schema updates and cli path fixes

README.md

@@ -97,11 +97,11 @@ and navigate to `build/viewer`
 
 **Lipid names**
 
-    node .\lib\cli\lipid-params -o src\mol-model\structure\model\types\lipids.ts
+    node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts
 
 **GraphQL schemas**
 
-    ./node_modules/.bin/graphql-codegen -c ./src/extensions/rcsb/graphql/codegen.yml
+    node node_modules//@graphql-codegen/cli/bin -c src/extensions/rcsb/graphql/codegen.yml
 
 ### Other scripts
 **Create chem comp bond table**
@@ -124,7 +124,7 @@ To see all available commands, use ``node lib/servers/model/preprocess -h``.
 
 Or
 
-    node ./lib/commonjs/cli/cif2bcif
+    node lib/commonjs/cli/cif2bcif
 
 ## Development
 

src/cli/chem-comp-bond/create-table.ts

@@ -220,7 +220,7 @@ async function run(out: string, binary = false) {
 
 const TABLE_NAME = 'CHEM_COMP_BONDS';
 
-const DATA_DIR = path.join(__dirname, '..', '..', '..', 'build/data');
+const DATA_DIR = path.join(__dirname, '..', '..', '..', '..', 'build/data');
 const CCD_PATH = path.join(DATA_DIR, 'components.cif');
 const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');
 const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif';

src/cli/cifschema/index.ts

@@ -160,7 +160,7 @@ async function ensureDicAvailable(dicPath: string, dicUrl: string) {
     }
 }
 
-const DIC_DIR = path.resolve(__dirname, '../../../build/dics/');
+const DIC_DIR = path.resolve(__dirname, '../../../../build/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`;
@@ -238,22 +238,22 @@ switch (args.preset) {
     case 'mmCIF':
         args.name = 'mmCIF';
         args.dic = 'mmCIF';
-        args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/mmcif-field-names.csv');
+        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');
+        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');
+        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');
+        args.fieldNamesPath = path.resolve(__dirname, '../../../../data/cif-field-names/cif-core-field-names.csv');
         break;
 }
 

src/cli/cifschema/util/generate.ts

@@ -17,15 +17,15 @@ function header (name: string, info: string, moldataImportPath: string) {
  * @author molstar/ciftools package
  */
 
-import { Database, Column } from '${moldataImportPath}/db'
+import { Database, Column } from '${moldataImportPath}/db';
 
-import Schema = Column.Schema`;
+import Schema = Column.Schema;`;
 }
 
 function footer (name: string) {
     return `
 export type ${name}_Schema = typeof ${name}_Schema;
-export interface ${name}_Database extends Database<${name}_Schema> {}`;
+export interface ${name}_Database extends Database<${name}_Schema> {};`;
 }
 
 function getTypeShorthands(schema: Database, fields?: Filter) {
@@ -122,7 +122,7 @@ export function generate (name: string, info: string, schema: Database, fields:
         });
         codeLines.push('    },');
     });
-    codeLines.push('}');
+    codeLines.push('};');
 
     if (addAliases) {
         codeLines.push('');
@@ -144,7 +144,7 @@ export function generate (name: string, info: string, schema: Database, fields:
             });
             codeLines.push('    ],');
         });
-        codeLines.push('}');
+        codeLines.push('};');
     }
 
     return `${header(name, info, moldataImportPath)}\n\n${getTypeShorthands(schema, fields)}\n\n${codeLines.join('\n')}\n${footer(name)}`;

src/cli/lipid-params/index.ts

@@ -11,7 +11,7 @@ import * as path from 'path';
 import fetch from 'node-fetch';
 import { UniqueArray } from '../../mol-data/generic';
 
-const LIPIDS_DIR = path.resolve(__dirname, '../../../build/lipids/');
+const LIPIDS_DIR = path.resolve(__dirname, '../../../../build/lipids/');
 
 const MARTINI_LIPIDS_PATH = path.resolve(LIPIDS_DIR, 'martini_lipids.itp');
 const MARTINI_LIPIDS_URL = 'http://www.cgmartini.nl/images/parameters/lipids/Collections/martini_v2.0_lipids_all_201506.itp';

src/mol-io/reader/cif/schema/bird.ts

@@ -1,14 +1,14 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.324, IHM 1.09, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.326, IHM 1.09, CARB draft.
  *
  * @author molstar/ciftools package
  */
 
 import { Database, Column } from '../../../../mol-data/db';
 
-import Schema = Column.Schema
+import Schema = Column.Schema;
 
 const str = Schema.str;
 const float = Schema.float;
@@ -66,7 +66,7 @@ export const BIRD_Schema = {
         /**
          * Broadly defines the function of the entity.
          */
-        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: Aliased<'Antagonist' | 'Antibiotic' | 'Anticancer' | 'Anticoagulant' | 'Antifungal' | 'Antigen' | 'Antiinflammatory' | 'Antimicrobial' | 'Antineoplastic' | 'Antiparasitic' | 'Antiretroviral' | 'Anthelmintic' | 'Antithrombotic' | 'Antitumor' | 'Antiviral' | 'CASPASE inhibitor' | 'Chaperone binding' | 'Enzyme inhibitor' | 'Drug delivery' | 'Glycan component' | 'Growth factor' | 'Immunosuppressant' | 'Inducer' | 'Inhibitor' | 'Lantibiotic' | 'Metabolism' | 'Metal transport' | 'Nutrient' | 'Oxidation-reduction' | 'Protein binding' | 'Receptor' | 'Substrate analog' | 'Thrombin inhibitor' | 'Trypsin inhibitor' | 'Toxin' | 'Unknown' | 'Water retention' | 'Anticoagulant, Antithrombotic' | 'Antibiotic, Antimicrobial' | 'Antibiotic, Anthelmintic' | 'Antibiotic, Antineoplastic' | 'Antimicrobial, Antiretroviral' | 'Antimicrobial, Antitumor' | 'Antimicrobial, Antiparasitic, Antibiotic' | 'Thrombin inhibitor, Trypsin inhibitor'>(str),
         /**
          * Evidence for the assignment of _pdbx_reference_molecule.class
          */
@@ -356,7 +356,7 @@ export const BIRD_Schema = {
         /**
          * The type of the polymer.
          */
-        type: Aliased<'peptide-like' | 'nucleic-acid-like' | 'polysaccharide-like'>(str),
+        type: Aliased<'peptide-like' | 'nucleic-acid-like' | 'polysaccharide-like' | 'oligosaccharide'>(str),
         /**
          * The database code for this source information
          */
@@ -496,4 +496,4 @@ export const BIRD_Schema = {
 };
 
 export type BIRD_Schema = typeof BIRD_Schema;
-export interface BIRD_Database extends Database<BIRD_Schema> {}
+export interface BIRD_Database extends Database<BIRD_Schema> {};

src/mol-io/reader/cif/schema/ccd.ts

@@ -1,14 +1,14 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.324, IHM 1.09, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.326, IHM 1.09, CARB draft.
  *
  * @author molstar/ciftools package
  */
 
 import { Database, Column } from '../../../../mol-data/db';
 
-import Schema = Column.Schema
+import Schema = Column.Schema;
 
 const str = Schema.str;
 const float = Schema.float;
@@ -397,4 +397,4 @@ export const CCD_Schema = {
 };
 
 export type CCD_Schema = typeof CCD_Schema;
-export interface CCD_Database extends Database<CCD_Schema> {}
+export interface CCD_Database extends Database<CCD_Schema> {};

src/mol-io/reader/cif/schema/cif-core.ts

@@ -8,7 +8,7 @@
 
 import { Database, Column } from '../../../../mol-data/db';
 
-import Schema = Column.Schema
+import Schema = Column.Schema;
 
 const int = Schema.int;
 const float = Schema.float;
@@ -792,4 +792,4 @@ export const CifCore_Aliases = {
 };
 
 export type CifCore_Schema = typeof CifCore_Schema;
-export interface CifCore_Database extends Database<CifCore_Schema> {}
+export interface CifCore_Database extends Database<CifCore_Schema> {};

src/mol-io/reader/cif/schema/mmcif.ts

@@ -1,14 +1,14 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.324, IHM 1.09, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.326, IHM 1.09, CARB draft.
  *
  * @author molstar/ciftools package
  */
 
 import { Database, Column } from '../../../../mol-data/db';
 
-import Schema = Column.Schema
+import Schema = Column.Schema;
 
 const str = Schema.str;
 const int = Schema.int;
@@ -2559,7 +2559,7 @@ export const mmCIF_Schema = {
         /**
          * This data item contains the descriptor type.
          */
-        type: Aliased<'LINUCS' | 'Glycam Condensed Sequence' | 'Glycam Condensed Core Sequence'>(str),
+        type: Aliased<'LINUCS' | 'Glycam Condensed Sequence' | 'Glycam Condensed Core Sequence' | 'WURCS'>(str),
         /**
          * This data item contains the name of the program
          * or library used to compute the descriptor.
@@ -2617,6 +2617,188 @@ export const mmCIF_Schema = {
          */
         ordinal: int,
     },
+    /**
+     * Data items in the PDBX_ENTITY_BRANCH_LIST category specify the list
+     * of monomers in a branched entity.  Allowance is made for the possibility
+     * of microheterogeneity in a sample by allowing a given sequence
+     * number to be correlated with more than one monomer ID. The
+     * corresponding ATOM_SITE entries should reflect this
+     * heterogeneity.
+     */
+    pdbx_entity_branch_list: {
+        /**
+         * This data item is a pointer to _entity.id in the ENTITY category.
+         */
+        entity_id: str,
+        /**
+         * A flag to indicate whether this monomer in the entity is
+         * heterogeneous in sequence.
+         */
+        hetero: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
+        /**
+         * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+         * category.
+         */
+        comp_id: str,
+        /**
+         * The value pair  _pdbx_entity_branch_list.num and _pdbx_entity_branch_list.comp_id
+         * must uniquely identify a record in the PDBX_ENTITY_BRANCH_LIST list.
+         */
+        num: int,
+    },
+    /**
+     * Data items in the PDBX_ENTITY_BRANCH_LINK category give details about
+     * the linkages between components within a branched entity.
+     */
+    pdbx_entity_branch_link: {
+        /**
+         * The value of _pdbx_entity_branch_link.link_id uniquely identifies
+         * linkages within the branched entity.
+         */
+        link_id: int,
+        /**
+         * A description of special aspects of this linkage.
+         */
+        details: str,
+        /**
+         * The entity id for this branched entity.
+         *
+         * This data item is a pointer to _pdbx_entity_branch_list.entity_id
+         * in the PDBX_ENTITY_BRANCH_LIST category.
+         */
+        entity_id: str,
+        /**
+         * The component number for the first component making the linkage.
+         *
+         * This data item is a pointer to _pdbx_entity_branch_list.num
+         * in the PDBX_ENTITY_BRANCH_LIST category.
+         */
+        entity_branch_list_num_1: int,
+        /**
+         * The component number for the second component making the linkage.
+         *
+         * This data item is a pointer to _pdbx_entity_branch_list.num
+         * in the PDBX_ENTITY_BRANCH_LIST category.
+         */
+        entity_branch_list_num_2: int,
+        /**
+         * The component identifier for the first component making the linkage.
+         *
+         * This data item is a pointer to _pdbx_entity_branch_list.comp_id
+         * in the PDBX_ENTITY_BRANCH_LIST category.
+         */
+        comp_id_1: str,
+        /**
+         * The component identifier for the second component making the linkage.
+         *
+         * This data item is a pointer to _pdbx_entity_branch_list.comp_id
+         * in the PDBX_ENTITY_BRANCH_LIST category.
+         */
+        comp_id_2: str,
+        /**
+         * The atom identifier/name for the first atom making the linkage.
+         */
+        atom_id_1: str,
+        /**
+         * The leaving atom identifier/name bonded to the first atom making the linkage.
+         */
+        leaving_atom_id_1: str,
+        /**
+         * The chiral configuration of the first atom making the linkage.
+         */
+        atom_stereo_config_1: Aliased<'R' | 'S' | 'N'>(str),
+        /**
+         * The atom identifier/name for the second atom making the linkage.
+         */
+        atom_id_2: str,
+        /**
+         * The leaving atom identifier/name bonded to the second atom making the linkage.
+         */
+        leaving_atom_id_2: str,
+        /**
+         * The chiral configuration of the second atom making the linkage.
+         */
+        atom_stereo_config_2: Aliased<'R' | 'S' | 'N'>(str),
+        /**
+         * The bond order target for the chemical linkage.
+         */
+        value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
+    },
+    /**
+     * Data items in the PDBX_ENTITY_BRANCH category specify the list
+     * of branched entities and the type.
+     */
+    pdbx_entity_branch: {
+        /**
+         * The entity id for this branched entity.
+         *
+         * This data item is a pointer to _entity.id
+         */
+        entity_id: str,
+        /**
+         * The type of this branched oligosaccharide.
+         */
+        type: Aliased<'oligosaccharide'>(str),
+    },
+    /**
+     * The PDBX_BRANCH_SCHEME category provides residue level nomenclature
+     * mapping for branch chain entities.
+     */
+    pdbx_branch_scheme: {
+        /**
+         * This data item is a pointer to _entity.id in the ENTITY category.
+         */
+        entity_id: str,
+        /**
+         * A flag to indicate whether this monomer in the entity is
+         * heterogeneous in sequence.
+         */
+        hetero: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
+        /**
+         * Pointer to _atom_site.label_asym_id.
+         */
+        asym_id: str,
+        /**
+         * This data item is a pointer to _atom_site.label_comp_id in the
+         * PDBX_ENTITY_BRANCH_LIST category.
+         */
+        mon_id: str,
+        /**
+         * This data item is a pointer to _pdbx_entity_branch_list.num in the
+         * PDBX_ENTITY_BRANCH_LIST category.
+         */
+        num: int,
+        /**
+         * This data item is a pointer to _atom_site.auth_asym_id in the
+         * ATOM_SITE category.
+         */
+        pdb_asym_id: str,
+        /**
+         * This data item is a pointer to _atom_site.auth_seq_id in the
+         * ATOM_SITE category.
+         */
+        pdb_seq_num: str,
+        /**
+         * This data item is a pointer to _atom_site.auth_comp_id in the
+         * ATOM_SITE category.
+         */
+        pdb_mon_id: str,
+        /**
+         * This data item is a pointer to _atom_site.pdbx_auth_asym_id in the
+         * ATOM_SITE category.
+         */
+        auth_asym_id: str,
+        /**
+         * This data item is a pointer to _atom_site.pdbx_auth_seq_id in the
+         * ATOM_SITE category.
+         */
+        auth_seq_num: str,
+        /**
+         * This data item is a pointer to _atom_site.pdbx_auth_comp_id in the
+         * ATOM_SITE category.
+         */
+        auth_mon_id: str,
+    },
     /**
      * Data items in the IHM_STARTING_MODEL_DETAILS category records the
      * details about structural models used as starting inputs in
@@ -4476,188 +4658,6 @@ export const mmCIF_Schema = {
          */
         dataset_list_id: int,
     },
-    /**
-     * Data items in the PDBX_ENTITY_BRANCH_LIST category specify the list
-     * of monomers in a branched entity.  Allowance is made for the possibility
-     * of microheterogeneity in a sample by allowing a given sequence
-     * number to be correlated with more than one monomer ID. The
-     * corresponding ATOM_SITE entries should reflect this
-     * heterogeneity.
-     */
-    pdbx_entity_branch_list: {
-        /**
-         * This data item is a pointer to _entity.id in the ENTITY category.
-         */
-        entity_id: str,
-        /**
-         * A flag to indicate whether this monomer in the entity is
-         * heterogeneous in sequence.
-         */
-        hetero: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
-        /**
-         * This data item is a pointer to _chem_comp.id in the CHEM_COMP
-         * category.
-         */
-        comp_id: str,
-        /**
-         * The value pair  _pdbx_entity_branch_list.num and _pdbx_entity_branch_list.comp_id
-         * must uniquely identify a record in the PDBX_ENTITY_BRANCH_LIST list.
-         */
-        num: int,
-    },
-    /**
-     * Data items in the PDBX_ENTITY_BRANCH_LINK category give details about
-     * the linkages between components within a branched entity.
-     */
-    pdbx_entity_branch_link: {
-        /**
-         * The value of _pdbx_entity_branch_link.link_id uniquely identifies
-         * linkages within the branched entity.
-         */
-        link_id: int,
-        /**
-         * A description of special aspects of this linkage.
-         */
-        details: str,
-        /**
-         * The entity id for this branched entity.
-         *
-         * This data item is a pointer to _pdbx_entity_branch_list.entity_id
-         * in the PDBX_ENTITY_BRANCH_LIST category.
-         */
-        entity_id: str,
-        /**
-         * The component number for the first component making the linkage.
-         *
-         * This data item is a pointer to _pdbx_entity_branch_list.num
-         * in the PDBX_ENTITY_BRANCH_LIST category.
-         */
-        entity_branch_list_num_1: int,
-        /**
-         * The component number for the second component making the linkage.
-         *
-         * This data item is a pointer to _pdbx_entity_branch_list.num
-         * in the PDBX_ENTITY_BRANCH_LIST category.
-         */
-        entity_branch_list_num_2: int,
-        /**
-         * The component identifier for the first component making the linkage.
-         *
-         * This data item is a pointer to _pdbx_entity_branch_list.comp_id
-         * in the PDBX_ENTITY_BRANCH_LIST category.
-         */
-        comp_id_1: str,
-        /**
-         * The component identifier for the second component making the linkage.
-         *
-         * This data item is a pointer to _pdbx_entity_branch_list.comp_id
-         * in the PDBX_ENTITY_BRANCH_LIST category.
-         */
-        comp_id_2: str,
-        /**
-         * The atom identifier/name for the first atom making the linkage.
-         */
-        atom_id_1: str,
-        /**
-         * The leaving atom identifier/name bonded to the first atom making the linkage.
-         */
-        leaving_atom_id_1: str,
-        /**
-         * The chiral configuration of the first atom making the linkage.
-         */
-        atom_stereo_config_1: Aliased<'R' | 'S' | 'N'>(str),
-        /**
-         * The atom identifier/name for the second atom making the linkage.
-         */
-        atom_id_2: str,
-        /**
-         * The leaving atom identifier/name bonded to the second atom making the linkage.
-         */
-        leaving_atom_id_2: str,
-        /**
-         * The chiral configuration of the second atom making the linkage.
-         */
-        atom_stereo_config_2: Aliased<'R' | 'S' | 'N'>(str),
-        /**
-         * The bond order target for the chemical linkage.
-         */
-        value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
-    },
-    /**
-     * Data items in the PDBX_ENTITY_BRANCH category specify the list
-     * of branched entities and the type.
-     */
-    pdbx_entity_branch: {
-        /**
-         * The entity id for this branched entity.
-         *
-         * This data item is a pointer to _entity.id
-         */
-        entity_id: str,
-        /**
-         * The type of this branched oligosaccharide.
-         */
-        type: Aliased<'oligosaccharide'>(str),
-    },
-    /**
-     * The PDBX_BRANCH_SCHEME category provides residue level nomenclature
-     * mapping for branch chain entities.
-     */
-    pdbx_branch_scheme: {
-        /**
-         * This data item is a pointer to _entity.id in the ENTITY category.
-         */
-        entity_id: str,
-        /**
-         * A flag to indicate whether this monomer in the entity is
-         * heterogeneous in sequence.
-         */
-        hetero: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
-        /**
-         * Pointer to _atom_site.label_asym_id.
-         */
-        asym_id: str,
-        /**
-         * This data item is a pointer to _atom_site.label_comp_id in the
-         * PDBX_ENTITY_BRANCH_LIST category.
-         */
-        mon_id: str,
-        /**
-         * This data item is a pointer to _pdbx_entity_branch_list.num in the
-         * PDBX_ENTITY_BRANCH_LIST category.
-         */
-        num: int,
-        /**
-         * This data item is a pointer to _atom_site.auth_asym_id in the
-         * ATOM_SITE category.
-         */
-        pdb_asym_id: str,
-        /**
-         * This data item is a pointer to _atom_site.auth_seq_id in the
-         * ATOM_SITE category.
-         */
-        pdb_seq_num: str,
-        /**
-         * This data item is a pointer to _atom_site.auth_comp_id in the
-         * ATOM_SITE category.
-         */
-        pdb_mon_id: str,
-        /**
-         * This data item is a pointer to _atom_site.pdbx_auth_asym_id in the
-         * ATOM_SITE category.
-         */
-        auth_asym_id: str,
-        /**
-         * This data item is a pointer to _atom_site.pdbx_auth_seq_id in the
-         * ATOM_SITE category.
-         */
-        auth_seq_num: str,
-        /**
-         * This data item is a pointer to _atom_site.pdbx_auth_comp_id in the
-         * ATOM_SITE category.
-         */
-        auth_mon_id: str,
-    },
     /**
      * PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components.
      */
@@ -4682,4 +4682,4 @@ export const mmCIF_Schema = {
 };
 
 export type mmCIF_Schema = typeof mmCIF_Schema;
-export interface mmCIF_Database extends Database<mmCIF_Schema> {}
+export interface mmCIF_Database extends Database<mmCIF_Schema> {};