improved gro format reading

src/mol-model-formats/structure/common/component.ts

@@ -0,0 +1,151 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { _parse_mmCif } from '../mmcif/parser';
+import { CifCategory, CifField } from '../../../mol-io/reader/cif';
+import { Table, Column } from '../../../mol-data/db';
+import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
+import { WaterNames } from '../../../mol-model/structure/model/types';
+import { SetUtils } from '../../../mol-util/set';
+
+type Component = Table.Row<Pick<mmCIF_Schema['chem_comp'], 'id' | 'name' | 'type'>>
+
+const ProteinAtomIdsList = [
+    new Set([ 'CA' ]),
+    new Set([ 'C' ]),
+    new Set([ 'N' ])
+]
+const RnaAtomIdsList = [
+    new Set([ 'P', 'O3\'', 'O3*' ]),
+    new Set([ 'C4\'', 'C4*' ]),
+    new Set([ 'O2\'', 'O2*', 'F2\'', 'F2*' ])
+]
+const DnaAtomIdsList = [
+    new Set([ 'P', 'O3\'', 'O3*' ]),
+    new Set([ 'C3\'', 'C3*' ]),
+    new Set([ 'O2\'', 'O2*', 'F2\'', 'F2*' ])
+]
+
+const StandardComponents = (function() {
+    const map = new Map<string, Component>()
+    const components: Component[] = [
+        { id: 'HIS', name: 'HISTIDINE', type: 'L-peptide linking' },
+        { id: 'ARG', name: 'ARGININE', type: 'L-peptide linking' },
+        { id: 'LYS', name: 'LYSINE', type: 'L-peptide linking' },
+        { id: 'ILE', name: 'ISOLEUCINE', type: 'L-peptide linking' },
+        { id: 'PHE', name: 'PHENYLALANINE', type: 'L-peptide linking' },
+        { id: 'LEU', name: 'LEUCINE', type: 'L-peptide linking' },
+        { id: 'TRP', name: 'TRYPTOPHAN', type: 'L-peptide linking' },
+        { id: 'ALA', name: 'ALANINE', type: 'L-peptide linking' },
+        { id: 'MET', name: 'METHIONINE', type: 'L-peptide linking' },
+        { id: 'CYS', name: 'CYSTEINE', type: 'L-peptide linking' },
+        { id: 'ASN', name: 'ASPARAGINE', type: 'L-peptide linking' },
+        { id: 'VAL', name: 'VALINE', type: 'L-peptide linking' },
+        { id: 'GLY', name: 'GLYCINE', type: 'peptide linking' },
+        { id: 'SER', name: 'SERINE', type: 'L-peptide linking' },
+        { id: 'GLN', name: 'GLUTAMINE', type: 'L-peptide linking' },
+        { id: 'TYR', name: 'TYROSINE', type: 'L-peptide linking' },
+        { id: 'ASP', name: 'ASPARTIC ACID', type: 'L-peptide linking' },
+        { id: 'GLU', name: 'GLUTAMIC ACID', type: 'L-peptide linking' },
+        { id: 'THR', name: 'THREONINE', type: 'L-peptide linking' },
+        { id: 'SEC', name: 'SELENOCYSTEINE', type: 'L-peptide linking' },
+        { id: 'PYL', name: 'PYRROLYSINE', type: 'L-peptide linking' },
+
+        { id: 'A', name: 'ADENOSINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
+        { id: 'C', name: 'CYTIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
+        { id: 'T', name: 'THYMIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
+        { id: 'G', name: 'GUANOSINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
+        { id: 'I', name: 'INOSINIC ACID', type: 'RNA linking' },
+        { id: 'U', name: 'URIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
+
+        { id: 'DA', name: '2\'-DEOXYADENOSINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
+        { id: 'DC', name: '2\'-DEOXYCYTIDINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
+        { id: 'DT', name: 'THYMIDINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
+        { id: 'DG', name: '2\'-DEOXYGUANOSINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
+        { id: 'DI', name: '2\'-DEOXYINOSINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
+        { id: 'DU', name: '2\'-DEOXYURIDINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
+    ]
+    components.forEach(c => map.set(c.id, c))
+    return map
+})()
+
+export class ComponentBuilder {
+    private comps = new Map<string, Component>()
+    private ids: string[] = []
+    private names: string[] = []
+    private types: mmCIF_Schema['chem_comp']['type']['T'][] = []
+
+    private set(c: Component) {
+        this.comps.set(c.id, c)
+        this.ids.push(c.id)
+        this.names.push(c.name)
+        this.types.push(c.type)
+    }
+
+    private getAtomIds(index: number) {
+        const atomIds = new Set<string>()
+        let prevSeqId = this.seqId.value(index)
+        while (index < this.seqId.rowCount) {
+            const seqId = this.seqId.value(index)
+            if (seqId !== prevSeqId) break
+            atomIds.add(this.atomId.value(index))
+            prevSeqId - seqId
+            index += 1
+        }
+        return atomIds
+    }
+
+    private hasAtomIds (atomIds: Set<string>, atomIdsList: Set<string>[]) {
+        for (let i = 0, il = atomIdsList.length; i < il; ++i) {
+            if (!SetUtils.areIntersecting(atomIds, atomIdsList[i])) {
+                return false
+            }
+        }
+        return true
+    }
+
+    private getType(atomIds: Set<string>): Component['type'] {
+        if (this.hasAtomIds(atomIds, ProteinAtomIdsList)) {
+            return 'peptide linking'
+        } else if (this.hasAtomIds(atomIds, RnaAtomIdsList)) {
+            return 'RNA linking'
+        } else if (this.hasAtomIds(atomIds, DnaAtomIdsList)) {
+            return 'DNA linking'
+        } else {
+            return 'other'
+        }
+    }
+
+    has(compId: string) { return this.comps.has(compId) }
+    get(compId: string) { return this.comps.get(compId) }
+
+    add(compId: string, index: number) {
+        if (!this.has(compId)) {
+            if (StandardComponents.has(compId)) {
+                this.set(StandardComponents.get(compId)!)
+            } else if (WaterNames.has(compId)) {
+                this.set({ id: compId, name: 'WATER', type: 'non-polymer' })
+            } else {
+                const atomIds = this.getAtomIds(index)
+                this.set({ id: compId, name: compId, type: this.getType(atomIds) })
+            }
+        }
+        return this.get(compId)!
+    }
+
+    getChemCompCategory() {
+        const chemComp: CifCategory.SomeFields<mmCIF_Schema['chem_comp']> = {
+            id: CifField.ofStrings(this.ids),
+            name: CifField.ofStrings(this.names),
+            type: CifField.ofStrings(this.types),
+        }
+        return CifCategory.ofFields('chem_comp', chemComp)
+    }
+
+    constructor(private seqId: Column<number>, private atomId: Column<string>) {
+
+    }
+}

src/mol-model-formats/structure/common/util.ts

@@ -0,0 +1,27 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { memoize1 } from '../../../mol-util/memoize';
+
+const ChainIdAlphabet = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+
+function _getChainId (index: number) {
+    const n = ChainIdAlphabet.length
+    let j = index
+    let k = 0
+    let chainId = ChainIdAlphabet[j % n]
+    while (j >= n) {
+        j = Math.floor(j / n)
+        chainId += ChainIdAlphabet[j % n]
+        k += 1
+    }
+    if (k >= 5) {
+        console.warn('getChainId overflow')
+    }
+    return chainId
+}
+
+export const getChainId = memoize1(_getChainId)

src/mol-model-formats/structure/gro.ts

@@ -13,62 +13,151 @@ import { CifCategory, CifField } from '../../mol-io/reader/cif';
 import { Column } from '../../mol-data/db';
 import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
 import { guessElementSymbolString } from './util';
+import { MoleculeType, getMoleculeType, isPolymer } from '../../mol-model/structure/model/types';
+import { ComponentBuilder } from './common/component';
+import { getChainId } from './common/util';
 
 // TODO multi model files
-// TODO seperate chains
-// TODO better entity handling
-// TODO improve performance
 
-function _entity(): { [K in keyof mmCIF_Schema['entity']]?: CifField } {
-    return {
-        id: CifField.ofStrings(['1', '2', '3']),
-        type: CifField.ofStrings(['polymer', 'non-polymer', 'water'])
+class EntityBuilder {
+    private count = 0
+    private ids: string[] = []
+    private types: string[] = []
+    private descriptions: string[] = []
+
+    private heteroMap = new Map<string, string>()
+    private chainMap = new Map<string, string>()
+    private waterId?: string
+
+    private set(type: string, description: string) {
+        this.count += 1
+        this.ids.push(`${this.count}`)
+        this.types.push(type)
+        this.descriptions.push(description)
+    }
+
+    getEntityId(compId: string, moleculeType: MoleculeType, chainId: string): string {
+        if (moleculeType === MoleculeType.water) {
+            if (this.waterId === undefined) {
+                this.set('water', 'Water')
+                this.waterId = `${this.count}`
+            }
+            return this.waterId;
+        } else if (isPolymer(moleculeType)) {
+            if (!this.chainMap.has(chainId)) {
+                this.set('polymer', `Polymer ${this.chainMap.size + 1}`)
+                this.chainMap.set(chainId, `${this.count}`)
+            }
+            return this.chainMap.get(chainId)!
+        } else {
+            if (!this.heteroMap.has(compId)) {
+                this.set('non-polymer', compId)
+                this.heteroMap.set(compId, `${this.count}`)
+            }
+            return this.heteroMap.get(compId)!
+        }
+    }
+
+    getEntityCategory() {
+        const entity: CifCategory.SomeFields<mmCIF_Schema['entity']> = {
+            id: CifField.ofStrings(this.ids),
+            type: CifField.ofStrings(this.types),
+            pdbx_description: CifField.ofStrings(this.descriptions),
+        }
+        return CifCategory.ofFields('entity', entity)
     }
 }
 
-function _atom_site(atoms: GroAtoms): { [K in keyof mmCIF_Schema['atom_site']]?: CifField } {
-    const auth_asym_id = CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str))
+function getCategories(atoms: GroAtoms) {
     const auth_atom_id = CifField.ofColumn(atoms.atomName)
     const auth_comp_id = CifField.ofColumn(atoms.residueName)
-    const auth_seq_id = CifField.ofColumn(atoms.residueNumber)
 
-    return {
+    const entityIds = new Array<string>(atoms.count)
+    const asymIds = new Array<string>(atoms.count)
+    const seqIds = new Uint32Array(atoms.count)
+    const ids = new Uint32Array(atoms.count)
+
+    const entityBuilder = new EntityBuilder()
+    const componentBuilder = new ComponentBuilder(atoms.residueNumber, atoms.atomName)
+
+    let currentEntityId = ''
+    let currentAsymIndex = 0
+    let currentAsymId = ''
+    let currentSeqId = 0
+    let prevMoleculeType = MoleculeType.unknown
+    let prevResidueNumber = -1
+
+    for (let i = 0, il = atoms.count; i < il; ++i) {
+        const residueNumber = atoms.residueNumber.value(i)
+        if (residueNumber !== prevResidueNumber) {
+            const compId = atoms.residueName.value(i)
+            const moleculeType = getMoleculeType(componentBuilder.add(compId, i).type, compId)
+
+            if (moleculeType !== prevMoleculeType || (
+                residueNumber !== prevResidueNumber + 1 && !(
+                    // gro format allows only for 5 character residueNumbers, handle overflow here
+                    prevResidueNumber === 99999 && residueNumber === 0
+                )
+            )) {
+                currentAsymId = getChainId(currentAsymIndex)
+                currentAsymIndex += 1
+                currentSeqId = 0
+            }
+
+            currentEntityId = entityBuilder.getEntityId(compId, moleculeType, currentAsymId)
+            currentSeqId += 1
+
+            prevResidueNumber = residueNumber
+            prevMoleculeType = moleculeType
+        }
+
+        entityIds[i] = currentEntityId
+        asymIds[i] = currentAsymId
+        seqIds[i] = currentSeqId
+        ids[i] = i
+    }
+
+    const auth_asym_id = CifField.ofColumn(Column.ofStringArray(asymIds))
+
+    const atom_site: CifCategory.SomeFields<mmCIF_Schema['atom_site']> = {
         auth_asym_id,
         auth_atom_id,
         auth_comp_id,
-        auth_seq_id,
+        auth_seq_id: CifField.ofColumn(atoms.residueNumber),
         B_iso_or_equiv: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.float)),
         Cartn_x: CifField.ofNumbers(Column.mapToArray(atoms.x, x => x * 10, Float32Array)),
         Cartn_y: CifField.ofNumbers(Column.mapToArray(atoms.y, y => y * 10, Float32Array)),
         Cartn_z: CifField.ofNumbers(Column.mapToArray(atoms.z, z => z * 10, Float32Array)),
         group_PDB: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
-        id: CifField.ofColumn(atoms.atomNumber),
+        id: CifField.ofColumn(Column.ofIntArray(ids)),
 
         label_alt_id: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
 
         label_asym_id: auth_asym_id,
         label_atom_id: auth_atom_id,
         label_comp_id: auth_comp_id,
-        label_seq_id: auth_seq_id,
-        label_entity_id: CifField.ofColumn(Column.ofConst('1', atoms.count, Column.Schema.str)),
+        label_seq_id: CifField.ofColumn(Column.ofIntArray(seqIds)),
+        label_entity_id: CifField.ofColumn(Column.ofStringArray(entityIds)),
 
         occupancy: CifField.ofColumn(Column.ofConst(1, atoms.count, Column.Schema.float)),
         type_symbol: CifField.ofStrings(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
-        // type_symbol: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
 
         pdbx_PDB_ins_code: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
         pdbx_PDB_model_num: CifField.ofColumn(Column.ofConst('1', atoms.count, Column.Schema.str)),
     }
+
+    return {
+        entity: entityBuilder.getEntityCategory(),
+        chem_comp: componentBuilder.getChemCompCategory(),
+        atom_site: CifCategory.ofFields('atom_site', atom_site)
+    }
 }
 
 async function groToMmCif(gro: GroFile) {
-    const categories = {
-        entity: CifCategory.ofFields('entity', _entity()),
-        atom_site: CifCategory.ofFields('atom_site', _atom_site(gro.structures[0].atoms))
-    } as any;
+    const categories = getCategories(gro.structures[0].atoms)
 
     return {
-        header: 'GRO',
+        header: gro.structures[0].header.title,
         categoryNames: Object.keys(categories),
         categories
     };

src/mol-model-formats/structure/pdb/entity.ts

@@ -81,7 +81,7 @@ export class EntityBuilder {
     private chainMap = new Map<string, string>()
     private waterId?: string
 
-    private add(type: string, description: string) {
+    private set(type: string, description: string) {
         this.count += 1
         this.ids.push(`${this.count}`)
         this.types.push(type)
@@ -92,13 +92,13 @@ export class EntityBuilder {
         if (isHet) {
             if (WaterNames.has(residueName)) {
                 if (this.waterId === undefined) {
-                    this.add('water', 'Water')
+                    this.set('water', 'Water')
                     this.waterId = `${this.count}`
                 }
                 return this.waterId;
             } else {
                 if (!this.heteroMap.has(residueName)) {
-                    this.add('non-polymer', residueName)
+                    this.set('non-polymer', residueName)
                     this.heteroMap.set(residueName, `${this.count}`)
                 }
                 return this.heteroMap.get(residueName)!
@@ -107,7 +107,7 @@ export class EntityBuilder {
             return this.compoundsMap.get(chainId)!
         } else {
             if (!this.chainMap.has(chainId)) {
-                this.add('polymer', chainId)
+                this.set('polymer', chainId)
                 this.chainMap.set(chainId, `${this.count}`)
             }
             return this.chainMap.get(chainId)!
@@ -126,7 +126,7 @@ export class EntityBuilder {
     setCompounds(compounds: Compound[]) {
         for (let i = 0, il = compounds.length; i < il; ++i) {
             const { chains, name } = compounds[i]
-            this.add('polymer', name)
+            this.set('polymer', name)
             for (let j = 0, jl = chains.length; j < jl; ++j) {
                 this.compoundsMap.set(chains[j], `${this.count}`)
             }

src/mol-model/structure/model/properties/atomic/hierarchy.ts

@@ -238,4 +238,8 @@ export namespace AtomicHierarchy {
     export function chainEndResidueIndexExcl(segs: AtomicSegments, cI: ChainIndex) {
         return segs.residueAtomSegments.index[segs.chainAtomSegments.offsets[cI + 1] - 1] + 1 as ResidueIndex;
     }
+
+    export function chainResidueCount(segs: AtomicSegments, cI: ChainIndex) {
+        return chainEndResidueIndexExcl(segs, cI) - chainStartResidueIndex(segs, cI)
+    }
 }

src/mol-model/structure/model/properties/utils/atomic-derived.ts

@@ -31,6 +31,7 @@ export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemi
             molType = getMoleculeType(chemCompMap.get(compId)!.type, compId)
             moleculeTypeMap.set(compId, molType)
         } else {
+            console.log('chemComp not found', compId)
             molType = getMoleculeType(getComponentType(compId), compId)
             // TODO if unknown molecule type, use atom names to guess molecule type
             moleculeTypeMap.set(compId, molType)

src/mol-model/structure/model/types.ts

@@ -185,6 +185,8 @@ export const BaseNames = SetUtils.unionMany(RnaBaseNames, DnaBaseNames, PeptideB
 export const isPurineBase = (compId: string) => PurineBaseNames.has(compId.toUpperCase())
 export const isPyrimidineBase = (compId: string) => PyrimidineBaseNames.has(compId.toUpperCase())
 
+export const PolymerNames = SetUtils.unionMany(AminoAcidNames, BaseNames)
+
 /** get the molecule type from component type and id */
 export function getMoleculeType(compType: string, compId: string) {
     compType = compType.toUpperCase()
@@ -227,12 +229,12 @@ export function getComponentType(compId: string): mmCIF_Schema['chem_comp']['typ
 
 export function getEntityType(compId: string): mmCIF_Schema['entity']['type']['T'] {
     compId = compId.toUpperCase()
-    if (AminoAcidNames.has(compId) || RnaBaseNames.has(compId) || DnaBaseNames.has(compId)) {
+    if (WaterNames.has(compId)) {
+        return 'water'
+    } else if (PolymerNames.has(compId)) {
         return 'polymer'
     } else if (SaccharideCompIdMap.has(compId)) {
         return 'branched'
-    } else if (WaterNames.has(compId)) {
-        return 'water'
     } else {
         return 'non-polymer'
     }

src/mol-util/set.ts

@@ -50,6 +50,13 @@ export namespace SetUtils {
         return intersection;
     }
 
+    export function areIntersecting<T>(setA: Set<T>, setB: Set<T>): boolean {
+        for (const elem of Array.from(setB)) {
+            if (setA.has(elem)) return true;
+        }
+        return false;
+    }
+
     /** Create set containing elements of set a that are not in set b. */
     export function difference<T>(setA: Set<T>, setB: Set<T>): Set<T> {
         const difference = new Set(setA);