From a81db69edc9e1ce25854156d8b05d515f64da5b1 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 8 Jun 2018 15:35:50 +0200
Subject: [PATCH] Only keep modified residue name mapping
---
src/apps/structure-info/model.ts | 11 ++--
.../structure/model/formats/mmcif.ts | 23 +++----
.../model/formats/mmcif/modified-residues.ts | 65 -------------------
src/mol-model/structure/model/model.ts | 5 +-
4 files changed, 20 insertions(+), 84 deletions(-)
delete mode 100644 src/mol-model/structure/model/formats/mmcif/modified-residues.ts
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 384758e57..ed012d465 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -128,11 +128,12 @@ export function printSequence(model: Model) {
export function printModRes(model: Model) {
console.log('\nModified Residues\n=============');
- const { residueIndices, keys, data } = model.properties.modifiedResidues;
- const { label_comp_id } = model.atomicHierarchy.residues;
- for (let i = 0; i < residueIndices.length; i++) {
- const rI = residueIndices[i], k = keys[i];
- console.log(`Idx: ${rI} ${data.parent_comp_id.value(k)} -> ${label_comp_id.value(rI)}`);
+ const map = model.properties.modifiedResidueNameMap;
+ const { label_comp_id, _rowCount } = model.atomicHierarchy.residues;
+ for (let i = 0; i < _rowCount; i++) {
+ const comp_id = label_comp_id.value(i);
+ if (!map.has(comp_id)) continue;
+ console.log(`[${i}] ${map.get(comp_id)} -> ${comp_id}`);
}
console.log();
}
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 7cbaedb7d..48d8c4754 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -11,7 +11,7 @@ import { Vec3 } from 'mol-math/linear-algebra';
import UUID from 'mol-util/uuid';
import Format from '../format';
import Model from '../model';
-import { AtomicConformation, AtomicData, AtomicSegments, AtomsSchema, ChainsSchema, ResiduesSchema, AtomicHierarchy } from '../properties/atomic';
+import { AtomicConformation, AtomicData, AtomicSegments, AtomsSchema, ChainsSchema, ResiduesSchema } from '../properties/atomic';
import { Entities } from '../properties/common';
import { ModelSymmetry } from '../properties/symmetry';
import { getAtomicKeys } from '../properties/utils/atomic-keys';
@@ -23,7 +23,6 @@ import { getSequence } from './mmcif/sequence';
import mmCIF_Format = Format.mmCIF
import { Task } from 'mol-task';
import { getSecondaryStructureMmCif } from './mmcif/secondary-structure';
-import { ModifiedResidues } from './mmcif/modified-residues';
function findModelBounds({ data }: mmCIF_Format, startIndex: number) {
const num = data.atom_site.pdbx_PDB_model_num;
@@ -119,13 +118,17 @@ function isHierarchyDataEqual(a: AtomicData, b: AtomicData) {
&& Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
}
-function modResProvider(format: mmCIF_Format, hierarchy: AtomicHierarchy, entities: Entities) {
- let modres: ModifiedResidues | undefined = void 0;
- return () => {
- if (modres) return modres;
- modres = new ModifiedResidues(format.data.pdbx_struct_mod_residue, hierarchy, entities);
- return modres;
+function modResMap(format: mmCIF_Format) {
+ const data = format.data.pdbx_struct_mod_residue;
+ const map = new Map<string, string>();
+ const comp_id = data.label_comp_id.isDefined ? data.label_comp_id : data.auth_comp_id;
+ const parent_id = data.parent_comp_id;
+
+ for (let i = 0; i < data._rowCount; i++) {
+ map.set(comp_id.value(i), parent_id.value(i));
}
+
+ return map;
}
function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model): Model {
@@ -156,8 +159,6 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
? format.data.entry.id.value(0)
: format.data._name;
- const modRes = modResProvider(format, atomicHierarchy, entities);
-
return {
id: UUID.create(),
label,
@@ -171,7 +172,7 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
coarseConformation: coarse.conformation,
properties: {
secondaryStructure: getSecondaryStructureMmCif(format.data, atomicHierarchy),
- get modifiedResidues() { return modRes() }
+ modifiedResidueNameMap: modResMap(format)
},
symmetry: getSymmetry(format)
};
diff --git a/src/mol-model/structure/model/formats/mmcif/modified-residues.ts b/src/mol-model/structure/model/formats/mmcif/modified-residues.ts
deleted file mode 100644
index 64f182b2b..000000000
--- a/src/mol-model/structure/model/formats/mmcif/modified-residues.ts
+++ /dev/null
@@ -1,65 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif'
-import { AtomicHierarchy } from '../../properties/atomic';
-import { Entities } from '../../properties/common';
-
-class ModifiedResidues {
- private residueIndexMap = new Map<number, number>();
-
- /** All residue indices within the given model that are modified. */
- readonly residueIndices: ReadonlyArray<number>;
- /** Indexed same as residueIndex and is key to ModifiedResidues.data table */
- readonly keys: ReadonlyArray<number>;
-
- /** Index into the data table. -1 if the residue is not modified. */
- getKey(residueIndex: number): number {
- return this.residueIndexMap.has(residueIndex) ? this.residueIndexMap.get(residueIndex)! : -1;
- }
-
- constructor(public data: mmCIF_Database['pdbx_struct_mod_residue'], hierarchy: AtomicHierarchy, entities: Entities) {
- if (data._rowCount === 0) {
- this.residueIndices = [];
- this.keys = [];
- return;
- }
-
- const { PDB_ins_code, auth_seq_id, _rowCount } = data;
-
- const asym_id = data.label_asym_id.isDefined ? data.label_asym_id : data.auth_asym_id;
- const comp_id = data.label_comp_id.isDefined ? data.label_comp_id : data.auth_comp_id;
-
- const entityIds = entities.data.id.toArray();
-
- const residueIndices: number[] = [];
- const keys: number[] = [];
-
- for (let i = 0; i < _rowCount; i++) {
- const aId = asym_id.value(i);
- const eIdx = getEntityId(hierarchy, entityIds, aId);
- if (eIdx < 0) continue;
- const key = hierarchy.findResidueKey(entityIds[eIdx], aId, comp_id.value(i), auth_seq_id.value(i), PDB_ins_code.value(i));
- if (key >= 0) {
- this.residueIndexMap.set(key, i);
- residueIndices[residueIndices.length] = key;
- keys[keys.length] = i;
- }
- }
-
- this.residueIndices = residueIndices;
- this.keys = keys;
- }
-}
-
-function getEntityId(hierarchy: AtomicHierarchy, ids: ArrayLike<string>, asym_id: string) {
- for (let i = 0, _i = ids.length; i < _i; i++) {
- if (hierarchy.findChainKey(ids[i], asym_id) >= 0) return i;
- }
- return -1;
-}
-
-export { ModifiedResidues }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 8f60531e6..799bb6643 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -15,8 +15,6 @@ import { SecondaryStructure } from './properties/seconday-structure';
//import from_gro from './formats/gro'
import from_mmCIF from './formats/mmcif'
-import { ModifiedResidues } from './formats/mmcif/modified-residues';
-
/**
* Interface to the "source data" of the molecule.
*
@@ -40,7 +38,8 @@ interface Model extends Readonly<{
/** Various parts of the code can "cache" custom properties here */
properties: {
readonly secondaryStructure: SecondaryStructure,
- readonly modifiedResidues: ModifiedResidues,
+ // maps modified residue name to its parent
+ readonly modifiedResidueNameMap: Map<string, string>,
[customName: string]: any
},
--
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