diff --git a/src/mol-model/volume/data.ts b/src/mol-model/volume/data.ts
index cda1035294766b00ea4edc8970c9bee925f1b95f..a5dce1067c2723641f138d791f7da5d61cb2afec 100644
--- a/src/mol-model/volume/data.ts
+++ b/src/mol-model/volume/data.ts
@@ -21,6 +21,13 @@ interface VolumeData {
}
namespace VolumeData {
+ export const Empty: VolumeData = {
+ cell: SpacegroupCell.Zero,
+ fractionalBox: Box3D.empty(),
+ data: Tensor.create(Tensor.Space([0, 0, 0], [0, 1, 2]), Tensor.Data1([])),
+ dataStats: { min: 0, max: 0, mean: 0, sigma: 0 }
+ }
+
const _scale = Mat4.zero(), _translate = Mat4.zero();
export function getGridToCartesianTransform(volume: VolumeData) {
const { data: { space } } = volume;
diff --git a/src/mol-plugin/behavior/static/state.ts b/src/mol-plugin/behavior/static/state.ts
index 420ae299c5cd9b6dec8b003d07c995071436ae86..f3d852d82e218b3cc1455ea579b70bd88032dae4 100644
--- a/src/mol-plugin/behavior/static/state.ts
+++ b/src/mol-plugin/behavior/static/state.ts
@@ -156,13 +156,5 @@ export function Snapshots(ctx: PluginContext) {
} catch (e) {
ctx.log.error(`Reading JSON state: ${e}`);
}
- // const element = document.createElement('a');
- // const json = JSON.stringify(ctx.state.getSnapshot(), null, 2);
- // element.setAttribute('href', 'data:application/json;charset=utf-8,' + encodeURIComponent(json));
- // element.setAttribute('download', `mol-star_state_${(name || getFormattedTime())}.json`);
- // element.style.display = 'none';
- // document.body.appendChild(element);
- // element.click();
- // document.body.removeChild(element);
});
}
\ 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 72a8d63f13c3e1ff3e77f564728817df78438b63..e0ac192283859f0b5ee745b275407970b16249dd 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -27,6 +27,11 @@ const TrajectoryFromMmCif = PluginStateTransform.BuiltIn({
from: SO.Format.Cif,
to: SO.Molecule.Trajectory,
params(a) {
+ if (!a) {
+ return {
+ blockHeader: PD.makeOptional(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.makeOptional(PD.Select(blocks[0] && blocks[0].header, blocks.map(b => [b.header, b.header] as [string, string]), { description: 'Header of the block to parse' }))
@@ -55,7 +60,12 @@ const ModelFromTrajectory = PluginStateTransform.BuiltIn({
display: { name: 'Model from Trajectory', description: 'Create a molecular structure from the specified model.' },
from: SO.Molecule.Trajectory,
to: SO.Molecule.Model,
- params: a => ({ modelIndex: PD.Converted(plus1, minus1, PD.Numeric(1, { min: 1, max: a.data.length, step: 1 }, { description: 'Model Index' })) })
+ params: a => {
+ if (!a) {
+ return { modelIndex: PD.Numeric(0, {}, { description: 'Zero-based index of the model' }) };
+ }
+ return { modelIndex: PD.Converted(plus1, minus1, PD.Numeric(1, { min: 1, max: a.data.length, step: 1 }, { description: 'Model Index' })) }
+ }
})({
isApplicable: a => a.data.length > 0,
apply({ a, params }) {
@@ -93,6 +103,9 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
from: SO.Molecule.Model,
to: SO.Molecule.Structure,
params(a) {
+ if (!a) {
+ return { id: PD.Text('', { label: 'Assembly Id', description: 'Assembly Id. If none specified (undefined or empty string), the asymmetric unit is used.' }) };
+ }
const model = a.data;
const ids = model.symmetry.assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]);
if (!ids.length) ids.push(['deposited', 'Deposited'])
@@ -104,7 +117,7 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
const model = a.data;
const id = params.id;
const asm = ModelSymmetry.findAssembly(model, id);
- if (id !== 'deposited' && !asm) throw new Error(`Assembly '${id}' not found`);
+ if (!!id && id !== 'deposited' && !asm) throw new Error(`Assembly '${id}' not found`);
const base = Structure.ofModel(model);
if (!asm) {
@@ -179,7 +192,10 @@ const CustomModelProperties = PluginStateTransform.BuiltIn({
display: { name: 'Custom Model Properties' },
from: SO.Molecule.Model,
to: SO.Molecule.Model,
- params: (a, ctx: PluginContext) => ({ properties: ctx.customModelProperties.getSelect(a.data) })
+ params: (a, ctx: PluginContext) => {
+ if (!a) return { properties: PD.MultiSelect([], [], { description: 'A list of property descriptor ids.' }) };
+ return { properties: ctx.customModelProperties.getSelect(a.data) };
+ }
})({
apply({ a, params }, ctx: PluginContext) {
return Task.create('Custom Props', async taskCtx => {
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index 83c33de0663d184c2fab2fe0576058d226d40320..4ffdfa8face12d2066213a6cd09a32e9c4a339a1 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -56,6 +56,26 @@ const StructureRepresentation3D = PluginStateTransform.BuiltIn({
params: (a, ctx: PluginContext) => {
const { registry, themeCtx } = ctx.structureRepresentation
const type = registry.get(registry.default.name);
+
+ if (!a) {
+ return {
+ type: PD.Mapped<any>(
+ registry.default.name,
+ registry.types,
+ name => PD.Group<any>(registry.get(name).getParams(themeCtx, Structure.Empty))),
+ colorTheme: PD.Mapped<any>(
+ type.defaultColorTheme,
+ themeCtx.colorThemeRegistry.types,
+ name => PD.Group<any>(themeCtx.colorThemeRegistry.get(name).getParams({ structure: Structure.Empty }))
+ ),
+ sizeTheme: PD.Mapped<any>(
+ type.defaultSizeTheme,
+ themeCtx.sizeThemeRegistry.types,
+ name => PD.Group<any>(themeCtx.sizeThemeRegistry.get(name).getParams({ structure: Structure.Empty }))
+ )
+ }
+ }
+
const dataCtx = { structure: a.data }
return ({
type: PD.Mapped<any>(
@@ -163,6 +183,26 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
params: (a, ctx: PluginContext) => {
const { registry, themeCtx } = ctx.volumeRepresentation
const type = registry.get(registry.default.name);
+
+ if (!a) {
+ return {
+ type: PD.Mapped<any>(
+ registry.default.name,
+ registry.types,
+ name => PD.Group<any>(registry.get(name).getParams(themeCtx, VolumeData.Empty ))),
+ colorTheme: PD.Mapped<any>(
+ type.defaultColorTheme,
+ themeCtx.colorThemeRegistry.types,
+ name => PD.Group<any>(themeCtx.colorThemeRegistry.get(name).getParams({ volume: VolumeData.Empty }))
+ ),
+ sizeTheme: PD.Mapped<any>(
+ type.defaultSizeTheme,
+ themeCtx.sizeThemeRegistry.types,
+ name => PD.Group<any>(themeCtx.sizeThemeRegistry.get(name).getParams({ volume: VolumeData.Empty }))
+ )
+ }
+ }
+
const dataCtx = { volume: a.data }
return ({
type: PD.Mapped<any>(
diff --git a/src/mol-state/transformer.ts b/src/mol-state/transformer.ts
index 05663bd8555f5da3b8ddcbaf23c0fd881acd5e74..d5952ee2e00684ea7ee9a17bfa80951ffae9f60a 100644
--- a/src/mol-state/transformer.ts
+++ b/src/mol-state/transformer.ts
@@ -151,7 +151,8 @@ export namespace Transformer {
name: string,
from: A | A[],
to: B | B[],
- params?: PD.For<P> | ((a: StateObject.From<A>, globalCtx: any) => PD.For<P>),
+ /** The source StateObject can be undefined: used for generating docs. */
+ params?: PD.For<P> | ((a: StateObject.From<A> | undefined, globalCtx: any) => PD.For<P>),
display?: string | { name: string, description?: string }
}