wip, carbohydrate related schema additions

data/mmcif-field-names.csv

@@ -41,6 +41,12 @@ 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
+
 cell.entry_id
 cell.length_a
 cell.length_b
@@ -76,6 +82,37 @@ entity_poly_seq.num
 entity_poly_seq.mon_id
 entity_poly_seq.hetero
 
+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.component_comp_id
+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_entity_descriptor.ordinal
+pdbx_entity_descriptor.entity_id
+pdbx_entity_descriptor.descriptor
+pdbx_entity_descriptor.type
+pdbx_entity_descriptor.program
+pdbx_entity_descriptor.program_version
+
 entry.id
 
 exptl.entry_id

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

 /**
  * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.298, IHM 0.134.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.299, IHM 0.134.
  *
  * @author mol-star package (src/apps/schema-generator/generate)
  */

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

 /**
  * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.298, IHM 0.134.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.299, IHM 0.134.
  *
  * @author mol-star package (src/apps/schema-generator/generate)
  */

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

 /**
  * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.298, IHM 0.134.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.299, IHM 0.134.
  *
  * @author mol-star package (src/apps/schema-generator/generate)
  */
@@ -1470,6 +1470,36 @@ export const mmCIF_Schema = {
          */
         'space_group_name_H-M': str,
     },
+    /**
+     * Data items in the CHEM_COMP_IDENTIFIER category provide
+     * identifiers for chemical components.
+     */
+    pdbx_chem_comp_identifier: {
+        /**
+         * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+         * category.
+         */
+        comp_id: str,
+        /**
+         * This data item contains the identifier value for this
+         * component.
+         */
+        identifier: str,
+        /**
+         * This data item contains the identifier type.
+         */
+        type: Aliased<'COMMON NAME' | 'SYSTEMATIC NAME' | 'CAS REGISTRY NUMBER' | 'PUBCHEM Identifier' | 'MDL Identifier' | 'SYNONYM'>(str),
+        /**
+         * This data item contains the name of the program
+         * or library used to compute the identifier.
+         */
+        program: str,
+        /**
+         * This data item contains the version of the program
+         * or library used to compute the identifier.
+         */
+        program_version: str,
+    },
     /**
      * Data items in the PDBX_STRUCT_MOD_RESIDUE category list the
      * modified polymer components in the entry and provide some
@@ -1886,6 +1916,40 @@ export const mmCIF_Schema = {
          */
         details: str,
     },
+    /**
+     * Data items in the PDBX_ENTITY_DESCRIPTOR category provide
+     * string descriptors of entity chemical structure.
+     */
+    pdbx_entity_descriptor: {
+        /**
+         * This data item is a pointer to _entity_poly.entity_id in the ENTITY
+         * category.
+         */
+        entity_id: str,
+        /**
+         * This data item contains the descriptor value for this
+         * entity.
+         */
+        descriptor: str,
+        /**
+         * This data item contains the descriptor type.
+         */
+        type: Aliased<'LINUCS' | 'IUPAC' | 'IUPAC Abbreviated'>(str),
+        /**
+         * This data item contains the name of the program
+         * or library used to compute the descriptor.
+         */
+        program: str,
+        /**
+         * This data item contains the version of the program
+         * or library used to compute the descriptor.
+         */
+        program_version: str,
+        /**
+         * Ordinal index for this category.
+         */
+        ordinal: int,
+    },
     /**
      * Data items in the IHM_STARTING_MODEL_DETAILS category records the
      * details about structural models used as starting inputs in