diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index 0721e70eb72d970d603ce0357c24d7110db514b8..f797e919cdb4f207224669ff11d095c9ace24f7f 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -12,7 +12,7 @@ import { Tensor, Vec3 } from '../../../mol-math/linear-algebra';
import { RuntimeContext } from '../../../mol-task';
import UUID from '../../../mol-util/uuid';
import { Model } from '../../../mol-model/structure/model/model';
-import { Entities } from '../../../mol-model/structure/model/properties/common';
+import { Entities, ChemicalComponent, MissingResidue } from '../../../mol-model/structure/model/properties/common';
import { CustomProperties } from '../../../mol-model/structure';
import { ModelSymmetry } from '../../../mol-model/structure/model/properties/symmetry';
import { createAssemblies } from './assembly';
@@ -23,7 +23,6 @@ import { getSecondaryStructure } from './secondary-structure';
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, getEntityType } from '../../../mol-model/structure/model/types';
import { ModelFormat } from '../format';
import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, SaccharideCompIdMap, UnknownSaccharideComponent } from '../../../mol-model/structure/structure/carbohydrates/constants';
@@ -98,14 +97,36 @@ function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['m
return { parentId, details };
}
+function getMissingResidues(format: mmCIF_Format): Model['properties']['missingResidues'] {
+ const map = new Map<string, MissingResidue>();
+ const c = format.data.pdbx_unobs_or_zero_occ_residues
+
+ const getKey = (model_num: number, asym_id: string, seq_id: number) => {
+ return `${model_num}|${asym_id}|${seq_id}`
+ }
+
+ for (let i = 0, il = c._rowCount; i < il; ++i) {
+ const key = getKey(c.PDB_model_num.value(i), c.label_asym_id.value(i), c.label_seq_id.value(i))
+ map.set(key, { polymer_flag: c.polymer_flag.value(i), occupancy_flag: c.occupancy_flag.value(i) })
+ }
+
+ return {
+ has: (model_num: number, asym_id: string, seq_id: number) => {
+ return map.has(getKey(model_num, asym_id, seq_id))
+ },
+ get: (model_num: number, asym_id: string, seq_id: number) => {
+ return map.get(getKey(model_num, asym_id, seq_id))
+ },
+ size: map.size
+ }
+}
+
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 } = format.data.chem_comp
- for (let i = 0, il = id.rowCount; i < il; ++i) {
- map.set(id.value(i), Table.getRow(format.data.chem_comp, i))
- }
+ const { id } = chem_comp
+ for (let i = 0, il = id.rowCount; i < il; ++i) {
+ map.set(id.value(i), Table.getRow(chem_comp, i))
}
return map
}
@@ -158,6 +179,7 @@ const getUniqueComponentNames = memoize1((format: mmCIF_Format) => {
export interface FormatData {
modifiedResidues: Model['properties']['modifiedResidues']
+ missingResidues: Model['properties']['missingResidues']
chemicalComponentMap: Model['properties']['chemicalComponentMap']
saccharideComponentMap: Model['properties']['saccharideComponentMap']
}
@@ -165,6 +187,7 @@ export interface FormatData {
function getFormatData(format: mmCIF_Format): FormatData {
return {
modifiedResidues: getModifiedResidueNameMap(format),
+ missingResidues: getMissingResidues(format),
chemicalComponentMap: getChemicalComponentMap(format),
saccharideComponentMap: getSaccharideComponentMap(format)
}
@@ -172,11 +195,12 @@ function getFormatData(format: mmCIF_Format): FormatData {
function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, formatData: FormatData, previous?: Model): Model {
const atomic = getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, formatData, previous);
+ const modelNum = atom_site.pdbx_PDB_model_num.value(0)
if (previous && atomic.sameAsPrevious) {
return {
...previous,
id: UUID.create22(),
- modelNum: atom_site.pdbx_PDB_model_num.value(0),
+ modelNum,
atomicConformation: atomic.conformation,
_dynamicPropertyData: Object.create(null)
};
@@ -192,7 +216,7 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIn
label,
entry: label,
sourceData: format,
- modelNum: atom_site.pdbx_PDB_model_num.value(0),
+ modelNum,
entities,
symmetry: getSymmetry(format),
sequence: getSequence(format.data, entities, atomic.hierarchy, formatData.modifiedResidues.parentId),
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index cd660879e8b16b92976667ff3db3f08998281709..22d1ae04e11f64f66543d5d8b0c134c875afe6bb 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -10,12 +10,11 @@ import StructureSequence from './properties/sequence';
import { AtomicHierarchy, AtomicConformation } from './properties/atomic';
import { ModelSymmetry } from './properties/symmetry';
import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
-import { Entities } from './properties/common';
+import { Entities, ChemicalComponentMap, MissingResidues } from './properties/common';
import { CustomProperties } from '../common/custom-property';
import { SecondaryStructure } from './properties/seconday-structure';
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.
@@ -49,6 +48,8 @@ export interface Model extends Readonly<{
parentId: ReadonlyMap<string, string>,
details: ReadonlyMap<string, string>
}>,
+ /** map that holds details about unobserved or zero occurrence residues */
+ readonly missingResidues: MissingResidues,
/** maps residue name to `ChemicalComponent` data */
readonly chemicalComponentMap: ChemicalComponentMap
/** maps residue name to `SaccharideComponent` data */
diff --git a/src/mol-model/structure/model/properties/chemical-component.ts b/src/mol-model/structure/model/properties/chemical-component.ts
deleted file mode 100644
index bc31df3247cb888ddb504e5a414ca111a3858d99..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/model/properties/chemical-component.ts
+++ /dev/null
@@ -1,13 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
-import { Table } from '../../../../mol-data/db';
-
-export type ChemicalComponent = Table.Row<mmCIF_Schema['chem_comp']>
-export type ChemicalComponentMap = ReadonlyMap<string, ChemicalComponent>
-
-// TODO add data for common chemical components
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/common.ts b/src/mol-model/structure/model/properties/common.ts
index 8355c9dceddafd302dca593b5adee128b050d30b..577367b67163a6a931de616b0beb58f66c292eb8 100644
--- a/src/mol-model/structure/model/properties/common.ts
+++ b/src/mol-model/structure/model/properties/common.ts
@@ -1,13 +1,28 @@
/**
- * 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>
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { mmCIF_Database as mmCIF } from '../../../../mol-io/reader/cif/schema/mmcif'
+import { mmCIF_Database, mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif'
+import { Table } from '../../../../mol-data/db';
import { EntityIndex } from '../indexing';
export interface Entities {
- data: mmCIF['entity'],
+ data: mmCIF_Database['entity'],
getEntityIndex(id: string): EntityIndex
+}
+
+export type ChemicalComponent = Table.Row<mmCIF_Schema['chem_comp']>
+export type ChemicalComponentMap = ReadonlyMap<string, ChemicalComponent>
+
+export type MissingResidue = Table.Row<Pick<
+ mmCIF_Schema['pdbx_unobs_or_zero_occ_residues'],
+ 'polymer_flag' | 'occupancy_flag'>
+>
+export interface MissingResidues {
+ has(model_num: number, asym_id: string, seq_id: number): boolean
+ get(model_num: number, asym_id: string, seq_id: number): MissingResidue | undefined
+ readonly size: number
}
\ 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 11706d5ada50c1cab3eb8459e681e444d347908d..ae82751c4c6740d05e54a77e0efe7c09acce1a44 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-derived.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-derived.ts
@@ -5,11 +5,11 @@
*/
import { AtomicData } from '../atomic';
-import { ChemicalComponentMap } from '../chemical-component';
import { AtomicIndex, AtomicDerivedData } from '../atomic/hierarchy';
import { ElementIndex, ResidueIndex } from '../../indexing';
import { MoleculeType, getMoleculeType, getComponentType } from '../../types';
import { getAtomIdForAtomRole } from '../../../../../mol-model/structure/util';
+import { ChemicalComponentMap } from '../common';
export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemicalComponentMap: ChemicalComponentMap): AtomicDerivedData {
const { label_comp_id, _rowCount: n } = data.residues
diff --git a/src/mol-model/structure/model/properties/utils/coarse-ranges.ts b/src/mol-model/structure/model/properties/utils/coarse-ranges.ts
index e7fb45928f8fdddfced1307ac67ef670bd8832fc..74c5f432ea7e9ad99aa7f6c39aa7e11f712e6eba 100644
--- a/src/mol-model/structure/model/properties/utils/coarse-ranges.ts
+++ b/src/mol-model/structure/model/properties/utils/coarse-ranges.ts
@@ -7,8 +7,8 @@
import { CoarseRanges, CoarseElementData } from '../coarse/hierarchy';
import { Segmentation, Interval } from '../../../../../mol-data/int';
import SortedRanges from '../../../../../mol-data/int/sorted-ranges';
-import { ChemicalComponent } from '../chemical-component';
import { ElementIndex } from '../../indexing';
+import { ChemicalComponent } from '../common';
// TODO assumes all coarse elements are part of a polymer
// TODO add gaps at the ends of the chains by comparing to the polymer sequence data
diff --git a/src/mol-plugin/ui/sequence/polymer.ts b/src/mol-plugin/ui/sequence/polymer.ts
index a6302fd24498601fb5dc8924dc91be8bd6c2f8c8..03b1f60d09c59a3e7d8886b3013733bd950ebb56 100644
--- a/src/mol-plugin/ui/sequence/polymer.ts
+++ b/src/mol-plugin/ui/sequence/polymer.ts
@@ -9,13 +9,18 @@ import { SequenceWrapper } from './util';
import { OrderedSet, Interval } from '../../../mol-data/int';
import { Loci } from '../../../mol-model/loci';
import { Sequence } from '../../../mol-model/sequence';
-import { Color } from '../../../mol-util/color';
+import { MissingResidues } from '../../../mol-model/structure/model/properties/common';
+import { ColorNames } from '../../../mol-util/color/tables';
export type StructureUnit = { structure: Structure, unit: Unit }
export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
private readonly location: StructureElement
private readonly sequence: Sequence
+ private readonly missing: MissingResidues
+
+ private readonly modelNum: number
+ private readonly asymId: string
seqId(i: number) {
return this.sequence.offset + i + 1
@@ -24,7 +29,9 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
return this.sequence.sequence[i]
}
residueColor(i: number) {
- return Color(0)
+ return this.missing.has(this.modelNum, this.asymId, this.seqId(i))
+ ? ColorNames.grey
+ : ColorNames.black
}
eachResidue(loci: Loci, apply: (interval: Interval) => boolean) {
@@ -69,6 +76,10 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
this.sequence = sequence
this.location = StructureElement.create()
+ this.missing = data.unit.model.properties.missingResidues
+
+ this.modelNum = data.unit.model.modelNum
+ this.asymId = SP.chain.label_asym_id(l)
}
}