From fe1f3bd4bb3b0fc682ea39f4fdc73ba7d9be1c1c Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 10 Sep 2019 11:12:00 -0700
Subject: [PATCH] use structure.uniqueResidues, removed duplicated code
---
.../structure/mmcif/bonds/comp.ts | 23 ++-----------------
1 file changed, 2 insertions(+), 21 deletions(-)
diff --git a/src/mol-model-formats/structure/mmcif/bonds/comp.ts b/src/mol-model-formats/structure/mmcif/bonds/comp.ts
index 96e1288a8..028bc6e23 100644
--- a/src/mol-model-formats/structure/mmcif/bonds/comp.ts
+++ b/src/mol-model-formats/structure/mmcif/bonds/comp.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 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>
@@ -9,8 +9,6 @@ import { Model } from '../../../../mol-model/structure/model/model'
import { LinkType } from '../../../../mol-model/structure/model/types'
import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
import { mmCIF_Database } from '../../../../mol-io/reader/cif/schema/mmcif';
-import { Structure, Unit, StructureProperties, StructureElement } from '../../../../mol-model/structure';
-import { Segmentation } from '../../../../mol-data/int';
import { CifWriter } from '../../../../mol-io/writer/cif'
export interface ComponentBond {
@@ -29,7 +27,7 @@ export namespace ComponentBond {
const chem_comp_bond = getChemCompBond(ctx.structures[0].model);
if (!chem_comp_bond) return CifWriter.Category.Empty;
- const comp_names = getUniqueResidueNames(ctx.structures[0]);
+ const comp_names = ctx.structures[0].uniqueResidueNames;
const { comp_id, _rowCount } = chem_comp_bond;
const indices: number[] = [];
for (let i = 0; i < _rowCount; i++) {
@@ -144,21 +142,4 @@ export namespace ComponentBond {
model._staticPropertyData[PropName] = chemComp;
return chemComp;
}
-
- function getUniqueResidueNames(s: Structure) {
- const prop = StructureProperties.residue.label_comp_id;
- const names = new Set<string>();
- const loc = StructureElement.Location.create();
- for (const unit of s.units) {
- if (!Unit.isAtomic(unit)) continue;
- const residues = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
- loc.unit = unit;
- while (residues.hasNext) {
- const seg = residues.move();
- loc.element = unit.elements[seg.start];
- names.add(prop(loc));
- }
- }
- return names;
- }
}
\ No newline at end of file
--
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