From d8adf7c5defce0f01afaf5767fdb328b635b4df3 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 24 Oct 2018 15:42:52 -0700
Subject: [PATCH] get saccharide component from 'SNFG CARB SYMBOL'
pdbx_chem_comp_identifier.type when available
---
.../structure/model/formats/mmcif.ts | 27 ++++++++++++++++++-
src/mol-model/structure/model/model.ts | 3 +++
.../structure/carbohydrates/compute.ts | 10 ++++---
.../structure/carbohydrates/constants.ts | 15 +++++++++--
4 files changed, 49 insertions(+), 6 deletions(-)
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 309e19470..e97ee8a41 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -27,6 +27,7 @@ import { ChemicalComponent, ChemicalComponentMap } from '../properties/chemical-
import { ComponentType, getMoleculeType } from '../types';
import mmCIF_Format = Format.mmCIF
+import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, UnknownSaccharideComponent, SaccharideCompIdMap } from 'mol-model/structure/structure/carbohydrates/constants';
type AtomSite = mmCIF_Database['atom_site']
@@ -125,17 +126,41 @@ function getChemicalComponentMap(format: mmCIF_Format): ChemicalComponentMap {
return map
}
+function getSaccharideComponentMap(format: mmCIF_Format): SaccharideComponentMap {
+ const map = new Map<string, SaccharideComponent>();
+ const { pdbx_chem_comp_identifier } = format.data
+ if (pdbx_chem_comp_identifier._rowCount > 0) {
+ const { type, comp_id, identifier } = pdbx_chem_comp_identifier
+ for (let i = 0, il = pdbx_chem_comp_identifier._rowCount; i < il; ++i) {
+ if (type.value(i) === 'SNFG CARB SYMBOL') {
+ const snfgName = identifier.value(i)
+ const saccharideComp = SaccharidesSnfgMap.get(snfgName)
+ if (saccharideComp) {
+ map.set(comp_id.value(i), saccharideComp)
+ } else {
+ console.warn(`Unknown SNFG name '${snfgName}'`)
+ }
+ }
+ }
+ return map
+ } else {
+ return SaccharideCompIdMap
+ }
+}
+
export interface FormatData {
modifiedResidues: Model['properties']['modifiedResidues']
asymIdSerialMap: Model['properties']['asymIdSerialMap']
chemicalComponentMap: Model['properties']['chemicalComponentMap']
+ saccharideComponentMap: Model['properties']['saccharideComponentMap']
}
function getFormatData(format: mmCIF_Format): FormatData {
return {
modifiedResidues: getModifiedResidueNameMap(format),
asymIdSerialMap: getAsymIdSerialMap(format),
- chemicalComponentMap: getChemicalComponentMap(format)
+ chemicalComponentMap: getChemicalComponentMap(format),
+ saccharideComponentMap: getSaccharideComponentMap(format)
}
}
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index bd9810c19..1eaad6e45 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -16,6 +16,7 @@ import { SecondaryStructure } from './properties/seconday-structure';
import from_mmCIF from './formats/mmcif'
import { ChemicalComponentMap } from './properties/chemical-component';
+import { SaccharideComponentMap } from '../structure/carbohydrates/constants';
/**
* Interface to the "source data" of the molecule.
@@ -50,6 +51,8 @@ export interface Model extends Readonly<{
readonly asymIdSerialMap: ReadonlyMap<string, number>
/** maps residue name to `ChemicalComponent` data */
readonly chemicalComponentMap: ChemicalComponentMap
+ /** maps residue name to `SaccharideComponent` data */
+ readonly saccharideComponentMap: SaccharideComponentMap
},
customProperties: CustomProperties,
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 1c0a7f7ea..6048fc52c 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -11,13 +11,13 @@ import { IntAdjacencyGraph } from 'mol-math/graph';
import { Vec3 } from 'mol-math/linear-algebra';
import PrincipalAxes from 'mol-math/linear-algebra/matrix/principal-axes';
import { fillSerial } from 'mol-util/array';
-import { ResidueIndex } from '../../model';
+import { ResidueIndex, Model } from '../../model';
import { ElementSymbol, MoleculeType } from '../../model/types';
import { getAtomicMoleculeType, getPositionMatrix } from '../../util';
import StructureElement from '../element';
import Structure from '../structure';
import Unit from '../unit';
-import { SaccharideNameMap, UnknownSaccharideComponent } from './constants';
+import { SaccharideCompIdMap, UnknownSaccharideComponent, SaccharideComponent, SaccharidesSnfgMap } from './constants';
import { CarbohydrateElement, CarbohydrateLink, Carbohydrates, CarbohydrateTerminalLink, PartialCarbohydrateElement } from './data';
import { UnitRings, UnitRing } from '../unit/rings';
import { ElementIndex } from '../../model/indexing';
@@ -118,6 +118,10 @@ function filterFusedRings(unitRings: UnitRings, rings: UnitRings.Index[] | undef
}
}
+function getSaccharideComp(compId: string, model: Model): SaccharideComponent {
+ return model.properties.saccharideComponentMap.get(compId) || UnknownSaccharideComponent
+}
+
export function computeCarbohydrates(structure: Structure): Carbohydrates {
const links: CarbohydrateLink[] = []
const terminalLinks: CarbohydrateTerminalLink[] = []
@@ -162,7 +166,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
while (residueIt.hasNext) {
const { index: residueIndex } = residueIt.move();
- const saccharideComp = SaccharideNameMap.get(label_comp_id.value(residueIndex)) || UnknownSaccharideComponent
+ const saccharideComp = getSaccharideComp(label_comp_id.value(residueIndex), model)
if (saccharideComp === UnknownSaccharideComponent) {
if (getAtomicMoleculeType(unit.model, residueIndex) !== MoleculeType.saccharide) continue
}
diff --git a/src/mol-model/structure/structure/carbohydrates/constants.ts b/src/mol-model/structure/structure/carbohydrates/constants.ts
index d68c1f81a..5c74ddfaf 100644
--- a/src/mol-model/structure/structure/carbohydrates/constants.ts
+++ b/src/mol-model/structure/structure/carbohydrates/constants.ts
@@ -174,6 +174,15 @@ const Monosaccharides: SaccharideComponent[] = [
{ abbr: 'Psi', name: 'Psicose', color: SaccharideColors.Pink, type: SaccharideType.Assigned },
]
+export const SaccharidesSnfgMap = (function () {
+ const map = new Map<string, SaccharideComponent>()
+ for (let i = 0, il = Monosaccharides.length; i < il; ++i) {
+ const saccharide = Monosaccharides[i]
+ map.set(saccharide.abbr, saccharide)
+ }
+ return map
+})()
+
export const MonosaccharidesColorTable: [string, Color][] = [
['Glc-family', SaccharideColors.Blue],
['Man-family', SaccharideColors.Green],
@@ -287,7 +296,7 @@ const CommonSaccharideNames: { [k: string]: string[] } = {
Psi: [],
}
-export const SaccharideNameMap = (function () {
+export const SaccharideCompIdMap = (function () {
const map = new Map<string, SaccharideComponent>()
for (let i = 0, il = Monosaccharides.length; i < il; ++i) {
const saccharide = Monosaccharides[i]
@@ -299,4 +308,6 @@ export const SaccharideNameMap = (function () {
}
}
return map
-})()
\ No newline at end of file
+})()
+
+export type SaccharideComponentMap = ReadonlyMap<string, SaccharideComponent>
--
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