophore, Polypeptide'>(str),
+ type_evidence_code: str,
+ class: Aliased<'Antagonist' | 'Antibiotic' | 'Anticancer' | 'Anticoagulant' | 'Antifungal' | 'Antiinflammatory' | 'Antimicrobial' | 'Antineoplastic' | 'Antiparasitic' | 'Antiretroviral' | 'Anthelmintic' | 'Antithrombotic' | 'Antitumor' | 'Antiviral' | 'CASPASE inhibitor' | 'Chaperone binding' | 'Enzyme inhibitor' | 'Growth factor' | 'Immunosuppressant' | 'Inhibitor' | 'Lantibiotic' | 'Metabolism' | 'Metal transport' | 'Oxidation-reduction' | 'Receptor' | 'Thrombin inhibitor' | 'Trypsin inhibitor' | 'Toxin' | 'Unknown' | 'Anticoagulant, Antithrombotic' | 'Antibiotic, Antimicrobial' |'Antibiotic, Anthelmintic' | 'Antibiotic, Antineoplastic' | 'Antimicrobial, Antiretroviral' | 'Antimicrobial, Antitumor' | 'Antimicrobial, Antiparasitic, Antibiotic' | 'Thrombin inhibitor, Trypsin inhibitor'>(str),
+ class_evidence_code: str,
+ name: str,
+ represent_as: Aliased<'polymer' | 'single molecule'>(str),
+ chem_comp_id: str,
+ description: str,
+ representative_PDB_id_code: str,
+ release_status: Aliased<'REL' | 'HOLD' | 'OBS' | 'WAIT'>(str),
+ replaces: str,
+ replaced_by: str,
+ },
+ pdbx_reference_entity_list: {
+ prd_id: str,
+ ref_entity_id: str,
+ type: str,
+ details: str,
+ component_id: int,
+ },
+ pdbx_reference_entity_nonpoly: {
+ prd_id: str,
+ ref_entity_id: str,
+ name: str,
+ chem_comp_id: str,
+ },
+ pdbx_reference_entity_link: {
+ link_id: int,
+ prd_id: str,
+ details: str,
+ ref_entity_id_1: str,
+ ref_entity_id_2: str,
+ entity_seq_num_1: int,
+ entity_seq_num_2: int,
+ comp_id_1: str,
+ comp_id_2: str,
+ atom_id_1: str,
+ atom_id_2: str,
+ value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
+ component_1: int,
+ component_2: int,
+ link_class: Aliased<'PP' | 'PN' | 'NP' | 'NN'>(str),
+ },
+ pdbx_reference_entity_poly_link: {
+ link_id: int,
+ prd_id: str,
+ ref_entity_id: str,
+ component_id: int,
+ entity_seq_num_1: int,
+ entity_seq_num_2: int,
+ comp_id_1: str,
+ comp_id_2: str,
+ atom_id_1: str,
+ atom_id_2: str,
+ value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
+ },
+ pdbx_reference_entity_poly: {
+ prd_id: str,
+ ref_entity_id: str,
+ type: Aliased<'peptide-like' | 'nucleic-acid-like' | 'polysaccharide-like'>(str),
+ db_code: str,
+ db_name: str,
+ },
+ pdbx_reference_entity_poly_seq: {
+ prd_id: str,
+ ref_entity_id: str,
+ mon_id: str,
+ parent_mon_id: str,
+ num: int,
+ observed: Aliased<'Y' | 'N'>(str),
+ hetero: Aliased<'Y' | 'N'>(str),
+ },
+ pdbx_reference_entity_sequence: {
+ prd_id: str,
+ ref_entity_id: str,
+ type: str,
+ NRP_flag: Aliased<'Y' | 'N'>(str),
+ one_letter_codes: str,
+ },
+ pdbx_reference_entity_src_nat: {
+ prd_id: str,
+ ref_entity_id: str,
+ ordinal: int,
+ organism_scientific: str,
+ taxid: str,
+ db_code: str,
+ db_name: str,
+ },
+ pdbx_prd_audit: {
+ prd_id: str,
+ date: str,
+ processing_site: str,
+ action_type: Aliased<'Initial release' | 'Create molecule' | 'Modify type' | 'Modify class' | 'Modify molecule name' | 'Modify representation' | 'Modify sequence' | 'Modify linkage' | 'Modify taxonomy organism' | 'Modify audit' | 'Other modification' | 'Obsolete molecule'>(str),
+ },
+}
+
+export type BIRD_Schema = typeof BIRD_Schema;
+export interface BIRD_Database extends Database<BIRD_Schema> { }
\ No newline at end of file
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index 4ce9bf75b287dd437b776191930793338ad94b6c..208353c5e617d784b815784c3901339bca248465 100644
--- a/src/mol-io/reader/cif/schema/ccd.ts
+++ b/src/mol-io/reader/cif/schema/ccd.ts
@@ -18,17 +18,18 @@ const coord = Schema.coord;
const Aliased = Schema.Aliased;
// const Matrix = Schema.Matrix;
// const Vector = Schema.Vector;
+const List = Schema.List;
export const CCD_Schema = {
chem_comp: {
formula: str,
formula_weight: float,
id: str,
- mon_nstd_parent_comp_id: str,
+ mon_nstd_parent_comp_id: List(',', x => x),
name: str,
one_letter_code: str,
three_letter_code: str,
- type: str,
+ type: Aliased<'D-peptide linking' | 'L-peptide linking' | 'D-peptide NH3 amino terminus' | 'L-peptide NH3 amino terminus' | 'D-peptide COOH carboxy terminus' | 'L-peptide COOH carboxy terminus' | 'DNA linking' | 'RNA linking' | 'L-RNA linking' | 'L-DNA linking' | 'DNA OH 5 prime terminus' | 'RNA OH 5 prime terminus' | 'DNA OH 3 prime terminus' | 'RNA OH 3 prime terminus' | 'D-saccharide 1,4 and 1,4 linking' | 'L-saccharide 1,4 and 1,4 linking' | 'D-saccharide 1,4 and 1,6 linking' | 'L-saccharide 1,4 and 1,6 linking' | 'L-saccharide' | 'D-saccharide' | 'saccharide' | 'non-polymer' | 'peptide linking' | 'peptide-like' | 'L-gamma-peptide, C-delta linking' | 'D-gamma-peptide, C-delta linking' | 'L-beta-peptide, C-gamma linking' | 'D-beta-peptide, C-gamma linking' | 'other'>(str),
pdbx_synonyms: str,
pdbx_type: str,
pdbx_ambiguous_flag: str,
@@ -42,7 +43,7 @@ export const CCD_Schema = {
pdbx_model_coordinates_missing_flag: Aliased<'Y' | 'N'>(str),
pdbx_initial_date: str,
pdbx_modified_date: str,
- pdbx_processing_site: str,
+ pdbx_processing_site: Aliased<'PDBE' | 'EBI' | 'PDBJ' | 'RCSB'>(str),
},
chem_comp_atom: {
alt_atom_id: str,
@@ -74,14 +75,14 @@ export const CCD_Schema = {
pdbx_chem_comp_descriptor: {
comp_id: str,
descriptor: str,
- type: str,
+ type: Aliased<'SMILES_CANNONICAL' | 'SMILES_CANONICAL' | 'SMILES' | 'SMILES' | 'InChI' | 'InChI_MAIN' | 'InChI_MAIN_FORMULA' | 'InChI_MAIN_CONNECT' | 'InChI_MAIN_HATOM' | 'InChI_CHARGE' | 'InChI_STEREO' | 'InChI_ISOTOPE' | 'InChI_FIXEDH' | 'InChI_RECONNECT' | 'InChIKey'>(str),
program: str,
program_version: str,
},
pdbx_chem_comp_identifier: {
comp_id: str,
identifier: str,
- type: str,
+ type: Aliased<'COMMON NAME' | 'SYSTEMATIC NAME' | 'CAS REGISTRY NUMBER' | 'PUBCHEM Identifier' | 'MDL Identifier' | 'SYNONYM'>(str),
program: str,
program_version: str,
},
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index ef249f5edc63bc5c525a27384dafec81ffc0895d..20988c52dccc5c4b77a2b6afea34c64d4082a59c 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -18,6 +18,7 @@ const coord = Schema.coord;
const Aliased = Schema.Aliased;
const Matrix = Schema.Matrix;
const Vector = Schema.Vector;
+const List = Schema.List;
export const mmCIF_Schema = {
atom_site: {
@@ -29,7 +30,7 @@ export const mmCIF_Schema = {
Cartn_x: coord,
Cartn_y: coord,
Cartn_z: coord,
- group_PDB: str,
+ group_PDB: Aliased<'ATOM' | 'HETATM'>(str),
id: int,
label_alt_id: str,
label_asym_id: str,
@@ -73,11 +74,11 @@ export const mmCIF_Schema = {
pdbx_number_of_molecules: float,
pdbx_mutation: str,
pdbx_fragment: str,
- pdbx_ec: str,
+ pdbx_ec: List(',', x => x),
},
exptl: {
entry_id: str,
- method: str,
+ method: Aliased<'X-RAY DIFFRACTION' | 'NEUTRON DIFFRACTION' | 'FIBER DIFFRACTION' | 'ELECTRON CRYSTALLOGRAPHY' | 'ELECTRON MICROSCOPY' | 'SOLUTION NMR' | 'SOLID-STATE NMR' | 'SOLUTION SCATTERING' | 'POWDER DIFFRACTION' | 'INFRARED SPECTROSCOPY' | 'EPR' | 'FLUORESCENCE TRANSFER' | 'THEORETICAL MODEL'>(str),
},
struct_conf: {
beg_label_asym_id: str,
@@ -186,14 +187,14 @@ export const mmCIF_Schema = {
},
pdbx_struct_oper_list: {
id: str,
- type: str,
+ type: Aliased<'identity operation' | 'point symmetry operation' | 'helical symmetry operation' | 'crystal symmetry operation' | '3D crystal symmetry operation' | '2D crystal symmetry operation' | 'transform to point frame' | 'transform to helical frame' | 'transform to crystal frame' | 'transform to 2D crystal frame' | 'transform to 3D crystal frame' | 'build point asymmetric unit' | 'build helical asymmetric unit' | 'build 2D crystal asymmetric unit' | 'build 3D crystal asymmetric unit'>(str),
name: str,
symmetry_operation: str,
matrix: Matrix(3, 3),
vector: Vector(3),
},
pdbx_struct_assembly_gen: {
- asym_id_list: str,
+ asym_id_list: List(',', x => x),
assembly_id: str,
oper_expression: str,
},
diff --git a/src/mol-model/structure/model/formats/gro.ts b/src/mol-model/structure/model/formats/gro.ts
index 9958d2a72ae0f656effe86ddc7bcd59eb86f588a..be9be255caea248d52d389e4ea486f053ec621e7 100644
--- a/src/mol-model/structure/model/formats/gro.ts
+++ b/src/mol-model/structure/model/formats/gro.ts
@@ -51,12 +51,12 @@ function createHierarchyData(atomsData: Atoms, offsets: HierarchyOffsets): Hiera
});
const residues = Table.view(Table.ofColumns(Hierarchy.ResiduesSchema, {
- group_PDB: Column.Undefined(atomsData.count, Column.Schema.str),
+ group_PDB: Column.Undefined(atomsData.count, Column.Schema.Aliased<'ATOM' | 'HETATM'>(Column.Schema.str)),
label_comp_id: atomsData.residueName,
auth_comp_id: atomsData.residueName,
label_seq_id: atomsData.residueNumber,
auth_seq_id: atomsData.residueNumber,
- pdbx_PDB_ins_code: Column.Undefined(atomsData.count, Column.Schema.str)
+ pdbx_PDB_ins_code: Column.Undefined(atomsData.count, Column.Schema.str),
}), Hierarchy.ResiduesSchema, offsets.residues);
// Optimize the numeric columns
Table.columnToArray(residues, 'label_seq_id', Int32Array);