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Commit 9b1c299d authored by Alexander Rose's avatar Alexander Rose
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pair-restraint cleanup & fixes

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src/mol-model/structure/model/formats/mmcif/pair-restraint.ts
+ 2
− 151
View file @ 9b1c299d
......@@ -4,154 +4,5 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
// ihm_predicted_contact_restraint: {
// id: int,
// entity_id_1: str,
// entity_id_2: str,
// asym_id_1: str,
// asym_id_2: str,
// comp_id_1: str,
// comp_id_2: str,
// seq_id_1: int,
// seq_id_2: int,
// atom_id_1: str,
// atom_id_2: str,
// distance_upper_limit: float,
// probability: float,
// restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound'>(str),
// model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
// dataset_list_id: int,
// software_id: int,
// },
// ihm_cross_link_restraint: {
// id: int,
// group_id: int,
// entity_id_1: str,
// entity_id_2: str,
// asym_id_1: str,
// asym_id_2: str,
// comp_id_1: str,
// comp_id_2: str,
// seq_id_1: int,
// seq_id_2: int,
// atom_id_1: str,
// atom_id_2: str,
// restraint_type: Aliased<'harmonic' | 'upper bound' | 'lower bound'>(str),
// conditional_crosslink_flag: Aliased<'ALL' | 'ANY'>(str),
// model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
// distance_threshold: float,
// psi: float,
// sigma_1: float,
// sigma_2: float,
// },
import Model from '../../model'
import { Table } from 'mol-data/db'
import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
import { findAtomIndexByLabelName } from './util';
import { Element, Unit } from '../../../structure';
function findAtomIndex(model: Model, entityId: string, asymId: string, compId: string, seqId: number, atomId: string) {
if (!model.atomicHierarchy.atoms.auth_atom_id.isDefined) return -1
const residueIndex = model.atomicHierarchy.findResidueKey(entityId, compId, asymId, seqId, '')
if (residueIndex < 0) return -1
return findAtomIndexByLabelName(model, residueIndex, atomId, '') as Element
}
// function findElementIndex(model: Model, entityId: string, asymId: string, compId: string, seqId: number, atomId: string) {
// }
// function key(entityId: string, asymId: string, compId: string, seqId: number, atomId: string) {
// return `${entityId}|${asymId}|${compId}|${seqId}|${atomId}`
// }
export interface IHMCrossLinkRestraint {
getIndicesByElement: (element: Element, kind: Unit.Kind) => number[]
data: Table<mmCIF_Schema['ihm_cross_link_restraint']>
}
export namespace IHMCrossLinkRestraint {
export const PropName = '__CrossLinkRestraint__';
export function fromModel(model: Model): IHMCrossLinkRestraint | undefined {
if (model.properties[PropName]) return model.properties[PropName]
if (model.sourceData.kind !== 'mmCIF') return
const { ihm_cross_link_restraint } = model.sourceData.data;
if (!ihm_cross_link_restraint._rowCount) return
const p1 = {
entity_id: ihm_cross_link_restraint.entity_id_1,
asym_id: ihm_cross_link_restraint.asym_id_1,
comp_id: ihm_cross_link_restraint.comp_id_1,
seq_id: ihm_cross_link_restraint.seq_id_1,
atom_id: ihm_cross_link_restraint.atom_id_1,
}
const p2: typeof p1 = {
entity_id: ihm_cross_link_restraint.entity_id_2,
asym_id: ihm_cross_link_restraint.asym_id_2,
comp_id: ihm_cross_link_restraint.comp_id_2,
seq_id: ihm_cross_link_restraint.seq_id_2,
atom_id: ihm_cross_link_restraint.atom_id_2,
}
function _add(map: Map<Element, number[]>, element: Element, row: number) {
const indices = map.get(element)
if (indices) indices.push(row)
else map.set(element, [ row ])
}
function add(row: number, ps: typeof p1) {
const entityId = ps.entity_id.value(row)
const asymId = ps.asym_id.value(row)
const seqId = ps.seq_id.value(row)
if (ihm_cross_link_restraint.model_granularity.value(row) === 'by-atom') {
const atomicElement = findAtomIndex(model, entityId, asymId, ps.comp_id.value(row), seqId, ps.atom_id.value(row))
if (atomicElement >= 0) _add(atomicElementMap, atomicElement as Element, row)
} else if (model.coarseHierarchy.isDefined) {
const sphereElement = model.coarseHierarchy.spheres.findSequenceKey(entityId, asymId, seqId)
if (sphereElement >= 0) {
_add(sphereElementMap, sphereElement as Element, row)
} else {
const gaussianElement = model.coarseHierarchy.gaussians.findSequenceKey(entityId, asymId, seqId)
if (gaussianElement >= 0) _add(gaussianElementMap, gaussianElement as Element, row)
}
}
}
function getMapByKind(kind: Unit.Kind) {
switch (kind) {
case Unit.Kind.Atomic: return atomicElementMap;
case Unit.Kind.Spheres: return sphereElementMap;
case Unit.Kind.Gaussians: return gaussianElementMap;
}
}
/** map from atomic element to cross link indices */
const atomicElementMap: Map<Element, number[]> = new Map()
/** map from sphere element to cross link indices */
const sphereElementMap: Map<Element, number[]> = new Map()
/** map from gaussian element to cross link indices */
const gaussianElementMap: Map<Element, number[]> = new Map()
const emptyIndexArray: number[] = [];
for (let i = 0; i < ihm_cross_link_restraint._rowCount; ++i) {
add(i, p1)
add(i, p2)
}
const crossLinkRestraint = {
getIndicesByElement: (element: Element, kind: Unit.Kind) => {
const map = getMapByKind(kind)
const idx = map.get(element)
return idx !== undefined ? idx : emptyIndexArray
},
data: ihm_cross_link_restraint
}
model.properties[PropName] = crossLinkRestraint
return crossLinkRestraint
}
}
\ No newline at end of file
export * from './pair-restraints/cross-links'
// export * from './pair-restraints/predicted-contacts'
\ No newline at end of file
src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts 0 → 100644
+ 108
− 0
View file @ 9b1c299d
/**
* Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import Model from '../../../model'
import { Table } from 'mol-data/db'
import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
import { findAtomIndexByLabelName } from '../util';
import { Element, Unit } from '../../../../structure';
function findAtomIndex(model: Model, entityId: string, asymId: string, compId: string, seqId: number, atomId: string) {
if (!model.atomicHierarchy.atoms.auth_atom_id.isDefined) return -1
const residueIndex = model.atomicHierarchy.findResidueKey(entityId, compId, asymId, seqId, '')
if (residueIndex < 0) return -1
return findAtomIndexByLabelName(model, residueIndex, atomId, '') as Element
}
export interface IHMCrossLinkRestraint {
getIndicesByElement: (element: Element, kind: Unit.Kind) => number[]
data: Table<mmCIF_Schema['ihm_cross_link_restraint']>
}
export namespace IHMCrossLinkRestraint {
export const PropName = '__CrossLinkRestraint__';
export function fromModel(model: Model): IHMCrossLinkRestraint | undefined {
if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName]
if (model.sourceData.kind !== 'mmCIF') return
const { ihm_cross_link_restraint } = model.sourceData.data;
if (!ihm_cross_link_restraint._rowCount) return
const p1 = {
entity_id: ihm_cross_link_restraint.entity_id_1,
asym_id: ihm_cross_link_restraint.asym_id_1,
comp_id: ihm_cross_link_restraint.comp_id_1,
seq_id: ihm_cross_link_restraint.seq_id_1,
atom_id: ihm_cross_link_restraint.atom_id_1,
}
const p2: typeof p1 = {
entity_id: ihm_cross_link_restraint.entity_id_2,
asym_id: ihm_cross_link_restraint.asym_id_2,
comp_id: ihm_cross_link_restraint.comp_id_2,
seq_id: ihm_cross_link_restraint.seq_id_2,
atom_id: ihm_cross_link_restraint.atom_id_2,
}
function _add(map: Map<Element, number[]>, element: Element, row: number) {
const indices = map.get(element)
if (indices) indices.push(row)
else map.set(element, [ row ])
}
function add(row: number, ps: typeof p1) {
const entityId = ps.entity_id.value(row)
const asymId = ps.asym_id.value(row)
const seqId = ps.seq_id.value(row)
if (ihm_cross_link_restraint.model_granularity.value(row) === 'by-atom') {
const atomicElement = findAtomIndex(model, entityId, asymId, ps.comp_id.value(row), seqId, ps.atom_id.value(row))
if (atomicElement >= 0) _add(atomicElementMap, atomicElement as Element, row)
} else if (model.coarseHierarchy.isDefined) {
const sphereElement = model.coarseHierarchy.spheres.findSequenceKey(entityId, asymId, seqId)
if (sphereElement >= 0) {
_add(sphereElementMap, sphereElement as Element, row)
} else {
const gaussianElement = model.coarseHierarchy.gaussians.findSequenceKey(entityId, asymId, seqId)
if (gaussianElement >= 0) _add(gaussianElementMap, gaussianElement as Element, row)
}
}
}
function getMapByKind(kind: Unit.Kind) {
switch (kind) {
case Unit.Kind.Atomic: return atomicElementMap;
case Unit.Kind.Spheres: return sphereElementMap;
case Unit.Kind.Gaussians: return gaussianElementMap;
}
}
/** map from atomic element to cross link indices */
const atomicElementMap: Map<Element, number[]> = new Map()
/** map from sphere element to cross link indices */
const sphereElementMap: Map<Element, number[]> = new Map()
/** map from gaussian element to cross link indices */
const gaussianElementMap: Map<Element, number[]> = new Map()
const emptyIndexArray: number[] = [];
for (let i = 0; i < ihm_cross_link_restraint._rowCount; ++i) {
add(i, p1)
add(i, p2)
}
const crossLinkRestraint = {
getIndicesByElement: (element: Element, kind: Unit.Kind) => {
const map = getMapByKind(kind)
const idx = map.get(element)
return idx !== undefined ? idx : emptyIndexArray
},
data: ihm_cross_link_restraint
}
model._staticPropertyData[PropName] = crossLinkRestraint
return crossLinkRestraint
}
}
\ No newline at end of file
src/mol-model/structure/model/formats/mmcif/pair-restraints/predicted-contacts.ts 0 → 100644
+ 26
− 0
View file @ 9b1c299d
/**
* Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
// TODO
// ihm_predicted_contact_restraint: {
// id: int,
// entity_id_1: str,
// entity_id_2: str,
// asym_id_1: str,
// asym_id_2: str,
// comp_id_1: str,
// comp_id_2: str,
// seq_id_1: int,
// seq_id_2: int,
// atom_id_1: str,
// atom_id_2: str,
// distance_upper_limit: float,
// probability: float,
// restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound'>(str),
// model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
// dataset_list_id: int,
// software_id: int,
// },
src/mol-view/stage.ts
+ 3
− 3
View file @ 9b1c299d
......@@ -43,14 +43,14 @@ export class Stage {
// this.loadPdbid('1jj2')
// this.loadPdbid('4umt') // ligand has bond with order 3
// this.loadPdbid('1crn') // small
this.loadPdbid('1crn') // small
// this.loadPdbid('1rb8') // virus
// this.loadPdbid('1blu') // metal coordination
// this.loadPdbid('3pqr') // inter unit bonds
// this.loadPdbid('4v5a') // ribosome
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`)
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`)
}
async loadMmcifUrl (url: string) {
......@@ -59,7 +59,7 @@ export class Stage {
const structureEntity = await ModelToStructure.apply(this.ctx, modelEntity)
StructureToSpacefill.apply(this.ctx, structureEntity, { ...spacefillProps, visible: true })
// StructureToBallAndStick.apply(this.ctx, structureEntity, ballAndStickProps)
StructureToBallAndStick.apply(this.ctx, structureEntity, ballAndStickProps)
StructureToDistanceRestraint.apply(this.ctx, structureEntity, ballAndStickProps)
this.globalContext.components.sequenceView.setState({ structure: structureEntity.value });
......
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