From ba3eee8cade12ec09e90808ca89e8825b3c42834 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Sun, 10 Mar 2019 15:57:46 +0100
Subject: [PATCH] adder more static label options to structures, various fixes
---
src/mol-plugin/state/actions/structure.ts | 8 ++++----
src/mol-plugin/state/animation/built-in.ts | 6 ++++++
src/mol-plugin/state/transforms/data.ts | 14 +++++++-------
src/mol-plugin/state/transforms/misc.ts | 2 +-
src/mol-plugin/state/transforms/model.ts | 12 ++++++------
src/mol-plugin/state/transforms/representation.ts | 13 +++++++++----
src/mol-plugin/state/transforms/volume.ts | 4 ++--
src/mol-plugin/ui/controls/parameters.tsx | 3 ++-
src/mol-plugin/util/structure-labels.ts | 15 ++++++++++-----
src/mol-util/param-definition.ts | 7 ++++---
10 files changed, 51 insertions(+), 33 deletions(-)
diff --git a/src/mol-plugin/state/actions/structure.ts b/src/mol-plugin/state/actions/structure.ts
index 76b4b0d9f..714adecf2 100644
--- a/src/mol-plugin/state/actions/structure.ts
+++ b/src/mol-plugin/state/actions/structure.ts
@@ -69,8 +69,8 @@ export const GroProvider: DataFormatProvider<any> = {
//
const DownloadStructurePdbIdSourceOptions = PD.Group({
- supportProps: PD.asOptional(PD.Boolean(false)),
- asTrajectory: PD.asOptional(PD.Boolean(false, { description: 'Load all entries into a single trajectory.' }))
+ supportProps: PD.Optional(PD.Boolean(false)),
+ asTrajectory: PD.Optional(PD.Boolean(false, { description: 'Load all entries into a single trajectory.' }))
});
export { DownloadStructure };
@@ -97,7 +97,7 @@ const DownloadStructure = StateAction.build({
format: PD.Select('cif', [['cif', 'CIF'], ['pdb', 'PDB']]),
isBinary: PD.Boolean(false),
options: PD.Group({
- supportProps: PD.asOptional(PD.Boolean(false))
+ supportProps: PD.Optional(PD.Boolean(false))
})
}, { isFlat: true })
}, {
@@ -242,7 +242,7 @@ export const UpdateTrajectory = StateAction.build({
display: { name: 'Update Trajectory' },
params: {
action: PD.Select<'advance' | 'reset'>('advance', [['advance', 'Advance'], ['reset', 'Reset']]),
- by: PD.asOptional(PD.Numeric(1, { min: -1, max: 1, step: 1 }))
+ by: PD.Optional(PD.Numeric(1, { min: -1, max: 1, step: 1 }))
}
})(({ params, state }) => {
const models = state.selectQ(q => q.ofTransformer(StateTransforms.Model.ModelFromTrajectory));
diff --git a/src/mol-plugin/state/animation/built-in.ts b/src/mol-plugin/state/animation/built-in.ts
index 0c58a509e..308bc1bd6 100644
--- a/src/mol-plugin/state/animation/built-in.ts
+++ b/src/mol-plugin/state/animation/built-in.ts
@@ -113,6 +113,9 @@ export const AnimateAssemblyUnwind = PluginStateAnimation.create({
const update = state.build();
let changed = false;
for (const r of reprs) {
+ // TODO: find a better way to handle this, perhaps add a different state object??
+ if (r.transform.transformer === StateTransforms.Representation.StructureLabels3D) continue;
+
const unwinds = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D, r.transform.ref));
if (unwinds.length > 0) continue;
@@ -180,6 +183,9 @@ export const AnimateUnitsExplode = PluginStateAnimation.create({
const update = state.build();
let changed = false;
for (const r of reprs) {
+ // TODO: find a better way to handle this, perhaps add a different state object??
+ if (r.transform.transformer === StateTransforms.Representation.StructureLabels3D) continue;
+
const explodes = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Representation.ExplodeStructureRepresentation3D, r.transform.ref));
if (explodes.length > 0) continue;
diff --git a/src/mol-plugin/state/transforms/data.ts b/src/mol-plugin/state/transforms/data.ts
index d04b01d59..aa0554a56 100644
--- a/src/mol-plugin/state/transforms/data.ts
+++ b/src/mol-plugin/state/transforms/data.ts
@@ -25,8 +25,8 @@ const Download = PluginStateTransform.BuiltIn({
to: [SO.Data.String, SO.Data.Binary],
params: {
url: PD.Text('https://www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif', { description: 'Resource URL. Must be the same domain or support CORS.' }),
- label: PD.asOptional(PD.Text('')),
- isBinary: PD.asOptional(PD.Boolean(false, { description: 'If true, download data as binary (string otherwise)' }))
+ label: PD.Optional(PD.Text('')),
+ isBinary: PD.Optional(PD.Boolean(false, { description: 'If true, download data as binary (string otherwise)' }))
}
})({
apply({ params: p }, globalCtx: PluginContext) {
@@ -58,10 +58,10 @@ const DownloadBlob = PluginStateTransform.BuiltIn({
sources: PD.ObjectList({
id: PD.Text('', { label: 'Unique ID' }),
url: PD.Text('https://www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif', { description: 'Resource URL. Must be the same domain or support CORS.' }),
- isBinary: PD.asOptional(PD.Boolean(false, { description: 'If true, download data as binary (string otherwise)' })),
- canFail: PD.asOptional(PD.Boolean(false, { description: 'Indicate whether the download can fail and not be included in the blob as a result.' }))
+ isBinary: PD.Optional(PD.Boolean(false, { description: 'If true, download data as binary (string otherwise)' })),
+ canFail: PD.Optional(PD.Boolean(false, { description: 'Indicate whether the download can fail and not be included in the blob as a result.' }))
}, e => `${e.id}: ${e.url}`),
- maxConcurrency: PD.asOptional(PD.Numeric(4, { min: 1, max: 12, step: 1 }, { description: 'The maximum number of concurrent downloads.' }))
+ maxConcurrency: PD.Optional(PD.Numeric(4, { min: 1, max: 12, step: 1 }, { description: 'The maximum number of concurrent downloads.' }))
}
})({
apply({ params }, plugin: PluginContext) {
@@ -102,8 +102,8 @@ const ReadFile = PluginStateTransform.BuiltIn({
to: [SO.Data.String, SO.Data.Binary],
params: {
file: PD.File(),
- label: PD.asOptional(PD.Text('')),
- isBinary: PD.asOptional(PD.Boolean(false, { description: 'If true, open file as as binary (string otherwise)' }))
+ label: PD.Optional(PD.Text('')),
+ isBinary: PD.Optional(PD.Boolean(false, { description: 'If true, open file as as binary (string otherwise)' }))
}
})({
apply({ params: p }) {
diff --git a/src/mol-plugin/state/transforms/misc.ts b/src/mol-plugin/state/transforms/misc.ts
index 86f3d9611..69aac3a93 100644
--- a/src/mol-plugin/state/transforms/misc.ts
+++ b/src/mol-plugin/state/transforms/misc.ts
@@ -18,7 +18,7 @@ const CreateGroup = PluginStateTransform.BuiltIn({
to: SO.Group,
params: {
label: PD.Text('Group'),
- description: PD.asOptional(PD.Text(''))
+ description: PD.Optional(PD.Text(''))
}
})({
apply({ params }) {
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 57dd2bfa1..dd54e9dc4 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -71,12 +71,12 @@ const TrajectoryFromMmCif = PluginStateTransform.BuiltIn({
params(a) {
if (!a) {
return {
- blockHeader: PD.asOptional(PD.Text(void 0, { description: 'Header of the block to parse. If none is specifed, the 1st data block in the file is used.' }))
+ blockHeader: PD.Optional(PD.Text(void 0, { description: 'Header of the block to parse. If none is specifed, the 1st data block in the file is used.' }))
};
}
const { blocks } = a.data;
return {
- blockHeader: PD.asOptional(PD.Select(blocks[0] && blocks[0].header, blocks.map(b => [b.header, b.header] as [string, string]), { description: 'Header of the block to parse' }))
+ blockHeader: PD.Optional(PD.Select(blocks[0] && blocks[0].header, blocks.map(b => [b.header, b.header] as [string, string]), { description: 'Header of the block to parse' }))
};
}
})({
@@ -181,12 +181,12 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
to: SO.Molecule.Structure,
params(a) {
if (!a) {
- return { id: PD.asOptional(PD.Text('', { label: 'Assembly Id', description: 'Assembly Id. Value \'deposited\' can be used to specify deposited asymmetric unit.' })) };
+ return { id: PD.Optional(PD.Text('', { label: 'Assembly Id', description: 'Assembly Id. Value \'deposited\' can be used to specify deposited asymmetric unit.' })) };
}
const model = a.data;
const ids = model.symmetry.assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]);
ids.push(['deposited', 'Deposited']);
- return { id: PD.asOptional(PD.Select(ids[0][0], ids, { label: 'Asm Id', description: 'Assembly Id' })) };
+ return { id: PD.Optional(PD.Select(ids[0][0], ids, { label: 'Asm Id', description: 'Assembly Id' })) };
}
})({
apply({ a, params }, plugin: PluginContext) {
@@ -258,7 +258,7 @@ const StructureSelection = PluginStateTransform.BuiltIn({
to: SO.Molecule.Structure,
params: {
query: PD.Value<Expression>(MolScriptBuilder.struct.generator.all, { isHidden: true }),
- label: PD.asOptional(PD.Text('', { isHidden: true }))
+ label: PD.Optional(PD.Text('', { isHidden: true }))
}
})({
apply({ a, params, cache }) {
@@ -295,7 +295,7 @@ const UserStructureSelection = PluginStateTransform.BuiltIn({
to: SO.Molecule.Structure,
params: {
query: PD.ScriptExpression({ language: 'mol-script', expression: '(sel.atom.atom-groups :residue-test (= atom.resname ALA))' }),
- label: PD.asOptional(PD.Text(''))
+ label: PD.Optional(PD.Text(''))
}
})({
apply({ a, params, cache }) {
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index d13614ea4..b5c9e1a82 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -202,9 +202,13 @@ const StructureLabels3D = PluginStateTransform.BuiltIn({
target: PD.MappedStatic('residues', {
'elements': PD.Group({ }),
'residues': PD.Group({ }),
- 'static-text': PD.Group({ value: PD.Text('') }, { isFlat: true })
+ 'static-text': PD.Group({
+ value: PD.Text(''),
+ size: PD.Optional(PD.Numeric(1, { min: 1, max: 1000, step: 0.1 })),
+ // TODO: this changes the position while rotated etc... fix
+ position: PD.Optional(Text.Params.attachment)
+ }, { isFlat: true })
}),
- // PD.Select<'elements' | 'residues'>('residues', [['residues', 'Residues'], ['elements', 'Elements']]),
options: PD.Group({
...Text.Params,
@@ -215,8 +219,9 @@ const StructureLabels3D = PluginStateTransform.BuiltIn({
})
}
})({
- canAutoUpdate({ a, oldParams, newParams }) {
- return newParams.target.name === 'static-text' || newParams.target.name === oldParams.target.name
+ canAutoUpdate({ oldParams, newParams }) {
+ return (oldParams.target.name === 'static-text' && newParams.target.name === 'static-text' && oldParams.target.params.value === newParams.target.params.value)
+ || newParams.target.name === oldParams.target.name;
},
apply({ a, params }) {
return Task.create('Structure Labels', async ctx => {
diff --git a/src/mol-plugin/state/transforms/volume.ts b/src/mol-plugin/state/transforms/volume.ts
index 399293a21..6861dc237 100644
--- a/src/mol-plugin/state/transforms/volume.ts
+++ b/src/mol-plugin/state/transforms/volume.ts
@@ -68,12 +68,12 @@ const VolumeFromDensityServerCif = PluginStateTransform.BuiltIn({
params(a) {
if (!a) {
return {
- blockHeader: PD.asOptional(PD.Text(void 0, { description: 'Header of the block to parse. If none is specifed, the 1st data block in the file is used.' }))
+ blockHeader: PD.Optional(PD.Text(void 0, { description: 'Header of the block to parse. If none is specifed, the 1st data block in the file is used.' }))
};
}
const blocks = a.data.blocks.slice(1); // zero block contains query meta-data
return {
- blockHeader: PD.asOptional(PD.Select(blocks[0] && blocks[0].header, blocks.map(b => [b.header, b.header] as [string, string]), { description: 'Header of the block to parse' }))
+ blockHeader: PD.Optional(PD.Select(blocks[0] && blocks[0].header, blocks.map(b => [b.header, b.header] as [string, string]), { description: 'Header of the block to parse' }))
};
}
})({
diff --git a/src/mol-plugin/ui/controls/parameters.tsx b/src/mol-plugin/ui/controls/parameters.tsx
index 8267741e1..72135f24d 100644
--- a/src/mol-plugin/ui/controls/parameters.tsx
+++ b/src/mol-plugin/ui/controls/parameters.tsx
@@ -181,7 +181,8 @@ export class NumberInputControl extends React.PureComponent<ParamProps<PD.Numeri
export class NumberRangeControl extends SimpleParam<PD.Numeric> {
onChange = (v: number) => { this.update(v); }
renderControl() {
- return <Slider value={this.props.value} min={this.props.param.min!} max={this.props.param.max!}
+ const value = typeof this.props.value === 'undefined' ? this.props.param.defaultValue : this.props.value;
+ return <Slider value={value} min={this.props.param.min!} max={this.props.param.max!}
step={this.props.param.step} onChange={this.onChange} disabled={this.props.isDisabled} onEnter={this.props.onEnter} />
}
}
diff --git a/src/mol-plugin/util/structure-labels.ts b/src/mol-plugin/util/structure-labels.ts
index af3b335de..c6e944b29 100644
--- a/src/mol-plugin/util/structure-labels.ts
+++ b/src/mol-plugin/util/structure-labels.ts
@@ -50,20 +50,25 @@ function getLabelsShape(ctx: RuntimeContext, data: LabelsData, props: PD.Values<
const boundaryHelper = new BoundaryHelper();
function getLabelData(structure: Structure, params: StateTransformer.Params<StructureLabels3D>): LabelsData {
if (params.target.name === 'static-text') {
- return getLabelDataStatic(structure, params.target.params.value);
+ return getLabelDataStatic(structure, params.target.params.value, params.target.params.size || 1, params.target.params.position || 'middle-center');
} else {
return getLabelDataComputed(structure, params.target.name);
}
}
-function getLabelDataStatic(structure: Structure, text: string): LabelsData {
+function getLabelDataStatic(structure: Structure, text: string, size: number, position: Text.Params['attachment']['defaultValue']): LabelsData {
const boundary = structure.boundary.sphere;
+ let oX = 0, oY = 0;
+ if (position.indexOf('left') >= 0) oX = -boundary.radius;
+ if (position.indexOf('right') >= 0) oX = boundary.radius;
+ if (position.indexOf('top') >= 0) oY = boundary.radius;
+ if (position.indexOf('bottom') >= 0) oY = -boundary.radius;
return {
texts: [text],
- positions: [boundary.center],
- sizes: [1],
- depths: [boundary.radius]
+ positions: [Vec3.add(Vec3.zero(), boundary.center, Vec3.create(oX, oY, 0))],
+ sizes: [size],
+ depths: [boundary.radius + Math.sqrt(oX * oX + oY * oY)]
};
}
diff --git a/src/mol-util/param-definition.ts b/src/mol-util/param-definition.ts
index e2ce230f3..a7f08f3cf 100644
--- a/src/mol-util/param-definition.ts
+++ b/src/mol-util/param-definition.ts
@@ -36,9 +36,10 @@ export namespace ParamDefinition {
type: T['type']
}
- export function asOptional<T>(p: Base<T>): Base<T | undefined> {
- p.isOptional = true;
- return p;
+ export function Optional<T>(p: Base<T>): Base<T | undefined> {
+ const ret = { ...p };
+ ret.isOptional = true;
+ return ret;
}
export interface Value<T> extends Base<T> {
--
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