cif schema updates

README.md

@@ -80,12 +80,11 @@ and navigate to `build/viewer`
 
 ### Code generation
 **CIF schemas**
+Install CIFTools `npm install ciftools -g`
 
-    export NODE_PATH="build/src"; node build/src/apps/schema-generator/schema-from-cif-dic.js -ts -o src/mol-io/reader/cif/schema/mmcif.ts --fieldNamesPath data/mmcif-field-names.csv --name mmCIF
-
-    export NODE_PATH="build/src"; node build/src/apps/schema-generator/schema-from-cif-dic.js -ts -o src/mol-io/reader/cif/schema/ccd.ts --fieldNamesPath data/ccd-field-names.csv --name CCD
-
-    export NODE_PATH="build/src"; node build/src/apps/schema-generator/schema-from-cif-dic.js -ts -o src/mol-io/reader/cif/schema/bird.ts --fieldNamesPath data/bird-field-names.csv --name BIRD
+    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
 
 **GraphQL schemas**
 

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

 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.309, IHM 0.141, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.311, IHM 1.0, CARB draft.
  *
- * @author mol-star package (src/apps/schema-generator/generate)
+ * @author molstar/ciftools package
  */
 
 import { Database, Column } from '../../../../mol-data/db'
@@ -84,6 +84,10 @@ export const BIRD_Schema = {
          * corresponding to the chemical definition for the molecule.
          */
         chem_comp_id: str,
+        /**
+         * Special details about this molecule.
+         */
+        compound_details: str,
         /**
          * Description of this molecule.
          */

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

 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.309, IHM 0.141, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.311, IHM 1.0, CARB draft.
  *
- * @author mol-star package (src/apps/schema-generator/generate)
+ * @author molstar/ciftools package
  */
 
 import { Database, Column } from '../../../../mol-data/db'
@@ -167,6 +167,10 @@ export const CCD_Schema = {
          * Date component was last modified.
          */
         pdbx_modified_date: str,
+        /**
+         * This data item holds the current release status for the component.
+         */
+        pdbx_release_status: Aliased<'REL' | 'HOLD' | 'HPUB' | 'OBS' | 'DEL' | 'REF_ONLY'>(str),
         /**
          * This data item identifies the deposition site that processed
          * this chemical component defintion.

src/mol-model-formats/structure/mmcif/parser.ts

@@ -329,6 +329,17 @@ function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
     return ret;
 }
 
+function getModelGroupName(model_id: number, format: mmCIF_Format) {
+    const { ihm_model_group, ihm_model_group_link } = format.data;
+
+    const link = Table.pickRow(ihm_model_group_link, i => ihm_model_group_link.model_id.value(i) === model_id)
+    if (link) {
+        const group = Table.pickRow(ihm_model_group, i => ihm_model_group.id.value(i) === link.group_id)
+        if (group) return group.name
+    }
+    return ''
+}
+
 async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: FormatData) {
     // when `atom_site.ihm_model_id` is undefined fall back to `atom_site.pdbx_PDB_model_num`
     const atom_sites_modelColumn = format.data.atom_site.ihm_model_id.isDefined ? format.data.atom_site.ihm_model_id : format.data.atom_site.pdbx_PDB_model_num
@@ -345,7 +356,7 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: Fo
 
     const models: Model[] = [];
 
-    const { model_id, model_name, model_group_name } = ihm_model_list;
+    const { model_id, model_name } = ihm_model_list;
     for (let i = 0; i < ihm_model_list._rowCount; i++) {
         const id = model_id.value(i);
 
@@ -364,7 +375,7 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: Fo
         const data: IHMData = {
             model_id: id,
             model_name: model_name.value(i),
-            model_group_name: model_group_name.value(i),
+            model_group_name: getModelGroupName(id, format),
             entities: entities,
             atom_site,
             atom_site_sourceIndex,