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Commit 221e3ce6 authored by Michal Malý's avatar Michal Malý
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ReDNATCO plugin stage 7

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src/apps/rednatco/commands.ts
+ 5
− 4
View file @ 221e3ce6
export namespace Commands {
export type Type = 'select-step'|'switch-model';
export type Type = 'redraw'|'select-step'|'switch-model';
export type Redraw = { type: 'redraw' }
export function Redraw(): Redraw { return { type: 'redraw' }; }
export type SelectStep = {
type: 'select-step';
......@@ -19,7 +22,5 @@ export namespace Commands {
export type SwitchModel = { type: 'switch-model', model: number };
export function SwitchModel(model: number): SwitchModel { return { type: 'switch-model', model }; }
export type Cmd = SelectStep|SwitchModel;
export type Cmd = Redraw|SelectStep|SwitchModel;
}
src/apps/rednatco/index.html
+ 1
− 1
View file @ 221e3ce6
......@@ -9,7 +9,7 @@
<script type="text/javascript" src="./molstar.js"></script>
<script>
async function loadStructure() {
const resp = await fetch('./1bna_v41C35A23.cif');
const resp = await fetch('./1hmh_v41C35A23.cif');
const data = await resp.text();
molstar.ReDNATCOMspApi.loadStructure(data);
......
src/apps/rednatco/index.tsx
+ 108
− 64
View file @ 221e3ce6
......@@ -15,7 +15,7 @@ import { ConfalPyramidsParams } from '../../extensions/dnatco/confal-pyramids/re
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, StructureSelection, Trajectory } from '../../mol-model/structure';
import { ElementIndex, 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';
......@@ -61,6 +61,10 @@ type StepInfo = {
name: string;
assignedNtC: string;
closestNtC: string; // Fallback for cases where assignedNtC is NANT
resNo1: number;
resNo2: number;
altId1?: string;
altId2?: string;
}
function capitalize(s: string) {
......@@ -70,11 +74,37 @@ function capitalize(s: string) {
}
function dinucleotideBackbone(loci: StructureElement.Loci) {
function dinucleotideBackbone(loci: StructureElement.Loci, altId1?: string, altId2?: string) {
const es = loci.elements[0];
const loc = Location.create(loci.structure, es.unit, es.unit.elements[OrderedSet.getAt(es.indices, 0)]);
const len = OrderedSet.size(es.indices);
const indices = [];
const indices = new Array<ElementIndex>();
const gather = (atoms: string[], start: number, end: number, altId?: string) => {
for (const atom of atoms) {
let idx = start;
for (; idx < end; idx++) {
loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
const _atom = StructureProperties.atom.label_atom_id(loc);
if (atom === _atom) {
if (altId) {
const _altId = StructureProperties.atom.label_alt_id(loc);
if (_altId !== '' && _altId !== altId)
continue;
}
indices.push(loc.element);
break;
}
}
if (idx === end) {
console.error(`Cannot find backbone atom ${atom} in first residue of a step`);
return false;
}
}
return true;
};
// Find split between first and second residue
const resNo1 = StructureProperties.residue.auth_seq_id(loc);
......@@ -92,50 +122,22 @@ function dinucleotideBackbone(loci: StructureElement.Loci) {
// Gather ElementIndices for backbone atoms of the first residue
loc.element = es.unit.elements[OrderedSet.getAt(es.indices, 0)];
const comp1 = StructureProperties.atom.label_comp_id(loc);
const ring1 = RefCfmr.CompoundRings[comp1 as keyof RefCfmr.CompoundRings];
const ring1 = RefCfmr.CompoundRings[StructureProperties.atom.label_comp_id(loc) as keyof RefCfmr.CompoundRings];
if (!ring1)
return [];
const first = RefCfmr.BackboneAtoms.first.concat(RefCfmr.BackboneAtoms[ring1]);
for (const atom of first) {
let idx = 0;
for (; idx < secondIdx; idx++) {
loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
const _atom = StructureProperties.atom.label_atom_id(loc);
if (atom === _atom) {
indices.push(loc.element);
break;
}
}
if (idx === secondIdx) {
console.error(`Cannot find backbone atom ${atom} in first residue of a step`);
return [];
}
}
if (!gather(first, 0, secondIdx, altId1))
return [];
loc.element = es.unit.elements[OrderedSet.getAt(es.indices, secondIdx)];
const comp2 = StructureProperties.atom.label_comp_id(loc);
const ring2 = RefCfmr.CompoundRings[comp2 as keyof RefCfmr.CompoundRings];
const ring2 = RefCfmr.CompoundRings[StructureProperties.atom.label_comp_id(loc) as keyof RefCfmr.CompoundRings];
if (!ring2)
return [];
const second = RefCfmr.BackboneAtoms.second.concat(RefCfmr.BackboneAtoms[ring2]);
for (const atom of second) {
let idx = secondIdx;
for (; idx < len; idx++) {
loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
const _atom = StructureProperties.atom.label_atom_id(loc);
if (atom === _atom) {
indices.push(loc.element);
break;
}
}
if (idx === len) {
console.error(`Cannot find backbone atom ${atom} in second residue of a step`);
return [];
}
}
if (!gather(second, secondIdx, len, altId2))
return [];
return indices;
}
......@@ -371,11 +373,8 @@ class ReDNATCOMspViewer {
return parent.obj?.type.name === 'Structure' ? parent.obj : undefined;
}
private ntcRef(id: number|undefined, where: 'sel'|'prev'|'next') {
if (id === undefined)
return undefined;
const info = this.steps[id];
return rcref(info.assignedNtC === 'NANT' ? info.closestNtC : info.assignedNtC, where);
private ntcRef(step: StepInfo, where: 'sel'|'prev'|'next') {
return rcref(step.assignedNtC === 'NANT' ? step.closestNtC : step.assignedNtC, where);
}
private pyramidsParams(colors: NtCColors.Conformers, visible: Map<string, boolean>, transparent: boolean) {
......@@ -433,6 +432,32 @@ class ReDNATCOMspViewer {
PluginCommands.Camera.SetSnapshot(this.plugin, { snapshot, durationMs: AnimationDurationMsec });
}
private stepNext(currentIdx: number) {
if (currentIdx === this.steps.length - 1)
return void 0;
const currentStep = this.steps[currentIdx];
const cand1 = this.steps[currentIdx + 1];
if (!currentStep.altId2 || !cand1.altId1 || currentStep.altId2 === cand1.altId1)
return cand1; // Current step is "altId'd" and the candidate step has a matching altId
if (currentIdx + 2 === this.steps.length)
return cand1; // Current step is "altId'd", candidate step has a mismatching altId but there are no more steps to try
const cand2 = this.steps[currentIdx + 2];
return cand2.resNo1 === currentStep.resNo2 ? cand2 : cand1;
}
private stepPrev(currentIdx: number) {
if (currentIdx === 0)
return void 0;
const currentStep = this.steps[currentIdx];
const cand1 = this.steps[currentIdx - 1];
if (!currentStep.altId1 || !cand1.altId2 || currentStep.altId1 === cand1.altId2)
return cand1; // Current step is "altId'd" and the candidate step has a matching altId
if (currentIdx - 2 < 0)
return cand1; // Current step is "altId'd", candidate step has a mismatching altId but there are no more steps to try
const cand2 = this.steps[currentIdx - 2];
return cand2.resNo2 === currentStep.resNo1 ? cand2 : cand1;
}
private substructureVisuals(representation: 'ball-and-stick'|'cartoon') {
switch (representation) {
case 'cartoon':
......@@ -454,9 +479,9 @@ class ReDNATCOMspViewer {
}
}
private superpose(reference: StructureElement.Loci, stru: StructureElement.Loci) {
private superpose(reference: StructureElement.Loci, stru: StructureElement.Loci, altId1?: string, altId2?: string) {
const refElems = dinucleotideBackbone(reference);
const struElems = dinucleotideBackbone(stru);
const struElems = dinucleotideBackbone(stru, altId1, altId2);
return Superpose.superposition(
{ elements: refElems, conformation: reference.elements[0].unit.conformation },
......@@ -579,7 +604,7 @@ class ReDNATCOMspViewer {
await b.commit();
}
gatherNtCInfo(): { steps: StepInfo[], stepNames: Map<string, number> }|undefined {
gatherStepInfo(): { steps: StepInfo[], stepNames: Map<string, number> }|undefined {
const obj = this.plugin.state.data.cells.get(IDs.ID('model', '', BaseRef))?.obj;
if (!obj)
return void 0;
......@@ -597,16 +622,24 @@ class ReDNATCOMspViewer {
const _ids = tableStep.getField('id');
const _names = tableStep.getField('name');
const _authSeqId1 = tableStep.getField('auth_seq_id_1');
const _authSeqId2 = tableStep.getField('auth_seq_id_2');
const _labelAltId1 = tableStep.getField('label_alt_id_1');
const _labelAltId2 = tableStep.getField('label_alt_id_2');
const _stepIds = tableSum.getField('step_id');
const _assignedNtCs = tableSum.getField('assigned_NtC');
const _closestNtCs = tableSum.getField('closest_NtC');
if (!_ids || !_names || !_stepIds || !_assignedNtCs || !_closestNtCs) {
if (!_ids || !_names || !_stepIds || !_assignedNtCs || !_closestNtCs || !_labelAltId1 || !_labelAltId2 || !_authSeqId1 || !_authSeqId2) {
console.warn('Expected fields are not present in NtC categories');
return void 0;
}
const ids = _ids.toIntArray();
const names = _names.toStringArray();
const authSeqId1 = _authSeqId1.toIntArray();
const authSeqId2 = _authSeqId2.toIntArray();
const labelAltId1 = _labelAltId1.toStringArray();
const labelAltId2 = _labelAltId2.toStringArray();
const stepIds = _stepIds.toIntArray();
const assignedNtCs = _assignedNtCs.toStringArray();
const closestNtCs = _closestNtCs.toStringArray();
......@@ -622,9 +655,13 @@ class ReDNATCOMspViewer {
if (stepIds[jdx] === id) {
const assignedNtC = assignedNtCs[jdx];
const closestNtC = closestNtCs[jdx];
const resNo1 = authSeqId1[jdx];
const resNo2 = authSeqId2[jdx];
const altId1 = labelAltId1[jdx] === '' ? void 0 : labelAltId1[jdx];
const altId2 = labelAltId2[jdx] === '' ? void 0 : labelAltId2[jdx];
// We're assuming that steps are ID'd with a contigious, monotonic sequence starting from 1
steps[id - 1] = { name, assignedNtC, closestNtC };
steps[id - 1] = { name, assignedNtC, closestNtC, resNo1, resNo2, altId1, altId2 };
stepNames.set(name, id - 1);
break;
}
......@@ -751,7 +788,7 @@ class ReDNATCOMspViewer {
this.haveMultipleModels = this.getModelCount() > 1;
const ntcInfo = this.gatherNtCInfo();
const ntcInfo = this.gatherStepInfo();
if (!ntcInfo) {
this.steps.length = 0;
this.stepNames.clear();
......@@ -836,8 +873,8 @@ class ReDNATCOMspViewer {
const stepDesc = Step.fromName(stepName);
if (!stepDesc)
return;
const stepId = this.stepNames.get(stepName);
if (stepId === undefined) {
const stepIdx = this.stepNames.get(stepName);
if (stepIdx === undefined) {
console.error(`Unknown step name ${stepName}`);
return;
}
......@@ -868,15 +905,16 @@ class ReDNATCOMspViewer {
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;
const step = this.steps[stepIdx];
const stepPrev = this.stepPrev(stepIdx);
const stepNext = this.stepNext(stepIdx);
const ntcRefSel = this.ntcRef(stepId, 'sel');
const ntcRefPrev = this.ntcRef(stepIdPrev, 'prev');
const ntcRefNext = this.ntcRef(stepIdNext, 'next');
const ntcRefSel = step ? this.ntcRef(step, 'sel') : void 0;
const ntcRefPrev = stepPrev ? this.ntcRef(stepPrev, 'prev') : void 0;
const ntcRefNext = stepNext ? this.ntcRef(stepNext, 'next') : void 0;
if (!ntcRefSel) {
console.error(`stepId ${stepId} does not map to a known step`);
console.error(`stepIdx ${stepIdx} does not map to a known step`);
return;
}
......@@ -885,12 +923,12 @@ class ReDNATCOMspViewer {
.delete(IDs.ID('superposition', '', NtCSupPrev))
.delete(IDs.ID('superposition', '', NtCSupNext));
const addReference = (ntcRef: string, superposRef: string, loci: Loci, color: number) => {
const addReference = (ntcRef: string, superposRef: string, loci: Loci, altId1: string|undefined, altId2: string|undefined, 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));
if (loci.kind === 'element-loci' && Step.is(loci)) {
const { bTransform, rmsd } = this.superpose(refLoci, loci);
const { bTransform, rmsd } = this.superpose(refLoci, loci, altId1, altId2);
if (isNaN(bTransform[0])) {
console.error(`Cannot superpose reference conformer ${ntcRef} onto selection`);
return;
......@@ -909,11 +947,15 @@ class ReDNATCOMspViewer {
}
};
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);
const rmsd = addReference(ntcRefSel, NtCSupSel, selLoci, stepDesc.altId1, stepDesc.altId2, 0x008000);
if (ntcRefPrev) {
const { altId1, altId2 } = stepPrev!;
addReference(ntcRefPrev, NtCSupPrev, Loci.normalize(Traverse.residue(-1, altId1, selLoci), 'two-residues'), altId1, altId2, 0x0000FF);
}
if (ntcRefNext) {
const { altId1, altId2 } = stepNext!;
addReference(ntcRefNext, NtCSupNext, Loci.normalize(Traverse.residue(1, altId1, selLoci), 'two-residues'), altId1, altId2, 0x00FFFF);
}
b.commit();
......@@ -986,7 +1028,9 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
if (!this.viewer)
return;
if (cmd.type === 'select-step') {
if (cmd.type === 'redraw')
window.dispatchEvent(new Event('resize'));
else 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())
......
src/apps/rednatco/traverse.ts
+ 7
− 6
View file @ 221e3ce6
......@@ -7,16 +7,17 @@ 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) {
export function residueAltIds(structure: Structure, unit: Unit, residue: Residue) {
const altIds = new Array<string>();
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;
if (altId !== '' && !altIds.includes(altId))
altIds.push(altId);
}
return void 0;
return altIds;
}
export function findResidue(asymId: string, seqId: number, altId: string|undefined, loci: StructureElement.Loci, source: 'label'|'auth') {
......@@ -46,8 +47,8 @@ export namespace Traverse {
const _seqId = getSeqId(loc);
if (_seqId === seqId) {
if (altId) {
const _altId = residueAltId(loci.structure, e.unit, residue);
if (_altId && _altId !== altId)
const _altIds = residueAltIds(loci.structure, e.unit, residue);
if (!_altIds.includes(altId))
continue;
}
......
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