From 79e4030ab460829d7d79c608d40f48bb6da88945 Mon Sep 17 00:00:00 2001
From: dsehnal <david.sehnal@gmail.com>
Date: Mon, 12 Dec 2022 18:35:52 +0100
Subject: [PATCH] fix qa assignment
---
.../model-archive/quality-assessment/prop.ts | 21 ++++++++++++++++---
.../model/properties/atomic/hierarchy.ts | 8 +++++++
.../model/properties/utils/atomic-index.ts | 8 +++++++
3 files changed, 34 insertions(+), 3 deletions(-)
diff --git a/src/extensions/model-archive/quality-assessment/prop.ts b/src/extensions/model-archive/quality-assessment/prop.ts
index ce8c1a397..80723c160 100644
--- a/src/extensions/model-archive/quality-assessment/prop.ts
+++ b/src/extensions/model-archive/quality-assessment/prop.ts
@@ -14,6 +14,7 @@ import { CustomPropSymbol } from '../../../mol-script/language/symbol';
import { Type } from '../../../mol-script/language/type';
import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
+import { AtomicIndex } from '../../../mol-model/structure/model/properties/atomic';
export { QualityAssessment };
@@ -71,14 +72,28 @@ namespace QualityAssessment {
localNames.set(ma_qa_metric.id.value(i), name);
}
+ const residueKey: AtomicIndex.ResidueLabelKey = {
+ label_entity_id: '',
+ label_asym_id: '',
+ label_seq_id: 0,
+ pdbx_PDB_ins_code: undefined,
+ };
+
for (let i = 0, il = ma_qa_metric_local._rowCount; i < il; i++) {
if (model_id.value(i) !== model.modelNum) continue;
const labelAsymId = label_asym_id.value(i);
const entityIndex = index.findEntity(labelAsymId);
- const rI = index.findResidue(model.entities.data.id.value(entityIndex), labelAsymId, label_seq_id.value(i));
- const name = localNames.get(metric_id.value(i))!;
- localMetrics.get(name)!.set(rI, metric_value.value(i));
+
+ residueKey.label_entity_id = model.entities.data.id.value(entityIndex);
+ residueKey.label_asym_id = labelAsymId;
+ residueKey.label_seq_id = label_seq_id.value(i);
+
+ const rI = index.findResidueLabel(residueKey);
+ if (rI >= 0) {
+ const name = localNames.get(metric_id.value(i))!;
+ localMetrics.get(name)!.set(rI, metric_value.value(i));
+ }
}
return {
diff --git a/src/mol-model/structure/model/properties/atomic/hierarchy.ts b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
index 5346163be..4ef8d5279 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -166,6 +166,14 @@ export interface AtomicIndex {
findResidue(key: AtomicIndex.ResidueKey): ResidueIndex,
findResidue(label_entity_id: string, label_asym_id: string, auth_seq_id: number, pdbx_PDB_ins_code?: string): ResidueIndex,
+
+ /**
+ * Index of the 1st occurence of this residue using "all-label" address.
+ * Doesn't work for "ligands" as they don't have a label seq id assigned.
+ * @returns index or -1 if not present.
+ */
+ findResidueLabel(key: AtomicIndex.ResidueLabelKey): ResidueIndex,
+
/**
* Index of the 1st occurence of this residue.
* @param key.pdbx_PDB_ins_code Empty string for undefined
diff --git a/src/mol-model/structure/model/properties/utils/atomic-index.ts b/src/mol-model/structure/model/properties/utils/atomic-index.ts
index 8f603282b..cbd09a722 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-index.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-index.ts
@@ -124,6 +124,14 @@ class Index implements AtomicIndex {
return rm.has(id) ? rm.get(id)! : -1 as ResidueIndex;
}
+ findResidueLabel(key: AtomicIndex.ResidueLabelKey): ResidueIndex {
+ const cI = this.findChainLabel(key);
+ if (cI < 0) return -1 as ResidueIndex;
+ const rm = this.map.chain_index_label_seq_id.get(cI)!;
+ const id = getResidueId(key.label_seq_id, key.pdbx_PDB_ins_code || '');
+ return rm.has(id) ? rm.get(id)! : -1 as ResidueIndex;
+ }
+
findResidueAuth(key: AtomicIndex.ResidueAuthKey): ResidueIndex {
const cI = this.findChainAuth(key);
if (cI < 0) return -1 as ResidueIndex;
--
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