diff --git a/src/mol-plugin/command.ts b/src/mol-plugin/command.ts
index ec948ef858251ab75850ecb96604d26dc1040481..880d8d053971d169d06c5a406cebed20d33c215d 100644
--- a/src/mol-plugin/command.ts
+++ b/src/mol-plugin/command.ts
@@ -4,12 +4,42 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import * as State from './command/state';
-import * as Camera from './command/camera';
+import { Camera } from 'mol-canvas3d/camera';
+import { PluginCommand } from './command/base';
+import { Transform, State } from 'mol-state';
+import { StateAction } from 'mol-state/action';
-export * from './command/command';
+export * from './command/base';
export const PluginCommands = {
- State,
- Camera
+ State: {
+ SetCurrentObject: PluginCommand<{ state: State, ref: Transform.Ref }>(),
+ ApplyAction: PluginCommand<{ state: State, action: StateAction.Instance, ref?: Transform.Ref }>(),
+ Update: PluginCommand<{ state: State, tree: State.Tree | State.Builder }>(),
+
+ RemoveObject: PluginCommand<{ state: State, ref: Transform.Ref }>(),
+
+ ToggleExpanded: PluginCommand<{ state: State, ref: Transform.Ref }>({ isImmediate: true }),
+ ToggleVisibility: PluginCommand<{ state: State, ref: Transform.Ref }>({ isImmediate: true }),
+
+ Snapshots: {
+ Add: PluginCommand<{ name?: string, description?: string }>({ isImmediate: true }),
+ Remove: PluginCommand<{ id: string }>({ isImmediate: true }),
+ Apply: PluginCommand<{ id: string }>({ isImmediate: true }),
+ Clear: PluginCommand<{}>({ isImmediate: true }),
+
+ Upload: PluginCommand<{ name?: string, description?: string, serverUrl: string }>({ isImmediate: true }),
+ Fetch: PluginCommand<{ url: string }>()
+ }
+ },
+ Camera: {
+ Reset: PluginCommand<{}>({ isImmediate: true }),
+ SetSnapshot: PluginCommand<{ snapshot: Camera.Snapshot, durationMs?: number }>({ isImmediate: true }),
+ Snapshots: {
+ Add: PluginCommand<{ name?: string, description?: string }>({ isImmediate: true }),
+ Remove: PluginCommand<{ id: string }>({ isImmediate: true }),
+ Apply: PluginCommand<{ id: string }>({ isImmediate: true }),
+ Clear: PluginCommand<{}>({ isImmediate: true }),
+ }
+ }
}
\ No newline at end of file
diff --git a/src/mol-plugin/command/command.ts b/src/mol-plugin/command/base.ts
similarity index 100%
rename from src/mol-plugin/command/command.ts
rename to src/mol-plugin/command/base.ts
diff --git a/src/mol-plugin/command/camera.ts b/src/mol-plugin/command/camera.ts
deleted file mode 100644
index b5138f9d66519b0ef0beb33447641d3db22cdb7d..0000000000000000000000000000000000000000
--- a/src/mol-plugin/command/camera.ts
+++ /dev/null
@@ -1,18 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { PluginCommand } from './command';
-import { Camera } from 'mol-canvas3d/camera';
-
-export const Reset = PluginCommand<{}>({ isImmediate: true });
-export const SetSnapshot = PluginCommand<{ snapshot: Camera.Snapshot, durationMs?: number }>({ isImmediate: true });
-
-export const Snapshots = {
- Add: PluginCommand<{ name?: string, description?: string }>({ isImmediate: true }),
- Remove: PluginCommand<{ id: string }>({ isImmediate: true }),
- Apply: PluginCommand<{ id: string }>({ isImmediate: true }),
- Clear: PluginCommand<{ }>({ isImmediate: true }),
-}
\ No newline at end of file
diff --git a/src/mol-plugin/command/state.ts b/src/mol-plugin/command/state.ts
deleted file mode 100644
index e9b092b00e04e65e1c910d6bde8c73325de761f7..0000000000000000000000000000000000000000
--- a/src/mol-plugin/command/state.ts
+++ /dev/null
@@ -1,31 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { PluginCommand } from './command';
-import { Transform, State } from 'mol-state';
-import { StateAction } from 'mol-state/action';
-
-export const SetCurrentObject = PluginCommand<{ state: State, ref: Transform.Ref }>();
-export const ApplyAction = PluginCommand<{ state: State, action: StateAction.Instance, ref?: Transform.Ref }>();
-export const Update = PluginCommand<{ state: State, tree: State.Tree | State.Builder }>();
-
-// export const UpdateObject = PluginCommand<{ ref: Transform.Ref, params: any }>('ms-data', 'update-object');
-
-export const RemoveObject = PluginCommand<{ state: State, ref: Transform.Ref }>();
-
-export const ToggleExpanded = PluginCommand<{ state: State, ref: Transform.Ref }>({ isImmediate: true });
-
-export const ToggleVisibility = PluginCommand<{ state: State, ref: Transform.Ref }>({ isImmediate: true });
-
-export const Snapshots = {
- Add: PluginCommand<{ name?: string, description?: string }>({ isImmediate: true }),
- Remove: PluginCommand<{ id: string }>({ isImmediate: true }),
- Apply: PluginCommand<{ id: string }>({ isImmediate: true }),
- Clear: PluginCommand<{ }>({ isImmediate: true }),
-
- Upload: PluginCommand<{ name?: string, description?: string, serverUrl: string }>({ isImmediate: true }),
- Fetch: PluginCommand<{ url: string }>()
-}
\ No newline at end of file
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 29471e0c80abb6bb4ce1da3ee9a22b5c15d48d94..7a87cb5049d4271438b60081eeb0aab8bbaacff9 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -25,10 +25,10 @@ const DefaultSpec: PluginSpec = {
PluginSpec.Action(CreateStructureFromPDBe),
PluginSpec.Action(StateTransforms.Data.Download),
PluginSpec.Action(StateTransforms.Data.ParseCif),
- PluginSpec.Action(StateTransforms.Model.CreateStructureAssembly),
- PluginSpec.Action(StateTransforms.Model.CreateStructure),
- PluginSpec.Action(StateTransforms.Model.CreateModelFromTrajectory),
- PluginSpec.Action(StateTransforms.Visuals.CreateStructureRepresentation)
+ PluginSpec.Action(StateTransforms.Model.StructureAssemblyFromModel),
+ PluginSpec.Action(StateTransforms.Model.StructureFromModel),
+ PluginSpec.Action(StateTransforms.Model.ModelFromTrajectory),
+ PluginSpec.Action(StateTransforms.Representation.StructureRepresentation3D)
],
behaviors: [
PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci),
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index 65914ce4c61fe9b3ce28b580288e686e4ae45dc4..754282bbcc7794854a741e4752f348d8b20b3e64 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -36,11 +36,11 @@ export const CreateStructureFromPDBe = StateAction.create<PluginStateObject.Root
const newTree = b.toRoot()
.apply(StateTransforms.Data.Download, { url })
.apply(StateTransforms.Data.ParseCif)
- .apply(StateTransforms.Model.ParseTrajectoryFromMmCif, {})
- .apply(StateTransforms.Model.CreateModelFromTrajectory, { modelIndex: 0 })
- .apply(StateTransforms.Model.CreateStructureAssembly)
+ .apply(StateTransforms.Model.TrajectoryFromMmCif, {})
+ .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
+ .apply(StateTransforms.Model.StructureAssemblyFromModel)
// .apply(StateTransforms.Model.CreateStructureSelection, { query, label: 'ALA residues' })
- .apply(StateTransforms.Visuals.CreateStructureRepresentation, {
+ .apply(StateTransforms.Representation.StructureRepresentation3D, {
type: {
name: 'cartoon',
params: PD.getDefaultValues(CartoonParams)
@@ -62,13 +62,14 @@ export const UpdateTrajectory = StateAction.create<PluginStateObject.Root, void,
by: PD.Numeric(1, { min: -1, max: 1, step: 1 }, { isOptional: true })
}),
apply({ params, state }) {
- const models = state.select(q => q.rootsOfType(PluginStateObject.Molecule.Model).filter(c => c.transform.transformer === StateTransforms.Model.CreateModelFromTrajectory));
+ const models = state.select(q => q.rootsOfType(PluginStateObject.Molecule.Model)
+ .filter(c => c.transform.transformer === StateTransforms.Model.ModelFromTrajectory));
const update = state.build();
if (params.action === 'reset') {
for (const m of models) {
- update.to(m.transform.ref).update(StateTransforms.Model.CreateModelFromTrajectory,
+ update.to(m.transform.ref).update(StateTransforms.Model.ModelFromTrajectory,
() => ({ modelIndex: 0}));
}
} else {
@@ -76,7 +77,7 @@ export const UpdateTrajectory = StateAction.create<PluginStateObject.Root, void,
const parent = StateSelection.findAncestorOfType(state.tree, state.cells, m.transform.ref, [PluginStateObject.Molecule.Trajectory]);
if (!parent || !parent.obj) continue;
const traj = parent.obj as PluginStateObject.Molecule.Trajectory;
- update.to(m.transform.ref).update(StateTransforms.Model.CreateModelFromTrajectory,
+ update.to(m.transform.ref).update(StateTransforms.Model.ModelFromTrajectory,
old => {
let modelIndex = (old.modelIndex + params.by!) % traj.data.length;
if (modelIndex < 0) modelIndex += traj.data.length;
diff --git a/src/mol-plugin/state/transforms.ts b/src/mol-plugin/state/transforms.ts
index c2b27831faceaef6ca37bcefe0e530a559598134..c6914174cf71c4d92ec64916da5341ea78ff6b84 100644
--- a/src/mol-plugin/state/transforms.ts
+++ b/src/mol-plugin/state/transforms.ts
@@ -6,10 +6,10 @@
import * as Data from './transforms/data'
import * as Model from './transforms/model'
-import * as Visuals from './transforms/visuals'
+import * as Representation from './transforms/representation'
export const StateTransforms = {
Data,
Model,
- Visuals
+ Representation
}
\ No newline at end of file
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 3a4a7963993809f53642b98cfab6f88a1de84fb8..3a5e74757c439500f17cef0661de628ba361cc6a 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -7,17 +7,16 @@
import { PluginStateTransform } from '../objects';
import { PluginStateObject as SO } from '../objects';
import { Task } from 'mol-task';
-import { Model, Format, Structure, ModelSymmetry, StructureSymmetry, QueryContext, StructureSelection } from 'mol-model/structure';
+import { Model, Format, Structure, ModelSymmetry, StructureSymmetry, QueryContext, StructureSelection as Sel } from 'mol-model/structure';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import Expression from 'mol-script/language/expression';
import { compile } from 'mol-script/runtime/query/compiler';
-import { Mat4 } from 'mol-math/linear-algebra';
import { MolScriptBuilder } from 'mol-script/language/builder';
-export { ParseTrajectoryFromMmCif }
-namespace ParseTrajectoryFromMmCif { export interface Params { blockHeader?: string } }
-const ParseTrajectoryFromMmCif = PluginStateTransform.Create<SO.Data.Cif, SO.Molecule.Trajectory, ParseTrajectoryFromMmCif.Params>({
- name: 'parse-trajectory-from-mmcif',
+export { TrajectoryFromMmCif }
+namespace TrajectoryFromMmCif { export interface Params { blockHeader?: string } }
+const TrajectoryFromMmCif = PluginStateTransform.Create<SO.Data.Cif, SO.Molecule.Trajectory, TrajectoryFromMmCif.Params>({
+ name: 'trajectory-from-mmcif',
display: {
name: 'Models from mmCIF',
description: 'Identify and create all separate models in the specified CIF data block'
@@ -45,11 +44,11 @@ const ParseTrajectoryFromMmCif = PluginStateTransform.Create<SO.Data.Cif, SO.Mol
}
});
-export { CreateModelFromTrajectory }
+export { ModelFromTrajectory }
const plus1 = (v: number) => v + 1, minus1 = (v: number) => v - 1;
-namespace CreateModelFromTrajectory { export interface Params { modelIndex: number } }
-const CreateModelFromTrajectory = PluginStateTransform.Create<SO.Molecule.Trajectory, SO.Molecule.Model, CreateModelFromTrajectory.Params>({
- name: 'create-model-from-trajectory',
+namespace ModelFromTrajectory { export interface Params { modelIndex: number } }
+const ModelFromTrajectory = PluginStateTransform.Create<SO.Molecule.Trajectory, SO.Molecule.Model, ModelFromTrajectory.Params>({
+ name: 'model-from-trajectory',
display: {
name: 'Model from Trajectory',
description: 'Create a molecular structure from the specified model.'
@@ -66,19 +65,18 @@ const CreateModelFromTrajectory = PluginStateTransform.Create<SO.Molecule.Trajec
}
});
-export { CreateStructure }
-namespace CreateStructure { export interface Params { transform3d?: Mat4 } }
-const CreateStructure = PluginStateTransform.Create<SO.Molecule.Model, SO.Molecule.Structure, CreateStructure.Params>({
- name: 'create-structure-from-model',
+export { StructureFromModel }
+namespace StructureFromModel { export interface Params { } }
+const StructureFromModel = PluginStateTransform.Create<SO.Molecule.Model, SO.Molecule.Structure, StructureFromModel.Params>({
+ name: 'structure-from-model',
display: {
name: 'Structure from Model',
description: 'Create a molecular structure from the specified model.'
},
from: [SO.Molecule.Model],
to: [SO.Molecule.Structure],
- apply({ a, params }) {
+ apply({ a }) {
let s = Structure.ofModel(a.data);
- if (params.transform3d) s = Structure.transform(s, params.transform3d);
const label = { label: a.data.label, description: s.elementCount === 1 ? '1 element' : `${s.elementCount} elements` };
return new SO.Molecule.Structure(s, label);
}
@@ -88,10 +86,10 @@ function structureDesc(s: Structure) {
return s.elementCount === 1 ? '1 element' : `${s.elementCount} elements`;
}
-export { CreateStructureAssembly }
-namespace CreateStructureAssembly { export interface Params { /** if not specified, use the 1st */ id?: string } }
-const CreateStructureAssembly = PluginStateTransform.Create<SO.Molecule.Model, SO.Molecule.Structure, CreateStructureAssembly.Params>({
- name: 'create-structure-assembly',
+export { StructureAssemblyFromModel }
+namespace StructureAssemblyFromModel { export interface Params { /** if not specified, use the 1st */ id?: string } }
+const StructureAssemblyFromModel = PluginStateTransform.Create<SO.Molecule.Model, SO.Molecule.Structure, StructureAssemblyFromModel.Params>({
+ name: 'structure-assembly-from-model',
display: {
name: 'Structure Assembly',
description: 'Create a molecular structure assembly.'
@@ -119,10 +117,10 @@ const CreateStructureAssembly = PluginStateTransform.Create<SO.Molecule.Model, S
}
});
-export { CreateStructureSelection }
-namespace CreateStructureSelection { export interface Params { query: Expression, label?: string } }
-const CreateStructureSelection = PluginStateTransform.Create<SO.Molecule.Structure, SO.Molecule.Structure, CreateStructureSelection.Params>({
- name: 'create-structure-selection',
+export { StructureSelection }
+namespace StructureSelection { export interface Params { query: Expression, label?: string } }
+const StructureSelection = PluginStateTransform.Create<SO.Molecule.Structure, SO.Molecule.Structure, StructureSelection.Params>({
+ name: 'structure-selection',
display: {
name: 'Structure Selection',
description: 'Create a molecular structure from the specified model.'
@@ -130,14 +128,14 @@ const CreateStructureSelection = PluginStateTransform.Create<SO.Molecule.Structu
from: [SO.Molecule.Structure],
to: [SO.Molecule.Structure],
params: () => ({
- query: PD.Value<Expression>(MolScriptBuilder.struct.generator.all),
- label: PD.Text('', { isOptional: true })
+ query: PD.Value<Expression>(MolScriptBuilder.struct.generator.all, { isHidden: true }),
+ label: PD.Text('', { isOptional: true, isHidden: true })
}),
apply({ a, params }) {
// TODO: use cache, add "update"
- const compiled = compile<StructureSelection>(params.query);
+ const compiled = compile<Sel>(params.query);
const result = compiled(new QueryContext(a.data));
- const s = StructureSelection.unionStructure(result);
+ const s = Sel.unionStructure(result);
const label = { label: `${params.label || 'Selection'}`, description: structureDesc(s) };
return new SO.Molecule.Structure(s, label);
}
diff --git a/src/mol-plugin/state/transforms/visuals.ts b/src/mol-plugin/state/transforms/representation.ts
similarity index 87%
rename from src/mol-plugin/state/transforms/visuals.ts
rename to src/mol-plugin/state/transforms/representation.ts
index cf1d4ee95bac8977817c3fe23c74cf714ac2f51f..cd51ffcbcf7c09e928055be01cd891955acb4554 100644
--- a/src/mol-plugin/state/transforms/visuals.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -11,14 +11,14 @@ import { PluginStateObject as SO } from '../objects';
import { PluginContext } from 'mol-plugin/context';
import { ParamDefinition as PD } from 'mol-util/param-definition';
-export { CreateStructureRepresentation }
-namespace CreateStructureRepresentation {
+export { StructureRepresentation3D }
+namespace StructureRepresentation3D {
export interface Params {
type: { name: string, params: any /** todo is there "common type" */ },
}
}
-const CreateStructureRepresentation = PluginStateTransform.Create<SO.Molecule.Structure, SO.Molecule.Representation3D, CreateStructureRepresentation.Params>({
- name: 'create-structure-representation',
+const StructureRepresentation3D = PluginStateTransform.Create<SO.Molecule.Structure, SO.Molecule.Representation3D, StructureRepresentation3D.Params>({
+ name: 'structure-representation-3d',
display: { name: '3D Representation' },
from: [SO.Molecule.Structure],
to: [SO.Molecule.Representation3D],
diff --git a/src/mol-plugin/ui/controls/parameters.tsx b/src/mol-plugin/ui/controls/parameters.tsx
index 86c955cb0c2336f8e10b27e87406da2cf36ee82f..de4a6afbb493272cf0572f679557a3ff4262d7b5 100644
--- a/src/mol-plugin/ui/controls/parameters.tsx
+++ b/src/mol-plugin/ui/controls/parameters.tsx
@@ -27,6 +27,7 @@ export class ParameterControls<P extends PD.Params> extends React.PureComponent<
return <div style={{ width: '100%' }}>
{Object.keys(params).map(key => {
const param = params[key];
+ if (param.isHidden) return null;
const Control = controlFor(param);
if (!Control) return null;
return <Control param={param} key={key} onChange={this.props.onChange} onEnter={this.props.onEnter} isDisabled={this.props.isDisabled} name={key} value={values[key]} />
diff --git a/src/mol-plugin/ui/state/common.tsx b/src/mol-plugin/ui/state/common.tsx
index ca64bbf00308c28366a9261e1596e163017fd81a..d58978b55e65a0edcddab82fce23ebe1aa6ebc51 100644
--- a/src/mol-plugin/ui/state/common.tsx
+++ b/src/mol-plugin/ui/state/common.tsx
@@ -53,6 +53,14 @@ namespace StateTransformParameters {
export type Class = React.ComponentClass<Props>
+ function areParamsEmpty(params: PD.Params) {
+ const keys = Object.keys(params);
+ for (const k of keys) {
+ if (!params[k].isHidden) return false;
+ }
+ return true;
+ }
+
export function infoFromAction(plugin: PluginContext, state: State, action: StateAction, nodeRef: Transform.Ref): Props['info'] {
const source = state.cells.get(nodeRef)!.obj!;
const params = action.definition.params ? action.definition.params(source, plugin) : { };
@@ -60,7 +68,7 @@ namespace StateTransformParameters {
return {
initialValues,
params,
- isEmpty: Object.keys(params).length === 0
+ isEmpty: areParamsEmpty(params)
};
}
@@ -72,7 +80,7 @@ namespace StateTransformParameters {
return {
initialValues: transform.params,
params,
- isEmpty: Object.keys(params).length === 0
+ isEmpty: areParamsEmpty(params)
}
}
}
diff --git a/src/mol-util/param-definition.ts b/src/mol-util/param-definition.ts
index 8bb45df5b470cdb53cbe3acb8d691de78ed21b92..e508a72c7e8aaffd8d4cc988ceb7fd50b66a9a71 100644
--- a/src/mol-util/param-definition.ts
+++ b/src/mol-util/param-definition.ts
@@ -14,7 +14,8 @@ export namespace ParamDefinition {
export interface Info {
label?: string,
description?: string,
- isOptional?: boolean
+ isOptional?: boolean,
+ isHidden?: boolean
}
function setInfo<T extends Info>(param: T, info?: Info): T {
@@ -22,6 +23,7 @@ export namespace ParamDefinition {
if (info.description) param.description = info.description;
if (info.label) param.label = info.label;
if (info.isOptional) param.isOptional = info.isOptional;
+ if (info.isHidden) param.isHidden = info.isHidden;
return param;
}