diff --git a/src/apps/rednatco/api-impl.ts b/src/apps/rednatco/api-impl.ts
index fa36829f0dd9f3091b37389f0013c2d141db6b54..d9940fa8a9aa682c23732779d988afc26e2e226a 100644
--- a/src/apps/rednatco/api-impl.ts
+++ b/src/apps/rednatco/api-impl.ts
@@ -34,9 +34,9 @@ export class ReDNATCOMspApiImpl implements ReDNATCOMspApi.Object {
return !!this.target;
}
- loadStructure(coords: { data: string, type: 'cif'|'pdb' }, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6'|'ds' }|null) {
+ loadStructure(coords: { data: string, type: 'cif'|'pdb' }, densityMaps: { data: Uint8Array, type: 'ccp4'|'dsn6', kind: '2fo-fc'|'fo-fc'|'em' }[]|null) {
this.check();
- this.target!.loadStructure(coords, densityMap);
+ this.target!.loadStructure(coords, densityMaps);
}
query<T extends ReDNATCOMspApi.Queries.Type>(type: T): ReDNATCOMspApi.ResponseTypes[T] {
diff --git a/src/apps/rednatco/api.ts b/src/apps/rednatco/api.ts
index 07d281d5a2d2a82b5a18bf1e5b5915b9fa862fd8..09a30b75b6e6a3223376caf251c4952643874e06 100644
--- a/src/apps/rednatco/api.ts
+++ b/src/apps/rednatco/api.ts
@@ -126,7 +126,7 @@ export namespace ReDNATCOMspApi {
event: (evt: Event) => void;
init: (elemId: string, onEvent?: (evt: Event) => void) => void;
isReady: () => boolean;
- loadStructure: (coords: { data: string, type: 'cif'|'pdb'}, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6'|'ds' }|null) => void;
+ loadStructure: (coords: { data: string, type: 'cif'|'pdb'}, densityMaps: { data: Uint8Array, type: 'ccp4'|'dsn6', kind: '2fo-fc'|'fo-fc'|'em' }[]|null) => void;
query: <T extends Queries.Type>(type: T) => ResponseTypes[T];
}
}
diff --git a/src/apps/rednatco/controls.tsx b/src/apps/rednatco/controls.tsx
index 5c720989e87a9eb47959b79fdc2775e699001344..572d184203435c52797a7ab78c7fda5eda641234 100644
--- a/src/apps/rednatco/controls.tsx
+++ b/src/apps/rednatco/controls.tsx
@@ -1,5 +1,6 @@
import React from 'react';
-import { fuzzyCmp, numDecimals, reduceDecimals, stof } from './util';
+import { fuzzyCmp, luminance, numDecimals, reduceDecimals, stof } from './util';
+import { Color } from '../../mol-util/color';
const Zero = '0'.charCodeAt(0);
const Nine = '9'.charCodeAt(0);
@@ -57,6 +58,20 @@ export namespace CollapsibleVertical {
}
}
+export class ColorBox extends React.Component<{ caption: string, color: Color }> {
+ render() {
+ const lum = luminance(this.props.color);
+ return (
+ <div
+ className='rmsp-color-box'
+ style={{ backgroundColor: Color.toStyle(this.props.color) }}
+ >
+ <span style={{ color: lum > 0.6 ? 'black' : 'white', margin: '0.15em' }}>{this.props.caption}</span>
+ </div>
+ );
+ }
+}
+
export class PushButton extends React.Component<{ text: string, enabled: boolean, onClick: () => void }> {
render() {
return (
diff --git a/src/apps/rednatco/density-map-controls.tsx b/src/apps/rednatco/density-map-controls.tsx
index 750a3066e1ec638b1d54ddd9e1262325f734a8d7..e454a042511b16b17a4e2eb77d108f915e6a63e1 100644
--- a/src/apps/rednatco/density-map-controls.tsx
+++ b/src/apps/rednatco/density-map-controls.tsx
@@ -1,32 +1,74 @@
import React from 'react';
-import { CollapsibleVertical, RangeSlider, SpinBox, ToggleButton } from './controls';
-import { isoToFixed } from './util';
+import { ColorPicker } from './color-picker';
+import { CollapsibleVertical, ColorBox, RangeSlider, SpinBox, ToggleButton } from './controls';
+import { DensityMapDisplay, DensityMapKind } from './index';
+import { isoBounds, isoToFixed } from './util';
+import { ReDNATCOMspViewer as Viewer } from './viewer';
+import { Color } from '../../mol-util/color';
export class DensityMapControls extends React.Component<DensityMapControls.Props> {
- render() {
- return (
- <CollapsibleVertical caption='Density map'>
- <div className='rmsp-controls'>
+ private colors(index: number, colors: DensityMapDisplay['colors']) {
+ const elems = new Array<JSX.Element>();
+
+ for (let idx = 0; idx < colors.length; idx++) {
+ const c = colors[idx];
+ const e =
+ <div className='rmsp-control-item'
+ key={idx}
+ style={{ backgroundColor: Color.toHexString(c.color) }}
+ onClick={(evt) => {
+ ColorPicker.create(
+ evt,
+ c.color,
+ (color) => {
+ colors[idx] = { ...colors[idx], color: Color(color) },
+ this.props.changeColors(index, colors);
+ }
+ );
+ }}
+ >
+ <ColorBox
+ caption={c.name}
+ color={c.color}
+ />
+ </div>;
+ elems.push(e);
+ }
+
+ return elems;
+ }
+
+ private controls(display: DensityMapDisplay[]) {
+ const ctrls = new Array<JSX.Element>();
+
+ for (let idx = 0; idx < display.length; idx++) {
+ const isoRange = this.props.viewer.densityMapIsoRange(idx);
+ const _isoBounds = isoRange ? isoBounds(isoRange.min, isoRange.max) : { min: 0, max: 0, step: 0 };
+
+ const d = display[idx];
+ const elem = (
+ <React.Fragment key={idx}>
<div className='rmsp-controls-section-caption'>
- Representations:
+ {this.mapName(d.kind)}
</div>
<div className='rmsp-controls-line'>
<div className='rmsp-control-item'>
<ToggleButton
text='Wireframe'
- switchedOn={this.props.wireframe}
- onClick={() => this.props.toggleWireframe()}
+ switchedOn={d.representations.includes('wireframe')}
+ onClick={() => this.props.toggleWireframe(idx)}
enabled={true}
/>
</div>
<div className='rmsp-control-item'>
<ToggleButton
text='Solid'
- switchedOn={this.props.solid}
- onClick={() => this.props.toggleSolid()}
+ switchedOn={d.representations.includes('solid')}
+ onClick={() => this.props.toggleSolid(idx)}
enabled={true}
/>
</div>
+ { this.colors(idx, d.colors) }
</div>
<div className='rmsp-controls-section-caption'>
@@ -35,22 +77,22 @@ export class DensityMapControls extends React.Component<DensityMapControls.Props
<div className='rmsp-controls-line'>
<div className='rmsp-control-item'>
<RangeSlider
- min={this.props.isoMin}
- max={this.props.isoMax}
- step={this.props.isoStep}
- value={isoToFixed(this.props.iso, this.props.isoStep)}
- onChange={(v) => this.props.changeIso(v!)}
+ min={_isoBounds.min}
+ max={_isoBounds.max}
+ step={_isoBounds.step}
+ value={isoToFixed(d.isoValue, _isoBounds.step)}
+ onChange={(v) => this.props.changeIso(idx, v!)}
/>
</div>
- <div className='rmsp-control-item'>
+ <div className='rmsp-control-item-squished'>
<div style={{ display: 'grid', gridTemplateColumns: '4em 1fr' }}>
<SpinBox
- min={this.props.isoMin}
- max={this.props.isoMax}
- step={this.props.isoStep}
- maxNumDecimals={Math.log10(this.props.isoStep) >= 0 ? 0 : -Math.log10(this.props.isoStep)}
- value={isoToFixed(this.props.iso, this.props.isoStep)}
- onChange={(n) => this.props.changeIso(n)}
+ min={_isoBounds.min}
+ max={_isoBounds.max}
+ step={_isoBounds.step}
+ maxNumDecimals={Math.log10(_isoBounds.step) >= 0 ? 0 : -Math.log10(_isoBounds.step)}
+ value={isoToFixed(d.isoValue, _isoBounds.step)}
+ onChange={(n) => this.props.changeIso(idx, n)}
pathPrefix=''
/>
<div />
@@ -67,24 +109,48 @@ export class DensityMapControls extends React.Component<DensityMapControls.Props
min={0}
max={100}
step={1}
- value={(1.0 - this.props.alpha) * 100}
- onChange={(n) => this.props.changeAlpha(1.0 - (n! / 100))}
+ value={(1.0 - d.alpha) * 100}
+ onChange={(n) => this.props.changeAlpha(idx, 1.0 - (n! / 100))}
/>
</div>
- <div className='rmsp-control-item'>
+ <div className='rmsp-control-item-squished'>
<div style={{ display: 'grid', gridTemplateColumns: '4em 1fr' }}>
<SpinBox
min={0}
max={100}
step={1}
maxNumDecimals={0}
- value={(1.0 - this.props.alpha) * 100}
- onChange={(n) => this.props.changeAlpha(1.0 - (n / 100))}
+ value={(1.0 - d.alpha) * 100}
+ onChange={(n) => this.props.changeAlpha(idx, 1.0 - (n / 100))}
pathPrefix=''
/>
</div>
</div>
</div>
+ </React.Fragment>
+ );
+ ctrls.push(elem);
+ }
+
+ return ctrls;
+ }
+
+ private mapName(kind: DensityMapKind) {
+ switch (kind) {
+ case '2fo-fc':
+ return <span>2Fo-Fc</span>;
+ case 'fo-fc':
+ return <span>Fo-Fc</span>;
+ case 'em':
+ return <span>EM map</span>;
+ }
+ }
+
+ render() {
+ return (
+ <CollapsibleVertical caption='Density map'>
+ <div className='rmsp-controls'>
+ {this.controls(this.props.display)}
</div>
</CollapsibleVertical>
);
@@ -93,18 +159,13 @@ export class DensityMapControls extends React.Component<DensityMapControls.Props
export namespace DensityMapControls {
export interface Props {
- wireframe: boolean;
- solid: boolean;
- toggleWireframe: () => void;
- toggleSolid: () => void;
-
- isoMin: number;
- isoMax: number;
- isoStep: number;
- iso: number;
- changeIso: (iso: number) => void;
+ viewer: Viewer;
+ display: DensityMapDisplay[];
- alpha: number;
- changeAlpha: (alpha: number) => void;
+ toggleWireframe: (index: number) => void;
+ toggleSolid: (index: number) => void;
+ changeIso: (index: number, iso: number) => void;
+ changeAlpha: (index: number, alpha: number) => void;
+ changeColors: (index: number, colors: DensityMapDisplay['colors']) => void;
}
}
diff --git a/src/apps/rednatco/idents.ts b/src/apps/rednatco/idents.ts
index 91b5b4c91d599df50d24dd472a644c1cd9770b2d..4a0df1b229b2c4961595bc2f72c50b4f4b8dc440 100644
--- a/src/apps/rednatco/idents.ts
+++ b/src/apps/rednatco/idents.ts
@@ -18,9 +18,10 @@ export function ID(id: ID, sub: Substructure|'', ref: string) {
}
export type DensityID = 'data'|'volume'|'visual';
+// export type DensityKind = 'absolute'|'difference-positive'|'difference-negative';
-export function DensityID(id: DensityID, ref: string) {
- return `${ref}_density-map_${id}`;
+export function DensityID(index: number, id: DensityID, ref: string) {
+ return `${ref}_density-map_${index}_${id}`;
}
export function isVisual(ident: string) {
diff --git a/src/apps/rednatco/index.tsx b/src/apps/rednatco/index.tsx
index f341c19528a695b085896acc37a901899189cde4..010f6db2b581f98e1e82a9b0eb16d3076734416a 100644
--- a/src/apps/rednatco/index.tsx
+++ b/src/apps/rednatco/index.tsx
@@ -7,8 +7,8 @@ import { Filters } from './filters';
import { ReDNATCOMspViewer } from './viewer';
import { NtCColors } from './colors';
import { ColorPicker } from './color-picker';
-import { CollapsibleVertical, PushButton, ToggleButton } from './controls';
-import { isoBounds, luminance, toggleArray } from './util';
+import { CollapsibleVertical, ColorBox, PushButton, ToggleButton } from './controls';
+import { toggleArray } from './util';
import { Color } from '../../mol-util/color';
import { assertUnreachable } from '../../mol-util/type-helpers';
import './index.html';
@@ -27,10 +27,24 @@ const ConformersByClass = {
type ConformersByClass = typeof ConformersByClass;
const DefaultChainColor = Color(0xD9D9D9);
-const DefaultDensityMapAlpha = 0.5;
+const DefaultDensityMapAlpha = 0.25;
const DefaultWaterColor = Color(0x0BB2FF);
export type VisualRepresentations = 'ball-and-stick'|'cartoon';
export type DensityMapRepresentation = 'wireframe'|'solid';
+export type DensityMapKind = '2fo-fc'|'fo-fc'|'em';
+
+export const DefaultDensityDifferencePositiveColor = Color(0x00C300);
+export const DefaultDensityDifferenceNegativeColor = Color(0xC30000);
+export const DefaultDensityMapColor = Color(0x009DFF);
+const DefaultDensityMapDisplay = {
+ kind: '2fo-fc' as DensityMapKind,
+ representations: ['solid'] as DensityMapRepresentation[],
+ isoValue: 0,
+
+ alpha: DefaultDensityMapAlpha,
+ colors: [{ color: DefaultDensityMapColor, name: 'Color' }],
+};
+export type DensityMapDisplay = typeof DefaultDensityMapDisplay;
const Display = {
structures: {
@@ -53,13 +67,7 @@ const Display = {
chainColor: DefaultChainColor,
waterColor: DefaultWaterColor,
},
- densityMap: {
- representations: ['wireframe'] as DensityMapRepresentation[],
- isoValue: 0,
-
- alpha: DefaultDensityMapAlpha,
- color: 0x000000
- },
+ densityMaps: [] as DensityMapDisplay[],
};
export type Display = typeof Display;
@@ -69,20 +77,6 @@ function capitalize(s: string) {
return s[0].toLocaleUpperCase() + s.slice(1);
}
-class ColorBox extends React.Component<{ caption: string, color: Color }> {
- render() {
- const lum = luminance(this.props.color);
- return (
- <div
- className='rmsp-color-box'
- style={{ backgroundColor: Color.toStyle(this.props.color) }}
- >
- <span style={{ color: lum > 0.6 ? 'black' : 'white' }}>{this.props.caption}</span>
- </div>
- );
- }
-}
-
interface State {
display: Display;
showControls: boolean;
@@ -231,11 +225,32 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
}
}
- loadStructure(coords: { data: string, type: 'pdb'|'cif' }, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6'|'ds' }|null) {
+ loadStructure(coords: { data: string, type: 'pdb'|'cif' }, densityMaps: { data: Uint8Array, type: 'ccp4'|'dsn6', kind: '2fo-fc'|'fo-fc'|'em' }[]|null) {
if (this.viewer) {
- this.viewer.loadStructure(coords, densityMap, this.state.display).then(() => {
+ const display = { ...this.state.display };
+ if (densityMaps) {
+ display.densityMaps.length = densityMaps.length;
+ for (let idx = 0; idx < densityMaps.length; idx++) {
+ const dm = densityMaps[idx];
+
+ if (dm.kind === 'fo-fc') {
+ display.densityMaps[idx] = {
+ ...DefaultDensityMapDisplay,
+ kind: dm.kind,
+ colors: [
+ { color: DefaultDensityDifferencePositiveColor, name: '+ color' },
+ { color: DefaultDensityDifferenceNegativeColor, name: '- color' },
+ ],
+ };
+ } else
+ display.densityMaps[idx] = { ...DefaultDensityMapDisplay, kind: dm.kind };
+ }
+ } else
+ display.densityMaps.length = 0;
+
+ this.viewer.loadStructure(coords, densityMaps, display).then(() => {
this.presentConformers = this.viewer!.getPresentConformers();
- this.forceUpdate();
+ this.setState({ ...this.state, display });
ReDNATCOMspApi.event(Api.Events.StructureLoaded());
});
}
@@ -271,9 +286,6 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
const hasProtein = this.viewer?.has('structure', 'protein') ?? false;
const hasWater = this.viewer?.has('structure', 'water') ?? false;
- const isoRange = this.viewer?.densityMapIsoRange();
- const _isoBounds = isoRange ? isoBounds(isoRange.min, isoRange.max) : { min: 0, max: 0, step: 0 };
-
return (
<div className='rmsp-app'>
<div id={this.props.elemId + '-viewer'} className='rmsp-viewer'></div>
@@ -500,44 +512,44 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
</div>
</div>
</CollapsibleVertical>
- {this.viewer?.hasDensityMap()
+ {this.viewer?.hasDensityMaps()
? <DensityMapControls
- wireframe={this.state.display.densityMap.representations.includes('wireframe')}
- toggleWireframe={() => {
+ viewer={this.viewer}
+ display={this.state.display.densityMaps}
+ toggleWireframe={(index) => {
const display = { ...this.state.display };
- display.densityMap.representations = toggleArray(display.densityMap.representations, 'wireframe');
+ display.densityMaps[index].representations = toggleArray(display.densityMaps[index].representations, 'wireframe');
- this.viewer!.changeDensityMap(display);
+ this.viewer!.changeDensityMap(index, display);
this.setState({ ...this.state, display });
}}
- solid={this.state.display.densityMap.representations.includes('solid')}
- toggleSolid={() => {
+ toggleSolid={(index) => {
const display = { ...this.state.display };
- display.densityMap.representations = toggleArray(display.densityMap.representations, 'solid');
+ display.densityMaps[index].representations = toggleArray(display.densityMaps[index].representations, 'solid');
- this.viewer!.changeDensityMap(display);
+ this.viewer!.changeDensityMap(index, display);
this.setState({ ...this.state, display });
}}
-
- isoMin={_isoBounds.min}
- isoMax={_isoBounds.max}
- isoStep={_isoBounds.step}
- iso={this.state.display.densityMap.isoValue}
- changeIso={(v) => {
+ changeIso={(index, v) => {
const display = { ...this.state.display };
- display.densityMap.isoValue = v;
+ display.densityMaps[index].isoValue = v;
- this.viewer!.changeDensityMap(display);
+ this.viewer!.changeDensityMap(index, display);
this.setState({ ...this.state, display });
}}
+ changeAlpha={(index, alpha) => {
+ const display = { ...this.state.display };
+ display.densityMaps[index].alpha = alpha;
- alpha={this.state.display.densityMap.alpha}
- changeAlpha={(alpha) => {
+ this.viewer!.changeDensityMap(index, display);
+ this.setState({ ...this.state, display });
+ }}
+ changeColors={(index, colors) => {
const display = { ...this.state.display };
- display.densityMap.alpha = alpha;
+ display.densityMaps[index].colors = colors;
- this.viewer!.changeDensityMap(display);
+ this.viewer!.changeDensityMap(index, display);
this.setState({ ...this.state, display });
}}
/>
diff --git a/src/apps/rednatco/rednatco-molstar.css b/src/apps/rednatco/rednatco-molstar.css
index fddb76fdec5905731c5c7e0360845e52e3139919..5f33a4a53ebbb98fa22f0b20617dbd0a52db377a 100644
--- a/src/apps/rednatco/rednatco-molstar.css
+++ b/src/apps/rednatco/rednatco-molstar.css
@@ -79,6 +79,9 @@
flex: 1;
}
+.rmsp-control-item-squished {
+}
+
.rmsp-controls-line {
align-items: center;
display: flex;
diff --git a/src/apps/rednatco/viewer.ts b/src/apps/rednatco/viewer.ts
index aacf7a673e73650f3714bce1dc6b8f57325c09e2..a6c978d72a9b6ddd114f4e0b338ecce9b6976157 100644
--- a/src/apps/rednatco/viewer.ts
+++ b/src/apps/rednatco/viewer.ts
@@ -244,20 +244,28 @@ export class ReDNATCOMspViewer {
this.app = app;
}
- private densityMapVisuals(vis: Display['densityMap']) {
+ private densityMapVisuals(vis: Display['densityMaps'][0], visKind: 'absolute'|'positive'|'negative') {
+ const isoValue = visKind === 'absolute'
+ ? Volume.IsoValue.absolute(vis.isoValue)
+ : visKind === 'positive'
+ ? Volume.IsoValue.relative(vis.isoValue) : Volume.IsoValue.relative(-vis.isoValue);
+
+ const color = visKind === 'absolute' || visKind === 'positive'
+ ? vis.colors[0] : vis.colors[1]
+
return {
type: {
name: 'isosurface',
params: {
alpha: vis.alpha,
- isoValue: Volume.IsoValue.absolute(vis.isoValue),
+ isoValue,
visuals: vis.representations,
sizeFactor: 0.75,
}
},
colorTheme: {
name: 'uniform',
- params: { value: Color(vis.color) },
+ params: { value: Color(color.color) },
},
};
}
@@ -649,22 +657,41 @@ export class ReDNATCOMspViewer {
await b.commit();
}
- async changeDensityMap(display: Display) {
- if (!this.hasDensityMap())
+ async changeDensityMap(index: number, display: Display) {
+ if (!this.hasDensityMaps())
return;
- const b = this.plugin.state.data.build().to(IDs.DensityID('visual', BaseRef));
- const vis = display.densityMap;
+ const dm = display.densityMaps[index];
- b.update(
- StateTransforms.Representation.VolumeRepresentation3D,
- old => ({
- ...old,
- ...this.densityMapVisuals(vis),
- })
- );
-
- await b.commit();
+ if (dm.kind === 'fo-fc') {
+ await this.plugin.state.data.build().to(IDs.DensityID(index, 'visual', BaseRef + '_pos'))
+ .update(
+ StateTransforms.Representation.VolumeRepresentation3D,
+ old => ({
+ ...old,
+ ...this.densityMapVisuals(dm, 'positive'),
+ })
+ )
+ .to(IDs.DensityID(index, 'visual', BaseRef + '_neg'))
+ .update(
+ StateTransforms.Representation.VolumeRepresentation3D,
+ old => ({
+ ...old,
+ ...this.densityMapVisuals(dm, 'negative'),
+ })
+ )
+ .commit();
+ } else {
+ await this.plugin.state.data.build().to(IDs.DensityID(index, 'visual', BaseRef))
+ .update(
+ StateTransforms.Representation.VolumeRepresentation3D,
+ old => ({
+ ...old,
+ ...this.densityMapVisuals(dm, 'absolute'),
+ })
+ )
+ .commit();
+ }
}
currentModelNumber() {
@@ -674,8 +701,8 @@ export class ReDNATCOMspViewer {
return (model as StateObject<Model>).data.modelNum;
}
- densityMapIsoRange(ref = BaseRef): { min: number, max: number }|undefined {
- const cell = this.plugin.state.data.cells.get(IDs.DensityID('volume', ref));
+ densityMapIsoRange(index: number, ref = BaseRef): { min: number, max: number }|undefined {
+ const cell = this.plugin.state.data.cells.get(IDs.DensityID(index, 'volume', ref));
if (!cell || !cell.obj)
return void 0;
@@ -842,8 +869,8 @@ export class ReDNATCOMspViewer {
return !!this.plugin.state.data.cells.get(IDs.ID(id, sub, ref))?.obj?.data;
}
- hasDensityMap(ref = BaseRef) {
- return !!this.plugin.state.data.cells.get(IDs.DensityID('volume', ref))?.obj?.data;
+ hasDensityMaps(ref = BaseRef) {
+ return !!this.plugin.state.data.cells.get(IDs.DensityID(0, 'volume', ref))?.obj?.data;
}
isReady() {
@@ -852,7 +879,7 @@ export class ReDNATCOMspViewer {
async loadStructure(
coords: { data: string, type: 'pdb'|'cif' },
- densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6'|'ds' }|null,
+ densityMaps: { data: Uint8Array, type: 'ccp4'|'dsn6', kind: '2fo-fc'|'fo-fc'|'em' }[]|null,
display: Display
) {
// TODO: Remove the currently loaded structure
@@ -941,42 +968,54 @@ export class ReDNATCOMspViewer {
await b3.commit();
// Load density map, if any
- if (densityMap) {
- // This is ridiculous but anything saner breaks type checker
- if (densityMap.type === 'ccp4') {
- await this.plugin.state.data.build().toRoot()
- .apply(RawData, { data: densityMap.data }, { ref: IDs.DensityID('data', BaseRef) })
- .apply(StateTransforms.Data.ParseCcp4)
- .apply(StateTransforms.Volume.VolumeFromCcp4, {}, { ref: IDs.DensityID('volume', BaseRef) })
- .commit();
- } else if (densityMap.type === 'dsn6') {
- await this.plugin.state.data.build().toRoot()
- .apply(RawData, { data: densityMap.data }, { ref: IDs.DensityID('data', BaseRef) })
- .apply(StateTransforms.Data.ParseDsn6)
- .apply(StateTransforms.Volume.VolumeFromDsn6, {}, { ref: IDs.DensityID('volume', BaseRef) })
- .commit();
- } else if (densityMap.type === 'ds') {
- await this.plugin.state.data.build().toRoot()
- .apply(RawData, { data: densityMap.data }, { ref: IDs.DensityID('data', BaseRef) })
- .apply(StateTransforms.Data.ParseCif)
- .apply(StateTransforms.Volume.VolumeFromDensityServerCif, {}, { ref: IDs.DensityID('volume', BaseRef) })
- .commit();
- }
-
- const isoRange = this.densityMapIsoRange()!;
- const bounds = isoBounds(isoRange.min, isoRange.max);
- const iso = prettyIso(((isoRange.max - isoRange.min) / 2) + isoRange.min, bounds.step);
-
- display.densityMap.representations = ['wireframe'];
- display.densityMap.isoValue = iso;
+ if (densityMaps) {
+ for (let idx = 0; idx < densityMaps.length; idx++) {
+ const dm = densityMaps[idx];
+ if (dm.type === 'ccp4') {
+ await this.plugin.state.data.build().toRoot()
+ .apply(RawData, { data: dm.data }, { ref: IDs.DensityID(idx, 'data', BaseRef) })
+ .apply(StateTransforms.Data.ParseCcp4)
+ .apply(StateTransforms.Volume.VolumeFromCcp4, {}, { ref: IDs.DensityID(idx, 'volume', BaseRef) })
+ .commit();
+ } else if (dm.type === 'dsn6') {
+ await this.plugin.state.data.build().toRoot()
+ .apply(RawData, { data: dm.data }, { ref: IDs.DensityID(idx, 'data', BaseRef) })
+ .apply(StateTransforms.Data.ParseDsn6)
+ .apply(StateTransforms.Volume.VolumeFromDsn6, {}, { ref: IDs.DensityID(idx, 'volume', BaseRef) })
+ .commit();
+ }
- await this.plugin.state.data.build().to(IDs.DensityID('volume', BaseRef))
- .apply(
- StateTransforms.Representation.VolumeRepresentation3D,
- this.densityMapVisuals(display.densityMap),
- { ref: IDs.DensityID('visual', BaseRef) }
- )
- .commit();
+ const isoRange = this.densityMapIsoRange(idx)!;
+ const bounds = isoBounds(isoRange.min, isoRange.max);
+
+ if (dm.kind === 'fo-fc') {
+ display.densityMaps[idx].isoValue = prettyIso(isoRange.max * 0.67, bounds.step);
+
+ this.plugin.state.data.build().to(IDs.DensityID(idx, 'volume', BaseRef))
+ .apply(
+ StateTransforms.Representation.VolumeRepresentation3D,
+ this.densityMapVisuals(display.densityMaps[idx], 'positive'),
+ { ref: IDs.DensityID(idx, 'visual', BaseRef + '_pos') }
+ )
+ .to(IDs.DensityID(idx, 'volume', BaseRef))
+ .apply(
+ StateTransforms.Representation.VolumeRepresentation3D,
+ this.densityMapVisuals(display.densityMaps[idx], 'negative'),
+ { ref: IDs.DensityID(idx, 'visual', BaseRef + '_neg') }
+ )
+ .commit();
+ } else {
+ display.densityMaps[idx].isoValue = prettyIso(((isoRange.max - isoRange.min) / 2) + isoRange.min, bounds.step);
+
+ await this.plugin.state.data.build().to(IDs.DensityID(idx, 'volume', BaseRef))
+ .apply(
+ StateTransforms.Representation.VolumeRepresentation3D,
+ this.densityMapVisuals(display.densityMaps[idx], 'absolute'),
+ { ref: IDs.DensityID(idx, 'visual', BaseRef) }
+ )
+ .commit();
+ }
+ }
}
this.haveMultipleModels = this.getModelCount() > 1;