From a3c790a54960733f9515faa856cbbf889aae4995 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 22 Apr 2019 14:49:21 -0700
Subject: [PATCH] handle mmcif files without entity catagory
---
.../structure/mmcif/parser.ts | 52 +++++++++++++++++--
src/mol-model/structure/model/types.ts | 13 +++++
src/mol-model/structure/util.ts | 4 +-
src/mol-plugin/util/structure-labels.ts | 8 +--
src/mol-theme/color/residue-name.ts | 2 +-
src/mol-theme/label.ts | 6 +--
6 files changed, 70 insertions(+), 15 deletions(-)
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index 71063f94d..bf6d29319 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -24,11 +24,12 @@ import { getSequence } from './sequence';
import { sortAtomSite } from './sort';
import { StructConn } from './bonds/struct_conn';
import { ChemicalComponent } from 'mol-model/structure/model/properties/chemical-component';
-import { getMoleculeType, MoleculeType } from 'mol-model/structure/model/types';
+import { getMoleculeType, MoleculeType, getEntityType } from 'mol-model/structure/model/types';
import { ModelFormat } from '../format';
import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, SaccharideCompIdMap, UnknownSaccharideComponent } from 'mol-model/structure/structure/carbohydrates/constants';
import mmCIF_Format = ModelFormat.mmCIF
import { memoize1 } from 'mol-util/memoize';
+import { ElementIndex } from 'mol-model/structure/model';
export async function _parse_mmCif(format: mmCIF_Format, ctx: RuntimeContext) {
const formatData = getFormatData(format)
@@ -247,9 +248,50 @@ function findModelEnd(num: Column<number>, startIndex: number) {
return endIndex;
}
+function getEntities(format: mmCIF_Format): Entities {
+ let entityData: Table<mmCIF_Schema['entity']>
+
+ if (!format.data.entity.id.isDefined) {
+ const entityIds = new Set<string>()
+ const entityList: Partial<Table.Row<mmCIF_Schema['entity']>>[] = []
+
+ const { label_entity_id, label_comp_id } = format.data.atom_site;
+ for (let i = 0 as ElementIndex, il = format.data.atom_site._rowCount; i < il; i++) {
+ const entityId = label_entity_id.value(i);
+ if (!entityIds.has(entityId)) {
+ entityList.push({ id: entityId, type: getEntityType(label_comp_id.value(i)) })
+ entityIds.add(entityId)
+ }
+ }
+
+ const { entity_id: sphere_entity_id } = format.data.ihm_sphere_obj_site;
+ for (let i = 0 as ElementIndex, il = format.data.ihm_sphere_obj_site._rowCount; i < il; i++) {
+ const entityId = sphere_entity_id.value(i);
+ if (!entityIds.has(entityId)) {
+ entityList.push({ id: entityId, type: 'polymer' })
+ entityIds.add(entityId)
+ }
+ }
+
+ const { entity_id: gaussian_entity_id } = format.data.ihm_gaussian_obj_site;
+ for (let i = 0 as ElementIndex, il = format.data.ihm_gaussian_obj_site._rowCount; i < il; i++) {
+ const entityId = gaussian_entity_id.value(i);
+ if (!entityIds.has(entityId)) {
+ entityList.push({ id: entityId, type: 'polymer' })
+ entityIds.add(entityId)
+ }
+ }
+
+ entityData = Table.ofRows(mmCIF_Schema.entity, entityList)
+ } else {
+ entityData = format.data.entity;
+ }
+ return { data: entityData, getEntityIndex: Column.createIndexer(entityData.id) };
+}
+
async function readStandard(ctx: RuntimeContext, format: mmCIF_Format, formatData: FormatData) {
const atomCount = format.data.atom_site._rowCount;
- const entities: Entities = { data: format.data.entity, getEntityIndex: Column.createIndexer(format.data.entity.id) };
+ const entities = getEntities(format)
const models: Model[] = [];
let modelStart = 0;
@@ -282,13 +324,13 @@ function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
}
async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: FormatData) {
- const { ihm_model_list } = format.data;
- const entities: Entities = { data: format.data.entity, getEntityIndex: Column.createIndexer(format.data.entity.id) };
-
if (format.data.atom_site._rowCount && !format.data.atom_site.ihm_model_id.isDefined) {
throw new Error('expected _atom_site.ihm_model_id to be defined')
}
+ const { ihm_model_list } = format.data;
+ const entities = getEntities(format)
+
const atom_sites = splitTable(format.data.atom_site, format.data.atom_site.ihm_model_id);
// TODO: will coarse IHM records require sorting or will we trust it?
// ==> Probably implement a sort as as well and store the sourceIndex same as with atomSite
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index 8b5e1b947..b4c65a89d 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -219,6 +219,19 @@ export function getComponentType(compId: string): mmCIF_Schema['chem_comp']['typ
}
}
+export function getEntityType(compId: string): mmCIF_Schema['entity']['type']['T'] {
+ compId = compId.toUpperCase()
+ if (AminoAcidNames.has(compId) || RnaBaseNames.has(compId) || DnaBaseNames.has(compId)) {
+ return 'polymer'
+ } else if (SaccharideCompIdMap.has(compId)) {
+ return 'polymer' // TODO will be 'branched' in the future
+ } else if (WaterNames.has(compId)) {
+ return 'water'
+ } else {
+ return 'non-polymer'
+ }
+}
+
export function isPolymer(moleculeType: MoleculeType) {
return moleculeType === MoleculeType.protein || moleculeType === MoleculeType.DNA || moleculeType === MoleculeType.RNA || moleculeType === MoleculeType.PNA
}
diff --git a/src/mol-model/structure/util.ts b/src/mol-model/structure/util.ts
index 87e34b6e0..92069c444 100644
--- a/src/mol-model/structure/util.ts
+++ b/src/mol-model/structure/util.ts
@@ -56,13 +56,13 @@ export function residueLabel(model: Model, rI: number) {
export function elementLabel(model: Model, index: ElementIndex) {
const { atoms, residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy
const { label_atom_id } = atoms
- const { auth_seq_id, auth_comp_id } = residues
+ const { auth_seq_id, label_comp_id } = residues
const { auth_asym_id } = chains
const residueIndex = residueAtomSegments.index[index]
const chainIndex = chainAtomSegments.index[residueIndex]
- return `[${auth_comp_id.value(residueIndex)}]${auth_seq_id.value(residueIndex)}:${auth_asym_id.value(chainIndex)}.${label_atom_id.value(index)}`
+ return `[${label_comp_id.value(residueIndex)}]${auth_seq_id.value(residueIndex)}:${auth_asym_id.value(chainIndex)}.${label_atom_id.value(index)}`
}
// const centerPos = Vec3.zero()
diff --git a/src/mol-plugin/util/structure-labels.ts b/src/mol-plugin/util/structure-labels.ts
index 932569da9..1ec7fd2b6 100644
--- a/src/mol-plugin/util/structure-labels.ts
+++ b/src/mol-plugin/util/structure-labels.ts
@@ -78,8 +78,8 @@ function getLabelDataComputed(structure: Structure, level: 'elements' | 'residue
const l = StructureElement.create();
const { units } = structure;
- const { auth_atom_id } = StructureProperties.atom;
- const { auth_seq_id, auth_comp_id } = StructureProperties.residue;
+ const { label_atom_id } = StructureProperties.atom;
+ const { auth_seq_id, label_comp_id } = StructureProperties.residue;
const { auth_asym_id } = StructureProperties.chain;
const p = Vec3.zero();
@@ -97,7 +97,7 @@ function getLabelDataComputed(structure: Structure, level: 'elements' | 'residue
l.element = elements[j];
pos(l.element, p);
- data.texts.push(auth_atom_id(l));
+ data.texts.push(label_atom_id(l));
data.positions.push(Vec3.clone(p));
data.sizes.push(1);
data.depths.push(2);
@@ -124,7 +124,7 @@ function getLabelDataComputed(structure: Structure, level: 'elements' | 'residue
l.element = elements[start];
- data.texts.push(`${auth_comp_id(l)} ${auth_seq_id(l)}:${auth_asym_id(l)}`);
+ data.texts.push(`${label_comp_id(l)} ${auth_seq_id(l)}:${auth_asym_id(l)}`);
data.positions.push(Vec3.clone(boundaryHelper.center));
data.sizes.push(Math.max(1, boundaryHelper.radius / 5));
data.depths.push(boundaryHelper.radius);
diff --git a/src/mol-theme/color/residue-name.ts b/src/mol-theme/color/residue-name.ts
index 999bf2a9b..53f601d04 100644
--- a/src/mol-theme/color/residue-name.ts
+++ b/src/mol-theme/color/residue-name.ts
@@ -75,7 +75,7 @@ export function residueNameColor(residueName: string): Color {
function getAtomicCompId(unit: Unit.Atomic, element: ElementIndex) {
const { modifiedResidues } = unit.model.properties
- const compId = unit.model.atomicHierarchy.residues.auth_comp_id.value(unit.residueIndex[element])
+ const compId = unit.model.atomicHierarchy.residues.label_comp_id.value(unit.residueIndex[element])
const parentId = modifiedResidues.parentId.get(compId)
return parentId === undefined ? compId : parentId
}
diff --git a/src/mol-theme/label.ts b/src/mol-theme/label.ts
index 69b67a6b9..baeb5d978 100644
--- a/src/mol-theme/label.ts
+++ b/src/mol-theme/label.ts
@@ -66,9 +66,9 @@ export function elementLabel(location: StructureElement) {
if (Unit.isAtomic(location.unit)) {
const asym_id = Props.chain.auth_asym_id(location)
- const seq_id = Props.residue.auth_seq_id(location)
- const comp_id = Props.residue.auth_comp_id(location)
- const atom_id = Props.atom.auth_atom_id(location)
+ const seq_id = location.unit.model.atomicHierarchy.residues.auth_seq_id.isDefined ? Props.residue.auth_seq_id(location) : Props.residue.label_seq_id(location)
+ const comp_id = Props.residue.label_comp_id(location)
+ const atom_id = Props.atom.label_atom_id(location)
const alt_id = Props.atom.label_alt_id(location)
label = `[${comp_id}]${seq_id}:${asym_id}.${atom_id}${alt_id ? `%${alt_id}` : ''}`
} else if (Unit.isCoarse(location.unit)) {
--
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