From 76ee97301b13e7bee77244bb2fe14434dd541e37 Mon Sep 17 00:00:00 2001
From: dsehnal <david.sehnal@gmail.com>
Date: Mon, 7 Feb 2022 17:44:03 +0100
Subject: [PATCH] atom_site.pdbx_label_index support
---
data/cif-field-names/mmcif-field-names.csv | 1 +
src/mol-io/reader/cif/schema/mmcif.ts | 5 +++++
.../structure/export/categories/atom_site.ts | 13 +++++++++++++
.../structure/util/superposition-db-mapping.ts | 1 -
4 files changed, 19 insertions(+), 1 deletion(-)
diff --git a/data/cif-field-names/mmcif-field-names.csv b/data/cif-field-names/mmcif-field-names.csv
index 860ac4780..c5b1751cf 100644
--- a/data/cif-field-names/mmcif-field-names.csv
+++ b/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
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 94e387d62..cd21924ad 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/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.
*/
diff --git a/src/mol-model/structure/export/categories/atom_site.ts b/src/mol-model/structure/export/categories/atom_site.ts
index 77729c73e..6f082686b 100644
--- a/src/mol-model/structure/export/categories/atom_site.ts
+++ b/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 })
diff --git a/src/mol-model/structure/structure/util/superposition-db-mapping.ts b/src/mol-model/structure/structure/util/superposition-db-mapping.ts
index 725826622..2c220eae6 100644
--- a/src/mol-model/structure/structure/util/superposition-db-mapping.ts
+++ b/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';
--
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