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Detect metal-coordination when parsing pdb

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This commit is contained in:
Alexander Rose
2026-02-14 23:20:25 -08:00
parent f91f445631
commit e0c794b557
2 changed files with 14 additions and 3 deletions
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1
CHANGELOG.md
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@@ -28,6 +28,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Add `vertex` and `vertexInstance` granularity support for size themes
- Add `transform` and `domain` parameters to volume-value size theme
- Fix parsing of single charge type_symbols (e.g., N+) in cif-core
- Detect metal-coordination when parsing pdb
## [v5.6.1] - 2026-01-23
- Disable occlusion culling in `ImagePass` (#1758)

16
src/mol-model-formats/structure/pdb/conect.ts
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@@ -1,5 +1,5 @@
/**
* Copyright (c) 2021-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2021-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Yakov Pechersky <ffxen158@gmail.com>
@@ -9,6 +9,8 @@
import { CifCategory, CifField } from '../../../mol-io/reader/cif';
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { Tokens } from '../../../mol-io/reader/common/text/tokenizer';
import { isMetal } from '../../../mol-model/structure/model/properties/atomic/types';
import { ElementSymbol } from '../../../mol-model/structure/model/types';
export function parseConect(lines: Tokens, lineStart: number, lineEnd: number, sites: { [K in keyof mmCIF_Schema['atom_site']]?: CifField }): CifCategory {
const idMap: { [k: string]: number } = {};
@@ -71,8 +73,16 @@ export function parseConect(lines: Tokens, lineStart: number, lineEnd: number, s
}
bondIndex[idxB] = k - 1;
id.push(`covale${k}`);
conn_type_id.push('covale');
const atomIdA = sites.type_symbol!.str(idxA) as ElementSymbol;
const atomIdB = sites.type_symbol!.str(idxB) as ElementSymbol;
if (isMetal(atomIdA) || isMetal(atomIdB)) {
id.push(`metalc${k}`);
conn_type_id.push('metalc');
} else {
id.push(`covale${k}`);
conn_type_id.push('covale');
}
bondOrder.push(1);
ptnr1_label_asym_id.push(sites.label_asym_id!.str(idxA));