updated cif schemas

README.md

@@ -91,6 +91,7 @@ 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
 
 **GraphQL schemas**
 

data/cif-core.csv

@@ -1,60 +0,0 @@
-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

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

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.320, IHM 1.05, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.323, IHM 1.07, CARB draft.
  *
  * @author molstar/ciftools package
  */
@@ -78,7 +78,7 @@ export const BIRD_Schema = {
         /**
          * Defines how this entity is represented in PDB data files.
          */
-        represent_as: Aliased<'polymer' | 'single molecule'>(str),
+        represent_as: Aliased<'polymer' | 'single molecule' | 'branched'>(str),
         /**
          * For entities represented as single molecules, the identifier
          * corresponding to the chemical definition for the molecule.

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

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.320, IHM 1.05, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.323, IHM 1.07, CARB draft.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'cifCore' schema file. Dictionary versions: CifCore 3.0.11.
+ * Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.0.11.
  *
  * @author molstar/ciftools package
  */
@@ -14,7 +14,7 @@ const int = Schema.int;
 const float = Schema.float;
 const str = Schema.str;
 
-export const cifCore_Schema = {
+export const CifCore_Schema = {
     /**
      * The CATEGORY of data items used to describe the parameters of
      * the crystal unit cell and their measurement.
@@ -585,7 +585,7 @@ export const cifCore_Schema = {
     },
 }
 
-export const cifCore_Aliases = {
+export const CifCore_Aliases = {
     'space_group.name_H-M_full': [
         'symmetry_space_group_name_H-M',
     ],
@@ -633,5 +633,5 @@ export const cifCore_Aliases = {
     ],
 }
 
-export type cifCore_Schema = typeof cifCore_Schema;
-export interface cifCore_Database extends Database<cifCore_Schema> {}
+export type CifCore_Schema = typeof CifCore_Schema;
+export interface CifCore_Database extends Database<CifCore_Schema> {}

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

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.320, IHM 1.05, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.323, IHM 1.07, CARB draft.
  *
  * @author molstar/ciftools package
  */
@@ -1880,6 +1880,23 @@ export const mmCIF_Schema = {
          */
         name: str,
     },
+    /**
+     * PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences.
+     */
+    pdbx_chem_comp_synonyms: {
+        /**
+         * The synonym of this particular chemical component.
+         */
+        name: str,
+        /**
+         * The chemical component for which this synonym applies.
+         */
+        comp_id: str,
+        /**
+         * The provenance of this synonym.
+         */
+        provenance: Aliased<'AUTHOR' | 'DRUGBANK' | 'CHEBI' | 'CHEMBL' | 'PDB' | 'PUBCHEM'>(str),
+    },
     /**
      * Data items in the CHEM_COMP_IDENTIFIER category provide
      * identifiers for chemical components.
@@ -3665,7 +3682,7 @@ export const mmCIF_Schema = {
         /**
          * The type of crosslinker used.
          */
-        linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'DSSO' | 'DSG' | 'BSP' | 'BMSO' | 'DHSO' | 'Other'>(str),
+        linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'DSSO' | 'DSG' | 'BSP' | 'BMSO' | 'DHSO' | 'CYS' | 'Other'>(str),
         /**
          * Identifier to the crosslinking dataset.
          * This data item is a pointer to the _ihm_dataset_list.id in the
@@ -4584,23 +4601,6 @@ export const mmCIF_Schema = {
          */
         auth_mon_id: str,
     },
-    /**
-     * PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences.
-     */
-    pdbx_chem_comp_synonyms: {
-        /**
-         * The synonym of this particular chemical component.
-         */
-        name: str,
-        /**
-         * The chemical component for which this synonym applies.
-         */
-        comp_id: str,
-        /**
-         * The provenance of this synonym.
-         */
-        provenance: Aliased<'AUTHOR' | 'DRUGBANK' | 'CHEBI' | 'CHEMBL' | 'PDB' | 'PUBCHEM'>(str),
-    },
     /**
      * PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components.
      */