diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 17b7ee9cf9f4df0ad0ab90bc398af82163679569..11e899c90e65bdce4fc65332787f04346bc2850a 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -70,6 +70,7 @@ function getNcsOperators(format: mmCIF_Format) {
}
return opers;
}
+
function getModifiedResidueNameMap(format: mmCIF_Format) {
const data = format.data.pdbx_struct_mod_residue;
const map = new Map<string, string>();
@@ -121,8 +122,22 @@ function getChemicalComponentMap(format: mmCIF_Format) {
return map
}
-function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities: Entities, previous?: Model): Model {
- const atomic = getAtomicHierarchyAndConformation(format, atom_site, entities, previous);
+export interface FormatData {
+ modifiedResidueNameMap: Map<string, string>
+ asymIdSerialMap: Map<string, number>
+ chemicalComponentMap: Map<string, ChemicalComponent>
+}
+
+function getFormatData(format: mmCIF_Format): FormatData {
+ return {
+ modifiedResidueNameMap: getModifiedResidueNameMap(format),
+ asymIdSerialMap: getAsymIdSerialMap(format),
+ chemicalComponentMap: getChemicalComponentMap(format)
+ }
+}
+
+function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities: Entities, formatData: FormatData, previous?: Model): Model {
+ const atomic = getAtomicHierarchyAndConformation(format, atom_site, entities, formatData, previous);
if (previous && atomic.sameAsPrevious) {
return { ...previous, atomicConformation: atomic.conformation };
}
@@ -132,10 +147,6 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities
? format.data.entry.id.value(0)
: format.data._name;
- const modifiedResidueNameMap = getModifiedResidueNameMap(format);
- const asymIdSerialMap = getAsymIdSerialMap(format)
- const chemicalComponentMap = getChemicalComponentMap(format)
-
return {
id: UUID.create(),
label,
@@ -143,16 +154,14 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities
modelNum: atom_site.pdbx_PDB_model_num.value(0),
entities,
symmetry: getSymmetry(format),
- sequence: getSequence(format.data, entities, atomic.hierarchy, modifiedResidueNameMap),
+ sequence: getSequence(format.data, entities, atomic.hierarchy, formatData.modifiedResidueNameMap),
atomicHierarchy: atomic.hierarchy,
atomicConformation: atomic.conformation,
coarseHierarchy: coarse.hierarchy,
coarseConformation: coarse.conformation,
properties: {
secondaryStructure: getSecondaryStructureMmCif(format.data, atomic.hierarchy),
- modifiedResidueNameMap,
- asymIdSerialMap,
- chemicalComponentMap
+ ...formatData
},
customProperties: new CustomProperties(),
_staticPropertyData: Object.create(null),
@@ -160,12 +169,9 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities
};
}
-function createModelIHM(format: mmCIF_Format, data: IHMData): Model {
- const atomic = getAtomicHierarchyAndConformation(format, data.atom_site, data.entities);
- const coarse = getIHMCoarse(data);
- const modifiedResidueNameMap = getModifiedResidueNameMap(format);
- const asymIdSerialMap = getAsymIdSerialMap(format)
- const chemicalComponentMap = getChemicalComponentMap(format)
+function createModelIHM(format: mmCIF_Format, data: IHMData, formatData: FormatData): Model {
+ const atomic = getAtomicHierarchyAndConformation(format, data.atom_site, data.entities, formatData);
+ const coarse = getIHMCoarse(data, formatData);
return {
id: UUID.create(),
@@ -174,16 +180,14 @@ function createModelIHM(format: mmCIF_Format, data: IHMData): Model {
modelNum: data.model_id,
entities: data.entities,
symmetry: getSymmetry(format),
- sequence: getSequence(format.data, data.entities, atomic.hierarchy, modifiedResidueNameMap),
+ sequence: getSequence(format.data, data.entities, atomic.hierarchy, formatData.modifiedResidueNameMap),
atomicHierarchy: atomic.hierarchy,
atomicConformation: atomic.conformation,
coarseHierarchy: coarse.hierarchy,
coarseConformation: coarse.conformation,
properties: {
secondaryStructure: getSecondaryStructureMmCif(format.data, atomic.hierarchy),
- modifiedResidueNameMap,
- asymIdSerialMap,
- chemicalComponentMap
+ ...formatData
},
customProperties: new CustomProperties(),
_staticPropertyData: Object.create(null),
@@ -204,7 +208,7 @@ function findModelEnd(num: Column<number>, startIndex: number) {
return endIndex;
}
-async function readStandard(ctx: RuntimeContext, format: mmCIF_Format) {
+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) };
@@ -213,7 +217,7 @@ async function readStandard(ctx: RuntimeContext, format: mmCIF_Format) {
while (modelStart < atomCount) {
const modelEnd = findModelEnd(format.data.atom_site.pdbx_PDB_model_num, modelStart);
const atom_site = await sortAtomSite(ctx, format.data.atom_site, modelStart, modelEnd);
- const model = createStandardModel(format, atom_site, entities, models.length > 0 ? models[models.length - 1] : void 0);
+ const model = createStandardModel(format, atom_site, entities, formatData, models.length > 0 ? models[models.length - 1] : void 0);
attachProps(model);
models.push(model);
modelStart = modelEnd;
@@ -235,7 +239,7 @@ function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
return ret;
}
-async function readIHM(ctx: RuntimeContext, format: mmCIF_Format) {
+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) };
@@ -257,7 +261,7 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format) {
ihm_sphere_obj_site: sphere_sites.has(id) ? sphere_sites.get(id)! : Table.window(format.data.ihm_sphere_obj_site, format.data.ihm_sphere_obj_site._schema, 0, 0),
ihm_gaussian_obj_site: gauss_sites.has(id) ? gauss_sites.get(id)! : Table.window(format.data.ihm_gaussian_obj_site, format.data.ihm_gaussian_obj_site._schema, 0, 0)
};
- const model = createModelIHM(format, data);
+ const model = createModelIHM(format, data, formatData);
attachProps(model);
models.push(model);
}
@@ -266,9 +270,10 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format) {
}
function buildModels(format: mmCIF_Format): Task<ReadonlyArray<Model>> {
+ const formatData = getFormatData(format)
return Task.create('Create mmCIF Model', async ctx => {
const isIHM = format.data.ihm_model_list._rowCount > 0;
- return isIHM ? await readIHM(ctx, format) : await readStandard(ctx, format);
+ return isIHM ? await readIHM(ctx, format, formatData) : await readStandard(ctx, format, formatData);
});
}
diff --git a/src/mol-model/structure/model/formats/mmcif/atomic.ts b/src/mol-model/structure/model/formats/mmcif/atomic.ts
index e9f69f9e607507b6da761812cc92eb041a0d8008..677914582d91d39e0806903bea388fa2914ad54a 100644
--- a/src/mol-model/structure/model/formats/mmcif/atomic.ts
+++ b/src/mol-model/structure/model/formats/mmcif/atomic.ts
@@ -17,13 +17,16 @@ import { ElementSymbol } from '../../types';
import { Entities } from '../../properties/common';
import mmCIF_Format = Format.mmCIF
+import { getAtomicRanges } from '../../properties/utils/atomic-ranges';
+import { FormatData } from '../mmcif';
+
type AtomSite = mmCIF_Database['atom_site']
function findHierarchyOffsets(atom_site: AtomSite) {
- if (atom_site._rowCount === 0) return { residues: [], polymers: [], chains: [] };
+ if (atom_site._rowCount === 0) return { residues: [], chains: [] };
const start = 0, end = atom_site._rowCount;
- const residues = [start as Element], chains = [start as Element], polymers = [start as Element];
+ const residues = [start as Element], chains = [start as Element];
const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code, label_comp_id } = atom_site;
@@ -34,13 +37,11 @@ function findHierarchyOffsets(atom_site: AtomSite) {
|| !auth_seq_id.areValuesEqual(i - 1, i)
|| !pdbx_PDB_ins_code.areValuesEqual(i - 1, i)
|| !label_comp_id.areValuesEqual(i - 1, i);
- const newPolymer = newResidue && label_seq_id.value(i - 1) !== label_seq_id.value(i) - 1;
if (newResidue) residues[residues.length] = i as Element;
- if (newPolymer) polymers[polymers.length] = i as Element;
if (newChain) chains[chains.length] = i as Element;
}
- return { residues, polymers, chains };
+ return { residues, chains };
}
function createHierarchyData(atom_site: AtomSite, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): AtomicData {
@@ -78,7 +79,7 @@ function isHierarchyDataEqual(a: AtomicData, b: AtomicData) {
&& Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
}
-export function getAtomicHierarchyAndConformation(format: mmCIF_Format, atom_site: AtomSite, entities: Entities, previous?: Model) {
+export function getAtomicHierarchyAndConformation(format: mmCIF_Format, atom_site: AtomSite, entities: Entities, formatData: FormatData, previous?: Model) {
const hierarchyOffsets = findHierarchyOffsets(atom_site);
const hierarchyData = createHierarchyData(atom_site, hierarchyOffsets);
@@ -93,11 +94,11 @@ export function getAtomicHierarchyAndConformation(format: mmCIF_Format, atom_sit
const hierarchySegments: AtomicSegments = {
residueSegments: Segmentation.ofOffsets(hierarchyOffsets.residues, Interval.ofBounds(0, atom_site._rowCount)),
chainSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, Interval.ofBounds(0, atom_site._rowCount)),
- polymerSegments: Segmentation.ofOffsets(hierarchyOffsets.polymers, Interval.ofBounds(0, atom_site._rowCount)),
}
const hierarchyKeys = getAtomicKeys(hierarchyData, entities, hierarchySegments);
- const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments };
+ const hierarchyRanges = getAtomicRanges(hierarchyData, hierarchySegments, formatData.chemicalComponentMap);
+ const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments, ...hierarchyRanges };
return {
sameAsPrevious: false,
hierarchy,
diff --git a/src/mol-model/structure/model/formats/mmcif/ihm.ts b/src/mol-model/structure/model/formats/mmcif/ihm.ts
index 1c93c716194329740575cde23028e263816f727e..d9b401d46ead15b02552f13ae2709ca23075e9be 100644
--- a/src/mol-model/structure/model/formats/mmcif/ihm.ts
+++ b/src/mol-model/structure/model/formats/mmcif/ihm.ts
@@ -13,6 +13,8 @@ import { UUID } from 'mol-util';
import { Segmentation, Interval } from 'mol-data/int';
import { Mat3, Tensor } from 'mol-math/linear-algebra';
import { Element } from '../../../structure'
+import { getCoarseRanges } from '../../properties/utils/coarse-ranges';
+import { FormatData } from '../mmcif';
export interface IHMData {
model_id: number,
@@ -25,7 +27,7 @@ export interface IHMData {
export const EmptyIHMCoarse = { hierarchy: CoarseHierarchy.Empty, conformation: void 0 as any }
-export function getIHMCoarse(data: IHMData): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
+export function getIHMCoarse(data: IHMData, formatData: FormatData): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
const { ihm_sphere_obj_site, ihm_gaussian_obj_site } = data;
if (ihm_sphere_obj_site._rowCount === 0 && ihm_gaussian_obj_site._rowCount === 0) return EmptyIHMCoarse;
@@ -33,16 +35,18 @@ export function getIHMCoarse(data: IHMData): { hierarchy: CoarseHierarchy, confo
const sphereData = getData(ihm_sphere_obj_site);
const sphereConformation = getSphereConformation(ihm_sphere_obj_site);
const sphereKeys = getCoarseKeys(sphereData, data.entities);
+ const sphereRanges = getCoarseRanges(sphereData, formatData.chemicalComponentMap);
const gaussianData = getData(ihm_gaussian_obj_site);
const gaussianConformation = getGaussianConformation(ihm_gaussian_obj_site);
const gaussianKeys = getCoarseKeys(gaussianData, data.entities);
+ const gaussianRanges = getCoarseRanges(gaussianData, formatData.chemicalComponentMap);
return {
hierarchy: {
isDefined: true,
- spheres: { ...sphereData, ...sphereKeys },
- gaussians: { ...gaussianData, ...gaussianKeys },
+ spheres: { ...sphereData, ...sphereKeys, ...sphereRanges },
+ gaussians: { ...gaussianData, ...gaussianKeys, ...gaussianRanges },
},
conformation: {
id: UUID.create(),
@@ -81,19 +85,14 @@ function getGaussianConformation(data: mmCIF['ihm_gaussian_obj_site']): CoarseGa
}
function getSegments(asym_id: Column<string>, seq_id_begin: Column<number>, seq_id_end: Column<number>) {
- const polymerOffsets = [0 as Element], chainOffsets = [0 as Element];
+ const chainOffsets = [0 as Element];
for (let i = 1, _i = asym_id.rowCount; i < _i; i++) {
const newChain = !asym_id.areValuesEqual(i - 1, i);
- const newPolymer = newChain
- || seq_id_end.value(i - 1) !== seq_id_begin.value(i) - 1;
-
- if (newPolymer) polymerOffsets[polymerOffsets.length] = i as Element;
if (newChain) chainOffsets[chainOffsets.length] = i as Element;
}
return {
- chainSegments: Segmentation.ofOffsets(chainOffsets, Interval.ofBounds(0, asym_id.rowCount)),
- polymerSegments: Segmentation.ofOffsets(polymerOffsets, Interval.ofBounds(0, asym_id.rowCount))
+ chainSegments: Segmentation.ofOffsets(chainOffsets, Interval.ofBounds(0, asym_id.rowCount))
}
}
diff --git a/src/mol-model/structure/model/properties/atomic/hierarchy.ts b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
index 12c9de4c1ed01dfbaaa055a7d2e7756ced2ed743..8870dd849eac8e355595057099055fc13d65c5d9 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -9,6 +9,7 @@ import { Segmentation } from 'mol-data/int'
import { mmCIF_Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
import { ElementSymbol } from '../../types'
import { Element } from '../../../structure'
+import SortedRanges from 'mol-data/int/sorted-ranges';
export const AtomsSchema = {
type_symbol: Column.Schema.Aliased<ElementSymbol>(mmCIF.atom_site.type_symbol),
@@ -52,11 +53,6 @@ export interface AtomicSegments {
residueSegments: Segmentation<Element>,
/** Maps chainIndex to a range of atoms [segments[cI], segments[cI + 1]) */
chainSegments: Segmentation<Element>,
- /**
- * bonded/connected stretches of polymer chains, i.e. a chain will be
- * broken into multiple polymer segments if there are missing residues
- */
- polymerSegments: Segmentation<Element>
// TODO: include entity segments?
}
@@ -78,5 +74,10 @@ export interface AtomicKeys {
findResidueKey(entityId: string, label_asym_id: string, label_comp_id: string, auth_seq_id: number, pdbx_PDB_ins_code: string): number
}
-type _Hierarchy = AtomicData & AtomicSegments & AtomicKeys
+export interface AtomicRanges {
+ polymerRanges: SortedRanges<Element>
+ gapRanges: SortedRanges<Element>
+}
+
+type _Hierarchy = AtomicData & AtomicSegments & AtomicKeys & AtomicRanges
export interface AtomicHierarchy extends _Hierarchy { }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/coarse/hierarchy.ts b/src/mol-model/structure/model/properties/coarse/hierarchy.ts
index 57d3da0acaac976009976324824438a94ae7ee2e..f9057f34894e3604588df1325fa9f1a5ae2795af 100644
--- a/src/mol-model/structure/model/properties/coarse/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/coarse/hierarchy.ts
@@ -8,6 +8,7 @@
import { Column } from 'mol-data/db'
import { Segmentation } from 'mol-data/int';
import { Element } from '../../../structure'
+import SortedRanges from 'mol-data/int/sorted-ranges';
export interface CoarsedElementKeys {
// assign a key to each element
@@ -28,14 +29,14 @@ export interface CoarseElementData {
seq_id_end: Column<number>,
chainSegments: Segmentation<Element>,
- /**
- * bonded/connected stretches of polymer chains, i.e. a chain will be
- * broken into multiple polymer segments if there are missing residues
- */
- polymerSegments: Segmentation<Element>
}
-export type CoarseElements = CoarsedElementKeys & CoarseElementData
+export interface CoarseRanges {
+ polymerRanges: SortedRanges<Element>
+ gapRanges: SortedRanges<Element>
+}
+
+export type CoarseElements = CoarsedElementKeys & CoarseElementData & CoarseRanges
export interface CoarseHierarchy {
isDefined: boolean,
diff --git a/src/mol-model/structure/model/properties/utils/atomic-ranges.ts b/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a28eca281de545c9079cbea9618b19f7dbbdf9ae
--- /dev/null
+++ b/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
@@ -0,0 +1,69 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { AtomicSegments } from '../atomic';
+import { AtomicData, AtomicRanges } from '../atomic/hierarchy';
+import { Segmentation, Interval } from 'mol-data/int';
+import SortedRanges from 'mol-data/int/sorted-ranges';
+import { Element } from '../../../../structure';
+import { ChemicalComponent } from '../chemical-component';
+import { MoleculeType, isPolymer } from '../../types';
+
+export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, chemicalComponentMap: Map<string, ChemicalComponent>): AtomicRanges {
+ const polymerRanges: number[] = []
+ const gapRanges: number[] = []
+ const chainIt = Segmentation.transientSegments(segments.chainSegments, Interval.ofBounds(0, data.atoms._rowCount))
+ const residueIt = Segmentation.transientSegments(segments.residueSegments, Interval.ofBounds(0, data.atoms._rowCount))
+ const { label_seq_id, label_comp_id } = data.residues
+
+ let prevSeqId: number
+ let prevEnd: number
+ let startIndex: number
+
+ while (chainIt.hasNext) {
+ const chainSegment = chainIt.move();
+ residueIt.setSegment(chainSegment);
+ prevSeqId = -1
+ prevEnd = -1
+ startIndex = -1
+
+ while (residueIt.hasNext) {
+ const residueSegment = residueIt.move();
+ const residueIndex = residueSegment.index
+ const cc = chemicalComponentMap.get(label_comp_id.value(residueIndex))
+ const moleculeType = cc ? cc.moleculeType : MoleculeType.unknown
+ const seqId = label_seq_id.value(residueIndex)
+ if (isPolymer(moleculeType)) {
+ if (startIndex !== -1) {
+ if (seqId !== prevSeqId + 1) {
+ polymerRanges.push(startIndex, prevEnd - 1)
+ gapRanges.push(prevEnd - 1, residueSegment.start)
+ startIndex = residueSegment.start
+ } else if (!residueIt.hasNext) {
+ polymerRanges.push(startIndex, residueSegment.end - 1)
+ }
+ } else {
+ startIndex = residueSegment.start // start polymer
+ }
+ } else {
+ if (startIndex !== -1) {
+ polymerRanges.push(startIndex, prevEnd - 1)
+ startIndex = -1
+ }
+ }
+
+ prevEnd = residueSegment.end
+ prevSeqId = seqId
+ }
+ }
+
+ console.log(polymerRanges, gapRanges)
+
+ return {
+ polymerRanges: SortedRanges.ofSortedRanges(polymerRanges as Element[]),
+ gapRanges: SortedRanges.ofSortedRanges(gapRanges as Element[])
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/utils/coarse-ranges.ts b/src/mol-model/structure/model/properties/utils/coarse-ranges.ts
new file mode 100644
index 0000000000000000000000000000000000000000..635bc51847a5fbc6681ab6019e6016f988d605ee
--- /dev/null
+++ b/src/mol-model/structure/model/properties/utils/coarse-ranges.ts
@@ -0,0 +1,52 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { CoarseRanges, CoarseElementData } from '../coarse/hierarchy';
+import { Segmentation, Interval } from 'mol-data/int';
+import SortedRanges from 'mol-data/int/sorted-ranges';
+import { Element } from '../../../../structure';
+import { ChemicalComponent } from '../chemical-component';
+
+// TODO assumes all coarse elements are part of a polymer
+
+export function getCoarseRanges(data: CoarseElementData, chemicalComponentMap: Map<string, ChemicalComponent>): CoarseRanges {
+ const polymerRanges: number[] = []
+ const gapRanges: number[] = []
+ const chainIt = Segmentation.transientSegments(data.chainSegments, Interval.ofBounds(0, data.count))
+
+ const { seq_id_begin, seq_id_end } = data
+
+ while (chainIt.hasNext) {
+ const { start, end } = chainIt.move();
+ console.log('chain', start, end)
+
+ let startIndex = -1
+ let prevSeqEnd = -1
+ for (let i = start; i < end; ++i) {
+ const seqEnd = seq_id_end.value(i)
+ if (i === start) {
+ startIndex = i
+ prevSeqEnd = seq_id_end.value(i)
+ } else {
+ if (prevSeqEnd !== seq_id_begin.value(i) - 1) {
+ polymerRanges.push(startIndex, i - 1)
+ startIndex = i
+ }
+ }
+ if (i === end - 1) {
+ polymerRanges.push(startIndex, i)
+ }
+ prevSeqEnd = seqEnd
+ }
+ }
+
+ console.log(polymerRanges, gapRanges)
+
+ return {
+ polymerRanges: SortedRanges.ofSortedRanges(polymerRanges as Element[]),
+ gapRanges: SortedRanges.ofSortedRanges(gapRanges as Element[])
+ }
+}
\ No newline at end of file