diff --git a/src/extensions/dnatco/confal-pyramids/behavior.ts b/src/extensions/dnatco/confal-pyramids/behavior.ts
index 6293e2b6cd60b8710dd2c0c3f68ea074980b2b52..7c34704ae344e745aa3ad5b0e0fc948d199dd588 100644
--- a/src/extensions/dnatco/confal-pyramids/behavior.ts
+++ b/src/extensions/dnatco/confal-pyramids/behavior.ts
@@ -8,7 +8,7 @@
import { ConfalPyramidsColorThemeProvider } from './color';
import { ConfalPyramids, ConfalPyramidsProvider } from './property';
import { ConfalPyramidsRepresentationProvider } from './representation';
-import { Loci } from '../../../mol-model/loci';
+import { ConfalPyramidsTypes } from './types';
import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../mol-plugin-state/builder/structure/representation-preset';
import { StateObjectRef } from '../../../mol-state';
@@ -56,21 +56,10 @@ export const DnatcoConfalPyramids = PluginBehavior.create<{ autoAttach: boolean,
description: 'Schematic depiction of conformer class and confal value.',
},
ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showToolTip: boolean }> {
-
private provider = ConfalPyramidsProvider;
- private labelConfalPyramids = {
- label: (loci: Loci): string | undefined => {
- if (!this.params.showToolTip) return void 0;
-
- /* TODO: Implement this */
- return void 0;
- }
- };
-
register(): void {
this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
- this.ctx.managers.lociLabels.addProvider(this.labelConfalPyramids);
this.ctx.representation.structure.themes.colorThemeRegistry.add(ConfalPyramidsColorThemeProvider);
this.ctx.representation.structure.registry.add(ConfalPyramidsRepresentationProvider);
@@ -88,7 +77,6 @@ export const DnatcoConfalPyramids = PluginBehavior.create<{ autoAttach: boolean,
unregister() {
this.ctx.customModelProperties.unregister(ConfalPyramidsProvider.descriptor.name);
- this.ctx.managers.lociLabels.removeProvider(this.labelConfalPyramids);
this.ctx.representation.structure.registry.remove(ConfalPyramidsRepresentationProvider);
this.ctx.representation.structure.themes.colorThemeRegistry.remove(ConfalPyramidsColorThemeProvider);
@@ -101,3 +89,13 @@ export const DnatcoConfalPyramids = PluginBehavior.create<{ autoAttach: boolean,
showToolTip: PD.Boolean(true)
})
});
+
+export function confalPyramidLabel(halfPyramid: ConfalPyramidsTypes.HalfPyramid) {
+ const { step } = halfPyramid;
+ return `
+ <b>${step.auth_asym_id_1}</b> |
+ <b>${step.label_comp_id_1} ${step.auth_seq_id_1}${step.PDB_ins_code_1}${step.label_alt_id_1.length > 0 ? ` (alt ${step.label_alt_id_1})` : ''}
+ ${step.label_comp_id_2} ${step.auth_seq_id_2}${step.PDB_ins_code_2}${step.label_alt_id_2.length > 0 ? ` (alt ${step.label_alt_id_2})` : ''} </b><br />
+ <i>NtC:</i> ${step.NtC} | <i>Confal score:</i> ${step.confal_score} | <i>RMSD:</i> ${step.rmsd.toFixed(2)}
+ `;
+}
diff --git a/src/extensions/dnatco/confal-pyramids/color.ts b/src/extensions/dnatco/confal-pyramids/color.ts
index 8bc71f0f37a411013cb26c629561cf44aa1192dc..1cf4ad87052d33ce98c58c19fe73c39bc8f08726 100644
--- a/src/extensions/dnatco/confal-pyramids/color.ts
+++ b/src/extensions/dnatco/confal-pyramids/color.ts
@@ -247,8 +247,8 @@ export function ConfalPyramidsColorTheme(ctx: ThemeDataContext, props: PD.Values
function color(location: Location, isSecondary: boolean): Color {
if (CPT.isLocation(location)) {
- const { pyramid, isLower } = location.data;
- const key = pyramid.NtC + `_${isLower ? 'Lwr' : 'Upr'}` as keyof PyramidsColors;
+ const { step, isLower } = location.data;
+ const key = step.NtC + `_${isLower ? 'Lwr' : 'Upr'}` as keyof PyramidsColors;
return colorMap[key] ?? ErrorColor;
}
diff --git a/src/extensions/dnatco/confal-pyramids/property.ts b/src/extensions/dnatco/confal-pyramids/property.ts
index 4417ebbc18816abdf6cd7fece1af9077b7d88574..dc141990ba2db5304821a795ac5ceaa494df05f8 100644
--- a/src/extensions/dnatco/confal-pyramids/property.ts
+++ b/src/extensions/dnatco/confal-pyramids/property.ts
@@ -16,7 +16,7 @@ import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
-export type ConfalPyramids = PropertyWrapper<CPT.PyramidsData | undefined >;
+export type ConfalPyramids = PropertyWrapper<CPT.StepsData | undefined>;
export namespace ConfalPyramids {
export const Schema = {
@@ -106,18 +106,19 @@ export const ConfalPyramidsProvider: CustomModelProperty.Provider<ConfalPyramids
type StepsSummaryTable = Table<typeof ConfalPyramids.Schema.ndb_struct_ntc_step_summary>;
function createPyramidsFromCif(model: Model,
- steps: Table<typeof ConfalPyramids.Schema.ndb_struct_ntc_step>,
- stepsSummary: StepsSummaryTable): CPT.PyramidsData {
- const pyramids = new Array<CPT.Pyramid>();
+ cifSteps: Table<typeof ConfalPyramids.Schema.ndb_struct_ntc_step>,
+ stepsSummary: StepsSummaryTable): CPT.StepsData {
+ const steps = new Array<CPT.Step>();
const names = new Map<string, number>();
- const locations = new Array<CPT.Location>();
+ const halfPyramids = new Array<CPT.HalfPyramid>();
let hasMultipleModels = false;
const {
id, PDB_model_number, name,
auth_asym_id_1, auth_seq_id_1, label_comp_id_1, label_alt_id_1, PDB_ins_code_1,
auth_asym_id_2, auth_seq_id_2, label_comp_id_2, label_alt_id_2, PDB_ins_code_2,
- _rowCount } = steps;
+ _rowCount
+ } = cifSteps;
if (_rowCount !== stepsSummary._rowCount) throw new Error('Inconsistent mmCIF data');
@@ -126,9 +127,13 @@ function createPyramidsFromCif(model: Model,
if (model_num !== model.modelNum)
hasMultipleModels = true;
- const { _NtC, _confal_score } = getNtCAndConfalScore(id.value(i), i, stepsSummary);
+ const {
+ NtC,
+ confal_score,
+ rmsd
+ } = getSummaryData(id.value(i), i, stepsSummary);
- const pyramid = {
+ const step = {
PDB_model_number: model_num,
name: name.value(i),
auth_asym_id_1: auth_asym_id_1.value(i),
@@ -141,30 +146,36 @@ function createPyramidsFromCif(model: Model,
label_comp_id_2: label_comp_id_2.value(i),
label_alt_id_2: label_alt_id_2.value(i),
PDB_ins_code_2: PDB_ins_code_2.value(i),
- confal_score: _confal_score,
- NtC: _NtC
+ confal_score,
+ NtC,
+ rmsd,
};
- pyramids.push(pyramid);
- names.set(pyramid.name, pyramids.length - 1);
+ steps.push(step);
+ names.set(step.name, steps.length - 1);
- locations.push(CPT.Location(pyramid, false));
- locations.push(CPT.Location(pyramid, true));
+ halfPyramids.push({ step, isLower: false });
+ halfPyramids.push({ step, isLower: true });
}
- return { pyramids, names, locations, hasMultipleModels };
+ return { steps, names, halfPyramids, hasMultipleModels };
}
-function getNtCAndConfalScore(id: number, i: number, stepsSummary: StepsSummaryTable) {
- const { step_id, confal_score, assigned_NtC } = stepsSummary;
+function getSummaryData(id: number, i: number, stepsSummary: StepsSummaryTable) {
+ const {
+ step_id,
+ confal_score,
+ assigned_NtC,
+ cartesian_rmsd_closest_NtC_representative,
+ } = stepsSummary;
// Assume that step_ids in ntc_step_summary are in the same order as steps in ntc_step
for (let j = i; j < stepsSummary._rowCount; j++) {
- if (id === step_id.value(j)) return { _NtC: assigned_NtC.value(j), _confal_score: confal_score.value(j) };
+ if (id === step_id.value(j)) return { NtC: assigned_NtC.value(j), confal_score: confal_score.value(j), rmsd: cartesian_rmsd_closest_NtC_representative.value(j) };
}
// Safety net for cases where the previous assumption is not met
for (let j = 0; j < i; j++) {
- if (id === step_id.value(j)) return { _NtC: assigned_NtC.value(j), _confal_score: confal_score.value(j) };
+ if (id === step_id.value(j)) return { NtC: assigned_NtC.value(j), confal_score: confal_score.value(j), rmsd: cartesian_rmsd_closest_NtC_representative.value(j) };
}
throw new Error('Inconsistent mmCIF data');
}
diff --git a/src/extensions/dnatco/confal-pyramids/representation.ts b/src/extensions/dnatco/confal-pyramids/representation.ts
index b0ce90b53e355ad33fcf2379bbe4445949868ed8..d8194e8b4b37b8fbbb99817feed798cb31053ca3 100644
--- a/src/extensions/dnatco/confal-pyramids/representation.ts
+++ b/src/extensions/dnatco/confal-pyramids/representation.ts
@@ -16,14 +16,14 @@ import { PrimitiveBuilder } from '../../../mol-geo/primitive/primitive';
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
import { EmptyLoci, Loci } from '../../../mol-model/loci';
-import { Structure, StructureProperties, Unit } from '../../../mol-model/structure';
+import { Structure, Unit } from '../../../mol-model/structure';
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../../mol-repr/representation';
import { StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder, UnitsRepresentation } from '../../../mol-repr/structure/representation';
import { UnitsMeshParams, UnitsMeshVisual, UnitsVisual } from '../../../mol-repr/structure/units-visual';
import { VisualUpdateState } from '../../../mol-repr/util';
import { VisualContext } from '../../../mol-repr/visual';
-import { getAltResidueLociFromId, StructureGroup } from '../../../mol-repr/structure/visual/util/common';
+import { StructureGroup } from '../../../mol-repr/structure/visual/util/common';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Theme, ThemeRegistryContext } from '../../../mol-theme/theme';
import { NullLocation } from '../../../mol-model/location';
@@ -58,13 +58,13 @@ function createConfalPyramidsIterator(structureGroup: StructureGroup): LocationI
return LocationIterator(0, 1, 1, () => NullLocation);
}
- const { locations } = prop.data;
+ const { halfPyramids } = prop.data;
const getLocation = (groupIndex: number, instanceIndex: number) => {
- if (locations.length <= groupIndex) return NullLocation;
- return locations[groupIndex];
+ if (halfPyramids.length <= groupIndex) return NullLocation;
+ return CPT.Location(halfPyramids[groupIndex]);
};
- return LocationIterator(locations.length, instanceCount, 1, getLocation);
+ return LocationIterator(halfPyramids.length, instanceCount, 1, getLocation);
}
function createConfalPyramidsMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<ConfalPyramidsMeshParams>, mesh?: Mesh) {
@@ -73,16 +73,16 @@ function createConfalPyramidsMesh(ctx: VisualContext, unit: Unit, structure: Str
const prop = ConfalPyramidsProvider.get(structure.model).value;
if (prop === undefined || prop.data === undefined) return Mesh.createEmpty(mesh);
- const { pyramids } = prop.data;
- if (pyramids.length === 0) return Mesh.createEmpty(mesh);
+ const { steps } = prop.data;
+ if (steps.length === 0) return Mesh.createEmpty(mesh);
const mb = MeshBuilder.createState(512, 512, mesh);
- const handler = (pyramid: CPT.Pyramid, first: ConfalPyramidsUtil.FirstResidueAtoms, second: ConfalPyramidsUtil.SecondResidueAtoms, firsLocIndex: number, secondLocIndex: number) => {
+ const handler = (step: CPT.Step, first: ConfalPyramidsUtil.FirstResidueAtoms, second: ConfalPyramidsUtil.SecondResidueAtoms, firsLocIndex: number, secondLocIndex: number) => {
if (firsLocIndex === -1 || secondLocIndex === -1)
throw new Error('Invalid location index');
- const scale = (pyramid.confal_score - 20.0) / 100.0;
+ const scale = (step.confal_score - 20.0) / 100.0;
const O3 = first.O3.pos;
const OP1 = second.OP1.pos; const OP2 = second.OP2.pos; const O5 = second.O5.pos; const P = second.P.pos;
@@ -127,13 +127,12 @@ function getConfalPyramidLoci(pickingId: PickingId, structureGroup: StructureGro
const prop = ConfalPyramidsProvider.get(structure.model).value;
if (prop === undefined || prop.data === undefined) return EmptyLoci;
- const { locations } = prop.data;
+ const { halfPyramids } = prop.data;
- if (locations.length <= groupId) return EmptyLoci;
- const altId = StructureProperties.atom.label_alt_id(CPT.toElementLocation(locations[groupId]));
- const rI = unit.residueIndex[locations[groupId].element.element];
+ if (halfPyramids.length <= groupId) return EmptyLoci;
+ const hp = halfPyramids[groupId];
- return getAltResidueLociFromId(structure, unit, rI, altId);
+ return CPT.Loci(hp, [{}]);
}
function eachConfalPyramid(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
diff --git a/src/extensions/dnatco/confal-pyramids/types.ts b/src/extensions/dnatco/confal-pyramids/types.ts
index b7a94099885cb2aa5e37094cb6bb100c355b2392..0e59626927f632392491125ad3f6452bf93aa809 100644
--- a/src/extensions/dnatco/confal-pyramids/types.ts
+++ b/src/extensions/dnatco/confal-pyramids/types.ts
@@ -6,10 +6,13 @@
*/
import { DataLocation } from '../../../mol-model/location';
-import { ElementIndex, Structure, StructureElement, Unit } from '../../../mol-model/structure';
+import { DataLoci } from '../../../mol-model/loci';
+import { confalPyramidLabel } from './behavior';
export namespace ConfalPyramidsTypes {
- export type Pyramid = {
+ export const DataTag = 'dnatco-confal-half-pyramid';
+
+ export type Step = {
PDB_model_number: number,
name: string,
auth_asym_id_1: string,
@@ -23,38 +26,39 @@ export namespace ConfalPyramidsTypes {
label_alt_id_2: string,
PDB_ins_code_2: string,
confal_score: number,
- NtC: string
+ NtC: string,
+ rmsd: number,
}
- export interface PyramidsData {
- pyramids: Array<Pyramid>,
+ export interface StepsData {
+ steps: Array<Step>,
names: Map<string, number>,
- locations: Array<Location>,
+ halfPyramids: Array<HalfPyramid>,
hasMultipleModels: boolean
}
- export interface LocationData {
- readonly pyramid: Pyramid
- readonly isLower: boolean;
- }
-
- export interface Element {
- structure: Structure;
- unit: Unit.Atomic;
- element: ElementIndex;
+ export interface HalfPyramid {
+ step: Step,
+ isLower: boolean,
}
- export interface Location extends DataLocation<LocationData, Element> {}
+ export interface Location extends DataLocation<HalfPyramid, {}> {}
- export function Location(pyramid: Pyramid, isLower: boolean, structure?: Structure, unit?: Unit.Atomic, element?: ElementIndex) {
- return DataLocation('pyramid', { pyramid, isLower }, { structure: structure as any, unit: unit as any, element: element as any });
+ export function Location(halfPyramid: HalfPyramid) {
+ return DataLocation(DataTag, halfPyramid, {});
}
export function isLocation(x: any): x is Location {
- return !!x && x.kind === 'data-location' && x.tag === 'pyramid';
+ return !!x && x.kind === 'data-location' && x.tag === DataTag;
+ }
+
+ export interface Loci extends DataLoci<HalfPyramid, {}> {}
+
+ export function Loci(data: HalfPyramid, elements: ReadonlyArray<{}>): Loci {
+ return DataLoci(DataTag, data, elements, undefined, () => confalPyramidLabel(data));
}
- export function toElementLocation(location: Location) {
- return StructureElement.Location.create(location.element.structure, location.element.unit, location.element.element);
+ export function isLoci(x: any): x is Loci {
+ return !!x && x.kind === 'data-loci' && x.tag === DataTag;
}
}
diff --git a/src/extensions/dnatco/confal-pyramids/util.ts b/src/extensions/dnatco/confal-pyramids/util.ts
index 467734af416ccba7b34fdf65e64b3e80abf30535..698a34e6d83fe295da1ce6454d788905be90e864 100644
--- a/src/extensions/dnatco/confal-pyramids/util.ts
+++ b/src/extensions/dnatco/confal-pyramids/util.ts
@@ -42,7 +42,7 @@ export namespace ConfalPyramidsUtil {
ins_code: string,
};
- export type Handler = (pyramid: CPT.Pyramid, first: FirstResidueAtoms, second: SecondResidueAtoms, firstLocIndex: number, secondLocIndex: number) => void;
+ export type Handler = (pyramid: CPT.Step, first: FirstResidueAtoms, second: SecondResidueAtoms, firstLocIndex: number, secondLocIndex: number) => void;
function residueInfoFromLocation(loc: StructureElement.Location): ResidueInfo {
return {
@@ -77,11 +77,11 @@ export namespace ConfalPyramidsUtil {
}
class Utility {
- protected getPyramidByName(name: string): { pyramid: CPT.Pyramid | undefined, index: number } {
+ protected getPyramidByName(name: string): { pyramid: CPT.Step | undefined, index: number } {
const index = this.data.names.get(name);
if (index === undefined) return { pyramid: undefined, index: -1 };
- return { pyramid: this.data.pyramids[index], index };
+ return { pyramid: this.data.steps[index], index };
}
protected stepToName(entry_id: string, modelNum: number, locFirst: StructureElement.Location, locSecond: StructureElement.Location, fakeAltId_1: string, fakeAltId_2: string) {
@@ -107,7 +107,7 @@ export namespace ConfalPyramidsUtil {
this.modelNum = unit.model.modelNum;
}
- protected readonly data: CPT.PyramidsData;
+ protected readonly data: CPT.StepsData;
protected readonly hasMultipleModels: boolean;
protected readonly entryId: string;
protected readonly modelNum: number;
@@ -164,15 +164,7 @@ export namespace ConfalPyramidsUtil {
const name = this.stepToName(this.entryId, modelNum, firstLoc, secondLoc, first.O3.fakeAltId, second.OP1.fakeAltId);
const { pyramid, index } = this.getPyramidByName(name);
if (pyramid !== undefined) {
- const setLoc = (loc: CPT.Location, eI: ElementIndex) => {
- loc.element.structure = this.structure;
- loc.element.unit = this.unit;
- loc.element.element = eI;
- };
-
const locIndex = index * 2;
- setLoc(this.data.locations[locIndex], firstLoc.element);
- setLoc(this.data.locations[locIndex + 1], secondLoc.element);
this.handler(pyramid, first, second, locIndex, locIndex + 1);
ok = true;
}