diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 0fdb0d735ab1ac460b42fe91892aa3a35dce24fd..8d06ce4f5d3190c6ccd3706a90f48a8ec00cbb32 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -14,7 +14,7 @@ import { Model, Structure, StructureElement, Unit, StructureProperties, UnitRing
import { OrderedSet } from 'mol-data/int';
import { openCif, downloadCif } from './helpers';
import { Vec3 } from 'mol-math/linear-algebra';
-import { parse_mmCIF } from 'mol-model-parsers/structure/mmcif';
+import { trajecotryFromMmCIF } from 'mol-model-parsers/structure/mmcif';
import { ModelFormat } from 'mol-model-parsers/structure/format';
@@ -200,7 +200,7 @@ export function printModelStats(models: ReadonlyArray<Model>) {
}
export async function getModelsAndStructure(frame: CifFrame) {
- const models = await parse_mmCIF(ModelFormat.mmCIF(frame)).run();
+ const models = await trajecotryFromMmCIF(ModelFormat.mmCIF(frame)).run();
const structure = Structure.ofModel(models[0]);
return { models, structure };
}
diff --git a/src/mol-model-parsers/structure/mmcif.ts b/src/mol-model-parsers/structure/mmcif.ts
index bc10993ac5114966373df6aa3b722b3256c43dac..c3ea2870b77de63aa2218cb8db0e4604eeb52f1b 100644
--- a/src/mol-model-parsers/structure/mmcif.ts
+++ b/src/mol-model-parsers/structure/mmcif.ts
@@ -5,304 +5,12 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Column, Table } from 'mol-data/db';
-import { mmCIF_Database, mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
-import { Spacegroup, SpacegroupCell, SymmetryOperator } from 'mol-math/geometry';
-import { Tensor, Vec3 } from 'mol-math/linear-algebra';
-import { Task, 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 { CustomProperties } from 'mol-model/structure/model/properties/custom';
-import { ModelSymmetry } from 'mol-model/structure/model/properties/symmetry';
-import { createAssemblies } from './mmcif/assembly';
-import { getAtomicHierarchyAndConformation } from './mmcif/atomic';
-import { ComponentBond } from './mmcif/bonds';
-import { getIHMCoarse, EmptyIHMCoarse, IHMData } from './mmcif/ihm';
-import { getSecondaryStructureMmCif } from './mmcif/secondary-structure';
-import { getSequence } from './mmcif/sequence';
-import { sortAtomSite } from './mmcif/sort';
-import { StructConn } from './mmcif/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 { Task } from 'mol-task';
import { ModelFormat } from './format';
-import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, SaccharideCompIdMap, UnknownSaccharideComponent } from 'mol-model/structure/structure/carbohydrates/constants';
+import { _parse_mmCif } from './mmcif/parser';
import mmCIF_Format = ModelFormat.mmCIF
-export function parse_mmCIF(format: mmCIF_Format): Task<Model.Trajectory> {
- 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, formatData) : await readStandard(ctx, format, formatData);
- });
-}
-
-type AtomSite = mmCIF_Database['atom_site']
-
-function getSymmetry(format: mmCIF_Format): ModelSymmetry {
- const assemblies = createAssemblies(format);
- const spacegroup = getSpacegroup(format);
- const isNonStandardCrytalFrame = checkNonStandardCrystalFrame(format, spacegroup);
- return { assemblies, spacegroup, isNonStandardCrytalFrame, ncsOperators: getNcsOperators(format) };
-}
-
-function checkNonStandardCrystalFrame(format: mmCIF_Format, spacegroup: Spacegroup) {
- const { atom_sites } = format.data;
- if (atom_sites._rowCount === 0) return false;
- // TODO: parse atom_sites transform and check if it corresponds to the toFractional matrix
- return false;
-}
-
-function getSpacegroup(format: mmCIF_Format): Spacegroup {
- const { symmetry, cell } = format.data;
- if (symmetry._rowCount === 0 || cell._rowCount === 0) return Spacegroup.ZeroP1;
- const groupName = symmetry['space_group_name_H-M'].value(0);
- const spaceCell = SpacegroupCell.create(groupName,
- Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)),
- Vec3.scale(Vec3.zero(), Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
-
- return Spacegroup.create(spaceCell);
-}
-
-function getNcsOperators(format: mmCIF_Format) {
- const { struct_ncs_oper } = format.data;
- if (struct_ncs_oper._rowCount === 0) return void 0;
- const { id, matrix, vector } = struct_ncs_oper;
-
- const matrixSpace = mmCIF_Schema.struct_ncs_oper.matrix.space, vectorSpace = mmCIF_Schema.struct_ncs_oper.vector.space;
-
- const opers: SymmetryOperator[] = [];
- for (let i = 0; i < struct_ncs_oper._rowCount; i++) {
- const m = Tensor.toMat3(matrixSpace, matrix.value(i));
- const v = Tensor.toVec3(vectorSpace, vector.value(i));
- if (!SymmetryOperator.checkIfRotationAndTranslation(m, v)) continue;
- opers[opers.length] = SymmetryOperator.ofRotationAndOffset(`ncs_${id.value(i)}`, m, v);
- }
- return opers;
-}
-function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['modifiedResidues'] {
- const data = format.data.pdbx_struct_mod_residue;
- const parentId = new Map<string, string>();
- const details = new Map<string, string>();
- const comp_id = data.label_comp_id.isDefined ? data.label_comp_id : data.auth_comp_id;
- const parent_id = data.parent_comp_id, details_data = data.details;
-
- for (let i = 0; i < data._rowCount; i++) {
- const id = comp_id.value(i);
- parentId.set(id, parent_id.value(i));
- details.set(id, details_data.value(i));
- }
-
- return { parentId, details };
-}
-
-function getChemicalComponentMap(format: mmCIF_Format): ChemicalComponentMap {
- const map = new Map<string, ChemicalComponent>();
- const { id, type, name, pdbx_synonyms, formula, formula_weight } = format.data.chem_comp
- for (let i = 0, il = id.rowCount; i < il; ++i) {
- const _id = id.value(i)
- const _type = type.value(i)
- const cc: ChemicalComponent = {
- id: _id,
- type: ComponentType[_type],
- moleculeType: getMoleculeType(_type, _id),
- name: name.value(i),
- synonyms: pdbx_synonyms.value(i),
- formula: formula.value(i),
- formulaWeight: formula_weight.value(i),
- }
- map.set(_id, cc)
- }
- return map
-}
-
-function getSaccharideComponentMap(format: mmCIF_Format): SaccharideComponentMap {
- const map = new Map<string, SaccharideComponent>();
- const { pdbx_chem_comp_identifier } = format.data
- if (pdbx_chem_comp_identifier._rowCount > 0) {
- const { comp_id, type, identifier } = pdbx_chem_comp_identifier
- for (let i = 0, il = pdbx_chem_comp_identifier._rowCount; i < il; ++i) {
- if (type.value(i) === 'SNFG CARB SYMBOL') {
- const snfgName = identifier.value(i)
- const saccharideComp = SaccharidesSnfgMap.get(snfgName)
- if (saccharideComp) {
- map.set(comp_id.value(i), saccharideComp)
- } else {
- console.warn(`Unknown SNFG name '${snfgName}'`)
- }
- }
- }
- } else if (format.data.chem_comp._rowCount > 0) {
- const { id, type } = format.data.chem_comp
- for (let i = 0, il = id.rowCount; i < il; ++i) {
- const _id = id.value(i)
- const _type = type.value(i)
- if (SaccharideCompIdMap.has(_id)) {
- map.set(_id, SaccharideCompIdMap.get(_id)!)
- } else if (!map.has(_id) && getMoleculeType(_type, _id) === MoleculeType.saccharide) {
- map.set(_id, UnknownSaccharideComponent)
- }
- }
- } else {
- // TODO check if present in format.data.atom_site.label_comp_id
- SaccharideCompIdMap.forEach((v, k) => map.set(k, v))
- }
- return map
-}
-
-export interface FormatData {
- modifiedResidues: Model['properties']['modifiedResidues']
- chemicalComponentMap: Model['properties']['chemicalComponentMap']
- saccharideComponentMap: Model['properties']['saccharideComponentMap']
-}
-
-function getFormatData(format: mmCIF_Format): FormatData {
- return {
- modifiedResidues: getModifiedResidueNameMap(format),
- chemicalComponentMap: getChemicalComponentMap(format),
- saccharideComponentMap: getSaccharideComponentMap(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,
- id: UUID.create22(),
- modelNum: atom_site.pdbx_PDB_model_num.value(0),
- atomicConformation: atomic.conformation,
- _dynamicPropertyData: Object.create(null)
- };
- }
-
- const coarse = EmptyIHMCoarse;
- const label = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
- ? format.data.entry.id.value(0)
- : format.data._name;
-
- return {
- id: UUID.create22(),
- label,
- sourceData: format,
- modelNum: atom_site.pdbx_PDB_model_num.value(0),
- entities,
- symmetry: getSymmetry(format),
- sequence: getSequence(format.data, entities, atomic.hierarchy, formatData.modifiedResidues.parentId),
- atomicHierarchy: atomic.hierarchy,
- atomicConformation: atomic.conformation,
- coarseHierarchy: coarse.hierarchy,
- coarseConformation: coarse.conformation,
- properties: {
- secondaryStructure: getSecondaryStructureMmCif(format.data, atomic.hierarchy),
- ...formatData
- },
- customProperties: new CustomProperties(),
- _staticPropertyData: Object.create(null),
- _dynamicPropertyData: Object.create(null)
- };
-}
-
-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.create22(),
- label: data.model_name,
- sourceData: format,
- modelNum: data.model_id,
- entities: data.entities,
- symmetry: getSymmetry(format),
- sequence: getSequence(format.data, data.entities, atomic.hierarchy, formatData.modifiedResidues.parentId),
- atomicHierarchy: atomic.hierarchy,
- atomicConformation: atomic.conformation,
- coarseHierarchy: coarse.hierarchy,
- coarseConformation: coarse.conformation,
- properties: {
- secondaryStructure: getSecondaryStructureMmCif(format.data, atomic.hierarchy),
- ...formatData
- },
- customProperties: new CustomProperties(),
- _staticPropertyData: Object.create(null),
- _dynamicPropertyData: Object.create(null)
- };
-}
-
-function attachProps(model: Model) {
- ComponentBond.attachFromMmCif(model);
- StructConn.attachFromMmCif(model);
-}
-
-function findModelEnd(num: Column<number>, startIndex: number) {
- const rowCount = num.rowCount;
- if (!num.isDefined) return rowCount;
- let endIndex = startIndex + 1;
- while (endIndex < rowCount && num.areValuesEqual(startIndex, endIndex)) endIndex++;
- return endIndex;
-}
-
-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 models: Model[] = [];
- let modelStart = 0;
- 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, formatData, models.length > 0 ? models[models.length - 1] : void 0);
- attachProps(model);
- models.push(model);
- modelStart = modelEnd;
- }
- return models;
-}
-
-function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
- const ret = new Map<number, T>()
- const rowCount = table._rowCount;
- let modelStart = 0;
- while (modelStart < rowCount) {
- const modelEnd = findModelEnd(col, modelStart);
- const id = col.value(modelStart);
- const window = Table.window(table, table._schema, modelStart, modelEnd) as T;
- ret.set(id, window);
- modelStart = modelEnd;
- }
- return ret;
-}
-
-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.ihm_model_id.isDefined) {
- throw new Error('expected _atom_site.ihm_model_id to be defined')
- }
-
- // TODO: will IHM require sorting or will we trust it?
- const atom_sites = splitTable(format.data.atom_site, format.data.atom_site.ihm_model_id);
- const sphere_sites = splitTable(format.data.ihm_sphere_obj_site, format.data.ihm_sphere_obj_site.model_id);
- const gauss_sites = splitTable(format.data.ihm_gaussian_obj_site, format.data.ihm_gaussian_obj_site.model_id);
-
- const models: Model[] = [];
-
- const { model_id, model_name } = ihm_model_list;
- for (let i = 0; i < ihm_model_list._rowCount; i++) {
- const id = model_id.value(i);
- const data: IHMData = {
- model_id: id,
- model_name: model_name.value(i),
- entities: entities,
- atom_site: atom_sites.has(id) ? atom_sites.get(id)! : Table.window(format.data.atom_site, format.data.atom_site._schema, 0, 0),
- 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, formatData);
- attachProps(model);
- models.push(model);
- }
-
- return models;
+export function trajecotryFromMmCIF(format: mmCIF_Format): Task<Model.Trajectory> {
+ return Task.create('Create mmCIF Model', ctx => _parse_mmCif(format, ctx));
}
\ No newline at end of file
diff --git a/src/mol-model-parsers/structure/mmcif/atomic.ts b/src/mol-model-parsers/structure/mmcif/atomic.ts
index 259933942c37b3615eae0ff08ae789b3ade7775e..7c4fbfbbfba1b8a266302d7bfbb2627186153ead 100644
--- a/src/mol-model-parsers/structure/mmcif/atomic.ts
+++ b/src/mol-model-parsers/structure/mmcif/atomic.ts
@@ -15,10 +15,10 @@ import { getAtomicIndex } from 'mol-model/structure/model/properties/utils/atomi
import { ElementSymbol } from 'mol-model/structure/model/types';
import { Entities } from 'mol-model/structure/model/properties/common';
import { getAtomicRanges } from 'mol-model/structure/model/properties/utils/atomic-ranges';
-import { FormatData } from '../mmcif';
import { getAtomicDerivedData } from 'mol-model/structure/model/properties/utils/atomic-derived';
import { ModelFormat } from '../format';
import mmCIF_Format = ModelFormat.mmCIF
+import { FormatData } from './parser';
type AtomSite = mmCIF_Database['atom_site']
diff --git a/src/mol-model-parsers/structure/mmcif/ihm.ts b/src/mol-model-parsers/structure/mmcif/ihm.ts
index 7ca51db554a8c12a6229e147e971684a451f66a1..731af9e3af83de9784c51bba90da32d0c15de777 100644
--- a/src/mol-model-parsers/structure/mmcif/ihm.ts
+++ b/src/mol-model-parsers/structure/mmcif/ihm.ts
@@ -14,7 +14,7 @@ import { Segmentation, Interval } from 'mol-data/int';
import { Mat3, Tensor } from 'mol-math/linear-algebra';
import { ElementIndex, ChainIndex } from 'mol-model/structure/model/indexing';
import { getCoarseRanges } from 'mol-model/structure/model/properties/utils/coarse-ranges';
-import { FormatData } from '../mmcif';
+import { FormatData } from './parser';
export interface IHMData {
model_id: number,
diff --git a/src/mol-model-parsers/structure/mmcif/parser.ts b/src/mol-model-parsers/structure/mmcif/parser.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a51afcb2787881faed93d3d3e48ffb94a744f69c
--- /dev/null
+++ b/src/mol-model-parsers/structure/mmcif/parser.ts
@@ -0,0 +1,306 @@
+/**
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Column, Table } from 'mol-data/db';
+import { mmCIF_Database, mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
+import { Spacegroup, SpacegroupCell, SymmetryOperator } from 'mol-math/geometry';
+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 { CustomProperties } from 'mol-model/structure/model/properties/custom';
+import { ModelSymmetry } from 'mol-model/structure/model/properties/symmetry';
+import { createAssemblies } from './assembly';
+import { getAtomicHierarchyAndConformation } from './atomic';
+import { ComponentBond } from './bonds';
+import { getIHMCoarse, EmptyIHMCoarse, IHMData } from './ihm';
+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 { ModelFormat } from '../format';
+import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, SaccharideCompIdMap, UnknownSaccharideComponent } from 'mol-model/structure/structure/carbohydrates/constants';
+import mmCIF_Format = ModelFormat.mmCIF
+
+export async function _parse_mmCif(format: mmCIF_Format, ctx: RuntimeContext) {
+ const formatData = getFormatData(format)
+ const isIHM = format.data.ihm_model_list._rowCount > 0;
+ return isIHM ? await readIHM(ctx, format, formatData) : await readStandard(ctx, format, formatData);
+}
+
+type AtomSite = mmCIF_Database['atom_site']
+
+function getSymmetry(format: mmCIF_Format): ModelSymmetry {
+ const assemblies = createAssemblies(format);
+ const spacegroup = getSpacegroup(format);
+ const isNonStandardCrytalFrame = checkNonStandardCrystalFrame(format, spacegroup);
+ return { assemblies, spacegroup, isNonStandardCrytalFrame, ncsOperators: getNcsOperators(format) };
+}
+
+function checkNonStandardCrystalFrame(format: mmCIF_Format, spacegroup: Spacegroup) {
+ const { atom_sites } = format.data;
+ if (atom_sites._rowCount === 0) return false;
+ // TODO: parse atom_sites transform and check if it corresponds to the toFractional matrix
+ return false;
+}
+
+function getSpacegroup(format: mmCIF_Format): Spacegroup {
+ const { symmetry, cell } = format.data;
+ if (symmetry._rowCount === 0 || cell._rowCount === 0) return Spacegroup.ZeroP1;
+ const groupName = symmetry['space_group_name_H-M'].value(0);
+ const spaceCell = SpacegroupCell.create(groupName,
+ Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)),
+ Vec3.scale(Vec3.zero(), Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
+
+ return Spacegroup.create(spaceCell);
+}
+
+function getNcsOperators(format: mmCIF_Format) {
+ const { struct_ncs_oper } = format.data;
+ if (struct_ncs_oper._rowCount === 0) return void 0;
+ const { id, matrix, vector } = struct_ncs_oper;
+
+ const matrixSpace = mmCIF_Schema.struct_ncs_oper.matrix.space, vectorSpace = mmCIF_Schema.struct_ncs_oper.vector.space;
+
+ const opers: SymmetryOperator[] = [];
+ for (let i = 0; i < struct_ncs_oper._rowCount; i++) {
+ const m = Tensor.toMat3(matrixSpace, matrix.value(i));
+ const v = Tensor.toVec3(vectorSpace, vector.value(i));
+ if (!SymmetryOperator.checkIfRotationAndTranslation(m, v)) continue;
+ opers[opers.length] = SymmetryOperator.ofRotationAndOffset(`ncs_${id.value(i)}`, m, v);
+ }
+ return opers;
+}
+function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['modifiedResidues'] {
+ const data = format.data.pdbx_struct_mod_residue;
+ const parentId = new Map<string, string>();
+ const details = new Map<string, string>();
+ const comp_id = data.label_comp_id.isDefined ? data.label_comp_id : data.auth_comp_id;
+ const parent_id = data.parent_comp_id, details_data = data.details;
+
+ for (let i = 0; i < data._rowCount; i++) {
+ const id = comp_id.value(i);
+ parentId.set(id, parent_id.value(i));
+ details.set(id, details_data.value(i));
+ }
+
+ return { parentId, details };
+}
+
+function getChemicalComponentMap(format: mmCIF_Format): ChemicalComponentMap {
+ const map = new Map<string, ChemicalComponent>();
+ const { id, type, name, pdbx_synonyms, formula, formula_weight } = format.data.chem_comp
+ for (let i = 0, il = id.rowCount; i < il; ++i) {
+ const _id = id.value(i)
+ const _type = type.value(i)
+ const cc: ChemicalComponent = {
+ id: _id,
+ type: ComponentType[_type],
+ moleculeType: getMoleculeType(_type, _id),
+ name: name.value(i),
+ synonyms: pdbx_synonyms.value(i),
+ formula: formula.value(i),
+ formulaWeight: formula_weight.value(i),
+ }
+ map.set(_id, cc)
+ }
+ return map
+}
+
+function getSaccharideComponentMap(format: mmCIF_Format): SaccharideComponentMap {
+ const map = new Map<string, SaccharideComponent>();
+ const { pdbx_chem_comp_identifier } = format.data
+ if (pdbx_chem_comp_identifier._rowCount > 0) {
+ const { comp_id, type, identifier } = pdbx_chem_comp_identifier
+ for (let i = 0, il = pdbx_chem_comp_identifier._rowCount; i < il; ++i) {
+ if (type.value(i) === 'SNFG CARB SYMBOL') {
+ const snfgName = identifier.value(i)
+ const saccharideComp = SaccharidesSnfgMap.get(snfgName)
+ if (saccharideComp) {
+ map.set(comp_id.value(i), saccharideComp)
+ } else {
+ console.warn(`Unknown SNFG name '${snfgName}'`)
+ }
+ }
+ }
+ } else if (format.data.chem_comp._rowCount > 0) {
+ const { id, type } = format.data.chem_comp
+ for (let i = 0, il = id.rowCount; i < il; ++i) {
+ const _id = id.value(i)
+ const _type = type.value(i)
+ if (SaccharideCompIdMap.has(_id)) {
+ map.set(_id, SaccharideCompIdMap.get(_id)!)
+ } else if (!map.has(_id) && getMoleculeType(_type, _id) === MoleculeType.saccharide) {
+ map.set(_id, UnknownSaccharideComponent)
+ }
+ }
+ } else {
+ // TODO check if present in format.data.atom_site.label_comp_id
+ SaccharideCompIdMap.forEach((v, k) => map.set(k, v))
+ }
+ return map
+}
+
+export interface FormatData {
+ modifiedResidues: Model['properties']['modifiedResidues']
+ chemicalComponentMap: Model['properties']['chemicalComponentMap']
+ saccharideComponentMap: Model['properties']['saccharideComponentMap']
+}
+
+function getFormatData(format: mmCIF_Format): FormatData {
+ return {
+ modifiedResidues: getModifiedResidueNameMap(format),
+ chemicalComponentMap: getChemicalComponentMap(format),
+ saccharideComponentMap: getSaccharideComponentMap(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,
+ id: UUID.create22(),
+ modelNum: atom_site.pdbx_PDB_model_num.value(0),
+ atomicConformation: atomic.conformation,
+ _dynamicPropertyData: Object.create(null)
+ };
+ }
+
+ const coarse = EmptyIHMCoarse;
+ const label = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
+ ? format.data.entry.id.value(0)
+ : format.data._name;
+
+ return {
+ id: UUID.create22(),
+ label,
+ sourceData: format,
+ modelNum: atom_site.pdbx_PDB_model_num.value(0),
+ entities,
+ symmetry: getSymmetry(format),
+ sequence: getSequence(format.data, entities, atomic.hierarchy, formatData.modifiedResidues.parentId),
+ atomicHierarchy: atomic.hierarchy,
+ atomicConformation: atomic.conformation,
+ coarseHierarchy: coarse.hierarchy,
+ coarseConformation: coarse.conformation,
+ properties: {
+ secondaryStructure: getSecondaryStructureMmCif(format.data, atomic.hierarchy),
+ ...formatData
+ },
+ customProperties: new CustomProperties(),
+ _staticPropertyData: Object.create(null),
+ _dynamicPropertyData: Object.create(null)
+ };
+}
+
+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.create22(),
+ label: data.model_name,
+ sourceData: format,
+ modelNum: data.model_id,
+ entities: data.entities,
+ symmetry: getSymmetry(format),
+ sequence: getSequence(format.data, data.entities, atomic.hierarchy, formatData.modifiedResidues.parentId),
+ atomicHierarchy: atomic.hierarchy,
+ atomicConformation: atomic.conformation,
+ coarseHierarchy: coarse.hierarchy,
+ coarseConformation: coarse.conformation,
+ properties: {
+ secondaryStructure: getSecondaryStructureMmCif(format.data, atomic.hierarchy),
+ ...formatData
+ },
+ customProperties: new CustomProperties(),
+ _staticPropertyData: Object.create(null),
+ _dynamicPropertyData: Object.create(null)
+ };
+}
+
+function attachProps(model: Model) {
+ ComponentBond.attachFromMmCif(model);
+ StructConn.attachFromMmCif(model);
+}
+
+function findModelEnd(num: Column<number>, startIndex: number) {
+ const rowCount = num.rowCount;
+ if (!num.isDefined) return rowCount;
+ let endIndex = startIndex + 1;
+ while (endIndex < rowCount && num.areValuesEqual(startIndex, endIndex)) endIndex++;
+ return endIndex;
+}
+
+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 models: Model[] = [];
+ let modelStart = 0;
+ 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, formatData, models.length > 0 ? models[models.length - 1] : void 0);
+ attachProps(model);
+ models.push(model);
+ modelStart = modelEnd;
+ }
+ return models;
+}
+
+function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
+ const ret = new Map<number, T>()
+ const rowCount = table._rowCount;
+ let modelStart = 0;
+ while (modelStart < rowCount) {
+ const modelEnd = findModelEnd(col, modelStart);
+ const id = col.value(modelStart);
+ const window = Table.window(table, table._schema, modelStart, modelEnd) as T;
+ ret.set(id, window);
+ modelStart = modelEnd;
+ }
+ return ret;
+}
+
+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.ihm_model_id.isDefined) {
+ throw new Error('expected _atom_site.ihm_model_id to be defined')
+ }
+
+ // TODO: will IHM require sorting or will we trust it?
+ const atom_sites = splitTable(format.data.atom_site, format.data.atom_site.ihm_model_id);
+ const sphere_sites = splitTable(format.data.ihm_sphere_obj_site, format.data.ihm_sphere_obj_site.model_id);
+ const gauss_sites = splitTable(format.data.ihm_gaussian_obj_site, format.data.ihm_gaussian_obj_site.model_id);
+
+ const models: Model[] = [];
+
+ const { model_id, model_name } = ihm_model_list;
+ for (let i = 0; i < ihm_model_list._rowCount; i++) {
+ const id = model_id.value(i);
+ const data: IHMData = {
+ model_id: id,
+ model_name: model_name.value(i),
+ entities: entities,
+ atom_site: atom_sites.has(id) ? atom_sites.get(id)! : Table.window(format.data.atom_site, format.data.atom_site._schema, 0, 0),
+ 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, formatData);
+ attachProps(model);
+ models.push(model);
+ }
+
+ return models;
+}
\ No newline at end of file
diff --git a/src/mol-model-parsers/structure/pdb.ts b/src/mol-model-parsers/structure/pdb.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a8695876900d671bf514d1c8ec01872fdcfbae31
--- /dev/null
+++ b/src/mol-model-parsers/structure/pdb.ts
@@ -0,0 +1,21 @@
+/**
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PdbFile } from 'mol-io/reader/pdb/schema';
+import { pdbToMmCif } from './pdb/to-cif';
+import { Model } from 'mol-model/structure/model';
+import { Task } from 'mol-task';
+import { ModelFormat } from './format';
+import { _parse_mmCif } from './mmcif/parser';
+
+export function trajectoryFromPDB(pdb: PdbFile): Task<Model.Trajectory> {
+ return Task.create('Parse PDB', async ctx => {
+ await ctx.update('Converting to mmCIF');
+ const cif = await pdbToMmCif(pdb);
+ const format = ModelFormat.mmCIF(cif);
+ return _parse_mmCif(format, ctx);
+ })
+}
diff --git a/src/mol-io/reader/pdb/to-cif.ts b/src/mol-model-parsers/structure/pdb/to-cif.ts
similarity index 92%
rename from src/mol-io/reader/pdb/to-cif.ts
rename to src/mol-model-parsers/structure/pdb/to-cif.ts
index c6862994be0c603ce22227635e62d292ec10c03f..799ab8c9a4ed7b7240a38c1134f9e2d6b30abe48 100644
--- a/src/mol-io/reader/pdb/to-cif.ts
+++ b/src/mol-model-parsers/structure/pdb/to-cif.ts
@@ -4,13 +4,11 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { CifField, CifCategory } from '../cif';
-import { mmCIF_Schema } from '../cif/schema/mmcif';
-import { TokenBuilder, Tokenizer } from '../common/text/tokenizer';
-import { PdbFile } from './schema';
-import { CifFile } from '../cif/data-model';
import { substringStartsWith } from 'mol-util/string';
-import { Task } from 'mol-task';
+import { CifField, CifCategory, CifFrame } from 'mol-io/reader/cif';
+import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
+import { TokenBuilder, Tokenizer } from 'mol-io/reader/common/text/tokenizer';
+import { PdbFile } from 'mol-io/reader/pdb/schema';
function toCategory(name: string, fields: { [name: string]: CifField | undefined }, rowCount: number): CifCategory {
return {
@@ -208,7 +206,7 @@ function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer, s: num
sites.index++;
}
-async function pdbToMmCIF(pdb: PdbFile): Promise<CifFile> {
+export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
const { lines } = pdb;
const { data, indices } = lines;
const tokenizer = Tokenizer(data);
@@ -260,19 +258,8 @@ async function pdbToMmCIF(pdb: PdbFile): Promise<CifFile> {
}
return {
- name: pdb.id,
- blocks: [{
- saveFrames: [],
- header: pdb.id || 'PDB',
- categoryNames: Object.keys(categories),
- categories
- }]
+ header: pdb.id || 'PDB',
+ categoryNames: Object.keys(categories),
+ categories
};
-}
-
-export function convertPDBtoMmCif(pdb: PdbFile): Task<CifFile> {
- return Task.create('Convert PDB to mmCIF', async ctx => {
- await ctx.update('Converting to mmCIF...');
- return pdbToMmCIF(pdb);
- });
}
\ No newline at end of file
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index 48c855fbcc57c4d8e3892d0715c743aee30c30b6..483e317e3e5edf2ee7ed63d51253082a772b520c 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -94,7 +94,7 @@ export const OpenStructure = StateAction.build({
function createModelTree(b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, format: 'pdb' | 'cif' = 'cif') {
const parsed = format === 'cif'
? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
- : b.apply(StateTransforms.Data.ConvertPDBtoMmCif).apply(StateTransforms.Model.TrajectoryFromMmCif);
+ : b.apply(StateTransforms.Model.TrajectoryFromPDB);
return parsed.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 });
}
diff --git a/src/mol-plugin/state/transforms/data.ts b/src/mol-plugin/state/transforms/data.ts
index c8395300b2d6b25a0e000220390ef33b51b0949f..59ed1b3a0d9e8e3eb3fb6fb615a4a3bfbb18b017 100644
--- a/src/mol-plugin/state/transforms/data.ts
+++ b/src/mol-plugin/state/transforms/data.ts
@@ -15,8 +15,6 @@ import { Transformer } from 'mol-state';
import { readFromFile } from 'mol-util/data-source';
import * as CCP4 from 'mol-io/reader/ccp4/parser'
import * as DSN6 from 'mol-io/reader/dsn6/parser'
-import { parsePDB } from 'mol-io/reader/pdb/parser';
-import { convertPDBtoMmCif } from 'mol-io/reader/pdb/to-cif';
export { Download }
type Download = typeof Download
@@ -97,24 +95,6 @@ const ParseCif = PluginStateTransform.BuiltIn({
}
});
-export { ConvertPDBtoMmCif }
-type ConvertPDBtoMmCif = typeof ConvertPDBtoMmCif
-const ConvertPDBtoMmCif = PluginStateTransform.BuiltIn({
- name: 'convert-pdb-to-mmcif',
- display: { name: 'Convert PDB string to mmCIF' },
- from: [SO.Data.String],
- to: SO.Format.Cif
-})({
- apply({ a }) {
- return Task.create('Parse CIF', async ctx => {
- const parsed = await parsePDB(a.data).runInContext(ctx);
- if (parsed.isError) throw new Error(parsed.message);
- const cif = await convertPDBtoMmCif(parsed.result).runInContext(ctx);
- return new SO.Format.Cif(cif);
- });
- }
-});
-
export { ParseCcp4 }
type ParseCcp4 = typeof ParseCcp4
const ParseCcp4 = PluginStateTransform.BuiltIn({
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 7f1dedacf625f8ea13f13e0f0f744f719412520b..1d2a96e8c8bf1e0de221251c0d0cb0ad6a97cc1d 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -19,8 +19,10 @@ import { stringToWords } from 'mol-util/string';
import { volumeFromCcp4 } from 'mol-model/volume/formats/ccp4';
import { Vec3 } from 'mol-math/linear-algebra';
import { volumeFromDsn6 } from 'mol-model/volume/formats/dsn6';
-import { parse_mmCIF } from 'mol-model-parsers/structure/mmcif';
+import { trajecotryFromMmCIF } from 'mol-model-parsers/structure/mmcif';
import { ModelFormat } from 'mol-model-parsers/structure/format';
+import { parsePDB } from 'mol-io/reader/pdb/parser';
+import { trajectoryFromPDB } from 'mol-model-parsers/structure/pdb';
export { TrajectoryFromMmCif }
type TrajectoryFromMmCif = typeof TrajectoryFromMmCif
@@ -47,7 +49,7 @@ const TrajectoryFromMmCif = PluginStateTransform.BuiltIn({
const header = params.blockHeader || a.data.blocks[0].header;
const block = a.data.blocks.find(b => b.header === header);
if (!block) throw new Error(`Data block '${[header]}' not found.`);
- const models = await parse_mmCIF(ModelFormat.mmCIF(block)).runInContext(ctx);
+ const models = await trajecotryFromMmCIF(ModelFormat.mmCIF(block)).runInContext(ctx);
if (models.length === 0) throw new Error('No models found.');
const props = { label: models[0].label, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
return new SO.Molecule.Trajectory(models, props);
@@ -55,6 +57,27 @@ const TrajectoryFromMmCif = PluginStateTransform.BuiltIn({
}
});
+
+export { TrajectoryFromPDB }
+type TrajectoryFromPDB = typeof TrajectoryFromPDB
+const TrajectoryFromPDB = PluginStateTransform.BuiltIn({
+ name: 'trajectory-from-pdb',
+ display: { name: 'Parse PDB string and create trajectory' },
+ from: [SO.Data.String],
+ to: SO.Molecule.Trajectory
+})({
+ apply({ a }) {
+ return Task.create('Parse PDB', async ctx => {
+ const parsed = await parsePDB(a.data).runInContext(ctx);
+ if (parsed.isError) throw new Error(parsed.message);
+ const models = await trajectoryFromPDB(parsed.result).runInContext(ctx);
+ const props = { label: models[0].label, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+ return new SO.Molecule.Trajectory(models, props);
+ });
+ }
+});
+
+
export { ModelFromTrajectory }
const plus1 = (v: number) => v + 1, minus1 = (v: number) => v - 1;
type ModelFromTrajectory = typeof ModelFromTrajectory
diff --git a/src/perf-tests/lookup3d.ts b/src/perf-tests/lookup3d.ts
index b74a2d4bbea45f2986085e1701ab3a2358d593e8..fb75917fc0d9299310e6c4c79ef5c673f1cd03cd 100644
--- a/src/perf-tests/lookup3d.ts
+++ b/src/perf-tests/lookup3d.ts
@@ -8,7 +8,7 @@ import { GridLookup3D } from 'mol-math/geometry';
// import { sortArray } from 'mol-data/util';
import { OrderedSet } from 'mol-data/int';
import { ModelFormat } from 'mol-model-parsers/structure/format';
-import { parse_mmCIF } from 'mol-model-parsers/structure/mmcif';
+import { trajecotryFromMmCIF } from 'mol-model-parsers/structure/mmcif';
require('util.promisify').shim();
const readFileAsync = util.promisify(fs.readFile);
@@ -34,7 +34,7 @@ export async function readCIF(path: string) {
}
const mmcif = ModelFormat.mmCIF(parsed.result.blocks[0]);
- const models = await parse_mmCIF(mmcif).run();
+ const models = await trajecotryFromMmCIF(mmcif).run();
const structures = models.map(Structure.ofModel);
return { mmcif: mmcif.data, models, structures };
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 91c326e4efc2dfc62037e9586d45923ec6f97928..60f485c27ecc8ead2305c85ee7f45973f16b28be 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -17,7 +17,7 @@ import { Structure, Model, Queries as Q, StructureElement, StructureSelection, S
import to_mmCIF from 'mol-model/structure/export/mmcif'
import { Vec3 } from 'mol-math/linear-algebra';
import { ModelFormat } from 'mol-model-parsers/structure/format';
-import { parse_mmCIF } from 'mol-model-parsers/structure/mmcif';
+import { trajecotryFromMmCIF } from 'mol-model-parsers/structure/mmcif';
// import { printUnits } from 'apps/structure-info/model';
// import { EquivalenceClasses } from 'mol-data/util';
@@ -76,7 +76,7 @@ export async function readCIF(path: string) {
console.timeEnd('schema')
console.time('buildModels')
- const models = await parse_mmCIF(mmcif).run();
+ const models = await trajecotryFromMmCIF(mmcif).run();
console.timeEnd('buildModels')
const structures = models.map(Structure.ofModel);
diff --git a/src/servers/model/server/structure-wrapper.ts b/src/servers/model/server/structure-wrapper.ts
index 2e9944c5161d0ad4a31f953cdefc4306361b8e2b..b124bdd2869147a7aae429cb2487cabbe7243969 100644
--- a/src/servers/model/server/structure-wrapper.ts
+++ b/src/servers/model/server/structure-wrapper.ts
@@ -15,7 +15,7 @@ import * as zlib from 'zlib'
import { Job } from './jobs';
import { ConsoleLogger } from 'mol-util/console-logger';
import { ModelPropertiesProvider } from '../property-provider';
-import { parse_mmCIF } from 'mol-model-parsers/structure/mmcif';
+import { trajecotryFromMmCIF } from 'mol-model-parsers/structure/mmcif';
import { ModelFormat } from 'mol-model-parsers/structure/format';
require('util.promisify').shim();
@@ -110,7 +110,7 @@ export async function readStructureWrapper(key: string, sourceId: string | '_loc
const frame = (await parseCif(data)).blocks[0];
perf.end('parse');
perf.start('createModel');
- const models = await parse_mmCIF(ModelFormat.mmCIF(frame)).run();
+ const models = await trajecotryFromMmCIF(ModelFormat.mmCIF(frame)).run();
perf.end('createModel');
const modelMap = new Map<number, Model>();