atom_site.pdbx_label_index support

data/cif-field-names/mmcif-field-names.csv

@@ -24,6 +24,7 @@ atom_site.auth_asym_id
 atom_site.auth_seq_id
 atom_site.pdbx_PDB_model_num
 atom_site.ihm_model_id
+atom_site.pdbx_label_index
 atom_site.pdbx_sifts_xref_db_name
 atom_site.pdbx_sifts_xref_db_acc
 atom_site.pdbx_sifts_xref_db_num

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

@@ -215,6 +215,11 @@ export const mmCIF_Schema = {
          * formal charge assignment normally found in chemical diagrams.
          */
         pdbx_formal_charge: int,
+        /**
+         * This data item is an ordinal which identifies distinct chemical components in the atom_site category, both
+         * polymeric and non-polymeric.
+         */
+        pdbx_label_index: int,
         /**
          * The name of additional external databases with residue level mapping.
          */

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

@@ -30,6 +30,17 @@ function atom_site_auth_asym_id(e: StructureElement.Location) {
     return l + suffix;
 }
 
+
+const atom_site_pdbx_label_index = {
+    shouldInclude(s: AtomSiteData) {
+        return !!s.atom_site?.pdbx_label_index.isDefined;
+    },
+    value(e: StructureElement.Location, d: AtomSiteData) {
+        const srcIndex = d.sourceIndex.value(e.element);
+        return d.atom_site!.pdbx_label_index.value(srcIndex);
+    },
+};
+
 const SIFTS = {
     shouldInclude(s: AtomSiteData) {
         return SIFTSMapping.isAvailable(s.structure.models[0]);
@@ -113,6 +124,8 @@ const atom_site_fields = () => CifWriter.fields<StructureElement.Location, AtomS
 
     .int('pdbx_PDB_model_num', P.unit.model_num, { encoder: E.deltaRLE })
 
+    .int('pdbx_label_index', atom_site_pdbx_label_index.value, { shouldInclude: atom_site_pdbx_label_index.shouldInclude })
+
     // SIFTS
     .str('pdbx_sifts_xref_db_name', SIFTS.pdbx_sifts_xref_db_name.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_name.valueKind })
     .str('pdbx_sifts_xref_db_acc', SIFTS.pdbx_sifts_xref_db_acc.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_acc.valueKind })

src/mol-model/structure/structure/util/superposition-db-mapping.ts

@@ -5,7 +5,6 @@
  */
 
 import { Segmentation } from '../../../../mol-data/int';
-import { Mat4 } from '../../../../mol-math/linear-algebra';
 import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
 import { SIFTSMapping } from '../../../../mol-model-props/sequence/sifts-mapping';
 import { ElementIndex } from '../../model/indexing';