pair-restraint cleanup & fixes

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
-    }
-}
+export * from './pair-restraints/cross-links'
+// export * from './pair-restraints/predicted-contacts'

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
+    }
+}

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,
+// },

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 });