diff --git a/src/mol-model/structure/model/formats/mmcif/pair-restraint.ts b/src/mol-model/structure/model/formats/mmcif/pair-restraint.ts
index 5cfe9f4e3ed1147334b195d252bf156eed3541f9..40cec49d41786cc3576f29bca18c357e87cb715e 100644
--- a/src/mol-model/structure/model/formats/mmcif/pair-restraint.ts
+++ b/src/mol-model/structure/model/formats/mmcif/pair-restraint.ts
@@ -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
diff --git a/src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts b/src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts
new file mode 100644
index 0000000000000000000000000000000000000000..584a429ccb559cef0e7480f0db2b20734aaa13e0
--- /dev/null
+++ b/src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts
@@ -0,0 +1,108 @@
+/**
+ * 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
diff --git a/src/mol-model/structure/model/formats/mmcif/pair-restraints/predicted-contacts.ts b/src/mol-model/structure/model/formats/mmcif/pair-restraints/predicted-contacts.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d736eabdf2c073838585736ba735813d76143d75
--- /dev/null
+++ b/src/mol-model/structure/model/formats/mmcif/pair-restraints/predicted-contacts.ts
@@ -0,0 +1,26 @@
+/**
+ * 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,
+// },
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 337cfba32ac4c327fd5af0b89cb100efe607d58e..964b42c5c51487265fd9ea392c8d26215a24e3a7 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -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 });