From 176f80ea9be7d54ab933daa36c9f1306a00126c9 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sat, 18 Dec 2021 12:09:17 -0800
Subject: [PATCH] ensure trace element for polymer residues
---
.../model/properties/atomic/hierarchy.ts | 8 +++++++-
.../model/properties/utils/atomic-derived.ts | 7 +++++--
.../model/properties/utils/atomic-index.ts | 16 +++++++++++++++-
3 files changed, 27 insertions(+), 4 deletions(-)
diff --git a/src/mol-model/structure/model/properties/atomic/hierarchy.ts b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
index a40aba1b5..9d6340bb2 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -206,6 +206,12 @@ export interface AtomicIndex {
*/
findAtomsOnResidue(residueIndex: ResidueIndex, label_atom_ids: Set<string>): ElementIndex
+ /**
+ * Find element index of an atom on a given residue.
+ * @returns index or -1 if the atom is not present.
+ */
+ findElementOnResidue(residueIndex: ResidueIndex, type_symbol: ElementSymbol): ElementIndex
+
// TODO: add indices that support comp_id?
}
diff --git a/src/mol-model/structure/model/properties/utils/atomic-derived.ts b/src/mol-model/structure/model/properties/utils/atomic-derived.ts
index 18380b233..a2dc50223 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-derived.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-derived.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -7,7 +7,7 @@
import { AtomicData, AtomNumber } from '../atomic';
import { AtomicIndex, AtomicDerivedData, AtomicSegments } from '../atomic/hierarchy';
import { ElementIndex, ResidueIndex } from '../../indexing';
-import { MoleculeType, getMoleculeType, getComponentType, PolymerType, getPolymerType } from '../../types';
+import { MoleculeType, getMoleculeType, getComponentType, PolymerType, getPolymerType, isPolymer, ElementSymbol } from '../../types';
import { getAtomIdForAtomRole } from '../../../../../mol-model/structure/util';
import { ChemicalComponentMap } from '../common';
import { isProductionMode } from '../../../../../mol-util/debug';
@@ -63,6 +63,9 @@ export function getAtomicDerivedData(data: AtomicData, segments: AtomicSegments,
if (traceIndex === -1) {
const coarseAtomId = getAtomIdForAtomRole(polyType, 'coarseBackbone');
traceIndex = index.findAtomsOnResidue(i, coarseAtomId);
+ if (traceIndex === -1 && isPolymer(molType)) {
+ traceIndex = index.findElementOnResidue(i, ElementSymbol('C'));
+ }
}
traceElementIndex[i] = traceIndex;
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 3e82b9d5d..8f603282b 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-index.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-index.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -12,6 +12,7 @@ import { ChainIndex, ResidueIndex, EntityIndex, ElementIndex } from '../../index
import { AtomicIndex, AtomicHierarchy } from '../atomic/hierarchy';
import { cantorPairing } from '../../../../../mol-data/util';
import { Column } from '../../../../../mol-data/db';
+import { ElementSymbol } from '../../types';
function getResidueId(seq_id: number, ins_code: string) {
if (!ins_code) return seq_id;
@@ -43,6 +44,7 @@ interface Mapping {
label_atom_id: Column<string>,
auth_atom_id: Column<string>,
label_alt_id: Column<string>,
+ type_symbol: Column<ElementSymbol>,
segments: AtomicSegments,
chain_index_entity_index: EntityIndex[],
@@ -64,6 +66,7 @@ function createMapping(entities: Entities, data: AtomicData, segments: AtomicSeg
label_atom_id: data.atoms.label_atom_id,
auth_atom_id: data.atoms.auth_atom_id,
label_alt_id: data.atoms.label_alt_id,
+ type_symbol: data.atoms.type_symbol,
chain_index_entity_index: new Int32Array(data.chains._rowCount) as any,
entity_index_label_asym_id: new Map(),
chain_index_label_seq_id: new Map(),
@@ -173,6 +176,10 @@ class Index implements AtomicIndex {
return findAtomByNames(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.label_atom_id, label_atom_ids);
}
+ findElementOnResidue(rI: ResidueIndex, type_symbol: ElementSymbol) {
+ return findAtomByElement(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.type_symbol, type_symbol);
+ }
+
constructor(private map: Mapping) {
this.entityIndex = map.entities.getEntityIndex;
this.residueOffsets = this.map.segments.residueAtomSegments.offsets;
@@ -201,6 +208,13 @@ function findAtomByNameAndAltLoc(start: ElementIndex, end: ElementIndex, nameDat
return -1 as ElementIndex;
}
+function findAtomByElement(start: ElementIndex, end: ElementIndex, data: Column<ElementSymbol>, typeSymbol: ElementSymbol): ElementIndex {
+ for (let i = start; i < end; i++) {
+ if (data.value(i) === typeSymbol) return i;
+ }
+ return -1 as ElementIndex;
+}
+
export function getAtomicIndex(data: AtomicData, entities: Entities, segments: AtomicSegments): AtomicIndex {
const map = createMapping(entities, data, segments);
--
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