diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index 8a8e4012695ad8af3f777f8ea12e7bd1c6cb6c81..4a16920ba94f80923960add8ee65176df8d8eb66 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -23,8 +23,8 @@ import { getSecondaryStructureMmCif } from './secondary-structure';
import { getSequence } from './sequence';
import { sortAtomSite } from './sort';
import { StructConn } from './bonds/struct_conn';
-import { ChemicalComponent, ChemicalComponentMap } from 'mol-model/structure/model/properties/chemical-component';
-import { ComponentType, getMoleculeType, MoleculeType } from 'mol-model/structure/model/types';
+import { ChemicalComponent } from 'mol-model/structure/model/properties/chemical-component';
+import { getMoleculeType, MoleculeType } 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
@@ -96,24 +96,13 @@ function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['m
return { parentId, details };
}
-function getChemicalComponentMap(format: mmCIF_Format): ChemicalComponentMap {
+function getChemicalComponentMap(format: mmCIF_Format): Model['properties']['chemicalComponentMap'] {
const map = new Map<string, ChemicalComponent>();
const { chem_comp } = format.data
if (chem_comp._rowCount > 0) {
- const { id, type, name, pdbx_synonyms, formula, formula_weight } = format.data.chem_comp
+ const { id } = format.data.chem_comp
for (let i = 0, il = id.rowCount; i < il; ++i) {
- const _id = id.value(i)
- const _type = type.value(i)
- const cc: ChemicalComponent = {
- id: _id,
- type: ComponentType[_type],
- moleculeType: getMoleculeType(_type, _id),
- name: name.value(i),
- synonyms: pdbx_synonyms.value(i),
- formula: formula.value(i),
- formulaWeight: formula_weight.value(i),
- }
- map.set(_id, cc)
+ map.set(id.value(i), Table.getRow(format.data.chem_comp, i))
}
}
return map
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 9c44135df7b8e64b081ffa4c449622d0a4443635..c777d8d55fe61d75afc5b24f07e58dbfe0b4748e 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -12,9 +12,9 @@ import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
import { Entities } from './properties/common';
import { CustomProperties } from './properties/custom';
import { SecondaryStructure } from './properties/seconday-structure';
-import { ChemicalComponentMap } from './properties/chemical-component';
import { SaccharideComponentMap } from '../structure/carbohydrates/constants';
import { ModelFormat } from 'mol-model-formats/structure/format';
+import { ChemicalComponentMap } from './properties/chemical-component';
/**
* Interface to the "source data" of the molecule.
diff --git a/src/mol-model/structure/model/properties/chemical-component.ts b/src/mol-model/structure/model/properties/chemical-component.ts
index 35d34e571790872c8e1a110bc125705d7a4b49c4..15efa28fed123964a6f47efc6555f8343f6514c8 100644
--- a/src/mol-model/structure/model/properties/chemical-component.ts
+++ b/src/mol-model/structure/model/properties/chemical-component.ts
@@ -4,16 +4,10 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { MoleculeType, ComponentType } from '../types'
+import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
+import { Table } from 'mol-data/db';
-export interface ChemicalComponent {
- id: string
- type: ComponentType
- moleculeType: MoleculeType
- name: string
- synonyms: string[]
- formula: string
- formulaWeight: number
-}
+export type ChemicalComponent = Table.Row<mmCIF_Schema['chem_comp']>
+export type ChemicalComponentMap = ReadonlyMap<string, ChemicalComponent>
-export type ChemicalComponentMap = ReadonlyMap<string, ChemicalComponent>
\ No newline at end of file
+// TODO add data for common chemical components
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/utils/atomic-derived.ts b/src/mol-model/structure/model/properties/utils/atomic-derived.ts
index 5dcb94da5b0f869eee578eca33f241d1846c31af..f2e1833042eff059d102d7d25dd1d860eac8bce7 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-derived.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-derived.ts
@@ -23,12 +23,12 @@ export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemi
for (let i = 0; i < n; ++i) {
const compId = label_comp_id.value(i)
const chemCompMap = chemicalComponentMap
- const cc = chemCompMap.get(compId)
let molType: MoleculeType
- if (cc) {
- molType = cc.moleculeType
- } else if (moleculeTypeMap.has(compId)){
+ if (moleculeTypeMap.has(compId)){
molType = moleculeTypeMap.get(compId)!
+ } else if (chemCompMap.has(compId)) {
+ molType = getMoleculeType(chemCompMap.get(compId)!.type, compId)
+ moleculeTypeMap.set(compId, molType)
} else {
molType = getMoleculeType(getComponentType(compId), compId)
// TODO if unknown molecule type, use atom names to guess molecule type
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index 20d44428bb70f4bbfcc9d7d7ea7990a172e3a4cd..3c1bb8383903c32ee2bc27479c3c727d662f755f 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.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 Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -7,6 +7,7 @@
import BitFlags from 'mol-util/bit-flags'
import { SaccharideCompIdMap } from '../structure/carbohydrates/constants';
+import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
const _esCache = (function () {
const cache = Object.create(null);
@@ -100,29 +101,6 @@ export const NucleicBackboneAtoms = [
'O2*', 'O3*', 'O4*', 'O5*', 'C1*', 'C2*', 'C3*', 'C4*', 'C5*'
]
-/** Chemical component types as defined in the mmCIF CCD */
-export enum ComponentType {
- // protein
- 'D-peptide linking', 'L-peptide linking', 'D-peptide NH3 amino terminus',
- 'L-peptide NH3 amino terminus', 'D-peptide COOH carboxy terminus',
- 'L-peptide COOH carboxy terminus', 'peptide linking', 'peptide-like',
- 'L-gamma-peptide, C-delta linking', 'D-gamma-peptide, C-delta linking',
- 'L-beta-peptide, C-gamma linking', 'D-beta-peptide, C-gamma linking',
-
- // DNA
- 'DNA linking', 'L-DNA linking', 'DNA OH 5 prime terminus', 'DNA OH 3 prime terminus',
-
- // RNA
- 'RNA linking', 'L-RNA linking', 'RNA OH 5 prime terminus', 'RNA OH 3 prime terminus',
-
- // sacharide
- 'D-saccharide 1,4 and 1,4 linking', 'L-saccharide 1,4 and 1,4 linking',
- 'D-saccharide 1,4 and 1,6 linking', 'L-saccharide 1,4 and 1,6 linking', 'L-saccharide',
- 'D-saccharide', 'saccharide',
-
- 'non-polymer', 'other'
-}
-
/** Chemical component type names for protein */
export const ProteinComponentTypeNames = [
'D-PEPTIDE LINKING', 'L-PEPTIDE LINKING', 'D-PEPTIDE NH3 AMINO TERMINUS',
@@ -221,7 +199,7 @@ export function getMoleculeType(compType: string, compId: string) {
}
}
-export function getComponentType(compId: string) {
+export function getComponentType(compId: string): mmCIF_Schema['chem_comp']['type']['T'] {
compId = compId.toUpperCase()
if (AminoAcidNames.includes(compId)) {
return 'peptide linking'
@@ -245,6 +223,8 @@ export function isNucleic(moleculeType: MoleculeType) {
}
/**
+ * TODO write script that read CCD and outputs list of ion names
+ *
* all chemical components with the word "ion" in their name, Sep 2016
*
* SET SESSION group_concat_max_len = 1000000;
diff --git a/src/mol-model/structure/util.ts b/src/mol-model/structure/util.ts
index e688b99c2c88325f541e5184020b98dd5648bcd8..40b5c13dac895a5a43e62a51aee243f932886054 100644
--- a/src/mol-model/structure/util.ts
+++ b/src/mol-model/structure/util.ts
@@ -1,11 +1,11 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Model, ResidueIndex, ElementIndex } from './model';
-import { MoleculeType, AtomRole, MoleculeTypeAtomRoleId } from './model/types';
+import { MoleculeType, AtomRole, MoleculeTypeAtomRoleId, getMoleculeType } from './model/types';
import { Vec3 } from 'mol-math/linear-algebra';
import { Unit } from './structure';
import Matrix from 'mol-math/linear-algebra/matrix/matrix';
@@ -17,27 +17,22 @@ export function getCoarseBegCompId(unit: Unit.Spheres | Unit.Gaussians, element:
return seq.compId.value(seq_id_begin - 1) // 1-indexed
}
-export function getElementMoleculeType(unit: Unit, element: ElementIndex) {
- let compId = ''
+export function getElementMoleculeType(unit: Unit, element: ElementIndex): MoleculeType {
switch (unit.kind) {
case Unit.Kind.Atomic:
- compId = unit.model.atomicHierarchy.residues.label_comp_id.value(unit.residueIndex[element])
- break
+ return unit.model.atomicHierarchy.derived.residue.moleculeType[unit.residueIndex[element]]
case Unit.Kind.Spheres:
case Unit.Kind.Gaussians:
- compId = getCoarseBegCompId(unit, element)
- break
+ // TODO add unit.model.coarseHierarchy.derived.residue.moleculeType
+ const compId = getCoarseBegCompId(unit, element)
+ const cc = unit.model.properties.chemicalComponentMap.get(compId)
+ if (cc) return getMoleculeType(cc.type, compId)
}
- const chemCompMap = unit.model.properties.chemicalComponentMap
- const cc = chemCompMap.get(compId)
- return cc ? cc.moleculeType : MoleculeType.unknown
+ return MoleculeType.unknown
}
-export function getAtomicMoleculeType(model: Model, rI: ResidueIndex) {
- const compId = model.atomicHierarchy.residues.label_comp_id.value(rI)
- const chemCompMap = model.properties.chemicalComponentMap
- const cc = chemCompMap.get(compId)
- return cc ? cc.moleculeType : MoleculeType.unknown
+export function getAtomicMoleculeType(model: Model, rI: ResidueIndex): MoleculeType {
+ return model.atomicHierarchy.derived.residue.moleculeType[rI]
}
export function getAtomIdForAtomRole(moleculeType: MoleculeType, atomRole: AtomRole) {
diff --git a/src/mol-plugin/behavior/dynamic/labels.ts b/src/mol-plugin/behavior/dynamic/labels.ts
index 0faa3ffbd84254fac455c412c2e153fd3da2938f..7b8ccd1ba92cb413457de3fe1e6ae15b85944084 100644
--- a/src/mol-plugin/behavior/dynamic/labels.ts
+++ b/src/mol-plugin/behavior/dynamic/labels.ts
@@ -21,6 +21,7 @@ import { Unit, StructureElement, StructureProperties } from 'mol-model/structure
import { SetUtils } from 'mol-util/set';
import { arrayEqual } from 'mol-util';
import { MoleculeType } from 'mol-model/structure/model/types';
+import { getElementMoleculeType } from 'mol-model/structure/util';
// TODO
// - support more object types than structures
@@ -157,9 +158,7 @@ export const SceneLabels = PluginBehavior.create<SceneLabelsProps>({
}
if (p.levels.includes('ligand') && !u.polymerElements.length) {
- const compId = StructureProperties.residue.label_comp_id(l)
- const chemComp = u.model.properties.chemicalComponentMap.get(compId)
- const moleculeType = chemComp ? chemComp.moleculeType : MoleculeType.unknown
+ const moleculeType = getElementMoleculeType(u, u.elements[0])
if (moleculeType === MoleculeType.other || moleculeType === MoleculeType.saccharide) {
label = `${StructureProperties.entity.pdbx_description(l).join(', ')} (${getAsymId(u)(l)})`
}