mmcif, ccd & bird schema updates

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> { }

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,
     },

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,
     },

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);