From f740ba95b06ae28a444e6930ffe6e4078a1303a8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Mal=C3=BD?= <michal.maly@ibt.cas.cz>
Date: Mon, 21 Mar 2022 19:21:56 +0100
Subject: [PATCH] ReDNATCO plugin stage 5
---
src/apps/rednatco/commands.ts | 25 ++++
src/apps/rednatco/index.html | 2 +-
src/apps/rednatco/index.tsx | 275 +++++++++++++++++++++-------------
src/apps/rednatco/step.ts | 109 ++++++++++++++
src/apps/rednatco/traverse.ts | 92 ++++++++++++
5 files changed, 394 insertions(+), 109 deletions(-)
create mode 100644 src/apps/rednatco/commands.ts
create mode 100644 src/apps/rednatco/traverse.ts
diff --git a/src/apps/rednatco/commands.ts b/src/apps/rednatco/commands.ts
new file mode 100644
index 000000000..869955365
--- /dev/null
+++ b/src/apps/rednatco/commands.ts
@@ -0,0 +1,25 @@
+export namespace Commands {
+ export type Type = 'select-step'|'switch-model';
+
+ export type SelectStep = {
+ type: 'select-step';
+ stepName: string;
+ referenceNtC: string;
+ references: ('sel'|'prev'|'next')[];
+ }
+ export function SelectStep(stepName: string, referenceNtC = '', references = ['sel', 'prev', 'next']): SelectStep {
+ return {
+ type: 'select-step',
+ stepName,
+ referenceNtC,
+ references: references as ('sel'|'prev'|'next')[],
+ };
+ }
+
+ export type SwitchModel = { type: 'switch-model', model: number };
+ export function SwitchModel(model: number): SwitchModel { return { type: 'switch-model', model }; }
+
+ export type Cmd = SelectStep|SwitchModel;
+}
+
+
diff --git a/src/apps/rednatco/index.html b/src/apps/rednatco/index.html
index a2633701a..889b15a28 100644
--- a/src/apps/rednatco/index.html
+++ b/src/apps/rednatco/index.html
@@ -9,7 +9,7 @@
<script type="text/javascript" src="./molstar.js"></script>
<script>
async function loadStructure() {
- const resp = await fetch('./3vok_v32C35A23.cif');
+ const resp = await fetch('./1bna_v41C35A23.cif');
const data = await resp.text();
molstar.ReDNATCOMspApi.loadStructure(data);
diff --git a/src/apps/rednatco/index.tsx b/src/apps/rednatco/index.tsx
index d8f6b2c0f..172952e91 100644
--- a/src/apps/rednatco/index.tsx
+++ b/src/apps/rednatco/index.tsx
@@ -2,18 +2,20 @@ import React from 'react';
import ReactDOM from 'react-dom';
import { NtCColors } from './colors';
import { ColorPicker } from './color-picker';
+import { Commands } from './commands';
import { PushButton, ToggleButton } from './controls';
import * as IDs from './idents';
import * as RefCfmr from './reference-conformers';
import { ReferenceConformersPdbs } from './reference-conformers-pdbs';
import { Step } from './step';
import { Superpose } from './superpose';
+import { Traverse } from './traverse';
import { DnatcoConfalPyramids } from '../../extensions/dnatco';
import { ConfalPyramidsParams } from '../../extensions/dnatco/confal-pyramids/representation';
import { OrderedSet } from '../../mol-data/int/ordered-set';
import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
import { Loci } from '../../mol-model/loci';
-import { Model, Structure, StructureElement, StructureProperties, Trajectory } from '../../mol-model/structure';
+import { Model, Structure, StructureElement, StructureProperties, StructureSelection, Trajectory } from '../../mol-model/structure';
import { Location } from '../../mol-model/structure/structure/element/location';
import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
import { PluginBehavior, PluginBehaviors } from '../../mol-plugin/behavior';
@@ -30,7 +32,6 @@ import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
import { Representation } from '../../mol-repr/representation';
import { StateObjectCell, StateObject, StateSelection } from '../../mol-state';
import { StateTreeSpine } from '../../mol-state/tree/spine';
-import { Script } from '../../mol-script/script';
import { lociLabel } from '../../mol-theme/label';
import { Color } from '../../mol-util/color';
import { arrayMax } from '../../mol-util/array';
@@ -54,7 +55,6 @@ const NtCSupPrev = 'ntc-sup-prev';
const NtCSupSel = 'ntc-sup-sel';
const NtCSupNext = 'ntc-sup-next';
-const SelectAllScript = Script('(sel.atom.atoms true)', 'mol-script');
const SphereBoundaryHelper = new BoundaryHelper('98');
type StepInfo = {
@@ -171,8 +171,9 @@ const ConformersByClass = {
};
type ConformersByClass = typeof ConformersByClass;
+type VisualRepresentations = 'ball-and-stick'|'cartoon';
const Display = {
- representation: 'cartoon',
+ representation: 'cartoon' as VisualRepresentations,
showNucleic: true,
showProtein: false,
@@ -350,6 +351,13 @@ class ReDNATCOMspViewer {
interactionContext.self = this;
}
+ private currentModelNumber() {
+ const model = this.plugin.state.data.cells.get(IDs.ID('model', '', BaseRef))?.obj;
+ if (!model)
+ return -1;
+ return (model as StateObject<Model>).data.modelNum;
+ }
+
private getBuilder(id: IDs.ID, sub: IDs.Substructure|'' = '', ref = BaseRef) {
return this.plugin.state.data.build().to(IDs.ID(id, sub, ref));
}
@@ -401,7 +409,8 @@ class ReDNATCOMspViewer {
continue;
const parent = this.getStructureParent(cell);
if (parent) {
- const s = Loci.getBoundingSphere(Script.toLoci(SelectAllScript, parent.data));
+ const loci = StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(parent.data, parent.data));
+ const s = Loci.getBoundingSphere(loci);
if (s)
spheres.push(s);
}
@@ -424,6 +433,27 @@ class ReDNATCOMspViewer {
PluginCommands.Camera.SetSnapshot(this.plugin, { snapshot, durationMs: AnimationDurationMsec });
}
+ private substructureVisuals(representation: 'ball-and-stick'|'cartoon') {
+ switch (representation) {
+ case 'cartoon':
+ return {
+ type: {
+ name: 'cartoon',
+ params: { sizeFactor: 0.2, sizeAspectRatio: 0.35, aromaticBonds: false },
+ },
+ colorTheme: { name: 'chain-id', params: { asymId: 'auth' } },
+ };
+ case 'ball-and-stick':
+ return {
+ type: {
+ name: 'ball-and-stick',
+ params: { sizeFactor: 0.2, sizeAspectRatio: 0.35, aromaticBonds: false },
+ },
+ colorTheme: { name: 'element-symbol', params: { carbonColor: 'chain-id' } },
+ };
+ }
+ }
+
private superpose(reference: StructureElement.Loci, stru: StructureElement.Loci) {
const refElems = dinucleotideBackbone(reference);
const struElems = dinucleotideBackbone(stru);
@@ -525,9 +555,8 @@ class ReDNATCOMspViewer {
);
await b.commit();
}
- } else {
+ } else
await PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.data, ref: IDs.ID('pyramids', 'nucleic', BaseRef) });
- }
}
async changeRepresentation(display: Partial<Display>) {
@@ -541,7 +570,7 @@ class ReDNATCOMspViewer {
StateTransforms.Representation.StructureRepresentation3D,
old => ({
...old,
- type: { ...old.type, name: repr }
+ ...this.substructureVisuals(repr),
})
);
}
@@ -689,9 +718,7 @@ class ReDNATCOMspViewer {
bb.to(IDs.ID('structure', 'nucleic', BaseRef))
.apply(
StateTransforms.Representation.StructureRepresentation3D,
- {
- type: { name: display.representation ?? 'cartoon', params: { sizeFactor: 0.2, sizeAspectRatio: 0.35, aromaticBonds: false } },
- },
+ this.substructureVisuals('cartoon'),
{ ref: IDs.ID('visual', 'nucleic', BaseRef) }
);
if (display.showPyramids) {
@@ -707,9 +734,7 @@ class ReDNATCOMspViewer {
bb.to(IDs.ID('structure', 'protein', BaseRef))
.apply(
StateTransforms.Representation.StructureRepresentation3D,
- {
- type: { name: display.representation ?? 'cartoon', params: { sizeFactor: 0.2, sizeAspectRatio: 0.35, aromaticBonds: false } },
- },
+ this.substructureVisuals('cartoon'),
{ ref: IDs.ID('visual', 'protein', BaseRef) }
);
}
@@ -717,9 +742,7 @@ class ReDNATCOMspViewer {
bb.to(IDs.ID('structure', 'water', BaseRef))
.apply(
StateTransforms.Representation.StructureRepresentation3D,
- {
- type: { name: display.representation ?? 'ball-and-stick', params: { sizeFactor: 0.2, sizeAspectRatio: 0.35 } },
- },
+ this.substructureVisuals('ball-and-stick'),
{ ref: IDs.ID('visual', 'water', BaseRef) }
);
}
@@ -770,35 +793,81 @@ class ReDNATCOMspViewer {
onLociSelected(selected: Representation.Loci) {
const loci = Loci.normalize(selected.loci, 'two-residues');
- if (loci.kind === 'element-loci')
- this.superposeReferences(loci);
+ if (loci.kind === 'element-loci') {
+ // TODO: This cannot call superposeReferences directly
+ // Instead, we must make a callback via the API
+ // and have the listener decide what to do with this event
+ const stepDesc = Step.describe(loci);
+ if (!stepDesc)
+ return;
+ const stepName = Step.name(stepDesc, this.haveMultipleModels);
+ this.superposeReferences(stepName, '', []);
+ }
}
async switchModel(display: Partial<Display>) {
- const b = this.getBuilder('model', '', BaseRef);
- b.update(
- StateTransforms.Model.ModelFromTrajectory,
- old => ({
- ...old,
- modelIndex: display.modelNumber ? display.modelNumber - 1 : 0
- })
- );
+ if (display.modelNumber && display.modelNumber === this.currentModelNumber())
+ return;
+
+ const b = this.plugin.state.data.build()
+ .delete(IDs.ID('superposition', '', NtCSupSel))
+ .delete(IDs.ID('superposition', '', NtCSupPrev))
+ .delete(IDs.ID('superposition', '', NtCSupNext))
+ .to(IDs.ID('model', '', BaseRef))
+ .update(
+ StateTransforms.Model.ModelFromTrajectory,
+ old => ({
+ ...old,
+ modelIndex: display.modelNumber ? display.modelNumber - 1 : 0
+ })
+ );
await b.commit();
}
- superposeReferences(selected: StructureElement.Loci) {
- const step = Step.describe(selected);
- if (!step)
- return;
+ async superposeReferences(stepName: string, referenceNtc: string, references: ('sel'|'prev'|'next')[]) {
+ const ReferenceVisuals = (color: number) => {
+ return {
+ type: { name: 'ball-and-stick', params: { sizeFactor: 0.15, aromaticBonds: false } },
+ colorTheme: { name: 'uniform', params: { value: Color(color) } },
+ };
+ };
- const stepName = Step.name(step, this.haveMultipleModels);
+ const stepDesc = Step.fromName(stepName);
+ if (!stepDesc)
+ return;
const stepId = this.stepNames.get(stepName);
if (stepId === undefined) {
console.error(`Unknown step name ${stepName}`);
return;
}
+ if (stepDesc.model !== this.currentModelNumber()) {
+ const b = this.getBuilder('model')
+ .update(
+ StateTransforms.Model.ModelFromTrajectory,
+ old => ({
+ ...old,
+ modelIndex: stepDesc.model - 1,
+ })
+ );
+ await b.commit();
+ }
+
+ const entireStru = this.plugin.state.data.cells.get(IDs.ID('structure', 'nucleic', BaseRef))!.obj!;
+ const loci = Traverse.findResidue(
+ stepDesc.chain,
+ stepDesc.resNo1,
+ stepDesc.altId1,
+ StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(entireStru.data, entireStru.data)),
+ 'auth'
+ );
+ if (loci.kind !== 'element-loci')
+ return;
+ const selLoci = Loci.normalize(loci, 'two-residues');
+ if (selLoci.kind !== 'element-loci')
+ return;
+
const stepIdPrev = stepId === 0 ? void 0 : stepId - 1;
const stepIdNext = stepId === this.steps.length - 1 ? void 0 : stepId + 1;
@@ -807,7 +876,7 @@ class ReDNATCOMspViewer {
const ntcRefNext = this.ntcRef(stepIdNext, 'next');
if (!ntcRefSel) {
- console.error(`Seemingly invalid stepId ${stepId}`);
+ console.error(`stepId ${stepId} does not map to a known step`);
return;
}
@@ -816,74 +885,39 @@ class ReDNATCOMspViewer {
.delete(IDs.ID('superposition', '', NtCSupPrev))
.delete(IDs.ID('superposition', '', NtCSupNext));
- {
- const stru = this.plugin.state.data.cells.get(IDs.ID('structure', '', ntcRefSel))!.obj!;
- const loci = Script.toLoci(SelectAllScript, stru.data);
+ const addReference = (ntcRef: string, superposRef: string, loci: Loci, color: number) => {
+ const refStru = this.plugin.state.data.cells.get(IDs.ID('structure', '', ntcRef))!.obj!;
+ const refLoci = StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(refStru.data, refStru.data));
- const { bTransform } = this.superpose(loci, selected);
- if (isNaN(bTransform[0])) {
- console.error(`Cannot superpose reference conformer ${ntcRefSel} onto selection`);
- return;
- }
- b.to(IDs.ID('structure', '', ntcRefSel))
- .apply(
- StateTransforms.Model.TransformStructureConformation,
- { transform: { name: 'matrix', params: { data: bTransform, transpose: false } } },
- { ref: IDs.ID('superposition', '', NtCSupSel) }
- ).apply(
- StateTransforms.Representation.StructureRepresentation3D,
- { type: { name: 'ball-and-stick', params: { sizeFactor: 0.15 } } },
- { ref: IDs.ID('visual', '', NtCSupSel) }
- );
- }
-
- // TODO: These cannot be applied onto selection!!!
- if (ntcRefPrev) {
- const stru = this.plugin.state.data.cells.get(IDs.ID('structure', '', ntcRefPrev))!.obj!;
- const loci = Script.toLoci(SelectAllScript, stru.data);
-
- const { bTransform } = this.superpose(loci, selected);
- if (isNaN(bTransform[0])) {
- console.error(`Cannot superpose reference conformer ${ntcRefPrev} onto selection`);
- return;
- }
- b.to(IDs.ID('structure', '', ntcRefPrev))
- .apply(
- StateTransforms.Model.TransformStructureConformation,
- { transform: { name: 'matrix', params: { data: bTransform, transpose: false } } },
- { ref: IDs.ID('superposition', '', NtCSupPrev) }
- ).apply(
- StateTransforms.Representation.StructureRepresentation3D,
- { type: { name: 'ball-and-stick', params: { sizeFactor: 0.15 } } },
- { ref: IDs.ID('visual', '', NtCSupPrev) }
- );
- }
-
- // TODO: These cannot be applied onto selection!!!
- if (ntcRefNext) {
- const stru = this.plugin.state.data.cells.get(IDs.ID('structure', '', ntcRefNext))!.obj!;
- const loci = Script.toLoci(SelectAllScript, stru.data);
-
- const { bTransform } = this.superpose(loci, selected);
- if (isNaN(bTransform[0])) {
- console.error(`Cannot superpose reference conformer ${ntcRefNext} onto selection`);
- return;
+ if (loci.kind === 'element-loci' && Step.is(loci)) {
+ const { bTransform, rmsd } = this.superpose(refLoci, loci);
+ if (isNaN(bTransform[0])) {
+ console.error(`Cannot superpose reference conformer ${ntcRef} onto selection`);
+ return;
+ }
+ b.to(IDs.ID('structure', '', ntcRef))
+ .apply(
+ StateTransforms.Model.TransformStructureConformation,
+ { transform: { name: 'matrix', params: { data: bTransform, transpose: false } } },
+ { ref: IDs.ID('superposition', '', superposRef) }
+ ).apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ ReferenceVisuals(color),
+ { ref: IDs.ID('visual', '', superposRef) }
+ );
+ return rmsd;
}
- b.to(IDs.ID('structure', '', ntcRefNext))
- .apply(
- StateTransforms.Model.TransformStructureConformation,
- { transform: { name: 'matrix', params: { data: bTransform, transpose: false } } },
- { ref: IDs.ID('superposition', '', NtCSupNext) }
- ).apply(
- StateTransforms.Representation.StructureRepresentation3D,
- { type: { name: 'ball-and-stick', params: { sizeFactor: 0.15 } } },
- { ref: IDs.ID('visual', '', NtCSupNext) }
- );
- }
+ };
- // TODO: Superpose previous and next step too!!!
+ const rmsd = addReference(ntcRefSel, NtCSupSel, selLoci, 0x008000);
+ if (ntcRefPrev)
+ addReference(ntcRefPrev, NtCSupPrev, Loci.normalize(Traverse.residue(-1, stepDesc.altId1, selLoci), 'two-residues'), 0x0000FF);
+ if (ntcRefNext)
+ addReference(ntcRefNext, NtCSupNext, Loci.normalize(Traverse.residue(1, stepDesc.altId2, selLoci), 'two-residues'), 0x00FFFF);
b.commit();
+
+ return rmsd;
}
async toggleSubstructure(sub: IDs.Substructure, display: Partial<Display>) {
@@ -893,12 +927,11 @@ class ReDNATCOMspViewer {
if (show) {
const b = this.getBuilder('structure', sub);
+ const visuals = this.substructureVisuals(sub === 'water' ? 'ball-and-stick' : repr);
if (b) {
b.apply(
StateTransforms.Representation.StructureRepresentation3D,
- {
- type: { name: repr, params: { sizeFactor: 0.2, sizeAspectRatio: 0.35, aromaticBonds: false } }, // TODO: Use different params for water
- },
+ visuals,
{ ref: IDs.ID('visual', sub, BaseRef) }
);
await b.commit();
@@ -949,6 +982,26 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
this.setState({ ...this.state, display });
}
+ command(cmd: Commands.Cmd) {
+ if (!this.viewer)
+ return;
+
+ if (cmd.type === 'select-step') {
+ this.viewer.superposeReferences(cmd.stepName, cmd.referenceNtC, cmd.references);
+ } else if (cmd.type === 'switch-model') {
+ if (cmd.model < 1 || cmd.model > this.viewer.getModelCount())
+ return;
+
+ const display: Display = {
+ ...this.state.display,
+ modelNumber: cmd.model,
+ };
+
+ this.viewer.switchModel(display);
+ this.setState({ ...this.state, display });
+ }
+ }
+
constructor(props: ReDNATCOMsp.Props) {
super(props);
@@ -972,7 +1025,7 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
ReDNATCOMspViewer.create(elem!).then(viewer => {
this.viewer = viewer;
this.viewer.loadReferenceConformers().then(() => {
- ReDNATCOMspApi.bind(this);
+ ReDNATCOMspApi._bind(this);
if (this.props.onInited)
this.props.onInited();
@@ -1006,7 +1059,7 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
text={capitalize(this.state.display.representation)}
enabled={ready}
onClick={() => {
- const display = {
+ const display: Display = {
...this.state.display,
representation: this.state.display.representation === 'cartoon' ? 'ball-and-stick' : 'cartoon',
};
@@ -1025,7 +1078,7 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
enabled={hasNucleic}
switchedOn={this.state.display.showNucleic}
onClick={() => {
- const display = {
+ const display: Display = {
...this.state.display,
showNucleic: !this.state.display.showNucleic,
};
@@ -1040,7 +1093,7 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
enabled={hasProtein}
switchedOn={this.state.display.showProtein}
onClick={() => {
- const display = {
+ const display: Display = {
...this.state.display,
showProtein: !this.state.display.showProtein,
};
@@ -1055,7 +1108,7 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
enabled={hasWater}
switchedOn={this.state.display.showWater}
onClick={() => {
- const display = {
+ const display: Display = {
...this.state.display,
showWater: !this.state.display.showWater,
};
@@ -1075,7 +1128,7 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
enabled={ready}
switchedOn={this.state.display.showPyramids}
onClick={() => {
- const display = {
+ const display: Display = {
...this.state.display,
showPyramids: !this.state.display.showPyramids,
};
@@ -1089,7 +1142,7 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
text={this.state.display.pyramidsTransparent ? 'Transparent' : 'Solid'}
enabled={this.state.display.showPyramids}
onClick={() => {
- const display = {
+ const display: Display = {
...this.state.display,
pyramidsTransparent: !this.state.display.pyramidsTransparent,
};
@@ -1113,7 +1166,7 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
text={this.state.display.ballsTransparent ? 'Transparent' : 'Solid'}
enabled={this.state.display.showBalls}
onClick={() => {
- const display = {
+ const display: Display = {
...this.state.display,
ballsTransparent: !this.state.display.ballsTransparent,
};
@@ -1226,12 +1279,18 @@ class _ReDNATCOMspApi {
throw new Error('ReDNATCOMsp object not bound');
}
- bind(target: ReDNATCOMsp) {
+ _bind(target: ReDNATCOMsp) {
this.target = target;
}
+ command(cmd: Commands.Cmd) {
+ this.check();
+ this.target!.command(cmd);
+ }
+
init(elemId: string, onInited?: () => void) {
ReDNATCOMsp.init(elemId, onInited);
+ return this;
}
loadStructure(data: string) {
diff --git a/src/apps/rednatco/step.ts b/src/apps/rednatco/step.ts
index c35bdc271..a988acfad 100644
--- a/src/apps/rednatco/step.ts
+++ b/src/apps/rednatco/step.ts
@@ -21,6 +21,25 @@ export namespace Step {
return `${compId}${altId ? `.${altId}` : ''}_${seqId}${insCode ? `.${insCode}` : '' }`;
}
+ function residueDescription(a: string, b: string): { comp: string, altId?: string, resNo: number, insCode?: string }|undefined {
+ const toksA = a.split('.');
+ const toksB = b.split('.');
+
+ if (toksA.length > 2 || toksB.length > 2)
+ return void 0;
+
+ const resNo = parseInt(toksB[0]);
+ if (isNaN(resNo))
+ return void 0;
+
+ return {
+ comp: toksA[0],
+ altId: toksA.length === 2 ? toksA[1] : void 0,
+ resNo,
+ insCode: toksB.length === 2 ? toksB[1] : void 0,
+ };
+ }
+
export function describe(loci: StructureElement.Loci) {
const es = loci.elements[0]; // Ignore multiple selections
@@ -62,6 +81,96 @@ export namespace Step {
return description;
}
+ export function fromName(name: string) {
+ const description: Description = {
+ model: -1,
+ entryId: '',
+ chain: '',
+ resNo1: -1,
+ comp1: '',
+ altId1: void 0,
+ insCode1: void 0,
+ resNo2: -1,
+ comp2: '',
+ altId2: void 0,
+ insCode2: void 0,
+ };
+
+ const toks = name.split('_');
+ if (toks.length !== 6) {
+ console.error(`String ${name} is not valid step name`);
+ return void 0;
+ }
+
+ const entryTok = toks[0];
+ const chain = toks[1];
+ const res1TokA = toks[2];
+ const res1TokB = toks[3];
+ const res2TokA = toks[4];
+ const res2TokB = toks[5];
+
+ const ets = entryTok.split('-');
+ if (ets.length === 1) {
+ description.entryId = ets[0];
+ description.model = 1;
+ } else if (ets.length === 2) {
+ description.entryId = ets[0];
+ const m = parseInt(ets[1].slice(1));
+ if (isNaN(m)) {
+ console.error(`String ${name} is not valid step name`);
+ return void 0;
+ }
+ description.model = m;
+ } else {
+ console.error(`String ${name} is not valid step name`);
+ return void 0;
+ }
+
+ if (chain.length !== 1) {
+ console.error(`String ${name} is not valid step name`);
+ return void 0;
+ } else
+ description.chain = chain;
+
+ const res1 = residueDescription(res1TokA, res1TokB);
+ const res2 = residueDescription(res2TokA, res2TokB);
+ if (!res1 || !res2) {
+ console.error(`String ${name} is not valid step name`);
+ return void 0;
+ }
+
+ description.resNo1 = res1.resNo;
+ description.comp1 = res1.comp;
+ description.altId1 = res1.altId;
+ description.insCode1 = res1.insCode;
+ description.resNo2 = res2.resNo;
+ description.comp2 = res2.comp;
+ description.altId2 = res2.altId;
+ description.insCode2 = res2.insCode;
+
+ return description;
+ }
+
+ export function is(loci: StructureElement.Loci) {
+ const e = loci.elements[0];
+ const loc = Location.create(loci.structure, e.unit, e.unit.elements[OrderedSet.getAt(e.indices, 0)]);
+
+ const resNo1 = StructureProperties.residue.label_seq_id(loc);
+ const asymId = StructureProperties.chain.label_asym_id(loc);
+ for (let idx = 1; idx < OrderedSet.size(e.indices); idx++) {
+ loc.element = e.unit.elements[OrderedSet.getAt(e.indices, idx)];
+
+ const resNo = StructureProperties.residue.label_seq_id(loc);
+ if (resNo !== resNo1 + 1)
+ continue;
+ const _asymId = StructureProperties.chain.label_asym_id(loc);
+ if (_asymId === asymId)
+ return true;
+ }
+
+ return false;
+ }
+
export function name(description: Description, multipleModels: boolean) {
const res1 = nameResidue(description.resNo1, description.comp1, description.altId1, description.insCode1);
const res2 = nameResidue(description.resNo2, description.comp2, description.altId2, description.insCode2);
diff --git a/src/apps/rednatco/traverse.ts b/src/apps/rednatco/traverse.ts
new file mode 100644
index 000000000..316e4c3e9
--- /dev/null
+++ b/src/apps/rednatco/traverse.ts
@@ -0,0 +1,92 @@
+import { Segmentation } from '../../mol-data/int';
+import { OrderedSet } from '../../mol-data/int/ordered-set';
+import { EmptyLoci, Loci } from '../../mol-model/loci';
+import { ResidueIndex, Structure, StructureElement, StructureProperties, Unit } from '../../mol-model/structure';
+import { Location } from '../../mol-model/structure/structure/element/location';
+
+export namespace Traverse {
+ type Residue = Segmentation.Segment<ResidueIndex>;
+
+ export function residueAltId(structure: Structure, unit: Unit, residue: Residue) {
+ const loc = Location.create(structure, unit);
+ for (let rI = residue.start; rI < residue.end; rI++) {
+ loc.element = OrderedSet.getAt(unit.elements, rI);
+ const altId = StructureProperties.atom.label_alt_id(loc);
+ if (altId !== '')
+ return altId;
+ }
+
+ return void 0;
+ }
+
+ export function findResidue(asymId: string, seqId: number, altId: string|undefined, loci: StructureElement.Loci, source: 'label'|'auth') {
+ for (const e of loci.elements) {
+ const loc = Location.create(loci.structure, e.unit);
+
+ const getAsymId = source === 'label' ? StructureProperties.chain.label_asym_id : StructureProperties.chain.auth_asym_id;
+ const getSeqId = source === 'label' ? StructureProperties.residue.label_seq_id : StructureProperties.residue.auth_seq_id;
+
+ // Walk the entire unit and look for the requested residue
+ const chainIt = Segmentation.transientSegments(e.unit.model.atomicHierarchy.chainAtomSegments, e.unit.elements);
+ const residueIt = Segmentation.transientSegments(e.unit.model.atomicHierarchy.residueAtomSegments, e.unit.elements);
+
+ const elemIndex = (idx: number) => OrderedSet.getAt(e.unit.elements, idx);
+ while (chainIt.hasNext) {
+ const chain = chainIt.move();
+ loc.element = elemIndex(chain.start);
+ const _asymId = getAsymId(loc);
+ if (_asymId !== asymId)
+ continue; // Wrong chain, skip it
+
+ residueIt.setSegment(chain);
+ while (residueIt.hasNext) {
+ const residue = residueIt.move();
+ loc.element = elemIndex(residue.start);
+
+ const _seqId = getSeqId(loc);
+ if (_seqId === seqId) {
+ if (altId) {
+ const _altId = residueAltId(loci.structure, e.unit, residue);
+ if (_altId && _altId !== altId)
+ continue;
+ }
+
+ const start = residue.start as StructureElement.UnitIndex;
+ const end = residue.end as StructureElement.UnitIndex;
+ return StructureElement.Loci(
+ loci.structure,
+ [{ unit: e.unit, indices: OrderedSet.ofBounds(start, end) }]
+ );
+ }
+ }
+ }
+ }
+
+ return EmptyLoci;
+ }
+
+ export function residue(shift: number, altId: string|undefined, cursor: StructureElement.Loci) {
+ for (const e of cursor.elements) {
+ const entireUnit = cursor.structure.units[e.unit.id];
+ const loc = Location.create(cursor.structure, e.unit);
+
+ loc.element = e.unit.elements[OrderedSet.getAt(e.indices, 0)];
+ const asymId = StructureProperties.chain.label_asym_id(loc);
+ const seqId = StructureProperties.residue.label_seq_id(loc);
+
+ const from = 0 as StructureElement.UnitIndex;
+ const to = entireUnit.elements.length as StructureElement.UnitIndex;
+
+ const loci = findResidue(
+ asymId,
+ seqId + shift,
+ altId,
+ StructureElement.Loci(cursor.structure, [{ unit: entireUnit, indices: OrderedSet.ofBounds(from, to) }]),
+ 'label'
+ );
+ if (!Loci.isEmpty(loci))
+ return loci;
+ }
+ return EmptyLoci;
+ }
+}
--
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