atom_site mmCIF export helpers

src/mol-model/structure/export/categories/atom_site.ts

@@ -61,10 +61,18 @@ export const _atom_site: CifCategory<CifExportContext> = {
     }
 }
 
-export function residueIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement): CifField<K, D>[] {
+function prefixed(prefix: string, name: string) {
+    return prefix ? `${prefix}_${name}` : name;
+}
+
+function mappedProp<K, D>(loc: (key: K, data: D) => StructureElement, prop: (e: StructureElement) => any) {
+    return (k: K, d: D) => prop(loc(k, d));
+}
+
+export function residueIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement, prefix = ''): CifField<K, D>[] {
     return [
-        CifField.str('label_comp_id', (k, d) => P.residue.label_comp_id(getLocation(k, d))),
-        CifField.int('label_seq_id', (k, d) => P.residue.label_seq_id(getLocation(k, d)), {
+        CifField.str(prefixed(prefix, `label_comp_id`), mappedProp(getLocation, P.residue.label_comp_id)),
+        CifField.int(prefixed(prefix, `label_seq_id`), mappedProp(getLocation, P.residue.label_seq_id), {
             encoder: E.deltaRLE,
             valueKind: (k, d) => {
                 const e = getLocation(k, d);
@@ -72,13 +80,21 @@ export function residueIdFields<K, D>(getLocation: (key: K, data: D) => Structur
                 return m.atomicHierarchy.residues.label_seq_id.valueKind(m.atomicHierarchy.residueAtomSegments.index[e.element]);
             }
         }),
-        CifField.str('pdbx_PDB_ins_code', (k, d) => P.residue.pdbx_PDB_ins_code(getLocation(k, d))),
+        CifField.str(prefixed(prefix, `pdbx_PDB_ins_code`), mappedProp(getLocation, P.residue.pdbx_PDB_ins_code)),
 
-        CifField.str('label_asym_id', (k, d) => P.chain.label_asym_id(getLocation(k, d))),
-        CifField.str('label_entity_id', (k, d) => P.chain.label_entity_id(getLocation(k, d))),
+        CifField.str(prefixed(prefix, `label_asym_id`), mappedProp(getLocation, P.chain.label_asym_id)),
+        CifField.str(prefixed(prefix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id)),
 
-        CifField.str('auth_comp_id', (k, d) => P.residue.auth_comp_id(getLocation(k, d))),
-        CifField.int('auth_seq_id', (k, d) => P.residue.auth_seq_id(getLocation(k, d)), { encoder: E.deltaRLE }),
-        CifField.str('auth_asym_id', (k, d) => P.chain.auth_asym_id(getLocation(k, d))),
-    ]
+        CifField.str(prefixed(prefix, `auth_comp_id`), mappedProp(getLocation, P.residue.auth_comp_id)),
+        CifField.int(prefixed(prefix, `auth_seq_id`), mappedProp(getLocation, P.residue.auth_seq_id), { encoder: E.deltaRLE }),
+        CifField.str(prefixed(prefix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id))
+    ];
+}
+
+export function chainIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement, prefix = ''): CifField<K, D>[] {
+    return [
+        CifField.str(prefixed(prefix, `label_asym_id`), mappedProp(getLocation, P.chain.label_asym_id)),
+        CifField.str(prefixed(prefix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id)),
+        CifField.str(prefixed(prefix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id))
+    ];
 }

src/mol-model/structure/export/categories/secondary-structure.ts

@@ -7,11 +7,12 @@
 import { Segmentation } from 'mol-data/int';
 import { CifWriter } from 'mol-io/writer/cif';
 import { SecondaryStructure } from '../../model/properties/seconday-structure';
-import { StructureElement, Unit, StructureProperties as P } from '../../structure';
+import { StructureElement, Unit } from '../../structure';
 import { CifExportContext } from '../mmcif';
 import CifField = CifWriter.Field
 import CifCategory = CifWriter.Category
 import { Column } from 'mol-data/db';
+import { residueIdFields } from './atom_site';
 
 export const _struct_conf: CifCategory<CifExportContext> = {
     name: 'struct_conf',
@@ -37,8 +38,8 @@ function compare_ssr(x: SSElement<SecondaryStructure.Sheet>, y: SSElement<Second
 const struct_conf_fields: CifField[] = [
     CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('conf_type_id', (i, data) => data[i].element.type_id),
     CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('id', (i, data, idx) => `${data[i].element.type_id}${idx + 1}`),
-    ...residueIdFields('beg_', e => e.start),
-    ...residueIdFields('end_', e => e.end),
+    ...residueIdFields<number, SSElement<SecondaryStructure.Helix>[]>((i, e) => e[i].start, 'beg'),
+    ...residueIdFields<number, SSElement<SecondaryStructure.Helix>[]>((i, e) => e[i].end, 'end'),
     CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('pdbx_PDB_helix_class', (i, data) => data[i].element.helix_class),
     CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('details', (i, data) => data[i].element.details || '', {
         valueKind: (i, d) => !!d[i].element.details ? Column.ValueKind.Present : Column.ValueKind.Unknown
@@ -49,24 +50,11 @@ const struct_conf_fields: CifField[] = [
 const struct_sheet_range_fields: CifField[] = [
     CifField.str<number, SSElement<SecondaryStructure.Sheet>[]>('sheet_id', (i, data) => data[i].element.sheet_id),
     CifField.index('id'),
-    ...residueIdFields('beg_', e => e.start),
-    ...residueIdFields('end_', e => e.end),
+    ...residueIdFields<number, SSElement<SecondaryStructure.Sheet>[]>((i, e) => e[i].start, 'beg'),
+    ...residueIdFields<number, SSElement<SecondaryStructure.Sheet>[]>((i, e) => e[i].end, 'end'),
     CifField.str('symmetry', (i, data) => '', { valueKind: (i, d) => Column.ValueKind.Unknown })
 ];
 
-function residueIdFields(prefix: string, loc: (e: SSElement<any>) => StructureElement): CifField<number, SSElement<SecondaryStructure.Helix>[]>[] {
-    return [
-        CifField.str(`${prefix}label_comp_id`, (i, d) => P.residue.label_comp_id(loc(d[i]))),
-        CifField.int(`${prefix}label_seq_id`, (i, d) => P.residue.label_seq_id(loc(d[i]))),
-        CifField.str(`pdbx_${prefix}PDB_ins_code`, (i, d) => P.residue.pdbx_PDB_ins_code(loc(d[i]))),
-        CifField.str(`${prefix}label_asym_id`, (i, d) => P.chain.label_asym_id(loc(d[i]))),
-        CifField.str(`${prefix}label_entity_id`, (i, d) => P.chain.label_entity_id(loc(d[i]))),
-        CifField.str(`${prefix}auth_comp_id`, (i, d) => P.residue.auth_comp_id(loc(d[i]))),
-        CifField.int(`${prefix}auth_seq_id`, (i, d) => P.residue.auth_seq_id(loc(d[i]))),
-        CifField.str(`${prefix}auth_asym_id`, (i, d) => P.chain.auth_asym_id(loc(d[i])))
-    ];
-}
-
 interface SSElement<T extends SecondaryStructure.Element> {
     start: StructureElement,
     end: StructureElement,