diff --git a/.eslintrc.json b/.eslintrc.json
index b9185e66b77456dec5f90b5a0ba8c4217ceb6766..28e80614867167fe9c80bb988dc5fa9114552072 100644
--- a/.eslintrc.json
+++ b/.eslintrc.json
@@ -14,8 +14,9 @@
"rules": {
"@typescript-eslint/ban-types": "warn",
"@typescript-eslint/class-name-casing": "off",
+ "indent": "off",
"@typescript-eslint/indent": [
- "warn",
+ "error",
4
],
"@typescript-eslint/member-delimiter-style": [
@@ -33,7 +34,7 @@
],
"@typescript-eslint/prefer-namespace-keyword": "warn",
"@typescript-eslint/quotes": [
- "warn",
+ "error",
"single",
{
"avoidEscape": true,
@@ -44,22 +45,27 @@
"off",
null
],
- "@typescript-eslint/type-annotation-spacing": "warn",
+ "@typescript-eslint/type-annotation-spacing": "error",
"arrow-parens": [
"off",
"as-needed"
],
+ "brace-style": "off",
+ "@typescript-eslint/brace-style": [
+ "error",
+ "1tbs", { "allowSingleLine": true }
+ ],
"comma-dangle": "off",
"eqeqeq": [
- "warn",
+ "error",
"smart"
],
"import/order": "off",
"no-eval": "warn",
"no-new-wrappers": "warn",
- "no-trailing-spaces": "warn",
+ "no-trailing-spaces": "error",
"no-unsafe-finally": "warn",
- "no-var": "warn",
- "spaced-comment": "warn"
+ "no-var": "error",
+ "spaced-comment": "error"
}
}
\ No newline at end of file
diff --git a/data/cif-field-names/cif-core-field-names.csv b/data/cif-field-names/cif-core-field-names.csv
index 25ce0320c9e0e7c60a833309094d6a27814b7a4c..f935944d7166915cf4c16bd567919d42fe85e6d2 100644
--- a/data/cif-field-names/cif-core-field-names.csv
+++ b/data/cif-field-names/cif-core-field-names.csv
@@ -1,6 +1,12 @@
audit.block_doi
database_code.depnum_ccdc_archive
+database_code.depnum_ccdc_fiz
+database_code.ICSD
+database_code.MDF
+database_code.NBS
+database_code.CSD
+database_code.COD
chemical.name_systematic
chemical.name_common
@@ -19,6 +25,7 @@ atom_type_scat.source
space_group.crystal_system
space_group.name_H-M_full
+space_group.IT_number
space_group_symop.operation_xyz
cell.length_a
@@ -42,19 +49,28 @@ atom_site.calc_flag
atom_site.refinement_flags
atom_site.disorder_assembly
atom_site.disorder_group
-
atom_site.site_symmetry_multiplicity
atom_site_aniso.label
+atom_site_aniso.U
atom_site_aniso.U_11
atom_site_aniso.U_22
atom_site_aniso.U_33
atom_site_aniso.U_23
atom_site_aniso.U_13
atom_site_aniso.U_12
+atom_site_aniso.U_su
+atom_site_aniso.U_11_su
+atom_site_aniso.U_22_su
+atom_site_aniso.U_33_su
+atom_site_aniso.U_23_su
+atom_site_aniso.U_13_su
+atom_site_aniso.U_12_su
geom_bond.atom_site_label_1
geom_bond.atom_site_label_2
geom_bond.distance
+geom_bond.site_symmetry_1
geom_bond.site_symmetry_2
-geom_bond.publ_flag
\ No newline at end of file
+geom_bond.publ_flag
+geom_bond.valence
\ No newline at end of file
diff --git a/package.json b/package.json
index 34f59326c9d625d3b5eb83ea8e5da411d337b021..895748255601adfe3995d9b74f0c552b4eab1356 100644
--- a/package.json
+++ b/package.json
@@ -11,7 +11,7 @@
"url": "https://github.com/molstar/molstar/issues"
},
"scripts": {
- "lint": "eslint src/**/*.ts",
+ "lint": "eslint src/**/*.{ts,tsx}",
"test": "npm run lint && jest",
"build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
"build-tsc": "tsc --incremental",
diff --git a/src/apps/cifschema/index.ts b/src/apps/cifschema/index.ts
index 38602d919e917f21b660a37f6171afc65008f6e4..479192198c741b8d009b7b39c3fa8a6a1a54b290 100644
--- a/src/apps/cifschema/index.ts
+++ b/src/apps/cifschema/index.ts
@@ -159,7 +159,7 @@ async function ensureDicAvailable(dicPath: string, dicUrl: string) {
}
}
-const DIC_DIR = path.resolve(__dirname, '../dics/')
+const DIC_DIR = path.resolve(__dirname, '../../../build/dics/')
const MMCIF_DIC_PATH = `${DIC_DIR}/mmcif_pdbx_v50.dic`
const MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic'
const IHM_DIC_PATH = `${DIC_DIR}/ihm-extension.dic`
diff --git a/src/apps/cifschema/util/cif-dic.ts b/src/apps/cifschema/util/cif-dic.ts
index 2f43e75a00009ae4a2ab604c52c1fd401e6112db..0fd9318731f554c1978a440c3ba39227c4f44885 100644
--- a/src/apps/cifschema/util/cif-dic.ts
+++ b/src/apps/cifschema/util/cif-dic.ts
@@ -232,6 +232,32 @@ const FORCE_INT_FIELDS = [
'_struct_sheet_range.end_auth_seq_id',
];
+const FORCE_MATRIX_FIELDS_MAP: { [k: string]: string } = {
+ 'atom_site_aniso.U_11': 'U',
+ 'atom_site_aniso.U_22': 'U',
+ 'atom_site_aniso.U_33': 'U',
+ 'atom_site_aniso.U_23': 'U',
+ 'atom_site_aniso.U_13': 'U',
+ 'atom_site_aniso.U_12': 'U',
+ 'atom_site_aniso.U_11_su': 'U_su',
+ 'atom_site_aniso.U_22_su': 'U_su',
+ 'atom_site_aniso.U_33_su': 'U_su',
+ 'atom_site_aniso.U_23_su': 'U_su',
+ 'atom_site_aniso.U_13_su': 'U_su',
+ 'atom_site_aniso.U_12_su': 'U_su',
+}
+const FORCE_MATRIX_FIELDS = Object.keys(FORCE_MATRIX_FIELDS_MAP)
+
+const EXTRA_ALIASES: Database['aliases'] = {
+ 'atom_site_aniso.U': [
+ 'atom_site_anisotrop_U'
+ ],
+ 'atom_site_aniso.U_su': [
+ 'atom_site_aniso_U_esd',
+ 'atom_site_anisotrop_U_esd',
+ ],
+}
+
const COMMA_SEPARATED_LIST_FIELDS = [
'_atom_site.pdbx_struct_group_id',
'_chem_comp.mon_nstd_parent_comp_id',
@@ -280,9 +306,8 @@ const EXTRA_ENUM_VALUES: { [k: string]: string[] } = {
}
export function generateSchema(frames: CifFrame[], imports: Imports = new Map()): Database {
-
const tables: Database['tables'] = {}
- const aliases: Database['aliases'] = {}
+ const aliases: Database['aliases'] = { ...EXTRA_ALIASES }
const categories: FrameCategories = {}
const links: FrameLinks = {}
@@ -291,7 +316,7 @@ export function generateSchema(frames: CifFrame[], imports: Imports = new Map())
// get category metadata
frames.forEach(d => {
// category definitions in mmCIF start with '_' and don't include a '.'
- // category definitions in cif don't include a '.'
+ // category definitions in cifCore don't include a '.'
if (d.header[0] === '_' || d.header.includes('.')) return
const categoryName = d.header.toLowerCase()
// console.log(d.header, d.categoryNames, d.categories)
@@ -399,6 +424,10 @@ export function generateSchema(frames: CifFrame[], imports: Imports = new Map())
} else if (FORCE_INT_FIELDS.includes(d.header)) {
fields[itemName] = IntCol(description)
console.log(`forcing int: ${d.header}`)
+ } else if (FORCE_MATRIX_FIELDS.includes(d.header)) {
+ fields[itemName] = FloatCol(description)
+ fields[FORCE_MATRIX_FIELDS_MAP[d.header]] = MatrixCol(3, 3, description)
+ console.log(`forcing matrix: ${d.header}`)
} else if (subCategory === 'matrix') {
fields[itemName.replace(reMatrixField, '')] = MatrixCol(3, 3, description)
} else if (subCategory === 'vector') {
diff --git a/src/apps/viewer/extensions/cellpack/model.ts b/src/apps/viewer/extensions/cellpack/model.ts
index 0c985c078f74bf9d493b8182ac30839aca3ce79e..e43e7e5144c8472d01c49cef7f6ef8b7d86d647a 100644
--- a/src/apps/viewer/extensions/cellpack/model.ts
+++ b/src/apps/viewer/extensions/cellpack/model.ts
@@ -321,20 +321,19 @@ async function handleHivRna(ctx: { runtime: RuntimeContext, fetch: AjaxTask }, p
async function loadHivMembrane(plugin: PluginContext, runtime: RuntimeContext, state: State, params: LoadCellPackModelParams) {
const url = `${params.baseUrl}/membranes/hiv_lipids.bcif`
- const membraneBuilder = state.build().toRoot()
+ const membrane = await state.build().toRoot()
.apply(StateTransforms.Data.Download, { label: 'hiv_lipids', url, isBinary: true }, { state: { isGhost: true } })
.apply(StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
.apply(StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
.apply(StateTransforms.Model.ModelFromTrajectory, undefined, { state: { isGhost: true } })
.apply(StateTransforms.Model.StructureFromModel)
- await state.updateTree(membraneBuilder).runInContext(runtime)
+ .commit()
const membraneParams = {
representation: params.preset.representation,
}
- const membrane = state.build().to(membraneBuilder.ref)
- await plugin.updateDataState(membrane, { revertOnError: true });
- await CellpackMembranePreset.apply(membrane.selector, membraneParams, plugin)
+
+ await CellpackMembranePreset.apply(membrane, membraneParams, plugin)
}
async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, state: State, params: LoadCellPackModelParams) {
@@ -345,6 +344,10 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
.apply(StateTransforms.Data.Download, { url, isBinary: false, label: params.source.params }, { state: { isGhost: true } })
} else {
const file = params.source.params
+ if (file === null) {
+ plugin.log.error('No file selected')
+ return
+ }
cellPackJson = state.build().toRoot()
.apply(StateTransforms.Data.ReadFile, { file, isBinary: false, label: file.name }, { state: { isGhost: true } })
}
@@ -354,17 +357,19 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
.apply(ParseCellPack)
const cellPackObject = await state.updateTree(cellPackBuilder).runInContext(runtime)
- const { packings } = cellPackObject.data
+ const { packings } = cellPackObject.obj!.data
await handleHivRna({ runtime, fetch: plugin.fetch }, packings, params.baseUrl)
for (let i = 0, il = packings.length; i < il; ++i) {
const p = { packing: i, baseUrl: params.baseUrl, ingredientFiles: params.ingredients.files }
- const packing = state.build().to(cellPackBuilder.ref).apply(StructureFromCellpack, p)
- await plugin.updateDataState(packing, { revertOnError: true });
+ const packing = await state.build()
+ .to(cellPackBuilder.ref)
+ .apply(StructureFromCellpack, p)
+ .commit({ revertOnError: true })
- const structure = packing.selector.obj?.data
+ const structure = packing.obj?.data
if (structure) {
await CellPackInfoProvider.attach({ fetch: plugin.fetch, runtime }, structure, {
info: { packingsCount: packings.length, packingIndex: i }
@@ -375,7 +380,7 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
traceOnly: params.preset.traceOnly,
representation: params.preset.representation,
}
- await CellpackPackingPreset.apply(packing.selector, packingParams, plugin)
+ await CellpackPackingPreset.apply(packing, packingParams, plugin)
}
}
diff --git a/src/apps/viewer/extensions/cellpack/preset.ts b/src/apps/viewer/extensions/cellpack/preset.ts
index fdb94b64f8dd8d31e7431ff557e11b9b48c37ecf..fd6a2361da6931152d0ea1d692906d1a454e9f1e 100644
--- a/src/apps/viewer/extensions/cellpack/preset.ts
+++ b/src/apps/viewer/extensions/cellpack/preset.ts
@@ -46,7 +46,7 @@ export const CellpackPackingPreset = StructureRepresentationPresetProvider({
polymer: builder.buildRepresentation<any>(update, components.polymer, { type: params.representation, typeParams: { ...typeParams, ...reprProps }, color }, { tag: 'polymer' })
};
- await plugin.updateDataState(update, { revertOnError: true });
+ await update.commit({ revertOnError: true })
return { components, representations };
}
});
@@ -84,7 +84,7 @@ export const CellpackMembranePreset = StructureRepresentationPresetProvider({
membrane: builder.buildRepresentation(update, components.membrane, { type: 'gaussian-surface', typeParams: { ...typeParams, ...reprProps }, color: 'uniform', colorParams: { value: ColorNames.lightgrey } }, { tag: 'all' })
};
- await plugin.updateDataState(update, { revertOnError: true });
+ await update.commit({ revertOnError: true })
return { components, representations };
}
});
\ No newline at end of file
diff --git a/src/apps/viewer/extensions/cellpack/state.ts b/src/apps/viewer/extensions/cellpack/state.ts
index abd983c26808377cda7878eaa28a4c12a889c802..9908ede2657560f99f05847ea0f042e4453fc9bf 100644
--- a/src/apps/viewer/extensions/cellpack/state.ts
+++ b/src/apps/viewer/extensions/cellpack/state.ts
@@ -70,9 +70,11 @@ const StructureFromCellpack = PluginStateTransform.BuiltIn({
return Task.create('Structure from CellPack', async ctx => {
const packing = a.data.packings[params.packing]
const ingredientFiles: IngredientFiles = {}
- for (let i = 0, il = params.ingredientFiles.length; i < il; ++i) {
- const file = params.ingredientFiles.item(i)
- if (file) ingredientFiles[file.name] = file
+ if (params.ingredientFiles !== null) {
+ for (let i = 0, il = params.ingredientFiles.length; i < il; ++i) {
+ const file = params.ingredientFiles.item(i)
+ if (file) ingredientFiles[file.name] = file
+ }
}
const structure = await createStructureFromCellPack(packing, params.baseUrl, ingredientFiles).runInContext(ctx)
return new PSO.Molecule.Structure(structure, { label: packing.name })
diff --git a/src/examples/proteopedia-wrapper/ui/controls.tsx b/src/examples/proteopedia-wrapper/ui/controls.tsx
index ed402e5a13b47e441936f98f68dc8b5e058851c4..df970158b11b8c3b91a51caa96a110a265bb4303 100644
--- a/src/examples/proteopedia-wrapper/ui/controls.tsx
+++ b/src/examples/proteopedia-wrapper/ui/controls.tsx
@@ -13,7 +13,6 @@ import { StateElements } from '../helpers';
export function volumeStreamingControls(plugin: PluginContext, parent: Element) {
ReactDOM.render(<PluginContextContainer plugin={plugin}>
- <TransformUpdaterControl nodeRef={StateElements.VolumeStreaming} />
- </PluginContextContainer>,
- parent);
+ <TransformUpdaterControl nodeRef={StateElements.VolumeStreaming} />
+ </PluginContextContainer>, parent);
}
\ No newline at end of file
diff --git a/src/mol-data/generic/linked-list.ts b/src/mol-data/generic/linked-list.ts
index fbea58bd8d032c0b3aa6526df4ed8af6ba74e9a7..efd64e347c07ed662cf70248ebb73619c60c19fc 100644
--- a/src/mol-data/generic/linked-list.ts
+++ b/src/mol-data/generic/linked-list.ts
@@ -89,15 +89,13 @@ class LinkedListImpl<T> implements LinkedList<T> {
if (node.previous !== null) {
node.previous.next = node.next;
- }
- else if (/* first == item*/ node.previous === null) {
+ } else if (/* first == item*/ node.previous === null) {
this.first = node.next;
}
if (node.next !== null) {
node.next.previous = node.previous;
- }
- else if (/* last == item*/ node.next === null) {
+ } else if (/* last == item*/ node.next === null) {
this.last = node.previous;
}
diff --git a/src/mol-data/int/impl/ordered-set.ts b/src/mol-data/int/impl/ordered-set.ts
index 858d4abf7c15e29c1c81986db8ca8f97f2e2aac2..47a91eed2de4d0f8e2ffd07a6f7e29cab24e25a7 100644
--- a/src/mol-data/int/impl/ordered-set.ts
+++ b/src/mol-data/int/impl/ordered-set.ts
@@ -150,8 +150,11 @@ function unionII(a: I, b: I) {
const minA = I.min(a), minB = I.min(b);
if (areRangesIntersecting(a, b)) return I.ofRange(Math.min(minA, minB), Math.max(I.max(a), I.max(b)));
let lSize, lMin, rSize, rMin;
- if (minA < minB) { lSize = sizeA; lMin = minA; rSize = sizeB; rMin = minB; }
- else { lSize = sizeB; lMin = minB; rSize = sizeA; rMin = minA; }
+ if (minA < minB) {
+ lSize = sizeA; lMin = minA; rSize = sizeB; rMin = minB;
+ } else {
+ lSize = sizeB; lMin = minB; rSize = sizeA; rMin = minA;
+ }
const arr = new Int32Array(sizeA + sizeB);
for (let i = 0; i < lSize; i++) arr[i] = i + lMin;
for (let i = 0; i < rSize; i++) arr[i + lSize] = i + rMin;
@@ -328,9 +331,13 @@ export function indexedIntersect(idxA: OrderedSetImpl, a: S, b: S): OrderedSetIm
let j = startJ;
while (O < lenI && j < endJ) {
const x = a[getAt(idxA, O)], y = b[j];
- if (x < y) { O++; }
- else if (x > y) { j++; }
- else { commonCount++; O++; j++; }
+ if (x < y) {
+ O++;
+ } else if (x > y) {
+ j++;
+ } else {
+ commonCount++; O++; j++;
+ }
}
// no common elements
@@ -345,9 +352,13 @@ export function indexedIntersect(idxA: OrderedSetImpl, a: S, b: S): OrderedSetIm
j = startJ;
while (O < lenI && j < endJ) {
const x = a[getAt(idxA, O)], y = b[j];
- if (x < y) { O++; }
- else if (x > y) { j++; }
- else { indices[offset++] = j; O++; j++; }
+ if (x < y) {
+ O++;
+ } else if (x > y) {
+ j++;
+ } else {
+ indices[offset++] = j; O++; j++;
+ }
}
return ofSortedArray(indices);
diff --git a/src/mol-data/int/impl/sorted-array.ts b/src/mol-data/int/impl/sorted-array.ts
index 35e83338e1469e4ec62720d081bba2c4a68851ad..87eacf6b0b8c91243f00447a118b3b69cb801e67 100644
--- a/src/mol-data/int/impl/sorted-array.ts
+++ b/src/mol-data/int/impl/sorted-array.ts
@@ -146,8 +146,8 @@ export function areIntersecting(a: Nums, b: Nums) {
let { startI: i, startJ: j, endI, endJ } = getSuitableIntersectionRange(a, b);
while (i < endI && j < endJ) {
const x = a[i], y = b[j];
- if (x < y) { i++; }
- else if (x > y) { j++; }
+ if (x < y) i++;
+ else if (x > y) j++;
else return true;
}
return false;
@@ -164,9 +164,13 @@ export function isSubset(a: Nums, b: Nums) {
let equal = 0;
while (i < endI && j < endJ) {
const x = a[i], y = b[j];
- if (x < y) { i++; }
- else if (x > y) { j++; }
- else { i++; j++; equal++; }
+ if (x < y) {
+ i++;
+ } else if (x > y) {
+ j++;
+ } else {
+ i++; j++; equal++;
+ }
}
return equal === lenB;
}
@@ -197,9 +201,13 @@ export function union(a: Nums, b: Nums): Nums {
// insert the common part
while (i < endI && j < endJ) {
const x = a[i], y = b[j];
- if (x < y) { indices[offset++] = x; i++; }
- else if (x > y) { indices[offset++] = y; j++; }
- else { indices[offset++] = x; i++; j++; }
+ if (x < y) {
+ indices[offset++] = x; i++;
+ } else if (x > y) {
+ indices[offset++] = y; j++;
+ } else {
+ indices[offset++] = x; i++; j++;
+ }
}
// insert the remaining common part
@@ -224,9 +232,13 @@ function getCommonCount(a: Nums, b: Nums, startI: number, startJ: number, endI:
let commonCount = 0;
while (i < endI && j < endJ) {
const x = a[i], y = b[j];
- if (x < y) { i++; }
- else if (x > y) { j++; }
- else { i++; j++; commonCount++; }
+ if (x < y) {
+ i++;
+ } else if (x > y) {
+ j++;
+ } else {
+ i++; j++; commonCount++;
+ }
}
return commonCount;
}
@@ -251,9 +263,13 @@ export function intersect(a: Nums, b: Nums) {
let j = startJ;
while (i < endI && j < endJ) {
const x = a[i], y = b[j];
- if (x < y) { i++; }
- else if (x > y) { j++; }
- else { indices[offset++] = x; i++; j++; }
+ if (x < y) {
+ i++;
+ } else if (x > y) {
+ j++;
+ } else {
+ indices[offset++] = x; i++; j++;
+ }
}
return ofSortedArray(indices);
@@ -268,9 +284,13 @@ export function subtract(a: Nums, b: Nums) {
let commonCount = 0;
while (i < endI && j < endJ) {
const x = a[i], y = b[j];
- if (x < y) { i++; }
- else if (x > y) { j++; }
- else { i++; j++; commonCount++; }
+ if (x < y) {
+ i++;
+ } else if (x > y) {
+ j++;
+ } else {
+ i++; j++; commonCount++;
+ }
}
// A isnt intersecting B ===> A
@@ -288,9 +308,13 @@ export function subtract(a: Nums, b: Nums) {
j = sJ;
while (i < endI && j < endJ) {
const x = a[i], y = b[j];
- if (x < y) { indices[offset++] = x; i++; }
- else if (x > y) { j++; }
- else { i++; j++; }
+ if (x < y) {
+ indices[offset++] = x; i++;
+ } else if (x > y) {
+ j++;
+ } else {
+ i++; j++;
+ }
}
// insert the "tail"
@@ -323,9 +347,13 @@ export function indicesOf(a: Nums, b: Nums): Nums {
let commonCount = 0;
while (i < endI && j < endJ) {
const x = a[i], y = b[j];
- if (x < y) { i++; }
- else if (x > y) { j++; }
- else { i++; j++; commonCount++; }
+ if (x < y) {
+ i++;
+ } else if (x > y) {
+ j++;
+ } else {
+ i++; j++; commonCount++;
+ }
}
const lenA = a.length;
@@ -340,9 +368,13 @@ export function indicesOf(a: Nums, b: Nums): Nums {
j = sJ;
while (i < endI && j < endJ) {
const x = a[i], y = b[j];
- if (x < y) { i++; }
- else if (x > y) { j++; }
- else { indices[offset++] = i; i++; j++; }
+ if (x < y) {
+ i++;
+ } else if (x > y) {
+ j++;
+ } else {
+ indices[offset++] = i; i++; j++;
+ }
}
return ofSortedArray(indices);
diff --git a/src/mol-io/common/msgpack/encode.ts b/src/mol-io/common/msgpack/encode.ts
index 35231843a4eeb62d41f8a58d8242bc2eb42afd22..9fa997674258233b3d1b089c4469fcc179e8f6ef 100644
--- a/src/mol-io/common/msgpack/encode.ts
+++ b/src/mol-io/common/msgpack/encode.ts
@@ -88,8 +88,7 @@ function encodedSize(value: any) {
for (let i = 0; i < length; i++) {
size += encodedSize(value[i]);
}
- }
- else {
+ } else {
let keys = Object.keys(value);
length = keys.length;
for (let i = 0; i < length; i++) {
@@ -257,8 +256,7 @@ function encodeInternal(value: any, view: DataView, bytes: Uint8Array, offset: n
if (isArray) {
length = value.length;
- }
- else {
+ } else {
keys = Object.keys(value);
length = keys.length;
}
@@ -266,13 +264,11 @@ function encodeInternal(value: any, view: DataView, bytes: Uint8Array, offset: n
if (length < 0x10) {
view.setUint8(offset, length | (isArray ? 0x90 : 0x80));
size = 1;
- }
- else if (length < 0x10000) {
+ } else if (length < 0x10000) {
view.setUint8(offset, isArray ? 0xdc : 0xde);
view.setUint16(offset + 1, length);
size = 3;
- }
- else if (length < 0x100000000) {
+ } else if (length < 0x100000000) {
view.setUint8(offset, isArray ? 0xdd : 0xdf);
view.setUint32(offset + 1, length);
size = 5;
@@ -282,8 +278,7 @@ function encodeInternal(value: any, view: DataView, bytes: Uint8Array, offset: n
for (let i = 0; i < length; i++) {
size += encodeInternal(value[i], view, bytes, offset + size);
}
- }
- else {
+ } else {
for (let i = 0, _i = keys!.length; i < _i; i++) {
const key = keys![i];
size += encodeInternal(key, view, bytes, offset + size);
diff --git a/src/mol-io/common/utf8.ts b/src/mol-io/common/utf8.ts
index 83cc3f0754f1e5a7b5d28303c697aa59903d52c0..706fe90db5492faf6f8980958504c5a5aa29ae15 100644
--- a/src/mol-io/common/utf8.ts
+++ b/src/mol-io/common/utf8.ts
@@ -59,24 +59,21 @@ function _utf8Read(data: Uint8Array, offset: number, length: number) {
for (let i = offset, end = offset + length; i < end; i++) {
let byte = data[i];
- // One byte character
if ((byte & 0x80) === 0x00) {
+ // One byte character
chunk[chunkOffset++] = chars[byte];
- }
- // Two byte character
- else if ((byte & 0xe0) === 0xc0) {
+ } else if ((byte & 0xe0) === 0xc0) {
+ // Two byte character
chunk[chunkOffset++] = chars[((byte & 0x0f) << 6) | (data[++i] & 0x3f)];
- }
- // Three byte character
- else if ((byte & 0xf0) === 0xe0) {
+ } else if ((byte & 0xf0) === 0xe0) {
+ // Three byte character
chunk[chunkOffset++] = String.fromCharCode(
((byte & 0x0f) << 12) |
((data[++i] & 0x3f) << 6) |
((data[++i] & 0x3f) << 0)
);
- }
- // Four byte character
- else if ((byte & 0xf8) === 0xf0) {
+ } else if ((byte & 0xf8) === 0xf0) {
+ // Four byte character
chunk[chunkOffset++] = String.fromCharCode(
((byte & 0x07) << 18) |
((data[++i] & 0x3f) << 12) |
diff --git a/src/mol-io/reader/cif/data-model.ts b/src/mol-io/reader/cif/data-model.ts
index d354d65aaae2f27b4013590f1c2e9a73cfe7eaf5..fa7223cf6ebb326a6e20a4f615cf263a4f4b99cb 100644
--- a/src/mol-io/reader/cif/data-model.ts
+++ b/src/mol-io/reader/cif/data-model.ts
@@ -267,21 +267,40 @@ export namespace CifField {
}
}
-export function getTensor(category: CifCategory, field: string, space: Tensor.Space, row: number, zeroIndexed: boolean): Tensor.Data {
- const ret = space.create();
+export function tensorFieldNameGetter(field: string, rank: number, zeroIndexed: boolean, namingVariant: 'brackets' | 'underscore') {
const offset = zeroIndexed ? 0 : 1;
+ switch (rank) {
+ case 1:
+ return namingVariant === 'brackets'
+ ? (i: number) => `${field}[${i + offset}]`
+ : (i: number) => `${field}_${i + offset}`
+ case 2:
+ return namingVariant === 'brackets'
+ ? (i: number, j: number) => `${field}[${i + offset}][${j + offset}]`
+ : (i: number, j: number) => `${field}_${i + offset}${j + offset}`
+ case 3:
+ return namingVariant === 'brackets'
+ ? (i: number, j: number, k: number) => `${field}[${i + offset}][${j + offset}][${k + offset}]`
+ : (i: number, j: number, k: number) => `${field}_${i + offset}${j + offset}${k + offset}`
+ default:
+ throw new Error('Tensors with rank > 3 or rank 0 are currently not supported.');
+ }
+}
+
+export function getTensor(category: CifCategory, space: Tensor.Space, row: number, getName: (...args: number[]) => string): Tensor.Data {
+ const ret = space.create();
if (space.rank === 1) {
const rows = space.dimensions[0];
for (let i = 0; i < rows; i++) {
- const f = category.getField(`${field}[${i + offset}]`);
+ const f = category.getField(getName(i));
space.set(ret, i, !!f ? f.float(row) : 0.0);
}
} else if (space.rank === 2) {
const rows = space.dimensions[0], cols = space.dimensions[1];
for (let i = 0; i < rows; i++) {
for (let j = 0; j < cols; j++) {
- const f = category.getField(`${field}[${i + offset}][${j + offset}]`);
+ const f = category.getField(getName(i, j));
space.set(ret, i, j, !!f ? f.float(row) : 0.0);
}
}
@@ -290,12 +309,14 @@ export function getTensor(category: CifCategory, field: string, space: Tensor.Sp
for (let i = 0; i < d0; i++) {
for (let j = 0; j < d1; j++) {
for (let k = 0; k < d2; k++) {
- const f = category.getField(`${field}[${i + offset}][${j + offset}][${k + offset}]`);
+ const f = category.getField(getName(i, j, k));
space.set(ret, i, j, k, !!f ? f.float(row) : 0.0);
}
}
}
- } else throw new Error('Tensors with rank > 3 or rank 0 are currently not supported.');
+ } else {
+ throw new Error('Tensors with rank > 3 or rank 0 are currently not supported.');
+ }
return ret;
}
diff --git a/src/mol-io/reader/cif/schema.ts b/src/mol-io/reader/cif/schema.ts
index f465a8fd29828e99fe396cdaea1756325592afc8..1fba5439b4d564e612167f08d6b6f2ca86d8843c 100644
--- a/src/mol-io/reader/cif/schema.ts
+++ b/src/mol-io/reader/cif/schema.ts
@@ -88,18 +88,21 @@ function createListColumn<T extends number | string>(schema: Column.Schema.List<
function createTensorColumn(schema: Column.Schema.Tensor, category: Data.CifCategory, key: string): Column<Tensor.Data> {
const space = schema.space;
- const zeroOffset = category.fieldNames.indexOf(`${key}[0]`) >= 0;
+ const zeroOffset = (
+ category.fieldNames.includes(`${key}[0]`) ||
+ category.fieldNames.includes(`${key}[0][0]`) ||
+ category.fieldNames.includes(`${key}[0][0][0]`)
+ );
const fst = zeroOffset ? 0 : 1;
-
- let firstFieldName: string;
- switch (space.rank) {
- case 1: firstFieldName = `${key}[${fst}]`; break;
- case 2: firstFieldName = `${key}[${fst}][${fst}]`; break;
- case 3: firstFieldName = `${key}[${fst}][${fst}][${fst}]`; break;
- default: throw new Error('Tensors with rank > 3 or rank 0 are currently not supported.');
- }
- const first = category.getField(firstFieldName) || Column.Undefined(category.rowCount, schema);
- const value = (row: number) => Data.getTensor(category, key, space, row, zeroOffset);
+ const namingVariant = (
+ category.fieldNames.includes(`${key}_1`) ||
+ category.fieldNames.includes(`${key}_11`) ||
+ category.fieldNames.includes(`${key}_111`)
+ ) ? 'underscore' : 'brackets'
+
+ const getName = Data.tensorFieldNameGetter(key, space.rank, zeroOffset, namingVariant)
+ const first = category.getField(getName(fst, fst, fst)) || Column.Undefined(category.rowCount, schema);
+ const value = (row: number) => Data.getTensor(category, space, row, getName);
const toArray: Column<Tensor.Data>['toArray'] = params => ColumnHelpers.createAndFillArray(category.rowCount, value, params)
return {
diff --git a/src/mol-io/reader/cif/schema/cif-core.ts b/src/mol-io/reader/cif/schema/cif-core.ts
index 6b6cfe4c72dfe0a3dba41ca013e32dc00aee3e3b..940ddc947e39b5933e1b8520c8224c27b98aed2e 100644
--- a/src/mol-io/reader/cif/schema/cif-core.ts
+++ b/src/mol-io/reader/cif/schema/cif-core.ts
@@ -13,6 +13,7 @@ import Schema = Column.Schema
const int = Schema.int;
const float = Schema.float;
const str = Schema.str;
+const Matrix = Schema.Matrix;
export const CifCore_Schema = {
/**
@@ -181,6 +182,14 @@ export const CifCore_Schema = {
* trigonal system.
*/
crystal_system: str,
+ /**
+ * The number as assigned in International Tables for Crystallography
+ * Vol A, specifying the proper affine class (i.e. the orientation
+ * preserving affine class) of space groups (crystallographic space
+ * group type) to which the space group belongs. This number defines
+ * the space group type but not the coordinate system expressed.
+ */
+ IT_number: int,
/**
* The full international Hermann-Mauguin space-group symbol as
* defined in Section 2.2.3 and given as the second item of the
@@ -272,6 +281,29 @@ export const CifCore_Schema = {
* publication or should be placed in a table of significant angles.
*/
publ_flag: str,
+ /**
+ * The set of data items which specify the symmetry operation codes
+ * which must be applied to the atom sites involved in the geometry angle.
+ *
+ * The symmetry code of each atom site as the symmetry-equivalent position
+ * number 'n' and the cell translation number 'pqr'. These numbers are
+ * combined to form the code 'n pqr' or n_pqr.
+ *
+ * The character string n_pqr is composed as follows:
+ *
+ * n refers to the symmetry operation that is applied to the
+ * coordinates stored in _atom_site.fract_xyz. It must match a
+ * number given in _symmetry_equiv.pos_site_id.
+ *
+ * p, q and r refer to the translations that are subsequently
+ * applied to the symmetry transformed coordinates to generate
+ * the atom used in calculating the angle. These translations
+ * (x,y,z) are related to (p,q,r) by the relations
+ * p = 5 + x
+ * q = 5 + y
+ * r = 5 + z
+ */
+ site_symmetry_1: str,
/**
* The set of data items which specify the symmetry operation codes
* which must be applied to the atom sites involved in the geometry angle.
@@ -295,6 +327,10 @@ export const CifCore_Schema = {
* r = 5 + z
*/
site_symmetry_2: str,
+ /**
+ * Bond valence calculated from the bond distance.
+ */
+ valence: float,
},
/**
* The CATEGORY of data items used to record details about the
@@ -329,12 +365,38 @@ export const CifCore_Schema = {
* originate from that source.
*/
database_code: {
+ /**
+ * Code assigned by Crystallography Open Database (COD).
+ */
+ COD: str,
+ /**
+ * Code assigned by the Cambridge Structural Database.
+ */
+ CSD: str,
/**
* Deposition numbers assigned by the Cambridge Crystallographic
* Data Centre (CCDC) to files containing structural information
* archived by the CCDC.
*/
depnum_ccdc_archive: str,
+ /**
+ * Deposition numbers assigned by the Fachinformationszentrum
+ * Karlsruhe (FIZ) to files containing structural information
+ * archived by the Cambridge Crystallographic Data Centre (CCDC).
+ */
+ depnum_ccdc_fiz: str,
+ /**
+ * Code assigned by the Inorganic Crystal Structure Database.
+ */
+ ICSD: str,
+ /**
+ * Code assigned in the Metals Data File.
+ */
+ MDF: str,
+ /**
+ * Code assigned by the NBS (NIST) Crystal Data Database.
+ */
+ NBS: str,
},
/**
* The CATEGORY of data items used to describe atom site information
@@ -476,6 +538,33 @@ export const CifCore_Schema = {
* The unique elements of the real symmetric matrix are entered by row.
*/
U_11: float,
+ /**
+ * These are the standard anisotropic atomic displacement
+ * components in angstroms squared which appear in the
+ * structure factor term:
+ *
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
+ *
+ * h = the Miller indices
+ * a* = the reciprocal-space cell lengths
+ *
+ * The unique elements of the real symmetric matrix are entered by row.
+ */
+ U: Matrix(3, 3),
+ /**
+ * These are the standard uncertainty values (SU) for the standard
+ * form of the Uij anisotropic atomic displacement components (see
+ * _aniso_UIJ. Because these values are TYPE measurand, the su values
+ * may in practice be auto generated as part of the Uij calculation.
+ */
+ U_11_su: float,
+ /**
+ * These are the standard uncertainty values (SU) for the standard
+ * form of the Uij anisotropic atomic displacement components (see
+ * _aniso_UIJ. Because these values are TYPE measurand, the su values
+ * may in practice be auto generated as part of the Uij calculation.
+ */
+ U_su: Matrix(3, 3),
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
@@ -489,6 +578,13 @@ export const CifCore_Schema = {
* The unique elements of the real symmetric matrix are entered by row.
*/
U_12: float,
+ /**
+ * These are the standard uncertainty values (SU) for the standard
+ * form of the Uij anisotropic atomic displacement components (see
+ * _aniso_UIJ. Because these values are TYPE measurand, the su values
+ * may in practice be auto generated as part of the Uij calculation.
+ */
+ U_12_su: float,
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
@@ -502,6 +598,13 @@ export const CifCore_Schema = {
* The unique elements of the real symmetric matrix are entered by row.
*/
U_13: float,
+ /**
+ * These are the standard uncertainty values (SU) for the standard
+ * form of the Uij anisotropic atomic displacement components (see
+ * _aniso_UIJ. Because these values are TYPE measurand, the su values
+ * may in practice be auto generated as part of the Uij calculation.
+ */
+ U_13_su: float,
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
@@ -515,6 +618,13 @@ export const CifCore_Schema = {
* The unique elements of the real symmetric matrix are entered by row.
*/
U_22: float,
+ /**
+ * These are the standard uncertainty values (SU) for the standard
+ * form of the Uij anisotropic atomic displacement components (see
+ * _aniso_UIJ. Because these values are TYPE measurand, the su values
+ * may in practice be auto generated as part of the Uij calculation.
+ */
+ U_22_su: float,
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
@@ -528,6 +638,13 @@ export const CifCore_Schema = {
* The unique elements of the real symmetric matrix are entered by row.
*/
U_23: float,
+ /**
+ * These are the standard uncertainty values (SU) for the standard
+ * form of the Uij anisotropic atomic displacement components (see
+ * _aniso_UIJ. Because these values are TYPE measurand, the su values
+ * may in practice be auto generated as part of the Uij calculation.
+ */
+ U_23_su: float,
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
@@ -541,6 +658,13 @@ export const CifCore_Schema = {
* The unique elements of the real symmetric matrix are entered by row.
*/
U_33: float,
+ /**
+ * These are the standard uncertainty values (SU) for the standard
+ * form of the Uij anisotropic atomic displacement components (see
+ * _aniso_UIJ. Because these values are TYPE measurand, the su values
+ * may in practice be auto generated as part of the Uij calculation.
+ */
+ U_33_su: float,
},
/**
* The CATEGORY of data items used to describe atomic type information
@@ -586,6 +710,16 @@ export const CifCore_Schema = {
}
export const CifCore_Aliases = {
+ 'atom_site_aniso.U': [
+ 'atom_site_anisotrop_U',
+ ],
+ 'atom_site_aniso.U_su': [
+ 'atom_site_aniso_U_esd',
+ 'atom_site_anisotrop_U_esd',
+ ],
+ 'space_group.IT_number': [
+ 'symmetry_Int_Tables_number',
+ ],
'space_group.name_H-M_full': [
'symmetry_space_group_name_H-M',
],
@@ -616,21 +750,45 @@ export const CifCore_Aliases = {
'atom_site_aniso.U_11': [
'atom_site_anisotrop_U_11',
],
+ 'atom_site_aniso.U_11_su': [
+ 'atom_site_aniso_U_11_esd',
+ 'atom_site_anisotrop_U_11_esd',
+ ],
'atom_site_aniso.U_12': [
'atom_site_anisotrop_U_12',
],
+ 'atom_site_aniso.U_12_su': [
+ 'atom_site_aniso_U_12_esd',
+ 'atom_site_anisotrop_U_12_esd',
+ ],
'atom_site_aniso.U_13': [
'atom_site_anisotrop_U_13',
],
+ 'atom_site_aniso.U_13_su': [
+ 'atom_site_aniso_U_13_esd',
+ 'atom_site_anisotrop_U_13_esd',
+ ],
'atom_site_aniso.U_22': [
'atom_site_anisotrop_U_22',
],
+ 'atom_site_aniso.U_22_su': [
+ 'atom_site_aniso_U_22_esd',
+ 'atom_site_anisotrop_U_22_esd',
+ ],
'atom_site_aniso.U_23': [
'atom_site_anisotrop_U_23',
],
+ 'atom_site_aniso.U_23_su': [
+ 'atom_site_aniso_U_23_esd',
+ 'atom_site_anisotrop_U_23_esd',
+ ],
'atom_site_aniso.U_33': [
'atom_site_anisotrop_U_33',
],
+ 'atom_site_aniso.U_33_su': [
+ 'atom_site_aniso_U_33_esd',
+ 'atom_site_anisotrop_U_33_esd',
+ ],
}
export type CifCore_Schema = typeof CifCore_Schema;
diff --git a/src/mol-io/reader/common/text/number-parser.ts b/src/mol-io/reader/common/text/number-parser.ts
index 27adc16cc1396ac0defc6da5ceaae63991db7677..4f609cec74eaf9779186f09704a50875c1baf658 100644
--- a/src/mol-io/reader/common/text/number-parser.ts
+++ b/src/mol-io/reader/common/text/number-parser.ts
@@ -71,8 +71,9 @@ export function parseFloat(str: string, start: number, end: number) {
return neg * (ret + point / div);
} else if (c === 53 || c === 21) { // 'e'/'E'
return parseScientific(neg * ret, str, _start + 1, end);
+ } else {
+ break;
}
- else break;
}
return neg * ret;
}
@@ -137,8 +138,9 @@ export function getNumberType(str: string): NumberType {
return NumberType.NaN; // string starts with e/E or -e/-E
}
return getNumberTypeScientific(str, start + 1, end);
+ } else {
+ break;
}
- else break;
}
return start === end ? NumberType.Int : NumberType.NaN;
}
diff --git a/src/mol-io/writer/cif/encoder/binary.ts b/src/mol-io/writer/cif/encoder/binary.ts
index 9040dc7e67bbf5d6ad349edc298d9b9f4f7d7050..a80e1afeb8c9ccca75f3a6ffff755c80c6ae4b4d 100644
--- a/src/mol-io/writer/cif/encoder/binary.ts
+++ b/src/mol-io/writer/cif/encoder/binary.ts
@@ -188,8 +188,7 @@ function getFieldData(field: Field<any, any>, arrayCtor: ArrayCtor<string | numb
if (isStr)
array[offset] = '';
allPresent = false;
- }
- else {
+ } else {
mask[offset] = Column.ValueKind.Present;
array[offset] = getter(key, d, offset);
}
diff --git a/src/mol-math/graph/int-adjacency-graph.ts b/src/mol-math/graph/int-adjacency-graph.ts
index 600ab01f07e60e8746d2dbe17d205a299857ac56..04c62438d8758476b989641e0a869115e8739ade 100644
--- a/src/mol-math/graph/int-adjacency-graph.ts
+++ b/src/mol-math/graph/int-adjacency-graph.ts
@@ -54,8 +54,11 @@ export namespace IntAdjacencyGraph {
getEdgeIndex(i: VertexIndex, j: VertexIndex): number {
let a, b;
- if (i < j) { a = i; b = j; }
- else { a = j; b = i; }
+ if (i < j) {
+ a = i; b = j;
+ } else {
+ a = j; b = i;
+ }
for (let t = this.offset[a], _t = this.offset[a + 1]; t < _t; t++) {
if (this.b[t] === b) return t;
}
diff --git a/src/mol-math/linear-algebra/3d/mat4.ts b/src/mol-math/linear-algebra/3d/mat4.ts
index f2b9d7173bbddbbfda28bf11d4f5f4685aafbe1d..6fd4bd0316504952edb1f460cb45aa5a4fabd592 100644
--- a/src/mol-math/linear-algebra/3d/mat4.ts
+++ b/src/mol-math/linear-algebra/3d/mat4.ts
@@ -743,6 +743,8 @@ namespace Mat4 {
* Check if the matrix has the form
* [ Rotation Translation ]
* [ 0 1 ]
+ *
+ * Allows for improper rotations
*/
export function isRotationAndTranslation(a: Mat4, eps?: number) {
return _isRotationAndTranslation(a, typeof eps !== 'undefined' ? eps : EPSILON)
@@ -752,12 +754,14 @@ namespace Mat4 {
const a00 = a[0], a01 = a[1], a02 = a[2], a03 = a[3],
a10 = a[4], a11 = a[5], a12 = a[6], a13 = a[7],
a20 = a[8], a21 = a[9], a22 = a[10], a23 = a[11],
- /* a30 = a[12], a31 = a[13], a32 = a[14],*/ a33 = a[15];
+ a33 = a[15];
if (!equalEps(a33, 1, eps) || !equalEps(a03, 0, eps) || !equalEps(a13, 0, eps) || !equalEps(a23, 0, eps)) {
return false;
}
- const det3x3 = a00 * (a11 * a22 - a12 * a21) - a01 * (a10 * a22 - a12 * a20) + a02 * (a10 * a21 - a11 * a20);
+
+ // use `abs` to allow for improper rotations
+ const det3x3 = Math.abs(a00 * (a11 * a22 - a12 * a21) - a01 * (a10 * a22 - a12 * a20) + a02 * (a10 * a21 - a11 * a20));
if (!equalEps(det3x3, 1, eps)) {
return false;
}
diff --git a/src/mol-math/linear-algebra/matrix/evd.ts b/src/mol-math/linear-algebra/matrix/evd.ts
index 789d314e65b8076c3deb49b92d98cc090b32b0f1..7bd2056ae88331e749a83771f1981b249e937c84 100644
--- a/src/mol-math/linear-algebra/matrix/evd.ts
+++ b/src/mol-math/linear-algebra/matrix/evd.ts
@@ -77,8 +77,7 @@ function symmetricTridiagonalize(a: number[], d: number[], e: number[], order: n
a[(j * order) + i] = 0.0;
a[(i * order) + j] = 0.0;
}
- }
- else {
+ } else {
// Generate Householder vector.
for (let k = 0; k < i; k++) {
d[k] /= scale;
diff --git a/src/mol-model-formats/structure/_spec/cif-core.spec.ts b/src/mol-model-formats/structure/_spec/cif-core.spec.ts
index 5e73efda9e8e6ef5d64c39ccb4e10e585ae27c81..51c4b868da264e145e2e8e6da09437c2141a2fd8 100644
--- a/src/mol-model-formats/structure/_spec/cif-core.spec.ts
+++ b/src/mol-model-formats/structure/_spec/cif-core.spec.ts
@@ -44,6 +44,34 @@ _cell_measurement_temperature 100(2)
_cell_measurement_reflns_used 5934
_cell_measurement_theta_min 2.86
_cell_measurement_theta_max 64.30
+
+loop_
+_atom_site_aniso_label
+_atom_site_aniso_U_11
+_atom_site_aniso_U_22
+_atom_site_aniso_U_33
+_atom_site_aniso_U_23
+_atom_site_aniso_U_13
+_atom_site_aniso_U_12
+Pt1 0.0425(2) 0.0423(2) 0.0375(2) 0.00066(13) 0.01515(13) 0.00089(12)
+K1 0.0605(15) 0.0687(17) 0.0559(17) 0.000 0.0203(13) 0.000
+Cl2 0.0511(11) 0.0554(11) 0.0533(13) 0.0078(10) 0.0225(9) 0.0027(9)
+Cl3 0.0708(13) 0.0484(11) 0.0605(13) -0.0053(10) 0.0276(10) 0.0026(10)
+Cl1 0.0950(16) 0.0442(11) 0.0942(18) -0.0051(12) 0.0526(14) 0.0035(12)
+N9 0.045(3) 0.047(4) 0.035(4) 0.004(3) 0.014(3) -0.003(3)
+N7 0.040(3) 0.048(4) 0.036(3) 0.008(3) 0.004(3) -0.004(3)
+O2 0.052(3) 0.098(4) 0.046(4) -0.012(4) 0.006(3) -0.016(3)
+N3 0.041(3) 0.044(3) 0.044(4) 0.001(3) 0.008(3) -0.002(3)
+O6 0.053(3) 0.093(4) 0.052(3) 0.008(3) 0.021(3) -0.019(3)
+C4 0.044(4) 0.032(4) 0.050(5) 0.004(4) 0.011(4) 0.003(3)
+N1 0.049(4) 0.049(4) 0.040(4) 0.004(3) 0.014(3) -0.005(3)
+C8 0.050(4) 0.045(4) 0.033(4) -0.007(4) 0.000(3) -0.004(4)
+C5 0.036(4) 0.039(4) 0.045(5) 0.003(4) 0.013(3) -0.001(3)
+C2 0.047(4) 0.045(4) 0.039(5) -0.007(4) 0.011(4) -0.004(4)
+C7 0.041(4) 0.072(5) 0.055(5) 0.013(5) 0.006(4) -0.015(4)
+C1 0.061(5) 0.067(5) 0.043(5) -0.002(4) 0.017(4) -0.005(4)
+C3 0.038(4) 0.090(6) 0.054(5) 0.003(5) 0.013(4) -0.018(4)
+C6 0.045(4) 0.043(4) 0.038(4) 0.004(4) 0.008(3) -0.002(4)
`
describe('cif-core read', () => {
@@ -65,6 +93,7 @@ describe('cif-core read', () => {
const cifCore = CIF.schema.cifCore(block)
expect(cifCore.cell.length_a.value(0)).toBe(11.0829)
- expect.assertions(1)
+ expect(cifCore.atom_site_aniso.U.value(0)).toEqual(new Float64Array([ 0.0425, 0, 0, 0.00089, 0.0423, 0, 0.01515, 0.00066, 0.0375 ]))
+ expect.assertions(2)
});
});
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/cif-core.ts b/src/mol-model-formats/structure/cif-core.ts
new file mode 100644
index 0000000000000000000000000000000000000000..539ff633834b16392be84f588de2f2f3ea8df563
--- /dev/null
+++ b/src/mol-model-formats/structure/cif-core.ts
@@ -0,0 +1,201 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Column, Table } from '../../mol-data/db';
+import { Model, Symmetry } from '../../mol-model/structure/model';
+import { MoleculeType } from '../../mol-model/structure/model/types';
+import { RuntimeContext, Task } from '../../mol-task';
+import { createModels } from './basic/parser';
+import { BasicSchema, createBasic } from './basic/schema';
+import { ComponentBuilder } from './common/component';
+import { EntityBuilder } from './common/entity';
+import { ModelFormat } from './format';
+import { CifCore_Database } from '../../mol-io/reader/cif/schema/cif-core';
+import { CifFrame, CIF } from '../../mol-io/reader/cif';
+import { Spacegroup, SpacegroupCell } from '../../mol-math/geometry';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { ModelSymmetry } from './property/symmetry';
+import { IndexPairBonds } from './property/bonds/index-pair';
+import { AtomSiteAnisotrop } from './property/anisotropic';
+
+function getSpacegroupNameOrNumber(space_group: CifCore_Database['space_group']) {
+ const groupNumber = space_group.IT_number.value(0)
+ const groupName = space_group['name_H-M_full'].value(0)
+ if (!space_group.IT_number.isDefined) return groupName
+ if (!space_group['name_H-M_full'].isDefined) return groupNumber
+ return groupNumber
+}
+
+function getSymmetry(db: CifCore_Database): Symmetry {
+ const { cell, space_group } = db
+ const nameOrNumber = getSpacegroupNameOrNumber(space_group)
+ const spaceCell = SpacegroupCell.create(nameOrNumber,
+ Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)),
+ Vec3.scale(Vec3.zero(), Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
+
+ return {
+ spacegroup: Spacegroup.create(spaceCell),
+ assemblies : [],
+ isNonStandardCrytalFrame: false,
+ ncsOperators: []
+ }
+}
+
+async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: RuntimeContext): Promise<Model[]> {
+
+ const atomCount = db.atom_site._rowCount
+ const MOL = Column.ofConst('MOL', atomCount, Column.Schema.str);
+ const A = Column.ofConst('A', atomCount, Column.Schema.str);
+ const seq_id = Column.ofConst(1, atomCount, Column.Schema.int);
+
+ const symmetry = getSymmetry(db)
+ const m = symmetry.spacegroup.cell.fromFractional
+
+ const { fract_x, fract_y, fract_z } = db.atom_site
+ const x = new Float32Array(atomCount)
+ const y = new Float32Array(atomCount)
+ const z = new Float32Array(atomCount)
+ const v = Vec3()
+ for (let i = 0; i < atomCount; ++i) {
+ Vec3.set(v, fract_x.value(i), fract_y.value(i), fract_z.value(i))
+ Vec3.transformMat4(v, v, m)
+ x[i] = v[0], y[i] = v[1], z[i] = v[2]
+ }
+
+ const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
+ auth_asym_id: A,
+ auth_atom_id: db.atom_site.label,
+ auth_comp_id: MOL,
+ auth_seq_id: seq_id,
+ Cartn_x: Column.ofFloatArray(x),
+ Cartn_y: Column.ofFloatArray(y),
+ Cartn_z: Column.ofFloatArray(z),
+ id: Column.range(0, atomCount - 1),
+
+ label_asym_id: A,
+ label_atom_id: db.atom_site.label,
+ label_comp_id: MOL,
+ label_seq_id: seq_id,
+ label_entity_id: Column.ofConst('1', atomCount, Column.Schema.str),
+
+ occupancy: db.atom_site.occupancy,
+ type_symbol: db.atom_site.type_symbol,
+
+ pdbx_PDB_model_num: Column.ofConst(1, atomCount, Column.Schema.int),
+ }, atomCount);
+
+ const name = (
+ db.chemical.name_common.value(0) ||
+ db.chemical.name_systematic.value(0) ||
+ db.chemical_formula.sum.value(0)
+ )
+
+ const entityBuilder = new EntityBuilder()
+ entityBuilder.setNames([['MOL', name || 'Unknown Entity']])
+ entityBuilder.getEntityId('MOL', MoleculeType.Unknown, 'A');
+
+ const componentBuilder = new ComponentBuilder(seq_id, db.atom_site.type_symbol);
+ componentBuilder.setNames([['MOL', name || 'Unknown Molecule']])
+ componentBuilder.add('MOL', 0);
+
+ const basics = createBasic({
+ entity: entityBuilder.getEntityTable(),
+ chem_comp: componentBuilder.getChemCompTable(),
+ atom_site
+ });
+
+ const models = await createModels(basics, format, ctx);
+
+ if (models.length > 0) {
+ ModelSymmetry.Provider.set(models[0], symmetry)
+
+ const bondCount = db.geom_bond._rowCount
+ if(bondCount > 0) {
+ const labelIndexMap: { [label: string]: number } = {}
+ const { label } = db.atom_site
+ for (let i = 0, il = label.rowCount; i < il; ++i) {
+ labelIndexMap[label.value(i)] = i
+ }
+
+ const indexA: number[] = []
+ const indexB: number[] = []
+ const order: number[] = []
+ const symmetryA: string[] = []
+ const symmetryB: string[] = []
+
+ const { atom_site_label_1, atom_site_label_2, valence, site_symmetry_1, site_symmetry_2 } = db.geom_bond
+ for (let i = 0; i < bondCount; ++i) {
+ indexA[i] = labelIndexMap[atom_site_label_1.value(i)]
+ indexB[i] = labelIndexMap[atom_site_label_2.value(i)]
+ // TODO derive order from bond length if undefined
+ order[i] = valence.isDefined ? valence.value(i) : 1
+ symmetryA[i] = site_symmetry_1.value(i) || '1_555'
+ symmetryB[i] = site_symmetry_2.value(i) || '1_555'
+ }
+
+ IndexPairBonds.Provider.set(models[0], IndexPairBonds.fromData({ pairs: {
+ indexA: Column.ofIntArray(indexA),
+ indexB: Column.ofIntArray(indexB),
+ order: Column.ofIntArray(order),
+ symmetryA: Column.ofStringArray(symmetryA),
+ symmetryB: Column.ofStringArray(symmetryB)
+ }, count: indexA.length }));
+ }
+ }
+
+ return models;
+}
+
+function atomSiteAnisotropFromCifCore(model: Model) {
+ if (!CifCoreFormat.is(model.sourceData)) return;
+ const { atom_site, atom_site_aniso } = model.sourceData.data.db
+ const data = Table.ofPartialColumns(AtomSiteAnisotrop.Schema, {
+ U: atom_site_aniso.U,
+ U_esd: atom_site_aniso.U_su
+ }, atom_site_aniso._rowCount);
+ const elementToAnsiotrop = AtomSiteAnisotrop.getElementToAnsiotropFromLabel(atom_site.label, atom_site_aniso.label)
+ return { data, elementToAnsiotrop }
+}
+function atomSiteAnisotropApplicableCifCore(model: Model) {
+ if (!CifCoreFormat.is(model.sourceData)) return false;
+ return model.sourceData.data.db.atom_site_aniso.U.isDefined
+}
+AtomSiteAnisotrop.Provider.formatRegistry.add('cifCore', atomSiteAnisotropFromCifCore, atomSiteAnisotropApplicableCifCore)
+
+//
+
+export { CifCoreFormat };
+
+type CifCoreFormat = ModelFormat<CifCoreFormat.Data>
+
+namespace CifCoreFormat {
+ export type Data = { db: CifCore_Database, frame: CifFrame }
+ export function is(x: ModelFormat): x is CifCoreFormat {
+ return x.kind === 'cifCore'
+ }
+
+ export function fromFrame(frame: CifFrame, db?: CifCore_Database): CifCoreFormat {
+ if (!db) db = CIF.schema.cifCore(frame)
+
+ const name = (
+ db.database_code.depnum_ccdc_archive.value(0) ||
+ db.database_code.depnum_ccdc_fiz.value(0) ||
+ db.database_code.ICSD.value(0) ||
+ db.database_code.MDF.value(0) ||
+ db.database_code.NBS.value(0) ||
+ db.database_code.CSD.value(0) ||
+ db.database_code.COD.value(0) ||
+ db._name
+ )
+
+ return { kind: 'cifCore', name, data: { db, frame } };
+ }
+}
+
+export function trajectoryFromCifCore(frame: CifFrame): Task<Model.Trajectory> {
+ const format = CifCoreFormat.fromFrame(frame)
+ return Task.create('Parse CIF Core', ctx => getModels(format.data.db, format, ctx))
+}
diff --git a/src/mol-model-formats/structure/common/property.ts b/src/mol-model-formats/structure/common/property.ts
index 873e8bd5848a0bf1edd36a69f9001d4555c293fb..eeb7c1685087afda73ad67d57f309eab2329f20c 100644
--- a/src/mol-model-formats/structure/common/property.ts
+++ b/src/mol-model-formats/structure/common/property.ts
@@ -8,19 +8,27 @@ import { CustomPropertyDescriptor, Model } from '../../../mol-model/structure';
import { ModelFormat } from '../format';
class FormatRegistry<T> {
- map = new Map<ModelFormat['kind'], (model: Model) => T | undefined>()
+ private map = new Map<ModelFormat['kind'], (model: Model) => T | undefined>()
+ private applicable = new Map<ModelFormat['kind'], (model: Model) => boolean>()
- add(kind: ModelFormat['kind'], obtain: (model: Model) => T | undefined) {
+ add(kind: ModelFormat['kind'], obtain: (model: Model) => T | undefined, applicable?: (model: Model) => boolean) {
this.map.set(kind, obtain)
+ if (applicable) this.applicable.set(kind, applicable)
}
remove(kind: ModelFormat['kind']) {
this.map.delete(kind)
+ this.applicable.delete(kind)
}
get(kind: ModelFormat['kind']) {
return this.map.get(kind)
}
+
+ isApplicable(model: Model) {
+ const isApplicable = this.applicable.get(model.sourceData.kind)
+ return isApplicable ? isApplicable(model) : true
+ }
}
export { FormatPropertyProvider as FormatPropertyProvider }
@@ -28,6 +36,7 @@ export { FormatPropertyProvider as FormatPropertyProvider }
interface FormatPropertyProvider<T> {
readonly descriptor: CustomPropertyDescriptor
readonly formatRegistry: FormatRegistry<T>
+ isApplicable(model: Model): boolean
get(model: Model): T | undefined
set(model: Model, value: T): void
}
@@ -40,6 +49,9 @@ namespace FormatPropertyProvider {
return {
descriptor,
formatRegistry,
+ isApplicable(model: Model) {
+ return formatRegistry.isApplicable(model)
+ },
get(model: Model): T | undefined {
if (model._staticPropertyData[name]) return model._staticPropertyData[name]
if (model.customProperties.has(descriptor)) return
diff --git a/src/mol-model-formats/structure/mmcif.ts b/src/mol-model-formats/structure/mmcif.ts
index ae7c3deb8147f42d7a2f660493581d921cc68b31..70fc158950b14340b6819e826dd580de2584a2ed 100644
--- a/src/mol-model-formats/structure/mmcif.ts
+++ b/src/mol-model-formats/structure/mmcif.ts
@@ -9,7 +9,7 @@ import { Model } from '../../mol-model/structure/model/model';
import { Task } from '../../mol-task';
import { ModelFormat } from './format';
import { CifFrame, CIF } from '../../mol-io/reader/cif';
-import { mmCIF_Database, mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
+import { mmCIF_Database } from '../../mol-io/reader/cif/schema/mmcif';
import { createModels } from './basic/parser';
import { ModelSymmetry } from './property/symmetry';
import { ModelSecondaryStructure } from './property/secondary-structure';
@@ -34,11 +34,15 @@ ModelSecondaryStructure.Provider.formatRegistry.add('mmCIF', secondaryStructureF
function atomSiteAnisotropFromMmcif(model: Model) {
if (!MmcifFormat.is(model.sourceData)) return;
const { atom_site_anisotrop } = model.sourceData.data.db
- const data = Table.ofColumns(mmCIF_Schema['atom_site_anisotrop'], atom_site_anisotrop);
- const elementToAnsiotrop = AtomSiteAnisotrop.getElementToAnsiotrop(model, data)
+ const data = Table.ofColumns(AtomSiteAnisotrop.Schema, atom_site_anisotrop);
+ const elementToAnsiotrop = AtomSiteAnisotrop.getElementToAnsiotrop(model.atomicConformation.atomId, atom_site_anisotrop.id)
return { data, elementToAnsiotrop }
}
-AtomSiteAnisotrop.Provider.formatRegistry.add('mmCIF', atomSiteAnisotropFromMmcif)
+function atomSiteAnisotropApplicableMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return false;
+ return model.sourceData.data.db.atom_site_anisotrop.U.isDefined
+}
+AtomSiteAnisotrop.Provider.formatRegistry.add('mmCIF', atomSiteAnisotropFromMmcif, atomSiteAnisotropApplicableMmcif)
function componentBondFromMmcif(model: Model) {
if (!MmcifFormat.is(model.sourceData)) return;
diff --git a/src/mol-model-formats/structure/mol.ts b/src/mol-model-formats/structure/mol.ts
index 2e9f43f315a63db09bece852ca917c955e79dbe1..ea99af2616ffe2cd8f627c025293b887b4fd01a8 100644
--- a/src/mol-model-formats/structure/mol.ts
+++ b/src/mol-model-formats/structure/mol.ts
@@ -1,6 +1,7 @@
/**
* Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
+ * @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -19,7 +20,7 @@ import { IndexPairBonds } from './property/bonds/index-pair';
async function getModels(mol: MolFile, ctx: RuntimeContext): Promise<Model[]> {
const { atoms, bonds } = mol;
- const UNK = Column.ofConst('UNK', mol.atoms.count, Column.Schema.str);
+ const MOL = Column.ofConst('MOL', mol.atoms.count, Column.Schema.str);
const A = Column.ofConst('A', mol.atoms.count, Column.Schema.str);
const type_symbol = Column.asArrayColumn(atoms.type_symbol);
const seq_id = Column.ofConst(1, atoms.count, Column.Schema.int);
@@ -27,7 +28,7 @@ async function getModels(mol: MolFile, ctx: RuntimeContext): Promise<Model[]> {
const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
auth_asym_id: A,
auth_atom_id: type_symbol,
- auth_comp_id: UNK,
+ auth_comp_id: MOL,
auth_seq_id: seq_id,
Cartn_x: Column.asArrayColumn(atoms.x, Float32Array),
Cartn_y: Column.asArrayColumn(atoms.y, Float32Array),
@@ -36,7 +37,7 @@ async function getModels(mol: MolFile, ctx: RuntimeContext): Promise<Model[]> {
label_asym_id: A,
label_atom_id: type_symbol,
- label_comp_id: UNK,
+ label_comp_id: MOL,
label_seq_id: seq_id,
label_entity_id: Column.ofConst('1', atoms.count, Column.Schema.str),
@@ -47,12 +48,12 @@ async function getModels(mol: MolFile, ctx: RuntimeContext): Promise<Model[]> {
}, atoms.count);
const entityBuilder = new EntityBuilder()
- entityBuilder.setNames([['UNK', 'Unknown Entity']])
- entityBuilder.getEntityId('UNK', MoleculeType.Unknown, 'A');
+ entityBuilder.setNames([['MOL', 'Unknown Entity']])
+ entityBuilder.getEntityId('MOL', MoleculeType.Unknown, 'A');
const componentBuilder = new ComponentBuilder(seq_id, type_symbol);
- componentBuilder.setNames([['UNK', 'Unknown Residue']])
- componentBuilder.add('UNK', 0);
+ componentBuilder.setNames([['MOL', 'Unknown Molecule']])
+ componentBuilder.add('MOL', 0);
const basics = createBasic({
entity: entityBuilder.getEntityTable(),
diff --git a/src/mol-model-formats/structure/property/anisotropic.ts b/src/mol-model-formats/structure/property/anisotropic.ts
index 156fcb8926083d77d75dd277a22e48621530d972..86db66428977fba9e1c7910f4af8524fb9488911 100644
--- a/src/mol-model-formats/structure/property/anisotropic.ts
+++ b/src/mol-model-formats/structure/property/anisotropic.ts
@@ -4,15 +4,20 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Table } from '../../../mol-data/db';
-import { Model, CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { Table, Column } from '../../../mol-data/db';
+import { CustomPropertyDescriptor } from '../../../mol-model/structure';
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { CifWriter } from '../../../mol-io/writer/cif';
import { FormatPropertyProvider } from '../common/property';
+import { MmcifFormat } from '../mmcif';
export { AtomSiteAnisotrop }
-type Anisotrop = Table<mmCIF_Schema['atom_site_anisotrop']>
+const Anisotrop = {
+ U: mmCIF_Schema.atom_site_anisotrop.U,
+ U_esd: mmCIF_Schema.atom_site_anisotrop.U_esd
+}
+type Anisotrop = Table<typeof Anisotrop>
interface AtomSiteAnisotrop {
data: Anisotrop
@@ -21,6 +26,8 @@ interface AtomSiteAnisotrop {
}
namespace AtomSiteAnisotrop {
+ export const Schema = Anisotrop
+
export const Descriptor: CustomPropertyDescriptor = {
name: 'atom_site_anisotrop',
cifExport: {
@@ -30,8 +37,9 @@ namespace AtomSiteAnisotrop {
instance(ctx) {
const p = Provider.get(ctx.firstModel);
if (!p) return CifWriter.Category.Empty;
+ if (!MmcifFormat.is(ctx.firstModel.sourceData)) return CifWriter.Category.Empty;
// TODO filter to write only data for elements that exist in model
- return CifWriter.Category.ofTable(p.data);
+ return CifWriter.Category.ofTable(ctx.firstModel.sourceData.data.db.atom_site_anisotrop);
}
}]
}
@@ -39,22 +47,36 @@ namespace AtomSiteAnisotrop {
export const Provider = FormatPropertyProvider.create<AtomSiteAnisotrop>(Descriptor)
- export function getElementToAnsiotrop(model: Model, data: Anisotrop) {
- const { atomId } = model.atomicConformation
+ export function getElementToAnsiotrop(atomId: Column<number>, ansioId: Column<number>) {
const atomIdToElement = new Int32Array(atomId.rowCount)
atomIdToElement.fill(-1)
for (let i = 0, il = atomId.rowCount; i < il; i++) {
atomIdToElement[atomId.value(i)] = i
}
- const { id } = data
const elementToAnsiotrop = new Int32Array(atomId.rowCount)
elementToAnsiotrop.fill(-1)
- for (let i = 0, il = id.rowCount; i < il; ++i) {
- const ei = atomIdToElement[id.value(i)]
+ for (let i = 0, il = ansioId.rowCount; i < il; ++i) {
+ const ei = atomIdToElement[ansioId.value(i)]
if (ei !== -1) elementToAnsiotrop[ei] = i
}
return elementToAnsiotrop
}
+
+ export function getElementToAnsiotropFromLabel(atomLabel: Column<string>, ansioLabel: Column<string>) {
+ const atomLabelToElement: { [k: string]: number | undefined } = {}
+ for (let i = 0, il = atomLabel.rowCount; i < il; i++) {
+ atomLabelToElement[atomLabel.value(i)] = i
+ }
+
+ const elementToAnsiotrop = new Int32Array(atomLabel.rowCount)
+ elementToAnsiotrop.fill(-1)
+ for (let i = 0, il = ansioLabel.rowCount; i < il; ++i) {
+ const ei = atomLabelToElement[ansioLabel.value(i)]
+ if (ei !== undefined) elementToAnsiotrop[ei] = i
+ }
+
+ return elementToAnsiotrop
+ }
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/property/bonds/index-pair.ts b/src/mol-model-formats/structure/property/bonds/index-pair.ts
index 8cc29e892471b5d9847dffb075c82efbf1d52d9d..98d48fabedbe7b8f45d31142ea66c08c657a8acc 100644
--- a/src/mol-model-formats/structure/property/bonds/index-pair.ts
+++ b/src/mol-model-formats/structure/property/bonds/index-pair.ts
@@ -9,17 +9,26 @@ import { IntAdjacencyGraph } from '../../../../mol-math/graph';
import { Column } from '../../../../mol-data/db';
import { FormatPropertyProvider } from '../../common/property';
-export type IndexPairBonds = IntAdjacencyGraph<number, { readonly order: ArrayLike<number> }>
+export type IndexPairBondsProps = {
+ readonly order: ArrayLike<number>
+ readonly symmetryA: ArrayLike<string>
+ readonly symmetryB: ArrayLike<string>
+}
+export type IndexPairBonds = IntAdjacencyGraph<number, IndexPairBondsProps>
-function getGraph(indexA: ArrayLike<number>, indexB: ArrayLike<number>, _order: ArrayLike<number>, count: number): IndexPairBonds {
+function getGraph(indexA: ArrayLike<number>, indexB: ArrayLike<number>, props: Partial<IndexPairBondsProps>, count: number): IndexPairBonds {
const builder = new IntAdjacencyGraph.EdgeBuilder(count, indexA, indexB);
const order = new Int8Array(builder.slotCount);
+ const symmetryA = new Array(builder.slotCount);
+ const symmetryB = new Array(builder.slotCount);
for (let i = 0, _i = builder.edgeCount; i < _i; i++) {
builder.addNextEdge();
- builder.assignProperty(order, _order[i]);
+ builder.assignProperty(order, props.order ? props.order[i] : 1);
+ builder.assignProperty(symmetryA, props.symmetryA ? props.symmetryA[i] : '');
+ builder.assignProperty(symmetryB, props.symmetryB ? props.symmetryB[i] : '');
}
- return builder.createGraph({ order });
+ return builder.createGraph({ order, symmetryA, symmetryB });
}
export namespace IndexPairBonds {
@@ -33,7 +42,9 @@ export namespace IndexPairBonds {
pairs: {
indexA: Column<number>,
indexB: Column<number>
- order: Column<number>
+ order?: Column<number>,
+ symmetryA?: Column<string>,
+ symmetryB?: Column<string>,
},
count: number
}
@@ -42,7 +53,9 @@ export namespace IndexPairBonds {
const { pairs, count } = data
const indexA = pairs.indexA.toArray()
const indexB = pairs.indexB.toArray()
- const order = pairs.order.toArray()
- return getGraph(indexA, indexB, order, count);
+ const order = pairs.order && pairs.order.toArray()
+ const symmetryA = pairs.symmetryA && pairs.symmetryA.toArray()
+ const symmetryB = pairs.symmetryB && pairs.symmetryB.toArray()
+ return getGraph(indexA, indexB, { order, symmetryA, symmetryB }, count);
}
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/property/symmetry.ts b/src/mol-model-formats/structure/property/symmetry.ts
index 487509249aefa9567915ca4b994aa715cf4e7f6d..8e3615079eafff748a161e731837ab6c15e91033 100644
--- a/src/mol-model-formats/structure/property/symmetry.ts
+++ b/src/mol-model-formats/structure/property/symmetry.ts
@@ -8,7 +8,7 @@
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { Spacegroup, SpacegroupCell, SymmetryOperator } from '../../../mol-math/geometry';
import { Tensor, Vec3, Mat3 } from '../../../mol-math/linear-algebra';
-import { Symmetry as _ModelSymmetry } from '../../../mol-model/structure/model/properties/symmetry';
+import { Symmetry } from '../../../mol-model/structure/model/properties/symmetry';
import { createAssemblies } from './assembly';
import { CustomPropertyDescriptor } from '../../../mol-model/structure';
import { FormatPropertyProvider } from '../common/property';
@@ -21,7 +21,7 @@ namespace ModelSymmetry {
name: 'model_symmetry',
};
- export const Provider = FormatPropertyProvider.create<_ModelSymmetry>(Descriptor)
+ export const Provider = FormatPropertyProvider.create<Symmetry>(Descriptor)
type Data = {
symmetry: Table<mmCIF_Schema['symmetry']>
@@ -33,7 +33,7 @@ namespace ModelSymmetry {
pdbx_struct_oper_list: Table<mmCIF_Schema['pdbx_struct_oper_list']>
}
- export function fromData(data: Data): _ModelSymmetry {
+ export function fromData(data: Data): Symmetry {
const assemblies = createAssemblies(data.pdbx_struct_assembly, data.pdbx_struct_assembly_gen, data.pdbx_struct_oper_list);
const spacegroup = getSpacegroup(data.symmetry, data.cell);
const isNonStandardCrytalFrame = checkNonStandardCrystalFrame(data.atom_sites, spacegroup);
diff --git a/src/mol-model-props/rcsb/validation-report.ts b/src/mol-model-props/rcsb/validation-report.ts
index 1120193d7c07b537f7a26d31779f59c7403a22a4..1ed8f1c2b68ded2a22e26a9dc36618723b0bd648 100644
--- a/src/mol-model-props/rcsb/validation-report.ts
+++ b/src/mol-model-props/rcsb/validation-report.ts
@@ -111,6 +111,7 @@ namespace ValidationReport {
}
export async function open(ctx: CustomProperty.Context, model: Model, props: FileSourceProps): Promise<ValidationReport> {
+ if (props.input === null) throw new Error('No file given')
const xml = await readFromFile(props.input, 'xml').runInContext(ctx.runtime)
return fromXml(xml, model)
}
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index ba6574fbf07b34096833bc668ae0c88074381673..f9c39208313a08e56afe38d33fefd07e9ba746e9 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -24,6 +24,7 @@ import { createModels } from '../../../mol-model-formats/structure/basic/parser'
import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
import { ChainIndex } from './indexing';
import { SymmetryOperator } from '../../../mol-math/geometry';
+import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
/**
* Interface to the "source data" of the molecule.
@@ -159,19 +160,14 @@ export namespace Model {
)
}
+ const tmpAngles90 = Vec3.create(1.5708, 1.5708, 1.5708) // in radians
+ const tmpLengths1 = Vec3.create(1, 1, 1)
export function hasCrystalSymmetry(model: Model) {
- if (!MmcifFormat.is(model.sourceData)) return false
- const { db } = model.sourceData.data
- return (
- db.symmetry._rowCount === 1 && db.cell._rowCount === 1 && !(
- db.symmetry.Int_Tables_number.value(0) === 1 &&
- db.cell.angle_alpha.value(0) === 90 &&
- db.cell.angle_beta.value(0) === 90 &&
- db.cell.angle_gamma.value(0) === 90 &&
- db.cell.length_a.value(0) === 1 &&
- db.cell.length_b.value(0) === 1 &&
- db.cell.length_c.value(0) === 1
- )
+ const spacegroup = ModelSymmetry.Provider.get(model)?.spacegroup
+ return !!spacegroup && !(
+ spacegroup.num === 1 &&
+ Vec3.equals(spacegroup.cell.anglesInRadians, tmpAngles90) &&
+ Vec3.equals(spacegroup.cell.size, tmpLengths1)
)
}
diff --git a/src/mol-model/structure/query/utils/structure-set.ts b/src/mol-model/structure/query/utils/structure-set.ts
index 2e1cf2d1aa17d8cf22bdad066779d310c173dc22..9741f3f3533c7c3a30792985ec03d1353f7dfbc3 100644
--- a/src/mol-model/structure/query/utils/structure-set.ts
+++ b/src/mol-model/structure/query/utils/structure-set.ts
@@ -44,8 +44,11 @@ export function structureAreIntersecting(sA: Structure, sB: Structure): boolean
if (sA === sB) return true;
let a, b;
- if (sA.units.length < sB.units.length) { a = sA; b = sB; }
- else { a = sB; b = sA; }
+ if (sA.units.length < sB.units.length) {
+ a = sA; b = sB;
+ } else {
+ a = sB; b = sA;
+ }
const aU = a.units, bU = b.unitMap;
@@ -64,8 +67,11 @@ export function structureIntersect(sA: Structure, sB: Structure): Structure {
if (!structureAreIntersecting(sA, sB)) return Structure.Empty;
let a, b;
- if (sA.units.length < sB.units.length) { a = sA; b = sB; }
- else { a = sB; b = sA; }
+ if (sA.units.length < sB.units.length) {
+ a = sA; b = sB;
+ } else {
+ a = sB; b = sA;
+ }
const aU = a.units, bU = b.unitMap;
const units: Unit[] = [];
diff --git a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
index de7bb5f48a866bd459810fd446886a22837ce689..e76a48ba563a57a4bbe7f14d687072c3cb0d5bc9 100644
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -59,6 +59,8 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
const testDistanceSq = (bRadius + MAX_RADIUS) * (bRadius + MAX_RADIUS);
builder.startUnitPair(unitA, unitB)
+ const symmUnitA = unitA.conformation.operator.name
+ const symmUnitB = unitB.conformation.operator.name
for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
const aI = atomsA[_aI];
@@ -67,10 +69,14 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
if (Vec3.squaredDistance(imageA, bCenter) > testDistanceSq) continue;
if (!props.forceCompute && indexPairs) {
+ const { order, symmetryA, symmetryB } = indexPairs.edgeProps
for (let i = indexPairs.offset[aI], il = indexPairs.offset[aI + 1]; i < il; ++i) {
const _bI = SortedArray.indexOf(unitA.elements, indexPairs.b[i]) as StructureElement.UnitIndex;
if (_bI < 0) continue;
- builder.add(_aI, _bI, { order: indexPairs.edgeProps.order[i], flag: BondType.Flag.Covalent });
+ if (symmetryA[i] === symmetryB[i]) continue;
+ if (symmUnitA === symmetryA[i] && symmUnitB === symmetryB[i]) {
+ builder.add(_aI, _bI, { order: order[i], flag: BondType.Flag.Covalent });
+ }
}
continue // assume `indexPairs` supplies all bonds
}
@@ -137,7 +143,9 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
const thresholdAB = getElementPairThreshold(aeI, beI);
const pairingThreshold = thresholdAB > 0
? thresholdAB
- : beI < 0 ? thresholdA : Math.max(thresholdA, getElementThreshold(beI));
+ : beI < 0
+ ? thresholdA
+ : (thresholdA + getElementThreshold(beI)) / 2; // not sure if avg or min but max is too big
if (dist <= pairingThreshold) {
const atomIdB = label_atom_idB.value(bI);
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
index 7aee9b943ade919b54d5e5948470850f66d2d167..6ba3b6246e2626083145b321ed06eb16de86fdc1 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -60,12 +60,14 @@ function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUni
const aI = atoms[_aI];
if (!props.forceCompute && indexPairs) {
+ const { edgeProps } = indexPairs
for (let i = indexPairs.offset[aI], il = indexPairs.offset[aI + 1]; i < il; ++i) {
const _bI = SortedArray.indexOf(unit.elements, indexPairs.b[i]) as StructureElement.UnitIndex;
if (_bI < 0) continue;
+ if (edgeProps.symmetryA[i] !== edgeProps.symmetryB[i]) continue;
atomA[atomA.length] = _aI;
atomB[atomB.length] = _bI;
- order[order.length] = indexPairs.edgeProps.order[i];
+ order[order.length] = edgeProps.order[i];
flags[flags.length] = BondType.Flag.Covalent;
}
continue // assume `indexPairs` supplies all bonds
@@ -157,7 +159,9 @@ function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUni
const thresholdAB = getElementPairThreshold(aeI, beI);
const pairingThreshold = thresholdAB > 0
? thresholdAB
- : beI < 0 ? thresholdA : Math.max(thresholdA, getElementThreshold(beI));
+ : beI < 0
+ ? thresholdA
+ : (thresholdA + getElementThreshold(beI)) / 2; // not sure if avg or min but max is too big
if (dist <= pairingThreshold) {
atomA[atomA.length] = _aI;
diff --git a/src/mol-model/structure/structure/util/subset-builder.ts b/src/mol-model/structure/structure/util/subset-builder.ts
index 56f1d14c656537a228f79861e535ef3d4c67e6c5..13c082495431cd77080ffcf69dac37d03060e1fb 100644
--- a/src/mol-model/structure/structure/util/subset-builder.ts
+++ b/src/mol-model/structure/structure/util/subset-builder.ts
@@ -21,8 +21,9 @@ export class StructureSubsetBuilder {
addToUnit(parentId: number, e: ElementIndex) {
const unit = this.unitMap.get(parentId);
- if (!!unit) { unit[unit.length] = e; }
- else {
+ if (!!unit) {
+ unit[unit.length] = e;
+ } else {
this.unitMap.set(parentId, [e]);
this.ids[this.ids.length] = parentId;
}
diff --git a/src/mol-model/structure/structure/util/unique-subset-builder.ts b/src/mol-model/structure/structure/util/unique-subset-builder.ts
index 21ebf6788f3e3ab062685525f5ae9b09620bd1da..fb713a805fac427478b187ee865737c98db487b4 100644
--- a/src/mol-model/structure/structure/util/unique-subset-builder.ts
+++ b/src/mol-model/structure/structure/util/unique-subset-builder.ts
@@ -24,8 +24,7 @@ export class StructureUniqueSubsetBuilder {
const unit = this.unitMap.get(parentId);
if (!!unit) {
if (UniqueArray.add(unit, e, e)) this.elementCount++;
- }
- else {
+ } else {
const arr: UArray = UniqueArray.create();
UniqueArray.add(arr, e, e);
this.unitMap.set(parentId, arr);
diff --git a/src/mol-plugin-state/actions.ts b/src/mol-plugin-state/actions.ts
index 5491ef5cfdcb1f0e9c4c7575c888199f9e38f4cc..ce6c13d4193c80a5749755e8d74048991eca8e86 100644
--- a/src/mol-plugin-state/actions.ts
+++ b/src/mol-plugin-state/actions.ts
@@ -6,7 +6,7 @@
import * as Structure from './actions/structure'
import * as Volume from './actions/volume'
-import * as DataFormat from './actions/data-format'
+import * as DataFormat from './actions/file'
export const StateActions = {
Structure,
diff --git a/src/mol-plugin-state/actions/data-format.ts b/src/mol-plugin-state/actions/data-format.ts
deleted file mode 100644
index 3008bf6d0310ebe553a3d27004ee42d49993af97..0000000000000000000000000000000000000000
--- a/src/mol-plugin-state/actions/data-format.ts
+++ /dev/null
@@ -1,170 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import msgpackDecode from '../../mol-io/common/msgpack/decode';
-import { PluginContext } from '../../mol-plugin/context';
-import { State, StateAction, StateObjectRef } from '../../mol-state';
-import { Task } from '../../mol-task';
-import { FileInfo, getFileInfo } from '../../mol-util/file-info';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { PluginStateObject } from '../objects';
-import { PlyProvider } from './shape';
-import { DcdProvider, GroProvider, MmcifProvider, PdbProvider, Provider3dg, PsfProvider, MolProvider } from './structure';
-import { Ccp4Provider, DscifProvider, Dsn6Provider } from './volume';
-
-export class DataFormatRegistry<D extends PluginStateObject.Data.Binary | PluginStateObject.Data.String> {
- private _list: { name: string, provider: DataFormatProvider<D> }[] = []
- private _map = new Map<string, DataFormatProvider<D>>()
- private _extensions: Set<string> | undefined = undefined
- private _binaryExtensions: Set<string> | undefined = undefined
- private _options: [string, string][] | undefined = undefined
-
- get types(): [string, string][] {
- return this._list.map(e => [e.name, e.provider.label] as [string, string]);
- }
-
- get extensions() {
- if (this._extensions) return this._extensions
- const extensions = new Set<string>()
- this._list.forEach(({ provider }) => {
- provider.stringExtensions.forEach(ext => extensions.add(ext))
- provider.binaryExtensions.forEach(ext => extensions.add(ext))
- })
- this._extensions = extensions
- return extensions
- }
-
- get binaryExtensions() {
- if (this._binaryExtensions) return this._binaryExtensions
- const binaryExtensions = new Set<string>()
- this._list.forEach(({ provider }) => provider.binaryExtensions.forEach(ext => binaryExtensions.add(ext)))
- this._binaryExtensions = binaryExtensions
- return binaryExtensions
- }
-
- get options() {
- if (this._options) return this._options
- const options: [string, string][] = [['auto', 'Automatic']]
- this._list.forEach(({ name, provider }) => options.push([ name, provider.label ]))
- this._options = options
- return options
- }
-
- constructor() {
- this.add('3dg', Provider3dg)
- this.add('ccp4', Ccp4Provider)
- this.add('dcd', DcdProvider)
- this.add('dscif', DscifProvider)
- this.add('dsn6', Dsn6Provider)
- this.add('gro', GroProvider)
- this.add('mol', MolProvider)
- this.add('mmcif', MmcifProvider)
- this.add('pdb', PdbProvider)
- this.add('ply', PlyProvider)
- this.add('psf', PsfProvider)
- };
-
- private _clear() {
- this._extensions = undefined
- this._binaryExtensions = undefined
- this._options = undefined
- }
-
- add(name: string, provider: DataFormatProvider<D>) {
- this._clear()
- this._list.push({ name, provider })
- this._map.set(name, provider)
- }
-
- remove(name: string) {
- this._clear()
- this._list.splice(this._list.findIndex(e => e.name === name), 1)
- this._map.delete(name)
- }
-
- auto(info: FileInfo, dataStateObject: D) {
- for (let i = 0, il = this.list.length; i < il; ++i) {
- const { provider } = this._list[i]
- if (provider.isApplicable(info, dataStateObject.data)) return provider
- }
- throw new Error('no compatible data format provider available')
- }
-
- get(name: string): DataFormatProvider<D> {
- if (this._map.has(name)) {
- return this._map.get(name)!
- } else {
- throw new Error(`unknown data format name '${name}'`)
- }
- }
-
- get list() {
- return this._list
- }
-}
-
-export type DataFormatBuilderOptions = { visuals: boolean }
-
-export interface DataFormatProvider<D extends PluginStateObject.Data.Binary | PluginStateObject.Data.String> {
- label: string
- description: string
- stringExtensions: string[]
- binaryExtensions: string[]
- isApplicable(info: FileInfo, data: string | Uint8Array): boolean
- getDefaultBuilder(ctx: PluginContext, data: StateObjectRef<D>, options: DataFormatBuilderOptions, state: State): Task<void>
-}
-
-//
-
-export const OpenFiles = StateAction.build({
- display: { name: 'Open Files', description: 'Load one or more files and optionally create default visuals' },
- from: PluginStateObject.Root,
- params: (a, ctx: PluginContext) => {
- const { extensions, options } = ctx.dataFormat.registry
- return {
- files: PD.FileList({ accept: Array.from(extensions.values()).map(e => `.${e}`).join(',') + ',.gz,.zip', multiple: true }),
- format: PD.Select('auto', options),
- visuals: PD.Boolean(true, { description: 'Add default visuals' }),
- }
- }
-})(({ params, state }, plugin: PluginContext) => Task.create('Open Files', async taskCtx => {
- await state.transaction(async () => {
- for (let i = 0, il = params.files.length; i < il; ++i) {
- try {
- const file = params.files[i]
- const info = getFileInfo(file)
- const isBinary = plugin.dataFormat.registry.binaryExtensions.has(info.ext)
- const { data } = await plugin.builders.data.readFile({ file, isBinary });
- // const data = state.build().toRoot().apply(StateTransforms.Data.ReadFile, { file, isBinary });
- // const dataStateObject = await state.updateTree(data).runInContext(taskCtx);
- const provider = params.format === 'auto'
- ? plugin.dataFormat.registry.auto(info, data.cell?.obj!)
- : plugin.dataFormat.registry.get(params.format)
-
- // need to await so that the enclosing Task finishes after the update is done.
- await provider.getDefaultBuilder(plugin, data, { visuals: params.visuals }, state).runInContext(taskCtx)
- } catch (e) {
- plugin.log.error(e)
- }
- }
- }).runInContext(taskCtx);
-}));
-
-//
-
-type cifVariants = 'dscif' | -1
-export function guessCifVariant(info: FileInfo, data: Uint8Array | string): cifVariants {
- if (info.ext === 'bcif') {
- try {
- // TODO: find a way to run msgpackDecode only once
- // now it is run twice, here and during file parsing
- if (msgpackDecode(data as Uint8Array).encoder.startsWith('VolumeServer')) return 'dscif'
- } catch { }
- } else if (info.ext === 'cif') {
- if ((data as string).startsWith('data_SERVER\n#\n_density_server_result')) return 'dscif'
- }
- return -1
-}
\ No newline at end of file
diff --git a/src/mol-plugin-state/actions/file.ts b/src/mol-plugin-state/actions/file.ts
new file mode 100644
index 0000000000000000000000000000000000000000..693a315ebd1e6c5d7c877a0545913846443c978f
--- /dev/null
+++ b/src/mol-plugin-state/actions/file.ts
@@ -0,0 +1,58 @@
+/**
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginContext } from '../../mol-plugin/context';
+import { StateAction } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { getFileInfo } from '../../mol-util/file-info';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { PluginStateObject } from '../objects';
+
+export const OpenFiles = StateAction.build({
+ display: { name: 'Open Files', description: 'Load one or more files and optionally create default visuals' },
+ from: PluginStateObject.Root,
+ params: (a, ctx: PluginContext) => {
+ const { extensions, options } = ctx.dataFormats
+ return {
+ files: PD.FileList({ accept: Array.from(extensions.values()).map(e => `.${e}`).join(',') + ',.gz,.zip', multiple: true }),
+ format: PD.Select('auto', options),
+ visuals: PD.Boolean(true, { description: 'Add default visuals' }),
+ }
+ }
+})(({ params, state }, plugin: PluginContext) => Task.create('Open Files', async taskCtx => {
+ plugin.behaviors.layout.leftPanelTabName.next('data');
+
+ await state.transaction(async () => {
+ if (params.files === null) {
+ plugin.log.error('No file(s) selected')
+ return
+ }
+ for (let i = 0, il = params.files.length; i < il; ++i) {
+ try {
+ const file = params.files[i]
+ const info = getFileInfo(file)
+ const isBinary = plugin.dataFormats.binaryExtensions.has(info.ext)
+ const { data } = await plugin.builders.data.readFile({ file, isBinary });
+ const provider = params.format === 'auto'
+ ? plugin.dataFormats.auto(info, data.cell?.obj!)
+ : plugin.dataFormats.get(params.format)
+
+ if (!provider) {
+ plugin.log.warn(`OpenFiles: could not find data provider for '${info.name}.${info.ext}'`);
+ continue;
+ }
+
+ // need to await so that the enclosing Task finishes after the update is done.
+ const parsed = await provider.parse(plugin, data);
+ if (params.visuals) {
+ await provider.visuals?.(plugin, parsed);
+ }
+ } catch (e) {
+ plugin.log.error(e)
+ }
+ }
+ }).runInContext(taskCtx);
+}));
\ No newline at end of file
diff --git a/src/mol-plugin-state/actions/shape.ts b/src/mol-plugin-state/actions/shape.ts
deleted file mode 100644
index 9db4c919b32f09aa0f574c4e17127ed1d4f41b01..0000000000000000000000000000000000000000
--- a/src/mol-plugin-state/actions/shape.ts
+++ /dev/null
@@ -1,33 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { PluginContext } from '../../mol-plugin/context';
-import { State, StateBuilder } from '../../mol-state';
-import { Task } from '../../mol-task';
-import { FileInfo } from '../../mol-util/file-info';
-import { StateTransforms } from '../transforms';
-import { DataFormatProvider, DataFormatBuilderOptions } from './data-format';
-
-export const PlyProvider: DataFormatProvider<any> = {
- label: 'PLY',
- description: 'PLY',
- stringExtensions: ['ply'],
- binaryExtensions: [],
- isApplicable: (info: FileInfo, data: string) => {
- return info.ext === 'ply'
- },
- getDefaultBuilder: (ctx: PluginContext, data, options: DataFormatBuilderOptions, state: State) => {
- return Task.create('PLY default builder', async taskCtx => {
- let tree: StateBuilder.To<any> = state.build().to(data)
- .apply(StateTransforms.Data.ParsePly)
- .apply(StateTransforms.Model.ShapeFromPly)
- if (options.visuals) {
- tree = tree.apply(StateTransforms.Representation.ShapeRepresentation3D)
- }
- await state.updateTree(tree).runInContext(taskCtx)
- })
- }
-}
\ No newline at end of file
diff --git a/src/mol-plugin-state/actions/structure.ts b/src/mol-plugin-state/actions/structure.ts
index 297850ad1376b33cc770ca32fb03a02020fedd64..171504fce8e4cd4760885e8e67c60e21ebdeee02 100644
--- a/src/mol-plugin-state/actions/structure.ts
+++ b/src/mol-plugin-state/actions/structure.ts
@@ -8,140 +8,14 @@
import { PluginContext } from '../../mol-plugin/context';
import { StateAction, StateSelection, StateTransformer } from '../../mol-state';
import { Task } from '../../mol-task';
-import { FileInfo } from '../../mol-util/file-info';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { BuiltInTrajectoryFormat, BuildInTrajectoryFormats } from '../formats/trajectory';
+import { PresetStructureRepresentations } from '../builder/structure/representation-preset';
+import { BuiltInTrajectoryFormat, BuiltInTrajectoryFormats } from '../formats/trajectory';
import { RootStructureDefinition } from '../helpers/root-structure';
import { PluginStateObject } from '../objects';
import { StateTransforms } from '../transforms';
-import { Download, ParsePsf } from '../transforms/data';
-import { CoordinatesFromDcd, CustomModelProperties, CustomStructureProperties, TopologyFromPsf, TrajectoryFromModelAndCoordinates } from '../transforms/model';
-import { DataFormatProvider, guessCifVariant } from './data-format';
-import { PresetStructureRepresentations } from '../builder/structure/representation-preset';
-
-// TODO make unitcell creation part of preset
-
-export const MmcifProvider: DataFormatProvider<PluginStateObject.Data.String | PluginStateObject.Data.Binary> = {
- label: 'mmCIF',
- description: 'mmCIF',
- stringExtensions: ['cif', 'mmcif', 'mcif'],
- binaryExtensions: ['bcif'],
- isApplicable: (info: FileInfo, data: Uint8Array | string) => {
- if (info.ext === 'mmcif' || info.ext === 'mcif') return true
- // assume cif/bcif files that are not DensityServer CIF are mmCIF
- if (info.ext === 'cif' || info.ext === 'bcif') return guessCifVariant(info, data) !== 'dscif'
- return false
- },
- getDefaultBuilder: (ctx: PluginContext, data, options) => {
- return Task.create('mmCIF default builder', async () => {
- const trajectory = await ctx.builders.structure.parseTrajectory(data, 'mmcif');
- const representationPreset = options.visuals ? 'auto' : 'empty';
- await ctx.builders.structure.hierarchy.applyPreset(trajectory, 'default', { showUnitcell: options.visuals, representationPreset });
- })
- }
-}
-
-export const PdbProvider: DataFormatProvider<any> = {
- label: 'PDB',
- description: 'PDB',
- stringExtensions: ['pdb', 'ent'],
- binaryExtensions: [],
- isApplicable: (info: FileInfo, data: string) => {
- return info.ext === 'pdb' || info.ext === 'ent'
- },
- getDefaultBuilder: (ctx: PluginContext, data, options) => {
- return Task.create('PDB default builder', async () => {
- const trajectory = await ctx.builders.structure.parseTrajectory(data, 'pdb');
- const representationPreset = options.visuals ? 'auto' : 'empty';
- await ctx.builders.structure.hierarchy.applyPreset(trajectory, 'default', { showUnitcell: options.visuals, representationPreset });
- })
- }
-}
-
-export const GroProvider: DataFormatProvider<any> = {
- label: 'GRO',
- description: 'GRO',
- stringExtensions: ['gro'],
- binaryExtensions: [],
- isApplicable: (info: FileInfo, data: string) => {
- return info.ext === 'gro'
- },
- getDefaultBuilder: (ctx: PluginContext, data, options) => {
- return Task.create('GRO default builder', async () => {
- const trajectory = await ctx.builders.structure.parseTrajectory(data, 'gro');
- const representationPreset = options.visuals ? 'auto' : 'empty';
- await ctx.builders.structure.hierarchy.applyPreset(trajectory, 'default', { showUnitcell: options.visuals, representationPreset });
- })
- }
-}
-
-export const MolProvider: DataFormatProvider<any> = {
- label: 'MOL',
- description: 'MOL',
- stringExtensions: ['mol', 'sdf'],
- binaryExtensions: [],
- isApplicable: (info: FileInfo, data: string) => {
- return info.ext === 'mol' || info.ext === 'sdf'
- },
- getDefaultBuilder: (ctx: PluginContext, data, options) => {
- return Task.create('MOL default builder', async () => {
- const trajectory = await ctx.builders.structure.parseTrajectory(data, 'mol');
- const representationPreset = options.visuals ? 'atomic-detail' : 'empty';
- await ctx.builders.structure.hierarchy.applyPreset(trajectory, 'default', { showUnitcell: options.visuals, representationPreset });
- })
- }
-}
-
-export const Provider3dg: DataFormatProvider<any> = {
- label: '3DG',
- description: '3DG',
- stringExtensions: ['3dg'],
- binaryExtensions: [],
- isApplicable: (info: FileInfo, data: string) => {
- return info.ext === '3dg'
- },
- getDefaultBuilder: (ctx: PluginContext, data, options) => {
- return Task.create('3DG default builder', async () => {
- const trajectory = await ctx.builders.structure.parseTrajectory(data, '3dg');
- const representationPreset = options.visuals ? 'auto' : 'empty';
- await ctx.builders.structure.hierarchy.applyPreset(trajectory, 'default', { showUnitcell: options.visuals, representationPreset });
- })
- }
-}
-
-export const PsfProvider: DataFormatProvider<any> = {
- label: 'PSF',
- description: 'PSF',
- stringExtensions: ['psf'],
- binaryExtensions: [],
- isApplicable: (info: FileInfo, data: string) => {
- return info.ext === 'psf'
- },
- getDefaultBuilder: (ctx: PluginContext, data, options, state) => {
- return Task.create('PSF default builder', async taskCtx => {
- const build = state.build().to(data).apply(ParsePsf, {}, { state: { isGhost: true } }).apply(TopologyFromPsf)
- await state.updateTree(build).runInContext(taskCtx)
- })
- }
-}
-
-export const DcdProvider: DataFormatProvider<any> = {
- label: 'DCD',
- description: 'DCD',
- stringExtensions: [],
- binaryExtensions: ['dcd'],
- isApplicable: (info: FileInfo, data: string) => {
- return info.ext === 'dcd'
- },
- getDefaultBuilder: (ctx: PluginContext, data, options, state) => {
- return Task.create('DCD default builder', async taskCtx => {
- const build = state.build().to(data).apply(CoordinatesFromDcd);
- await state.updateTree(build).runInContext(taskCtx)
- })
- }
-}
-
-//
+import { Download } from '../transforms/data';
+import { CustomModelProperties, CustomStructureProperties, TrajectoryFromModelAndCoordinates } from '../transforms/model';
const DownloadModelRepresentationOptions = (plugin: PluginContext) => PD.Group({
type: RootStructureDefinition.getParams(void 0, 'auto').type,
@@ -192,7 +66,7 @@ const DownloadStructure = StateAction.build({
}, { isFlat: true, label: 'PubChem', description: 'Loads 3D conformer from PubChem.' }),
'url': PD.Group({
url: PD.Text(''),
- format: PD.Select<BuiltInTrajectoryFormat>('mmcif', PD.arrayToOptions(BuildInTrajectoryFormats.map(f => f[0]), f => f)),
+ format: PD.Select<BuiltInTrajectoryFormat>('mmcif', PD.arrayToOptions(BuiltInTrajectoryFormats.map(f => f[0]), f => f)),
isBinary: PD.Boolean(false),
options
}, { isFlat: true, label: 'URL' })
diff --git a/src/mol-plugin-state/actions/volume.ts b/src/mol-plugin-state/actions/volume.ts
index 2fc544875129850a318709e869fdc3e31c63d88b..6a5383c38ef38216495ed86a060d2646084577a2 100644
--- a/src/mol-plugin-state/actions/volume.ts
+++ b/src/mol-plugin-state/actions/volume.ts
@@ -5,102 +5,14 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { VolumeIsoValue } from '../../mol-model/volume';
import { PluginContext } from '../../mol-plugin/context';
-import { State, StateAction, StateBuilder, StateTransformer } from '../../mol-state';
+import { StateAction, StateTransformer } from '../../mol-state';
import { Task } from '../../mol-task';
-import { ColorNames } from '../../mol-util/color/names';
-import { FileInfo, getFileInfo } from '../../mol-util/file-info';
+import { getFileInfo } from '../../mol-util/file-info';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { PluginStateObject } from '../objects';
-import { StateTransforms } from '../transforms';
import { Download } from '../transforms/data';
-import { VolumeRepresentation3DHelpers } from '../transforms/representation';
-import { DataFormatProvider, guessCifVariant, DataFormatBuilderOptions } from './data-format';
-
-export const Ccp4Provider: DataFormatProvider<any> = {
- label: 'CCP4/MRC/BRIX',
- description: 'CCP4/MRC/BRIX',
- stringExtensions: [],
- binaryExtensions: ['ccp4', 'mrc', 'map'],
- isApplicable: (info: FileInfo, data: Uint8Array) => {
- return info.ext === 'ccp4' || info.ext === 'mrc' || info.ext === 'map'
- },
- getDefaultBuilder: (ctx: PluginContext, data, options: DataFormatBuilderOptions, state: State) => {
- return Task.create('CCP4/MRC/BRIX default builder', async taskCtx => {
- let tree: StateBuilder.To<any> = state.build().to(data)
- .apply(StateTransforms.Data.ParseCcp4, {}, { state: { isGhost: true } })
- .apply(StateTransforms.Volume.VolumeFromCcp4)
- if (options.visuals) {
- tree = tree.apply(StateTransforms.Representation.VolumeRepresentation3D)
- }
- await state.updateTree(tree).runInContext(taskCtx)
- })
- }
-}
-
-export const Dsn6Provider: DataFormatProvider<any> = {
- label: 'DSN6/BRIX',
- description: 'DSN6/BRIX',
- stringExtensions: [],
- binaryExtensions: ['dsn6', 'brix'],
- isApplicable: (info: FileInfo, data: Uint8Array) => {
- return info.ext === 'dsn6' || info.ext === 'brix'
- },
- getDefaultBuilder: (ctx: PluginContext, data, options: DataFormatBuilderOptions, state: State) => {
- return Task.create('DSN6/BRIX default builder', async taskCtx => {
- let tree: StateBuilder.To<any> = state.build().to(data)
- .apply(StateTransforms.Data.ParseDsn6, {}, { state: { isGhost: true } })
- .apply(StateTransforms.Volume.VolumeFromDsn6)
- if (options.visuals) {
- tree = tree.apply(StateTransforms.Representation.VolumeRepresentation3D)
- }
- await state.updateTree(tree).runInContext(taskCtx)
- })
- }
-}
-
-export const DscifProvider: DataFormatProvider<any> = {
- label: 'DensityServer CIF',
- description: 'DensityServer CIF',
- stringExtensions: ['cif'],
- binaryExtensions: ['bcif'],
- isApplicable: (info: FileInfo, data: Uint8Array | string) => {
- return guessCifVariant(info, data) === 'dscif' ? true : false
- },
- getDefaultBuilder: (ctx: PluginContext, data, options: DataFormatBuilderOptions, state: State) => {
- return Task.create('DensityServer CIF default builder', async taskCtx => {
- const cifBuilder = state.build().to(data).apply(StateTransforms.Data.ParseCif)
- const cifStateObject = await state.updateTree(cifBuilder).runInContext(taskCtx)
- const b = state.build().to(cifBuilder.ref);
- const blocks = cifStateObject.data.blocks.slice(1); // zero block contains query meta-data
- let tree: StateBuilder.To<any, any>
- if (blocks.length === 1) {
- tree = b
- .apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: blocks[0].header })
- if (options.visuals) {
- tree = tree.apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 0.3 }, 'uniform', { value: ColorNames.teal }))
- }
- } else if (blocks.length === 2) {
- tree = b
- .apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: blocks[0].header })
- if (options.visuals) {
- tree = tree.apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 0.3 }, 'uniform', { value: ColorNames.blue }))
- }
- const vol = tree.to(cifBuilder.ref)
- .apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: blocks[1].header })
- const posParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(3), alpha: 0.3 }, 'uniform', { value: ColorNames.green })
- tree = vol.apply(StateTransforms.Representation.VolumeRepresentation3D, posParams)
- const negParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(-3), alpha: 0.3 }, 'uniform', { value: ColorNames.red })
- tree = tree.to(vol.ref).apply(StateTransforms.Representation.VolumeRepresentation3D, negParams)
- } else {
- throw new Error('unknown number of blocks')
- }
-
- await state.updateTree(tree).runInContext(taskCtx);
- })
- }
-}
+import { DataFormatProvider } from '../formats/provider';
export { DownloadDensity };
type DownloadDensity = typeof DownloadDensity
@@ -108,7 +20,7 @@ const DownloadDensity = StateAction.build({
from: PluginStateObject.Root,
display: { name: 'Download Density', description: 'Load a density from the provided source and create its default visual.' },
params: (a, ctx: PluginContext) => {
- const { options } = ctx.dataFormat.registry
+ const { options } = ctx.dataFormats
return {
source: PD.MappedStatic('pdb-xray', {
'pdb-xray': PD.Group({
@@ -147,10 +59,10 @@ const DownloadDensity = StateAction.build({
})
}
}
-})(({ params, state }, ctx: PluginContext) => Task.create('Download Density', async taskCtx => {
+})(({ params }, plugin: PluginContext) => Task.create('Download Density', async taskCtx => {
const src = params.source;
let downloadParams: StateTransformer.Params<Download>;
- let provider: DataFormatProvider<any>
+ let provider: DataFormatProvider | undefined;
switch (src.name) {
case 'url':
@@ -196,24 +108,30 @@ const DownloadDensity = StateAction.build({
default: throw new Error(`${(src as any).name} not supported.`);
}
- const data = await ctx.builders.data.download(downloadParams);
+ const data = await plugin.builders.data.download(downloadParams);
switch (src.name) {
case 'url':
downloadParams = src.params;
- provider = src.params.format === 'auto' ? ctx.dataFormat.registry.auto(getFileInfo(downloadParams.url), data.cell?.obj!) : ctx.dataFormat.registry.get(src.params.format)
+ provider = src.params.format === 'auto' ? plugin.dataFormats.auto(getFileInfo(downloadParams.url), data.cell?.obj!) : plugin.dataFormats.get(src.params.format)
break;
case 'pdb-xray':
provider = src.params.provider.server === 'pdbe'
- ? ctx.dataFormat.registry.get('ccp4')
- : ctx.dataFormat.registry.get('dsn6')
+ ? plugin.dataFormats.get('ccp4')
+ : plugin.dataFormats.get('dsn6')
break;
case 'pdb-emd-ds':
case 'pdb-xray-ds':
- provider = ctx.dataFormat.registry.get('dscif')
+ provider = plugin.dataFormats.get('dscif')
break;
default: throw new Error(`${(src as any).name} not supported.`);
}
- await provider.getDefaultBuilder(ctx, data, { visuals: true }, state).runInContext(taskCtx)
+ if (!provider) {
+ plugin.log.warn('DownloadDensity: Format provider not found.');
+ return;
+ }
+
+ const volumes = await provider.parse(plugin, data);
+ await provider.visuals?.(plugin, volumes);
}));
\ No newline at end of file
diff --git a/src/mol-plugin-state/animation/built-in.ts b/src/mol-plugin-state/animation/built-in.ts
index f804def83bf3acc7c89461d0527636d1c8653c1b..f3fde2bb93d40f71e35ef8a1dac3943eeb0dfae2 100644
--- a/src/mol-plugin-state/animation/built-in.ts
+++ b/src/mol-plugin-state/animation/built-in.ts
@@ -105,7 +105,7 @@ export const AnimateAssemblyUnwind = PluginStateAnimation.create({
};
},
initialState: () => ({ t: 0 }),
- async setup(params, plugin) {
+ setup(params, plugin) {
const state = plugin.state.data;
const root = !params.target || params.target === 'all' ? StateTransform.RootRef : params.target;
const reprs = state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure.Representation3D, root));
@@ -123,9 +123,9 @@ export const AnimateAssemblyUnwind = PluginStateAnimation.create({
if (!changed) return;
- return plugin.updateDataState(update, { doNotUpdateCurrent: true });
+ return update.commit({ doNotUpdateCurrent: true });
},
- async teardown(_, plugin) {
+ teardown(_, plugin) {
const state = plugin.state.data;
const reprs = state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure.Representation3DState)
.withTag('animate-assembly-unwind'));
@@ -133,7 +133,7 @@ export const AnimateAssemblyUnwind = PluginStateAnimation.create({
const update = state.build();
for (const r of reprs) update.delete(r.transform.ref);
- return plugin.updateDataState(update);
+ return update.commit();
},
async apply(animState, t, ctx) {
const state = ctx.plugin.state.data;
@@ -190,9 +190,9 @@ export const AnimateUnitsExplode = PluginStateAnimation.create({
if (!changed) return;
- return plugin.updateDataState(update, { doNotUpdateCurrent: true });
+ return update.commit({ doNotUpdateCurrent: true });
},
- async teardown(_, plugin) {
+ teardown(_, plugin) {
const state = plugin.state.data;
const reprs = state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure.Representation3DState)
.withTag('animate-units-explode'));
@@ -200,7 +200,7 @@ export const AnimateUnitsExplode = PluginStateAnimation.create({
const update = state.build();
for (const r of reprs) update.delete(r.transform.ref);
- return plugin.updateDataState(update);
+ return update.commit();
},
async apply(animState, t, ctx) {
const state = ctx.plugin.state.data;
diff --git a/src/mol-plugin-state/builder/data.ts b/src/mol-plugin-state/builder/data.ts
index 45508c2526a1fd2e9139d10662f1ab2a8c0ae905..e628bf7aa9be06d73c001a60a36d4b4aead3349a 100644
--- a/src/mol-plugin-state/builder/data.ts
+++ b/src/mol-plugin-state/builder/data.ts
@@ -14,29 +14,25 @@ export class DataBuilder {
return this.plugin.state.data;
}
- async rawData(params: StateTransformer.Params<RawData>, options?: Partial<StateTransform.Options>) {
+ rawData(params: StateTransformer.Params<RawData>, options?: Partial<StateTransform.Options>) {
const data = this.dataState.build().toRoot().apply(RawData, params, options);
- await this.plugin.updateDataState(data, { revertOnError: true });
- return data.selector;
+ return data.commit({ revertOnError: true });
}
- async download(params: StateTransformer.Params<Download>, options?: Partial<StateTransform.Options>) {
+ download(params: StateTransformer.Params<Download>, options?: Partial<StateTransform.Options>) {
const data = this.dataState.build().toRoot().apply(Download, params, options);
- await this.plugin.updateDataState(data, { revertOnError: true });
- return data.selector;
+ return data.commit({ revertOnError: true });
}
- async downloadBlob(params: StateTransformer.Params<DownloadBlob>, options?: Partial<StateTransform.Options>) {
+ downloadBlob(params: StateTransformer.Params<DownloadBlob>, options?: Partial<StateTransform.Options>) {
const data = this.dataState.build().toRoot().apply(DownloadBlob, params, options);
- await this.plugin.updateDataState(data, { revertOnError: true });
- return data.selector;
+ return data.commit({ revertOnError: true });
}
async readFile(params: StateTransformer.Params<ReadFile>, options?: Partial<StateTransform.Options>) {
- const data = this.dataState.build().toRoot().apply(ReadFile, params, options);
- const fileInfo = getFileInfo(params.file);
- await this.plugin.updateDataState(data, { revertOnError: true });
- return { data: data.selector, fileInfo };
+ const data = await this.dataState.build().toRoot().apply(ReadFile, params, options).commit({ revertOnError: true });
+ const fileInfo = getFileInfo(params.file || '');
+ return { data: data, fileInfo };
}
constructor(public plugin: PluginContext) {
diff --git a/src/mol-plugin-state/builder/structure.ts b/src/mol-plugin-state/builder/structure.ts
index 82bb1af27c6d479f883a788893e5d16eeb6f0dad..001312e7aafc6de9dd299605d8be2fd0eb769467 100644
--- a/src/mol-plugin-state/builder/structure.ts
+++ b/src/mol-plugin-state/builder/structure.ts
@@ -26,27 +26,26 @@ export class StructureBuilder {
}
private async parseTrajectoryData(data: StateObjectRef<SO.Data.Binary | SO.Data.String>, format: BuiltInTrajectoryFormat | TrajectoryFormatProvider) {
- const provider = typeof format === 'string' ? this.plugin.dataFormat.trajectory.get(format) : format;
+ const provider = typeof format === 'string' ? this.plugin.dataFormats.get(format) as TrajectoryFormatProvider : format;
if (!provider) throw new Error(`'${format}' is not a supported data format.`);
const { trajectory } = await provider.parse(this.plugin, data);
return trajectory;
}
- private async parseTrajectoryBlob(data: StateObjectRef<SO.Data.Blob>, params: StateTransformer.Params<StateTransforms['Data']['ParseBlob']>) {
+ private parseTrajectoryBlob(data: StateObjectRef<SO.Data.Blob>, params: StateTransformer.Params<StateTransforms['Data']['ParseBlob']>) {
const state = this.dataState;
const trajectory = state.build().to(data)
.apply(StateTransforms.Data.ParseBlob, params, { state: { isGhost: true } })
.apply(StateTransforms.Model.TrajectoryFromBlob, void 0);
- await this.plugin.updateDataState(trajectory, { revertOnError: true });
- return trajectory.selector;
+ return trajectory.commit({ revertOnError: true });
}
readonly hierarchy = new TrajectoryHierarchyBuilder(this.plugin);
readonly representation = new StructureRepresentationBuilder(this.plugin);
- async parseTrajectory(data: StateObjectRef<SO.Data.Binary | SO.Data.String>, format: BuiltInTrajectoryFormat | TrajectoryFormatProvider): Promise<StateObjectSelector<SO.Molecule.Trajectory>>
- async parseTrajectory(blob: StateObjectRef<SO.Data.Blob>, params: StateTransformer.Params<StateTransforms['Data']['ParseBlob']>): Promise<StateObjectSelector<SO.Molecule.Trajectory>>
- async parseTrajectory(data: StateObjectRef, params: any) {
+ parseTrajectory(data: StateObjectRef<SO.Data.Binary | SO.Data.String>, format: BuiltInTrajectoryFormat | TrajectoryFormatProvider): Promise<StateObjectSelector<SO.Molecule.Trajectory>>
+ parseTrajectory(blob: StateObjectRef<SO.Data.Blob>, params: StateTransformer.Params<StateTransforms['Data']['ParseBlob']>): Promise<StateObjectSelector<SO.Molecule.Trajectory>>
+ parseTrajectory(data: StateObjectRef, params: any) {
const cell = StateObjectRef.resolveAndCheck(this.dataState, data as StateObjectRef);
if (!cell) throw new Error('Invalid data cell.');
@@ -57,24 +56,22 @@ export class StructureBuilder {
}
}
- async createModel(trajectory: StateObjectRef<SO.Molecule.Trajectory>, params?: StateTransformer.Params<StateTransforms['Model']['ModelFromTrajectory']>, initialState?: Partial<StateTransform.State>) {
+ createModel(trajectory: StateObjectRef<SO.Molecule.Trajectory>, params?: StateTransformer.Params<StateTransforms['Model']['ModelFromTrajectory']>, initialState?: Partial<StateTransform.State>) {
const state = this.dataState;
const model = state.build().to(trajectory)
.apply(StateTransforms.Model.ModelFromTrajectory, params || { modelIndex: 0 }, { state: initialState });
- await this.plugin.updateDataState(model, { revertOnError: true });
- return model.selector;
+ return model.commit({ revertOnError: true });
}
- async insertModelProperties(model: StateObjectRef<SO.Molecule.Model>, params?: StateTransformer.Params<StateTransforms['Model']['CustomModelProperties']>, initialState?: Partial<StateTransform.State>) {
+ insertModelProperties(model: StateObjectRef<SO.Molecule.Model>, params?: StateTransformer.Params<StateTransforms['Model']['CustomModelProperties']>, initialState?: Partial<StateTransform.State>) {
const state = this.dataState;
const props = state.build().to(model)
.apply(StateTransforms.Model.CustomModelProperties, params, { state: initialState });
- await this.plugin.updateDataState(props, { revertOnError: true });
- return props.selector;
+ return props.commit({ revertOnError: true });
}
- async tryCreateUnitcell(model: StateObjectRef<SO.Molecule.Model>, params?: StateTransformer.Params<StateTransforms['Representation']['ModelUnitcell3D']>, initialState?: Partial<StateTransform.State>) {
+ tryCreateUnitcell(model: StateObjectRef<SO.Molecule.Model>, params?: StateTransformer.Params<StateTransforms['Representation']['ModelUnitcell3D']>, initialState?: Partial<StateTransform.State>) {
const state = this.dataState;
const m = StateObjectRef.resolveAndCheck(state, model)?.obj?.data;
if (!m) return;
@@ -83,11 +80,10 @@ export class StructureBuilder {
const unitcell = state.build().to(model)
.apply(StateTransforms.Representation.ModelUnitcell3D, params, { state: initialState });
- await this.plugin.updateDataState(unitcell, { revertOnError: true });
- return unitcell.selector;
+ return unitcell.commit({ revertOnError: true });
}
- async createStructure(modelRef: StateObjectRef<SO.Molecule.Model>, params?: RootStructureDefinition.Params, initialState?: Partial<StateTransform.State>) {
+ createStructure(modelRef: StateObjectRef<SO.Molecule.Model>, params?: RootStructureDefinition.Params, initialState?: Partial<StateTransform.State>) {
const state = this.dataState;
if (!params) {
@@ -101,16 +97,14 @@ export class StructureBuilder {
const structure = state.build().to(modelRef)
.apply(StateTransforms.Model.StructureFromModel, { type: params || { name: 'assembly', params: { } } }, { state: initialState });
- await this.plugin.updateDataState(structure, { revertOnError: true });
- return structure.selector;
+ return structure.commit({ revertOnError: true });
}
- async insertStructureProperties(structure: StateObjectRef<SO.Molecule.Structure>, params?: StateTransformer.Params<StateTransforms['Model']['CustomStructureProperties']>) {
+ insertStructureProperties(structure: StateObjectRef<SO.Molecule.Structure>, params?: StateTransformer.Params<StateTransforms['Model']['CustomStructureProperties']>) {
const state = this.dataState;
const props = state.build().to(structure)
.apply(StateTransforms.Model.CustomStructureProperties, params);
- await this.plugin.updateDataState(props, { revertOnError: true });
- return props.selector;
+ return props.commit({ revertOnError: true });
}
isComponentTransform(cell: StateObjectCell) {
@@ -128,13 +122,12 @@ export class StructureBuilder {
tags: tags ? [...tags, keyTag] : [keyTag]
});
- await this.plugin.updateDataState(component);
+ await component.commit();
const selector = component.selector;
if (!selector.isOk || selector.cell?.obj?.data.elementCount === 0) {
- const del = state.build().delete(selector.ref);
- await this.plugin.updateDataState(del);
+ await state.build().delete(selector.ref).commit();
return;
}
diff --git a/src/mol-plugin-state/builder/structure/representation-preset.ts b/src/mol-plugin-state/builder/structure/representation-preset.ts
index a9088281f6afe32730a01f5784ca224b3c539de7..2def1be284f8fc8a97c5051888fe6dc1fd972428 100644
--- a/src/mol-plugin-state/builder/structure/representation-preset.ts
+++ b/src/mol-plugin-state/builder/structure/representation-preset.ts
@@ -121,7 +121,8 @@ const polymerAndLigand = StructureRepresentationPresetProvider({
coarse: builder.buildRepresentation(update, components.coarse, { type: 'spacefill', typeParams, color: color || 'polymer-id' }, { tag: 'coarse' })
};
- await plugin.updateDataState(update, { revertOnError: false });
+ await update.commit({ revertOnError: false });
+
return { components, representations };
}
});
@@ -148,7 +149,7 @@ const proteinAndNucleic = StructureRepresentationPresetProvider({
nucleic: builder.buildRepresentation(update, components.nucleic, { type: 'gaussian-surface', typeParams, color }, { tag: 'nucleic' })
};
- await plugin.updateDataState(update, { revertOnError: true });
+ await update.commit({ revertOnError: true });
return { components, representations };
}
});
@@ -189,7 +190,7 @@ const coarseSurface = StructureRepresentationPresetProvider({
polymer: builder.buildRepresentation(update, components.polymer, { type: 'gaussian-surface', typeParams: { ...typeParams, ...gaussianProps }, color }, { tag: 'polymer' })
};
- await plugin.updateDataState(update, { revertOnError: true });
+ await update.commit({ revertOnError: true });
return { components, representations };
}
});
@@ -214,7 +215,7 @@ const polymerCartoon = StructureRepresentationPresetProvider({
polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams, color }, { tag: 'polymer' })
};
- await plugin.updateDataState(update, { revertOnError: true });
+ await update.commit({ revertOnError: true });
return { components, representations };
}
});
@@ -239,7 +240,7 @@ const atomicDetail = StructureRepresentationPresetProvider({
all: builder.buildRepresentation(update, components.all, { type: 'ball-and-stick', typeParams, color }, { tag: 'all' })
};
- await plugin.updateDataState(update, { revertOnError: true });
+ await update.commit({ revertOnError: true });
return { components, representations };
}
});
diff --git a/src/mol-plugin-state/builder/structure/representation.ts b/src/mol-plugin-state/builder/structure/representation.ts
index 7bde496a8f0d5c61a776c63ef2904313185a3782..ef15aaa5b492920f6fb77501c398f5b5b0c9e2d4 100644
--- a/src/mol-plugin-state/builder/structure/representation.ts
+++ b/src/mol-plugin-state/builder/structure/representation.ts
@@ -117,7 +117,7 @@ export class StructureRepresentationBuilder {
const selector = this.buildRepresentation(repr, structure, props, options);
if (!selector) return;
- await this.plugin.updateDataState(repr);
+ await repr.commit();
return selector;
}
diff --git a/src/mol-plugin-state/formats/provider.ts b/src/mol-plugin-state/formats/provider.ts
new file mode 100644
index 0000000000000000000000000000000000000000..eaa33bfa06698efe82b3f7cdda12604a5dbe1adf
--- /dev/null
+++ b/src/mol-plugin-state/formats/provider.ts
@@ -0,0 +1,41 @@
+/**
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import msgpackDecode from '../../mol-io/common/msgpack/decode';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateObjectRef } from '../../mol-state';
+import { FileInfo } from '../../mol-util/file-info';
+import { PluginStateObject } from '../objects';
+
+export interface DataFormatProvider<P = any, R = any, V = any> {
+ label: string,
+ description: string,
+ category?: string,
+ stringExtensions?: string[],
+ binaryExtensions?: string[],
+ isApplicable?(info: FileInfo, data: string | Uint8Array): boolean,
+ parse(plugin: PluginContext, data: StateObjectRef<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, params?: P): Promise<R>,
+ visuals?(plugin: PluginContext, data: R): Promise<V> | undefined
+}
+
+export function DataFormatProvider<P extends DataFormatProvider>(provider: P): P { return provider; }
+
+type cifVariants = 'dscif' | 'coreCif' | -1
+export function guessCifVariant(info: FileInfo, data: Uint8Array | string): cifVariants {
+ if (info.ext === 'bcif') {
+ try {
+ // TODO: find a way to run msgpackDecode only once
+ // now it is run twice, here and during file parsing
+ if (msgpackDecode(data as Uint8Array).encoder.startsWith('VolumeServer')) return 'dscif'
+ } catch { }
+ } else if (info.ext === 'cif') {
+ const str = data as string
+ if (str.startsWith('data_SERVER\n#\n_density_server_result')) return 'dscif'
+ if (str.includes('atom_site_fract_x') || str.includes('atom_site.fract_x')) return 'coreCif'
+ }
+ return -1
+}
\ No newline at end of file
diff --git a/src/mol-plugin-state/formats/registry.ts b/src/mol-plugin-state/formats/registry.ts
index 5b6c3bc5c1328e31e940127f6997182825233e4e..9ed9f3fdf4e0f3f313f436fcb59b6ec6ba80d002 100644
--- a/src/mol-plugin-state/formats/registry.ts
+++ b/src/mol-plugin-state/formats/registry.ts
@@ -5,18 +5,20 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import msgpackDecode from '../../mol-io/common/msgpack/decode';
-import { PluginContext } from '../../mol-plugin/context';
-import { StateObjectRef } from '../../mol-state';
import { FileInfo } from '../../mol-util/file-info';
import { PluginStateObject } from '../objects';
+import { DataFormatProvider } from './provider';
+import { BuiltInTrajectoryFormats } from './trajectory';
+import { BuiltInVolumeFormats } from './volume';
+import { BuiltInShapeFormats } from './shape';
+import { BuiltInStructureFormats } from './structure';
-export class DataFormatRegistry<Provider extends DataFormatProvider> {
- private _list: { name: string, provider: Provider }[] = []
- private _map = new Map<string, Provider>()
+export class DataFormatRegistry {
+ private _list: { name: string, provider: DataFormatProvider }[] = []
+ private _map = new Map<string, DataFormatProvider>()
private _extensions: Set<string> | undefined = undefined
private _binaryExtensions: Set<string> | undefined = undefined
- private _options: [string, string][] | undefined = undefined
+ private _options: [string, string, string][] | undefined = undefined
get types(): [string, string][] {
return this._list.map(e => [e.name, e.provider.label] as [string, string]);
@@ -26,8 +28,8 @@ export class DataFormatRegistry<Provider extends DataFormatProvider> {
if (this._extensions) return this._extensions
const extensions = new Set<string>()
this._list.forEach(({ provider }) => {
- provider.stringExtensions.forEach(ext => extensions.add(ext))
- provider.binaryExtensions.forEach(ext => extensions.add(ext))
+ provider.stringExtensions?.forEach(ext => extensions.add(ext))
+ provider.binaryExtensions?.forEach(ext => extensions.add(ext))
})
this._extensions = extensions
return extensions
@@ -36,21 +38,24 @@ export class DataFormatRegistry<Provider extends DataFormatProvider> {
get binaryExtensions() {
if (this._binaryExtensions) return this._binaryExtensions
const binaryExtensions = new Set<string>()
- this._list.forEach(({ provider }) => provider.binaryExtensions.forEach(ext => binaryExtensions.add(ext)))
+ this._list.forEach(({ provider }) => provider.binaryExtensions?.forEach(ext => binaryExtensions.add(ext)))
this._binaryExtensions = binaryExtensions
return binaryExtensions
}
get options() {
if (this._options) return this._options
- const options: [string, string][] = [['auto', 'Automatic']]
- this._list.forEach(({ name, provider }) => options.push([ name, provider.label ]))
+ const options: [string, string, string][] = [['auto', 'Automatic', '']]
+ this._list.forEach(({ name, provider }) => options.push([ name, provider.label, provider.category || '' ]))
this._options = options
return options
}
- constructor(buildInFormats: ReadonlyArray<readonly [string, Provider]>) {
- for (const [id, p] of buildInFormats) this.add(id, p);
+ constructor() {
+ for (const [id, p] of BuiltInVolumeFormats) this.add(id, p);
+ for (const [id, p] of BuiltInStructureFormats) this.add(id, p);
+ for (const [id, p] of BuiltInShapeFormats) this.add(id, p);
+ for (const [id, p] of BuiltInTrajectoryFormats) this.add(id, p);
};
private _clear() {
@@ -59,7 +64,7 @@ export class DataFormatRegistry<Provider extends DataFormatProvider> {
this._options = undefined
}
- add(name: string, provider: Provider) {
+ add(name: string, provider: DataFormatProvider) {
this._clear()
this._list.push({ name, provider })
this._map.set(name, provider)
@@ -74,12 +79,16 @@ export class DataFormatRegistry<Provider extends DataFormatProvider> {
auto(info: FileInfo, dataStateObject: PluginStateObject.Data.Binary | PluginStateObject.Data.String) {
for (let i = 0, il = this.list.length; i < il; ++i) {
const { provider } = this._list[i];
- if (provider.isApplicable(info, dataStateObject.data)) return provider;
+
+ let hasExt = false;
+ if (provider.binaryExtensions && provider.binaryExtensions.indexOf(info.ext) >= 0) hasExt = true;
+ else if (provider.stringExtensions && provider.stringExtensions.indexOf(info.ext) >= 0) hasExt = true;
+ if (hasExt && (!provider.isApplicable || provider.isApplicable(info, dataStateObject.data))) return provider;
}
return;
}
- get(name: string): Provider | undefined {
+ get(name: string): DataFormatProvider | undefined {
if (this._map.has(name)) {
return this._map.get(name)!
} else {
@@ -90,27 +99,4 @@ export class DataFormatRegistry<Provider extends DataFormatProvider> {
get list() {
return this._list
}
-}
-
-export interface DataFormatProvider<P = any, R = any> {
- label: string
- description: string
- stringExtensions: string[]
- binaryExtensions: string[]
- isApplicable(info: FileInfo, data: string | Uint8Array): boolean
- parse(plugin: PluginContext, data: StateObjectRef<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, params?: P): Promise<R>
-}
-
-type cifVariants = 'dscif' | -1
-export function guessCifVariant(info: FileInfo, data: Uint8Array | string): cifVariants {
- if (info.ext === 'bcif') {
- try {
- // TODO: find a way to run msgpackDecode only once
- // now it is run twice, here and during file parsing
- if (msgpackDecode(data as Uint8Array).encoder.startsWith('VolumeServer')) return 'dscif'
- } catch { }
- } else if (info.ext === 'cif') {
- if ((data as string).startsWith('data_SERVER\n#\n_density_server_result')) return 'dscif'
- }
- return -1
}
\ No newline at end of file
diff --git a/src/mol-plugin-state/formats/shape.ts b/src/mol-plugin-state/formats/shape.ts
new file mode 100644
index 0000000000000000000000000000000000000000..cc02ee10c1a667708a130af62246f3b7174e25fc
--- /dev/null
+++ b/src/mol-plugin-state/formats/shape.ts
@@ -0,0 +1,35 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { StateTransforms } from '../transforms';
+import { DataFormatProvider } from './provider';
+
+const Category = 'Shape';
+
+export const PlyProvider = DataFormatProvider({
+ label: 'PLY',
+ description: 'PLY',
+ category: Category,
+ stringExtensions: ['ply'],
+ parse: async (plugin, data) => {
+ const format = plugin.state.data.build()
+ .to(data)
+ .apply(StateTransforms.Data.ParsePly, {}, { state: { isGhost: true } });
+
+ const shape = format.apply(StateTransforms.Model.ShapeFromPly);
+
+ await format.commit();
+
+ return { format: format.selector, shape: shape.selector };
+ }
+});
+
+export const BuiltInShapeFormats = [
+ ['ply', PlyProvider] as const,
+] as const
+
+export type BuildInShapeFormat = (typeof BuiltInShapeFormats)[number][0]
\ No newline at end of file
diff --git a/src/mol-plugin-state/formats/structure.ts b/src/mol-plugin-state/formats/structure.ts
new file mode 100644
index 0000000000000000000000000000000000000000..f534e20da4c09f68de15c62cc0ad558fd2c7fb8e
--- /dev/null
+++ b/src/mol-plugin-state/formats/structure.ts
@@ -0,0 +1,49 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { StateTransforms } from '../transforms';
+import { DataFormatProvider } from './provider';
+
+const Category = 'Structure';
+
+export const PsfProvider = DataFormatProvider({
+ label: 'PSF',
+ description: 'PSF',
+ category: Category,
+ stringExtensions: ['psf'],
+ parse: async (plugin, data) => {
+ const format = plugin.state.data.build()
+ .to(data)
+ .apply(StateTransforms.Data.ParsePsf, {}, { state: { isGhost: true } });
+ const topology = format.apply(StateTransforms.Model.TopologyFromPsf);
+
+ await format.commit();
+
+ return { format: format.selector, topology: topology.selector };
+ }
+});
+
+export const DcdProvider = DataFormatProvider({
+ label: 'DCD',
+ description: 'DCD',
+ category: Category,
+ binaryExtensions: ['dcd'],
+ parse: (plugin, data) => {
+ const coordinates = plugin.state.data.build()
+ .to(data)
+ .apply(StateTransforms.Model.CoordinatesFromDcd);
+
+ return coordinates.commit();
+ }
+});
+
+export const BuiltInStructureFormats = [
+ ['psf', PsfProvider] as const,
+ ['dcd', DcdProvider] as const,
+] as const
+
+export type BuildInStructureFormat = (typeof BuiltInStructureFormats)[number][0]
\ No newline at end of file
diff --git a/src/mol-plugin-state/formats/trajectory.ts b/src/mol-plugin-state/formats/trajectory.ts
index 9a735feab4a41f9ab53741e31097c2b49cd903b3..c888550f2c1808fefb31880dd10b630bb5d32141 100644
--- a/src/mol-plugin-state/formats/trajectory.ts
+++ b/src/mol-plugin-state/formats/trajectory.ts
@@ -5,105 +5,131 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { FileInfo } from '../../mol-util/file-info';
import { StateTransforms } from '../transforms';
-import { guessCifVariant, DataFormatProvider, DataFormatRegistry } from './registry';
+import { guessCifVariant, DataFormatProvider } from './provider';
import { StateTransformer, StateObjectRef } from '../../mol-state';
import { PluginStateObject } from '../objects';
+import { PluginContext } from '../../mol-plugin/context';
export interface TrajectoryFormatProvider<P extends { trajectoryTags?: string | string[] } = { trajectoryTags?: string | string[] }, R extends { trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory> } = { trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory> }>
extends DataFormatProvider<P, R> {
}
-export function TrajectoryFormatRegistry() {
- return new DataFormatRegistry<TrajectoryFormatProvider>(BuildInTrajectoryFormats);
+const Category = 'Trajectory';
+
+function defaultVisuals(plugin: PluginContext, data: { trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory> }) {
+ return plugin.builders.structure.hierarchy.applyPreset(data.trajectory, 'default');
}
export const MmcifProvider: TrajectoryFormatProvider = {
label: 'mmCIF',
description: 'mmCIF',
+ category: Category,
stringExtensions: ['cif', 'mmcif', 'mcif'],
binaryExtensions: ['bcif'],
- isApplicable: (info: FileInfo, data: Uint8Array | string) => {
+ isApplicable: (info, data) => {
if (info.ext === 'mmcif' || info.ext === 'mcif') return true
- // assume cif/bcif files that are not DensityServer CIF are mmCIF
- if (info.ext === 'cif' || info.ext === 'bcif') return guessCifVariant(info, data) !== 'dscif'
+ // assume undetermined cif/bcif files are mmCIF
+ if (info.ext === 'cif' || info.ext === 'bcif') return guessCifVariant(info, data) === -1
return false
},
parse: async (plugin, data, params) => {
const state = plugin.state.data;
const cif = state.build().to(data)
.apply(StateTransforms.Data.ParseCif, void 0, { state: { isGhost: true } })
- const trajectory = cif.apply(StateTransforms.Model.TrajectoryFromMmCif, void 0, { tags: params?.trajectoryTags })
- await plugin.updateDataState(trajectory, { revertOnError: true });
+ const trajectory = await cif
+ .apply(StateTransforms.Model.TrajectoryFromMmCif, void 0, { tags: params?.trajectoryTags })
+ .commit({ revertOnError: true });
+
if ((cif.selector.cell?.obj?.data.blocks.length || 0) > 1) {
plugin.state.data.updateCellState(cif.ref, { isGhost: false });
}
- return { trajectory: trajectory.selector };
- }
+
+ return { trajectory };
+ },
+ visuals: defaultVisuals
+}
+
+export const CifCoreProvider: TrajectoryFormatProvider = {
+ label: 'cifCore',
+ description: 'CIF Core',
+ category: Category,
+ stringExtensions: ['cif'],
+ isApplicable: (info, data) => {
+ if (info.ext === 'cif') return guessCifVariant(info, data) === 'coreCif'
+ return false
+ },
+ parse: async (plugin, data, params) => {
+ const state = plugin.state.data;
+ const cif = state.build().to(data)
+ .apply(StateTransforms.Data.ParseCif, void 0, { state: { isGhost: true } })
+ const trajectory = await cif
+ .apply(StateTransforms.Model.TrajectoryFromCifCore, void 0, { tags: params?.trajectoryTags })
+ .commit({ revertOnError: true });
+
+ if ((cif.selector.cell?.obj?.data.blocks.length || 0) > 1) {
+ plugin.state.data.updateCellState(cif.ref, { isGhost: false });
+ }
+ return { trajectory };
+ },
+ visuals: defaultVisuals
}
function directTrajectory(transformer: StateTransformer<PluginStateObject.Data.String | PluginStateObject.Data.Binary, PluginStateObject.Molecule.Trajectory>): TrajectoryFormatProvider['parse'] {
return async (plugin, data, params) => {
const state = plugin.state.data;
- const trajectory = state.build().to(data)
+ const trajectory = await state.build().to(data)
.apply(transformer, void 0, { tags: params?.trajectoryTags })
- await plugin.updateDataState(trajectory, { revertOnError: true });
- return { trajectory: trajectory.selector };
+ .commit({ revertOnError: true });
+ return { trajectory };
}
}
export const PdbProvider: TrajectoryFormatProvider = {
label: 'PDB',
description: 'PDB',
+ category: Category,
stringExtensions: ['pdb', 'ent'],
- binaryExtensions: [],
- isApplicable: (info: FileInfo, data: string) => {
- return info.ext === 'pdb' || info.ext === 'ent'
- },
- parse: directTrajectory(StateTransforms.Model.TrajectoryFromPDB)
+ parse: directTrajectory(StateTransforms.Model.TrajectoryFromPDB),
+ visuals: defaultVisuals
}
export const GroProvider: TrajectoryFormatProvider = {
label: 'GRO',
description: 'GRO',
+ category: Category,
stringExtensions: ['gro'],
binaryExtensions: [],
- isApplicable: (info: FileInfo, data: string) => {
- return info.ext === 'gro'
- },
- parse: directTrajectory(StateTransforms.Model.TrajectoryFromGRO)
+ parse: directTrajectory(StateTransforms.Model.TrajectoryFromGRO),
+ visuals: defaultVisuals
}
export const Provider3dg: TrajectoryFormatProvider = {
label: '3DG',
description: '3DG',
+ category: Category,
stringExtensions: ['3dg'],
- binaryExtensions: [],
- isApplicable: (info: FileInfo, data: string) => {
- return info.ext === '3dg'
- },
- parse: directTrajectory(StateTransforms.Model.TrajectoryFrom3DG)
+ parse: directTrajectory(StateTransforms.Model.TrajectoryFrom3DG),
+ visuals: defaultVisuals
}
export const MolProvider: TrajectoryFormatProvider = {
label: 'MOL',
description: 'MOL',
+ category: Category,
stringExtensions: ['mol', 'sdf'],
- binaryExtensions: [],
- isApplicable: (info: FileInfo, data: string) => {
- return info.ext === 'mol' || info.ext === 'sdf'
- },
- parse: directTrajectory(StateTransforms.Model.TrajectoryFromMOL)
+ parse: directTrajectory(StateTransforms.Model.TrajectoryFromMOL),
+ visuals: defaultVisuals
}
-export const BuildInTrajectoryFormats = [
+export const BuiltInTrajectoryFormats = [
['mmcif', MmcifProvider] as const,
+ ['cifCore', CifCoreProvider] as const,
['pdb', PdbProvider] as const,
['gro', GroProvider] as const,
['3dg', Provider3dg] as const,
['mol', MolProvider] as const
] as const
-export type BuiltInTrajectoryFormat = (typeof BuildInTrajectoryFormats)[number][0]
\ No newline at end of file
+export type BuiltInTrajectoryFormat = (typeof BuiltInTrajectoryFormats)[number][0]
\ No newline at end of file
diff --git a/src/mol-plugin-state/formats/volume.ts b/src/mol-plugin-state/formats/volume.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a70f3d285264b1dbba6dd5858e6530bda9a0e5f6
--- /dev/null
+++ b/src/mol-plugin-state/formats/volume.ts
@@ -0,0 +1,118 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { StateTransforms } from '../transforms';
+import { DataFormatProvider, guessCifVariant } from './provider';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateObjectSelector } from '../../mol-state';
+import { PluginStateObject } from '../objects';
+import { VolumeRepresentation3DHelpers } from '../transforms/representation';
+import { ColorNames } from '../../mol-util/color/names';
+import { VolumeIsoValue } from '../../mol-model/volume';
+
+const Category = 'Volume';
+
+async function defaultVisuals(plugin: PluginContext, data: { volume: StateObjectSelector<PluginStateObject.Volume.Data> }) {
+ const visual = plugin.build().to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D);
+ return [await visual.commit()];
+}
+
+export const Ccp4Provider = DataFormatProvider({
+ label: 'CCP4/MRC/BRIX',
+ description: 'CCP4/MRC/BRIX',
+ category: Category,
+ binaryExtensions: ['ccp4', 'mrc', 'map'],
+ parse: async (plugin, data) => {
+ const format = plugin.build()
+ .to(data)
+ .apply(StateTransforms.Data.ParseCcp4, {}, { state: { isGhost: true } });
+
+ const volume = format.apply(StateTransforms.Volume.VolumeFromCcp4);
+
+ await format.commit({ revertOnError: true });
+
+ return { format: format.selector, volume: volume.selector };
+ },
+ visuals: defaultVisuals
+});
+
+export const Dsn6Provider = DataFormatProvider({
+ label: 'DSN6/BRIX',
+ description: 'DSN6/BRIX',
+ category: Category,
+ binaryExtensions: ['dsn6', 'brix'],
+ parse: async (plugin, data) => {
+ const format = plugin.build()
+ .to(data)
+ .apply(StateTransforms.Data.ParseDsn6, {}, { state: { isGhost: true } });
+
+ const volume = format.apply(StateTransforms.Volume.VolumeFromDsn6);
+
+ await format.commit({ revertOnError: true });
+
+ return { format: format.selector, volume: volume.selector };
+ },
+ visuals: defaultVisuals
+});
+
+export const DscifProvider = DataFormatProvider({
+ label: 'DensityServer CIF',
+ description: 'DensityServer CIF',
+ category: Category,
+ stringExtensions: ['cif'],
+ binaryExtensions: ['bcif'],
+ isApplicable: (info, data) => {
+ return guessCifVariant(info, data) === 'dscif' ? true : false
+ },
+ parse: async (plugin, data) => {
+ const cifCell = await plugin.build().to(data).apply(StateTransforms.Data.ParseCif).commit()
+ const b = plugin.build().to(cifCell);
+ const blocks = cifCell.obj!.data.blocks.slice(1); // zero block contains query meta-data
+
+ if (blocks.length !== 1 && blocks.length !== 2) throw new Error('unknown number of blocks')
+
+ const volumes: StateObjectSelector<PluginStateObject.Volume.Data>[] = [];
+ for (const block of blocks) {
+ volumes.push(b.apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: block.header }).selector);
+ }
+
+ await b.commit();
+
+ return { volumes };
+ },
+ visuals: async (plugin, data: { volumes: StateObjectSelector<PluginStateObject.Volume.Data>[] }) => {
+ const { volumes } = data;
+ const tree = plugin.build();
+ const visuals: StateObjectSelector<PluginStateObject.Volume.Representation3D>[] = [];
+
+ if (volumes.length > 0) {
+ visuals[0] = tree
+ .to(volumes[0])
+ .apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 0.3 }, 'uniform', { value: ColorNames.teal }))
+ .selector;
+ }
+
+ if (volumes.length > 1) {
+ const posParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(3), alpha: 0.3 }, 'uniform', { value: ColorNames.green })
+ const negParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(-3), alpha: 0.3 }, 'uniform', { value: ColorNames.red })
+ visuals[visuals.length] = tree.to(volumes[1]).apply(StateTransforms.Representation.VolumeRepresentation3D, posParams).selector;
+ visuals[visuals.length] = tree.to(volumes[1]).apply(StateTransforms.Representation.VolumeRepresentation3D, negParams).selector;
+ }
+
+ await tree.commit();
+
+ return visuals;
+ }
+});
+
+export const BuiltInVolumeFormats = [
+ ['ccp4', Ccp4Provider] as const,
+ ['dns6', Dsn6Provider] as const,
+ ['dscif', DscifProvider] as const,
+] as const
+
+export type BuildInVolumeFormat = (typeof BuiltInVolumeFormats)[number][0]
\ No newline at end of file
diff --git a/src/mol-plugin-state/helpers/structure-overpaint.ts b/src/mol-plugin-state/helpers/structure-overpaint.ts
index cc977e3972750639d86c9099c2cfdeebaaa7e355..2049ee21756b5c77938ec8354bc772e4e4ee637f 100644
--- a/src/mol-plugin-state/helpers/structure-overpaint.ts
+++ b/src/mol-plugin-state/helpers/structure-overpaint.ts
@@ -55,7 +55,7 @@ export async function clearStructureOverpaint(plugin: PluginContext, components:
});
}
-async function eachRepr(plugin: PluginContext, components: StructureComponentRef[], callback: OverpaintEachReprCallback) {
+function eachRepr(plugin: PluginContext, components: StructureComponentRef[], callback: OverpaintEachReprCallback) {
const state = plugin.state.data;
const update = state.build();
for (const c of components) {
@@ -65,7 +65,7 @@ async function eachRepr(plugin: PluginContext, components: StructureComponentRef
}
}
- await plugin.updateDataState(update, { doNotUpdateCurrent: true });
+ return update.commit({ doNotUpdateCurrent: true });
}
/** filter overpaint layers for given structure */
diff --git a/src/mol-plugin-state/manager/structure/component.ts b/src/mol-plugin-state/manager/structure/component.ts
index 2adb9f75bac4f1e2c80a0d023b50cddef440c275..87868522ada71f7ed7dd75f41dffc5de39e8d00c 100644
--- a/src/mol-plugin-state/manager/structure/component.ts
+++ b/src/mol-plugin-state/manager/structure/component.ts
@@ -60,7 +60,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
}
return this.plugin.dataTransaction(async () => {
- await this.plugin.updateDataState(update);
+ await update.commit();
if (interactionChanged) await this.updateInterationProps();
});
}
@@ -89,11 +89,11 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
const oldParams = s.properties.cell.transform.params?.properties[InteractionsProvider.descriptor.name];
if (PD.areEqual(interactionParams, oldParams, this.state.options.interactions)) continue;
- const b = this.dataState.build();
- b.to(s.properties.cell).update(old => {
- old.properties[InteractionsProvider.descriptor.name] = this.state.options.interactions;
- });
- await this.plugin.updateDataState(b);
+ await this.dataState.build().to(s.properties.cell)
+ .update(old => {
+ old.properties[InteractionsProvider.descriptor.name] = this.state.options.interactions;
+ })
+ .commit();
} else {
const pd = this.plugin.customStructureProperties.getParams(s.cell.obj?.data);
const params = PD.getDefaultValues(pd);
@@ -113,7 +113,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
}, { canUndo: 'Preset' });
}
- private async syncPreset(root: StructureRef, preset?: StructureRepresentationPresetProvider.Result) {
+ private syncPreset(root: StructureRef, preset?: StructureRepresentationPresetProvider.Result) {
if (!preset || !preset.components) return this.clearComponents([root]);
const keptRefs = new Set<string>();
@@ -153,7 +153,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
}
}
- if (changed) return this.plugin.updateDataState(update);
+ if (changed) return update.commit();
}
clear(structures: ReadonlyArray<StructureRef>) {
@@ -247,7 +247,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
update.to(repr.cell).update(params);
}
- return this.plugin.updateDataState(update, { canUndo: 'Update Representation' });
+ return update.commit({ canUndo: 'Update Representation' });
}
/**
@@ -288,7 +288,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
}
}
- return this.plugin.updateDataState(update, { canUndo: 'Update Theme' });
+ return update.commit({ canUndo: 'Update Theme' });
}
addRepresentation(components: ReadonlyArray<StructureComponentRef>, type: string) {
@@ -313,6 +313,10 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
const xs = structures || this.currentStructures;
if (xs.length === 0) return;
+ const { showHydrogens, visualQuality: quality } = this.state.options;
+ const ignoreHydrogens = !showHydrogens;
+ const typeParams = { ignoreHydrogens, quality };
+
const componentKey = UUID.create22();
for (const s of xs) {
const component = await this.plugin.builders.structure.tryCreateComponentFromSelection(s.cell, params.selection, componentKey, {
@@ -320,7 +324,8 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
});
if (params.representation === 'none' || !component) continue;
await this.plugin.builders.structure.representation.addRepresentation(component, {
- type: this.plugin.representation.structure.registry.get(params.representation)
+ type: this.plugin.representation.structure.registry.get(params.representation),
+ typeParams
});
}
}, { canUndo: 'Add Selection' });
@@ -379,7 +384,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
deletes.delete(c.cell.transform.ref);
}
}
- return this.plugin.updateDataState(deletes, { canUndo: 'Clear Selections' });
+ return deletes.commit({ canUndo: 'Clear Selections' });
}
constructor(public plugin: PluginContext) {
diff --git a/src/mol-plugin-state/manager/structure/hierarchy.ts b/src/mol-plugin-state/manager/structure/hierarchy.ts
index 4eef242c5336979492db34327c679b2f57fff19f..51d78520263f4bf60ed01dc8f027313d380a4c82 100644
--- a/src/mol-plugin-state/manager/structure/hierarchy.ts
+++ b/src/mol-plugin-state/manager/structure/hierarchy.ts
@@ -155,7 +155,7 @@ export class StructureHierarchyManager extends PluginComponent {
if (refs.length === 0) return;
const deletes = this.plugin.state.data.build();
for (const r of refs) deletes.delete(typeof r === 'string' ? r : r.cell.transform.ref);
- return this.plugin.updateDataState(deletes, { canUndo: canUndo ? 'Remove' : false });
+ return deletes.commit({ canUndo: canUndo ? 'Remove' : false });
}
toggleVisibility(refs: ReadonlyArray<HierarchyRef>, action?: 'show' | 'hide') {
@@ -196,7 +196,7 @@ export class StructureHierarchyManager extends PluginComponent {
for (const m of trajectory.models) {
builder.delete(m.cell);
}
- return this.plugin.updateDataState(builder);
+ return builder.commit();
}
constructor(private plugin: PluginContext) {
diff --git a/src/mol-plugin-state/snapshots.ts b/src/mol-plugin-state/snapshots.ts
index b34bb3c97b59917cb8dcd363b06b6fe244f92a7f..9ae2b8ad4b4a05107e5fbeb6b95db8525db801a7 100644
--- a/src/mol-plugin-state/snapshots.ts
+++ b/src/mol-plugin-state/snapshots.ts
@@ -210,8 +210,9 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
if (this.state.isPlaying) {
this.stop();
this.plugin.state.animation.stop();
+ } else {
+ this.play();
}
- else this.play();
}
constructor(private plugin: PluginContext) {
diff --git a/src/mol-plugin-state/transforms/data.ts b/src/mol-plugin-state/transforms/data.ts
index d1b8ecf51bf98bfd652adf05597185587cf96399..b588dd00f0feeda11a281d76d1e5f438fc157be4 100644
--- a/src/mol-plugin-state/transforms/data.ts
+++ b/src/mol-plugin-state/transforms/data.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -11,7 +11,7 @@ import { Task } from '../../mol-task';
import { CIF } from '../../mol-io/reader/cif'
import { PluginContext } from '../../mol-plugin/context';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { StateTransformer } from '../../mol-state';
+import { StateTransformer, StateObject } from '../../mol-state';
import { readFromFile, ajaxGetMany } from '../../mol-util/data-source';
import * as CCP4 from '../../mol-io/reader/ccp4/parser'
import * as DSN6 from '../../mol-io/reader/dsn6/parser'
@@ -143,8 +143,12 @@ const ReadFile = PluginStateTransform.BuiltIn({
isBinary: PD.Optional(PD.Boolean(false, { description: 'If true, open file as as binary (string otherwise)' }))
}
})({
- apply({ params: p }) {
+ apply({ params: p }, plugin: PluginContext) {
return Task.create('Open File', async ctx => {
+ if (p.file === null) {
+ plugin.log.error('No file(s) selected')
+ return StateObject.Null;
+ }
const data = await readFromFile(p.file, p.isBinary ? 'binary' : 'string').runInContext(ctx);
return p.isBinary
? new SO.Data.Binary(data as Uint8Array, { label: p.label ? p.label : p.file.name })
@@ -153,7 +157,7 @@ const ReadFile = PluginStateTransform.BuiltIn({
},
update({ oldParams, newParams, b }) {
if (oldParams.label !== newParams.label) {
- (b.label as string) = newParams.label || oldParams.file.name;
+ (b.label as string) = newParams.label || oldParams.file?.name || '';
return StateTransformer.UpdateResult.Updated;
}
return StateTransformer.UpdateResult.Unchanged;
diff --git a/src/mol-plugin-state/transforms/model.ts b/src/mol-plugin-state/transforms/model.ts
index defe06b40b618fbbd92629418b82badf1a210918..2e0839e8fe2743e40aef426116d462d504da3ffc 100644
--- a/src/mol-plugin-state/transforms/model.ts
+++ b/src/mol-plugin-state/transforms/model.ts
@@ -34,6 +34,7 @@ import { StructureSelectionQueries } from '../helpers/structure-selection-query'
import { PluginStateObject as SO, PluginStateTransform } from '../objects';
import { parseMol } from '../../mol-io/reader/mol/parser';
import { trajectoryFromMol } from '../../mol-model-formats/structure/mol';
+import { trajectoryFromCifCore } from '../../mol-model-formats/structure/cif-core';
export { CoordinatesFromDcd };
export { TopologyFromPsf };
@@ -43,6 +44,7 @@ export { TrajectoryFromMmCif };
export { TrajectoryFromPDB };
export { TrajectoryFromGRO };
export { TrajectoryFromMOL };
+export { TrajectoryFromCifCore };
export { TrajectoryFrom3DG };
export { ModelFromTrajectory };
export { StructureFromTrajectory };
@@ -233,6 +235,37 @@ const TrajectoryFromMOL = PluginStateTransform.BuiltIn({
}
});
+type TrajectoryFromCifCore = typeof TrajectoryFromCifCore
+const TrajectoryFromCifCore = PluginStateTransform.BuiltIn({
+ name: 'trajectory-from-cif-core',
+ display: { name: 'Parse CIF Core', description: 'Identify and create all separate models in the specified CIF data block' },
+ from: SO.Format.Cif,
+ to: SO.Molecule.Trajectory,
+ params(a) {
+ if (!a) {
+ return {
+ 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.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' }))
+ };
+ }
+})({
+ apply({ a, params }) {
+ return Task.create('Parse CIF Core', async ctx => {
+ const header = params.blockHeader || a.data.blocks[0].header;
+ const block = a.data.blocks.find(b => b.header === header);
+ if (!block) throw new Error(`Data block '${[header]}' not found.`);
+ const models = await trajectoryFromCifCore(block).runInContext(ctx);
+ if (models.length === 0) throw new Error('No models found.');
+ const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+ return new SO.Molecule.Trajectory(models, props);
+ });
+ }
+});
+
type TrajectoryFrom3DG = typeof TrajectoryFrom3DG
const TrajectoryFrom3DG = PluginStateTransform.BuiltIn({
name: 'trajectory-from-3dg',
diff --git a/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx b/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx
index f623e05c9e4ed876884e5bd97a02743e49a4873e..1503f5531a09fe3935bab6858e651e82711a02a2 100644
--- a/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx
+++ b/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx
@@ -15,7 +15,7 @@ interface LineGraphComponentState {
}
export default class LineGraphComponent extends React.Component<any, LineGraphComponentState> {
- private myRef:any;
+ private myRef: any;
private height: number;
private width: number;
private padding: number;
@@ -123,11 +123,11 @@ export default class LineGraphComponent extends React.Component<any, LineGraphCo
// TODO: SET canSelectMultiple = fasle
}
- private handleClick = (id:number) => (event:any) => {
+ private handleClick = (id: number) => (event: any) => {
// TODO: add point to selected array
}
- private handleMouseDown = (id:number) => (event: any) => {
+ private handleMouseDown = (id: number) => (event: any) => {
if(id === 0 || id === this.state.points.length-1){
return;
}
@@ -164,17 +164,13 @@ export default class LineGraphComponent extends React.Component<any, LineGraphCo
if ((svgP.x < (padding) || svgP.x > (this.width+(padding))) && (svgP.y > (this.height+(padding)) || svgP.y < (padding))) {
updatedCopyPoint = Vec2.create(this.updatedX, this.updatedY);
- }
- else if (svgP.x < padding) {
+ } else if (svgP.x < padding) {
updatedCopyPoint = Vec2.create(padding, svgP.y);
- }
- else if( svgP.x > (this.width+(padding))) {
+ } else if( svgP.x > (this.width+(padding))) {
updatedCopyPoint = Vec2.create(this.width+padding, svgP.y);
- }
- else if (svgP.y > (this.height+(padding))) {
+ } else if (svgP.y > (this.height+(padding))) {
updatedCopyPoint = Vec2.create(svgP.x, this.height+padding);
- }
- else if (svgP.y < (padding)) {
+ } else if (svgP.y < (padding)) {
updatedCopyPoint = Vec2.create(svgP.x, padding);
} else {
updatedCopyPoint = Vec2.create(svgP.x, svgP.y);
@@ -230,8 +226,8 @@ export default class LineGraphComponent extends React.Component<any, LineGraphCo
this.change(points);
this.gElement.innerHTML = '';
this.ghostPoints = [];
- document.removeEventListener("mousemove", this.handleDrag, true);
- document.removeEventListener("mouseup", this.handlePointUpdate, true);
+ document.removeEventListener('mousemove', this.handleDrag, true);
+ document.removeEventListener('mouseup', this.handlePointUpdate, true);
}
private handleDoubleClick(event: any) {
@@ -267,8 +263,8 @@ export default class LineGraphComponent extends React.Component<any, LineGraphCo
this.change(points);
}
- private deletePoint = (i:number) => (event: any) => {
- if(i===0 || i===this.state.points.length-1){ return; }
+ private deletePoint = (i: number) => (event: any) => {
+ if(i===0 || i===this.state.points.length-1){ return; }
const points = this.state.points.filter((_,j) => j !== i);
points.sort((a, b) => {
if(a[0] === b[0]){
@@ -334,21 +330,21 @@ export default class LineGraphComponent extends React.Component<any, LineGraphCo
const points: any[] = [];
let point: Vec2;
for (let i = 0; i < this.state.points.length; i++){
- if(i != 0 && i != this.state.points.length-1){
+ if(i !== 0 && i !== this.state.points.length-1){
point = this.normalizePoint(this.state.points[i]);
points.push(<PointComponent
- key={i}
- id={i}
- x={point[0]}
- y={point[1]}
- nX={this.state.points[i][0]}
- nY={this.state.points[i][1]}
- selected={false}
- delete={this.deletePoint}
- onmouseover={this.props.onHover}
- onmousedown={this.handleMouseDown(i)}
- onclick={this.handleClick(i)}
- />);
+ key={i}
+ id={i}
+ x={point[0]}
+ y={point[1]}
+ nX={this.state.points[i][0]}
+ nY={this.state.points[i][1]}
+ selected={false}
+ delete={this.deletePoint}
+ onmouseover={this.props.onHover}
+ onmousedown={this.handleMouseDown(i)}
+ onclick={this.handleClick(i)}
+ />);
}
}
return points;
@@ -357,8 +353,8 @@ export default class LineGraphComponent extends React.Component<any, LineGraphCo
private renderLines() {
const points: Vec2[] = [];
let lines = [];
- let min:number;
- let maxX:number;
+ let min: number;
+ let maxX: number;
let maxY: number;
let normalizedX: number;
let normalizedY: number;
diff --git a/src/mol-plugin-ui/controls/slider.tsx b/src/mol-plugin-ui/controls/slider.tsx
index ba53065ece5c5435ce6577fe41c89495b137e5e0..12a66eeef40d88d2f402f7d7183fcffe7436651c 100644
--- a/src/mol-plugin-ui/controls/slider.tsx
+++ b/src/mol-plugin-ui/controls/slider.tsx
@@ -733,7 +733,7 @@ export class SliderBase extends React.Component<SliderBaseProps, SliderBaseState
ref: this.handleElements[i]
}));
if (!range) { handles.shift(); }
-
+
const sliderClassName = classNames({
[prefixCls!]: true,
[`${prefixCls}-with-marks`]: Object.keys(marks).length,
@@ -743,8 +743,8 @@ export class SliderBase extends React.Component<SliderBaseProps, SliderBaseState
});
return (
- <div ref={this.sliderElement} className={sliderClassName}
- onTouchStart={disabled ? noop : this.onTouchStart as any}
+ <div ref={this.sliderElement} className={sliderClassName}
+ onTouchStart={disabled ? noop : this.onTouchStart as any}
onMouseDown={disabled ? noop : this.onMouseDown as any}
>
<div className={`${prefixCls}-rail`} />
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
index 3d2cad2628ee2dce12dc17ea9a840b6c5efb7c3b..34aafbe151d4c7a34d7883f4faf11226a3a787dd 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
@@ -188,10 +188,9 @@ export const AssemblySymmetryPreset = StructureRepresentationPresetProvider({
}
});
-export async function tryCreateAssemblySymmetry(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, params?: StateTransformer.Params<AssemblySymmetry3D>, initialState?: Partial<StateTransform.State>) {
+export function tryCreateAssemblySymmetry(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, params?: StateTransformer.Params<AssemblySymmetry3D>, initialState?: Partial<StateTransform.State>) {
const state = plugin.state.data;
const assemblySymmetry = state.build().to(structure)
.applyOrUpdateTagged(AssemblySymmetry.Tag.Representation, AssemblySymmetry3D, params, { state: initialState });
- await plugin.updateDataState(assemblySymmetry, { revertOnError: true });
- return assemblySymmetry.selector
+ return assemblySymmetry.commit({ revertOnError: true });
}
\ No newline at end of file
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/ui/assembly-symmetry.tsx b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/ui/assembly-symmetry.tsx
index df69ba8f7e6fe0d301267ae809cc644716a92775..8931de1f6c53b9bc7a4d652d1eda63779d32689d 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/ui/assembly-symmetry.tsx
+++ b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/ui/assembly-symmetry.tsx
@@ -96,7 +96,7 @@ export class AssemblySymmetryControls extends CollapsableControls<{}, AssemblySy
b.to(s.properties.cell).update(old => {
old.properties[AssemblySymmetryProvider.descriptor.name] = values;
});
- await this.plugin.updateDataState(b);
+ await b.commit();
} else {
const pd = this.plugin.customStructureProperties.getParams(s.cell.obj?.data);
const params = PD.getDefaultValues(pd);
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts
index f5d23feae4bb21ab7aa3fbc43a0d6f4162fc352f..da8ff9dfb3c4f73134fe62bded4ba98fb2f03f81 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts
@@ -329,7 +329,7 @@ export const ValidationReportGeometryQualityPreset = StructureRepresentationPres
clashesSnfg3d = builder.buildRepresentation<any>(update, clashes, { type: ClashesRepresentationProvider.name, typeParams, color }, { tag: 'clashes-snfg-3d' });
}
- await plugin.updateDataState(update, { revertOnError: false });
+ await update.commit({ revertOnError: true });
return { components: { ...components, clashes }, representations: { ...representations, clashesBallAndStick, clashesSnfg3d } };
}
});
diff --git a/src/mol-plugin/behavior/dynamic/representation.ts b/src/mol-plugin/behavior/dynamic/representation.ts
index 41b0ad9abefdb2b2376131fd5a21ed910753f281..88494345213c5352da8ea9191042b01500ff05e9 100644
--- a/src/mol-plugin/behavior/dynamic/representation.ts
+++ b/src/mol-plugin/behavior/dynamic/representation.ts
@@ -184,7 +184,7 @@ export const DefaultLociLabelProvider = PluginBehavior.create({
label.push(name)
}
label.push(lociLabel(loci))
- return label.join('</br>')
+ return label.filter(l => !!l).join('</br>')
},
group: (label: LociLabel) => label.toString().replace(/Model [0-9]+/g, 'Models'),
priority: 100
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
index 9b9bd36e33be45b4256b415f0d68d8b10a83e137..c4a44118c52c170a42ccfb5e7f4b7b2fa9c6bc2c 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
@@ -99,7 +99,7 @@ export const InitVolumeStreaming = StateAction.build({
entries
});
- await plugin.updateDataState(infoTree);
+ await infoTree.commit();
const info = infoTree.selector;
if (!info.isOk) return;
diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index 1fd0735ec242773a71ea7581e7a7e29e3e4c6375..0009f66874e40495ae93ab646f07c7b593c8fe6b 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -11,10 +11,9 @@ import { merge } from 'rxjs';
import { Canvas3D, DefaultCanvas3DParams } from '../mol-canvas3d/canvas3d';
import { CustomProperty } from '../mol-model-props/common/custom-property';
import { Model, Structure } from '../mol-model/structure';
-import { DataFormatRegistry } from '../mol-plugin-state/actions/data-format';
import { DataBuilder } from '../mol-plugin-state/builder/data';
import { StructureBuilder } from '../mol-plugin-state/builder/structure';
-import { TrajectoryFormatRegistry } from '../mol-plugin-state/formats/trajectory';
+import { DataFormatRegistry } from '../mol-plugin-state/formats/registry';
import { StructureSelectionQueryRegistry } from '../mol-plugin-state/helpers/structure-selection-query';
import { CameraManager } from '../mol-plugin-state/manager/camera';
import { InteractivityManager } from '../mol-plugin-state/manager/interactivity';
@@ -30,7 +29,7 @@ import { StateTransformParameters } from '../mol-plugin-ui/state/common';
import { Representation } from '../mol-repr/representation';
import { StructureRepresentationRegistry } from '../mol-repr/structure/registry';
import { VolumeRepresentationRegistry } from '../mol-repr/volume/registry';
-import { State, StateBuilder, StateTree, StateTransform } from '../mol-state';
+import { StateTransform } from '../mol-state';
import { Progress, Task } from '../mol-task';
import { ColorTheme } from '../mol-theme/color';
import { SizeTheme } from '../mol-theme/size';
@@ -45,7 +44,7 @@ import { BuiltInPluginBehaviors } from './behavior';
import { PluginBehavior } from './behavior/behavior';
import { PluginCommandManager } from './command';
import { PluginCommands } from './commands';
-import { PluginConfigManager, PluginConfig } from './config';
+import { PluginConfig, PluginConfigManager } from './config';
import { LeftPanelTabName, PluginLayout } from './layout';
import { PluginSpec } from './spec';
import { PluginState } from './state';
@@ -56,6 +55,8 @@ import { ViewportScreenshotHelper } from './util/viewport-screenshot';
import { PLUGIN_VERSION, PLUGIN_VERSION_DATE } from './version';
export class PluginContext {
+ runTask = <T>(task: Task<T>) => this.tasks.run(task);
+
private disposed = false;
private ev = RxEventHelper.create();
private tasks = new TaskManager();
@@ -127,17 +128,17 @@ export class PluginContext {
}
} as const;
- readonly dataFormat = {
- trajectory: TrajectoryFormatRegistry(),
- // TODO: separate registries for format catgories
- registry: new DataFormatRegistry()
- } as const
+ readonly dataFormats = new DataFormatRegistry();
readonly builders = {
data: new DataBuilder(this),
structure: void 0 as any as StructureBuilder
};
+ build() {
+ return this.state.data.build();
+ }
+
readonly managers = {
structure: {
hierarchy: new StructureHierarchyManager(this),
@@ -218,18 +219,10 @@ export class PluginContext {
this.behaviors.interaction.selectionMode.next(mode);
}
- runTask<T>(task: Task<T>) {
- return this.tasks.run(task);
- }
-
dataTransaction(f: () => Promise<void> | void, options?: { canUndo?: string | boolean }) {
return this.runTask(this.state.data.transaction(f, options));
}
- updateDataState(tree: StateTree | StateBuilder, options?: Partial<State.UpdateOptions>) {
- return this.runTask(this.state.data.updateTree(tree, options));
- }
-
requestTaskAbort(progress: Progress, reason?: string) {
this.tasks.requestAbort(progress, reason);
}
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index d756ca8844610b7bf3ffa067140a0aa6d1a3c681..9b0e4d9d4ac447b920f6a30cdad7da9fa56db2e2 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -39,6 +39,7 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Action(StateTransforms.Data.ParseDsn6),
PluginSpec.Action(StateTransforms.Model.TrajectoryFromMmCif),
+ PluginSpec.Action(StateTransforms.Model.TrajectoryFromCifCore),
PluginSpec.Action(StateTransforms.Model.TrajectoryFromPDB),
PluginSpec.Action(StateTransforms.Model.TransformStructureConformation),
PluginSpec.Action(StateTransforms.Model.StructureCoordinateSystem),
diff --git a/src/mol-plugin/state.ts b/src/mol-plugin/state.ts
index f88a067f668a31270ff944cabb6bafb3b79e8a5f..d9bc28c7511dd34d4966640412de0d102bf228c1 100644
--- a/src/mol-plugin/state.ts
+++ b/src/mol-plugin/state.ts
@@ -108,8 +108,8 @@ class PluginState {
constructor(private plugin: import('./context').PluginContext) {
this.snapshots = new PluginStateSnapshotManager(plugin);
- this.data = State.create(new SO.Root({ }), { globalContext: plugin });
- this.behaviors = State.create(new PluginBehavior.Root({ }), { globalContext: plugin, rootState: { isLocked: true } });
+ this.data = State.create(new SO.Root({ }), { runTask: plugin.runTask, globalContext: plugin });
+ this.behaviors = State.create(new PluginBehavior.Root({ }), { runTask: plugin.runTask, globalContext: plugin, rootState: { isLocked: true } });
this.animation = new PluginAnimationManager(plugin);
}
diff --git a/src/mol-repr/structure/representation/ellipsoid.ts b/src/mol-repr/structure/representation/ellipsoid.ts
index 2ef2eca8a4cc2c9c4de4f98f90a0ce20d36401b0..90af41838d2ef6d1be2f46e6bb7a33074bdc16d1 100644
--- a/src/mol-repr/structure/representation/ellipsoid.ts
+++ b/src/mol-repr/structure/representation/ellipsoid.ts
@@ -28,7 +28,7 @@ export const EllipsoidParams = {
unitKinds: getUnitKindsParam(['atomic']),
sizeFactor: PD.Numeric(1, { min: 0.01, max: 10, step: 0.01 }),
sizeAspectRatio: PD.Numeric(0.1, { min: 0.01, max: 3, step: 0.01 }),
- bondCap: PD.Boolean(true),
+ linkCap: PD.Boolean(true),
visuals: PD.MultiSelect(['ellipsoid-mesh', 'intra-bond', 'inter-bond'], PD.objectToOptions(EllipsoidVisuals)),
}
export type EllipsoidParams = typeof EllipsoidParams
@@ -50,5 +50,5 @@ export const EllipsoidRepresentationProvider = StructureRepresentationProvider({
defaultValues: PD.getDefaultValues(EllipsoidParams),
defaultColorTheme: { name: 'element-symbol' },
defaultSizeTheme: { name: 'uniform' },
- isApplicable: (structure: Structure) => structure.elementCount > 0 && structure.models.some(m => m.customProperties.has(AtomSiteAnisotrop.Descriptor))
+ isApplicable: (structure: Structure) => structure.elementCount > 0 && structure.models.some(m => AtomSiteAnisotrop.Provider.isApplicable(m))
})
\ No newline at end of file
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index dbd42f193e2027b5ebe389c7ca7272f0d3e6a90e..4cac2762a67249d07aabb2e29d9e8c0427605205 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -228,36 +228,46 @@ const symbols = [
})(ctx)),
// ============= GENERATORS ================
- D(MolScript.structureQuery.generator.atomGroups, function structureQuery_generator_atomGroups(ctx, xs) { return Queries.generators.atoms({
- entityTest: xs['entity-test'],
- chainTest: xs['chain-test'],
- residueTest: xs['residue-test'],
- atomTest: xs['atom-test'],
- groupBy: xs['group-by']
- })(ctx) }),
+ D(MolScript.structureQuery.generator.atomGroups, function structureQuery_generator_atomGroups(ctx, xs) {
+ return Queries.generators.atoms({
+ entityTest: xs['entity-test'],
+ chainTest: xs['chain-test'],
+ residueTest: xs['residue-test'],
+ atomTest: xs['atom-test'],
+ groupBy: xs['group-by']
+ })(ctx)
+ }),
D(MolScript.structureQuery.generator.all, function structureQuery_generator_all(ctx) { return Queries.generators.all(ctx) }),
D(MolScript.structureQuery.generator.empty, function structureQuery_generator_empty(ctx) { return Queries.generators.none(ctx) }),
- D(MolScript.structureQuery.generator.bondedAtomicPairs, function structureQuery_generator_bondedAtomicPairs(ctx, xs) { return Queries.generators.bondedAtomicPairs(xs && xs[0])(ctx) }),
- D(MolScript.structureQuery.generator.rings, function structureQuery_generator_rings(ctx, xs) { return Queries.generators.rings(xs?.['fingerprint']?.(ctx) as any, xs?.['only-aromatic']?.(ctx))(ctx) }),
+ D(MolScript.structureQuery.generator.bondedAtomicPairs, function structureQuery_generator_bondedAtomicPairs(ctx, xs) {
+ return Queries.generators.bondedAtomicPairs(xs && xs[0])(ctx)
+ }),
+ D(MolScript.structureQuery.generator.rings, function structureQuery_generator_rings(ctx, xs) {
+ return Queries.generators.rings(xs?.['fingerprint']?.(ctx) as any, xs?.['only-aromatic']?.(ctx))(ctx)
+ }),
// ============= MODIFIERS ================
- D(MolScript.structureQuery.modifier.includeSurroundings, function structureQuery_modifier_includeSurroundings(ctx, xs) { return Queries.modifiers.includeSurroundings(xs[0] as any, {
- radius: xs['radius'](ctx),
- wholeResidues: !!(xs['as-whole-residues'] && xs['as-whole-residues'](ctx)),
- elementRadius: xs['atom-radius']
- })(ctx) }),
+ D(MolScript.structureQuery.modifier.includeSurroundings, function structureQuery_modifier_includeSurroundings(ctx, xs) {
+ return Queries.modifiers.includeSurroundings(xs[0] as any, {
+ radius: xs['radius'](ctx),
+ wholeResidues: !!(xs['as-whole-residues'] && xs['as-whole-residues'](ctx)),
+ elementRadius: xs['atom-radius']
+ })(ctx)
+ }),
D(MolScript.structureQuery.modifier.wholeResidues, function structureQuery_modifier_wholeResidues(ctx, xs) { return Queries.modifiers.wholeResidues(xs[0] as any)(ctx) }),
D(MolScript.structureQuery.modifier.union, function structureQuery_modifier_union(ctx, xs) { return Queries.modifiers.union(xs[0] as any)(ctx) }),
D(MolScript.structureQuery.modifier.expandProperty, function structureQuery_modifier_expandProperty(ctx, xs) { return Queries.modifiers.expandProperty(xs[0] as any, xs['property'])(ctx) }),
D(MolScript.structureQuery.modifier.exceptBy, function structureQuery_modifier_exceptBy(ctx, xs) { return Queries.modifiers.exceptBy(xs[0] as any, xs['by'] as any)(ctx) }),
- D(MolScript.structureQuery.modifier.includeConnected, function structureQuery_modifier_includeConnected(ctx, xs) { return Queries.modifiers.includeConnected({
- query: xs[0] as any,
- bondTest: xs['bond-test'],
- wholeResidues: !!(xs['as-whole-residues'] && xs['as-whole-residues'](ctx)),
- layerCount: (xs['layer-count'] && xs['layer-count'](ctx)) || 1
- })(ctx) }),
+ D(MolScript.structureQuery.modifier.includeConnected, function structureQuery_modifier_includeConnected(ctx, xs) {
+ return Queries.modifiers.includeConnected({
+ query: xs[0] as any,
+ bondTest: xs['bond-test'],
+ wholeResidues: !!(xs['as-whole-residues'] && xs['as-whole-residues'](ctx)),
+ layerCount: (xs['layer-count'] && xs['layer-count'](ctx)) || 1
+ })(ctx)
+ }),
// ============= COMBINATORS ================
diff --git a/src/mol-state/action.ts b/src/mol-state/action.ts
index 07547cf5a3d7b91c34afd74b31a26f36c2b0bc44..bd1d25767421c5a47ec8d85bd59f9c2251b23d80 100644
--- a/src/mol-state/action.ts
+++ b/src/mol-state/action.ts
@@ -78,7 +78,7 @@ namespace StateAction {
: void 0,
run({ cell, state, params }) {
const tree = state.build().to(cell.transform.ref).apply(transformer, params);
- return state.updateTree(tree) as Task<void>;
+ return state.updateTree(tree) as unknown as Task<void>;
}
})
}
diff --git a/src/mol-state/state.ts b/src/mol-state/state.ts
index 4383be5045aed5093b9775dc80391210ccf26c56..b72476c25ec0ffdb1a37039f3bd409c790ee402d 100644
--- a/src/mol-state/state.ts
+++ b/src/mol-state/state.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { StateObject, StateObjectCell } from './object';
+import { StateObject, StateObjectCell, StateObjectSelector } from './object';
import { StateTree } from './tree';
import { StateTransform } from './transform';
import { StateTransformer } from './transformer';
@@ -58,6 +58,8 @@ class State {
readonly actions = new StateActionManager();
+ readonly runTask: <T>(task: Task<T>) => Promise<T>;
+
get tree(): StateTree { return this._tree; }
get transforms() { return (this._tree as StateTree).transforms; }
get current() { return this.behaviors.currentObject.value.ref; }
@@ -232,7 +234,7 @@ class State {
* @param tree Tree instance or a tree builder instance
* @param doNotReportTiming Indicates whether to log timing of the individual transforms
*/
- updateTree<T extends StateObject>(tree: StateBuilder.To<T, any>, options?: Partial<State.UpdateOptions>): Task<T>
+ updateTree<T extends StateObject>(tree: StateBuilder.To<T, any>, options?: Partial<State.UpdateOptions>): Task<StateObjectSelector<T>>
updateTree(tree: StateTree | StateBuilder, options?: Partial<State.UpdateOptions>): Task<void>
updateTree(tree: StateTree | StateBuilder, options?: Partial<State.UpdateOptions>): Task<any> {
const params: UpdateParams = { tree, options };
@@ -247,6 +249,11 @@ class State {
if (!this.inTransaction) this.behaviors.isUpdating.next(true);
try {
+ if (StateBuilder.is(tree)) {
+ if (tree.editInfo.applied) throw new Error('This builder has already been applied. Create a new builder for further state updates');
+ tree.editInfo.applied = true;
+ }
+
this.reverted = false;
const ret = options && (options.revertIfAborted || options.revertOnError)
? await this._revertibleTreeUpdate(taskCtx, params, options)
@@ -255,7 +262,9 @@ class State {
if (ret.ctx.hadError) this.inTransactionError = true;
- return ret.cell;
+ if (!ret.cell) return;
+
+ return new StateObjectSelector(ret.cell.transform.ref, this);
} finally {
this._inUpdate = false;
this.updateQueue.handled(params);
@@ -294,7 +303,7 @@ class State {
updated = await update(ctx);
if (StateBuilder.isTo(params.tree)) {
const cell = this.select(params.tree.ref)[0];
- return { ctx, cell: cell && cell.obj };
+ return { ctx, cell };
}
return { ctx };
} finally {
@@ -335,10 +344,11 @@ class State {
return ctx;
}
- constructor(rootObject: StateObject, params?: { globalContext?: unknown, rootState?: StateTransform.State, historyCapacity?: number }) {
+ constructor(rootObject: StateObject, params: State.Params) {
this._tree = StateTree.createEmpty(StateTransform.createRoot(params && params.rootState)).asTransient();
const tree = this._tree;
const root = tree.root;
+ this.runTask = params.runTask;
if (params?.historyCapacity !== void 0) this.historyCapacity = params.historyCapacity;
@@ -363,6 +373,17 @@ class State {
}
namespace State {
+ export interface Params {
+ runTask<T>(task: Task<T>): Promise<T>,
+ globalContext?: unknown,
+ rootState?: StateTransform.State,
+ historyCapacity?: number
+ }
+
+ export function create(rootObject: StateObject, params: Params) {
+ return new State(rootObject, params);
+ }
+
export type Cells = ReadonlyMap<StateTransform.Ref, StateObjectCell>
export type Tree = StateTree
@@ -390,10 +411,6 @@ namespace State {
revertOnError: boolean,
canUndo: boolean | string
}
-
- export function create(rootObject: StateObject, params?: { globalContext?: unknown, rootState?: StateTransform.State }) {
- return new State(rootObject, params);
- }
}
const StateUpdateDefaultOptions: State.UpdateOptions = {
@@ -885,12 +902,7 @@ function runTask<T>(t: T | Task<T>, ctx: RuntimeContext) {
return t as T;
}
-function createObject(ctx: UpdateContext, cell: StateObjectCell, transformer: StateTransformer, a: StateObject, params: any) {
- if (!cell.cache) cell.cache = Object.create(null);
- return runTask(transformer.definition.apply({ a, params, cache: cell.cache, spine: ctx.spine, dependencies: resolveDependencies(ctx, cell) }, ctx.parent.globalContext), ctx.taskCtx);
-}
-
-function resolveDependencies(ctx: UpdateContext, cell: StateObjectCell) {
+function resolveDependencies(cell: StateObjectCell) {
if (cell.dependencies.dependsOn.length === 0) return void 0;
const deps = Object.create(null);
@@ -905,10 +917,15 @@ function resolveDependencies(ctx: UpdateContext, cell: StateObjectCell) {
return deps;
}
+function createObject(ctx: UpdateContext, cell: StateObjectCell, transformer: StateTransformer, a: StateObject, params: any) {
+ if (!cell.cache) cell.cache = Object.create(null);
+ return runTask(transformer.definition.apply({ a, params, cache: cell.cache, spine: ctx.spine, dependencies: resolveDependencies(cell) }, ctx.parent.globalContext), ctx.taskCtx);
+}
+
async function updateObject(ctx: UpdateContext, cell: StateObjectCell, transformer: StateTransformer, a: StateObject, b: StateObject, oldParams: any, newParams: any) {
if (!transformer.definition.update) {
return StateTransformer.UpdateResult.Recreate;
}
if (!cell.cache) cell.cache = Object.create(null);
- return runTask(transformer.definition.update({ a, oldParams, b, newParams, cache: cell.cache, spine: ctx.spine, dependencies: resolveDependencies(ctx, cell) }, ctx.parent.globalContext), ctx.taskCtx);
+ return runTask(transformer.definition.update({ a, oldParams, b, newParams, cache: cell.cache, spine: ctx.spine, dependencies: resolveDependencies(cell) }, ctx.parent.globalContext), ctx.taskCtx);
}
\ No newline at end of file
diff --git a/src/mol-state/state/builder.ts b/src/mol-state/state/builder.ts
index 1d168ae15598642b1dee94ceea85c53805cb2f05..e249ee738ec42ddcebf871da6dccf74aca584f81 100644
--- a/src/mol-state/state/builder.ts
+++ b/src/mol-state/state/builder.ts
@@ -21,6 +21,7 @@ interface StateBuilder {
namespace StateBuilder {
export interface EditInfo {
+ applied: boolean,
sourceTree: StateTree,
count: number,
lastUpdate?: StateTransform.Ref
@@ -102,7 +103,13 @@ namespace StateBuilder {
return this;
}
getTree(): StateTree { return buildTree(this.state); }
- constructor(tree: StateTree, state?: State) { this.state = { state, tree: tree.asTransient(), actions: [], editInfo: { sourceTree: tree, count: 0, lastUpdate: void 0 } } }
+
+ commit(options?: Partial<State.UpdateOptions>) {
+ if (!this.state.state) throw new Error('Cannot commit template tree');
+ return this.state.state.runTask(this.state.state.updateTree(this, options));
+ }
+
+ constructor(tree: StateTree, state?: State) { this.state = { state, tree: tree.asTransient(), actions: [], editInfo: { applied: false, sourceTree: tree, count: 0, lastUpdate: void 0 } } }
}
export class To<A extends StateObject, T extends StateTransformer = StateTransformer> implements StateBuilder {
@@ -252,6 +259,12 @@ namespace StateBuilder {
getTree(): StateTree { return buildTree(this.state); }
+ /** Returns selector to this node. */
+ commit(options?: Partial<State.UpdateOptions>): Promise<StateObjectSelector<A>> {
+ if (!this.state.state) throw new Error('Cannot commit template tree');
+ return this.state.state.runTask(this.state.state.updateTree(this, options));
+ }
+
constructor(private state: BuildState, ref: StateTransform.Ref, private root: Root) {
this.ref = ref;
if (!this.state.tree.transforms.has(ref)) {
diff --git a/src/mol-theme/label.ts b/src/mol-theme/label.ts
index e6f8276b00a6d64962cf97fadbea43d2ca686ff3..7152d13ea8dddd87bae874482aea6e02f1ebd9b7 100644
--- a/src/mol-theme/label.ts
+++ b/src/mol-theme/label.ts
@@ -28,7 +28,7 @@ export type LabelOptions = typeof DefaultLabelOptions
export function lociLabel(loci: Loci, options: Partial<LabelOptions> = {}): string {
switch (loci.kind) {
case 'structure-loci':
- return loci.structure.models.map(m => m.entry).join(', ')
+ return loci.structure.models.map(m => m.entry).filter(l => !!l).join(', ')
case 'element-loci':
return structureElementStatsLabel(StructureElement.Stats.ofLoci(loci), options)
case 'bond-loci':
@@ -148,7 +148,7 @@ export function _bundleLabel(bundle: Loci.Bundle<any>, options: LabelOptions) {
const labels = locations.map(l => _elementLabel(l, granularity, hidePrefix, reverse || condensed))
if (condensed) {
- return labels.map(l => l[0].replace(/\[.*\]/g, '').trim()).join(' \u2014 ')
+ return labels.map(l => l[0].replace(/\[.*\]/g, '').trim()).filter(l => !!l).join(' \u2014 ')
}
let offset = 0
@@ -167,22 +167,22 @@ export function _bundleLabel(bundle: Loci.Bundle<any>, options: LabelOptions) {
if (offset > 0) {
const offsetLabels = [labels[0].join(' | ')]
for (let j = 1, jl = labels.length; j < jl; ++j) {
- offsetLabels.push(labels[j].slice(offset).join(' | '))
+ offsetLabels.push(labels[j].slice(offset).filter(l => !!l).join(' | '))
}
return offsetLabels.join(' \u2014 ')
} else {
- return labels.map(l => l.join(' | ')).join('</br>')
+ return labels.map(l => l.filter(l => !!l).join(' | ')).filter(l => !!l).join('</br>')
}
} else {
const labels = bundle.loci.map(l => lociLabel(l, options))
- return labels.join(condensed ? ' \u2014 ' : '</br>')
+ return labels.filter(l => !!l).join(condensed ? ' \u2014 ' : '</br>')
}
}
export function elementLabel(location: StructureElement.Location, options: Partial<LabelOptions> = {}): string {
const o = { ...DefaultLabelOptions, ...options }
const _label = _elementLabel(location, o.granularity, o.hidePrefix, o.reverse || o.condensed)
- const label = o.condensed ? _label[0].replace(/\[.*\]/g, '').trim() : _label.join(' | ')
+ const label = o.condensed ? _label[0].replace(/\[.*\]/g, '').trim() : _label.filter(l => !!l).join(' | ')
return o.htmlStyling ? label : stripTags(label)
}
diff --git a/src/mol-util/make-dir.ts b/src/mol-util/make-dir.ts
index 051203d65191bfae0cd8c89b45409991b24119b7..a8f4ed6fb2c50a94e331f88583f71181a60f67bb 100644
--- a/src/mol-util/make-dir.ts
+++ b/src/mol-util/make-dir.ts
@@ -12,8 +12,9 @@ export function makeDir(path: string, root?: string): boolean {
root = (root || '') + dir + '/';
- try { fs.mkdirSync(root); }
- catch (e) {
+ try {
+ fs.mkdirSync(root);
+ } catch (e) {
if (!fs.statSync(root).isDirectory()) throw new Error(e);
}
diff --git a/src/mol-util/param-definition.ts b/src/mol-util/param-definition.ts
index b008677758a4837244ee0749b0b498cd2566266b..c98526d2f0535ea664f952aef4c60331c16ed392 100644
--- a/src/mol-util/param-definition.ts
+++ b/src/mol-util/param-definition.ts
@@ -147,22 +147,22 @@ export namespace ParamDefinition {
return setInfo<Mat4>({ type: 'mat4', defaultValue }, info)
}
- export interface FileParam extends Base<File> {
+ export interface FileParam extends Base<File | null> {
type: 'file'
accept?: string
}
export function File(info?: Info & { accept?: string, multiple?: boolean }): FileParam {
- const ret = setInfo<FileParam>({ type: 'file', defaultValue: void 0 as any }, info);
+ const ret = setInfo<FileParam>({ type: 'file', defaultValue: null }, info);
if (info?.accept) ret.accept = info.accept;
return ret;
}
- export interface FileListParam extends Base<FileList> {
+ export interface FileListParam extends Base<FileList | null> {
type: 'file-list'
accept?: string
}
export function FileList(info?: Info & { accept?: string, multiple?: boolean }): FileListParam {
- const ret = setInfo<FileListParam>({ type: 'file-list', defaultValue: void 0 as any }, info);
+ const ret = setInfo<FileListParam>({ type: 'file-list', defaultValue: null }, info);
if (info?.accept) ret.accept = info.accept;
return ret;
}
diff --git a/src/mol-util/param-mapping.ts b/src/mol-util/param-mapping.ts
index 14f985e7931f1624ebd0921359b136883337bcbf..861bb64c30795f7cd611a29d80c6da912ff4a43f 100644
--- a/src/mol-util/param-mapping.ts
+++ b/src/mol-util/param-mapping.ts
@@ -23,8 +23,7 @@ export function ParamMapping<S, T, Ctx>(def: {
values(t: T, ctx: Ctx): S,
update(s: S, t: Mutable<T>, ctx: Ctx): void,
apply?(t: T, ctx: Ctx): void | Promise<void>
- }) => ParamMapping<S, T, Ctx>
-{
+ }) => ParamMapping<S, T, Ctx> {
return ({ values, update, apply }) => ({
params: typeof def.params === 'function' ? def.params as any : ctx => def.params,
getTarget: def.target,
diff --git a/src/mol-util/zip/bin.ts b/src/mol-util/zip/bin.ts
index c3a41a16939fa40855fbec64b75657378a99c61f..6edbdc1c67d9831ce0a8d2db2b491c4fa1654fb6 100644
--- a/src/mol-util/zip/bin.ts
+++ b/src/mol-util/zip/bin.ts
@@ -91,11 +91,17 @@ export function sizeUTF8(str: string) {
let i = 0;
for(let ci = 0; ci < strl; ci++) {
const code = str.charCodeAt(ci);
- if ((code&(0xffffffff-(1<< 7)+1)) === 0) { i++ ; }
- else if((code&(0xffffffff-(1<<11)+1)) === 0) { i+=2; }
- else if((code&(0xffffffff-(1<<16)+1)) === 0) { i+=3; }
- else if((code&(0xffffffff-(1<<21)+1)) === 0) { i+=4; }
- else throw 'e';
+ if ((code&(0xffffffff-(1<< 7)+1)) === 0) {
+ i++ ;
+ } else if((code&(0xffffffff-(1<<11)+1)) === 0) {
+ i+=2;
+ } else if((code&(0xffffffff-(1<<16)+1)) === 0) {
+ i+=3;
+ } else if((code&(0xffffffff-(1<<21)+1)) === 0) {
+ i+=4;
+ } else {
+ throw 'e';
+ }
}
return i;
}
diff --git a/src/mol-util/zip/deflate.ts b/src/mol-util/zip/deflate.ts
index 464805474b8c7a6d1539fdb44e2e857576e83b43..25cec469ff31594089636c6020d0137e73425538 100644
--- a/src/mol-util/zip/deflate.ts
+++ b/src/mol-util/zip/deflate.ts
@@ -96,8 +96,9 @@ export function _deflateRaw(data: Uint8Array, out: Uint8Array, opos: number, lvl
const dgi = _goodIndex(dst, U.df0); U.dhst[ dgi]++; ebits += U.exb[lgi] + U.dxb[dgi];
lits[li] = (len<<23)|(i-cvrd); lits[li+1] = (dst<<16)|(lgi<<8)|dgi; li+=2;
cvrd = i + len;
+ } else {
+ U.lhst[data[i]]++;
}
- else { U.lhst[data[i]]++; }
lc++;
}
}
@@ -302,8 +303,9 @@ function _lenCodes(tree: number[], set: number[]) {
const zc = Math.min((lz+1-i)>>>1, 6);
set.push(16, zc-3);
i += zc*2-2;
+ } else {
+ set.push(l, 0);
}
- else set.push(l, 0);
}
return len>>>1;
}
diff --git a/src/mol-util/zip/zip.ts b/src/mol-util/zip/zip.ts
index 8d43d47719feab6fe21ab4bd50a7440f279225c0..081451dd0216d0a0402cb850997a3af241d20a27 100644
--- a/src/mol-util/zip/zip.ts
+++ b/src/mol-util/zip/zip.ts
@@ -105,8 +105,9 @@ async function _readLocal(runtime: RuntimeContext, data: Uint8Array, o: number,
const buf = new Uint8Array(usize);
await inflateRaw(runtime, file, buf);
out[name] = buf;
+ } else {
+ throw `unknown compression method: ${cmpr}`;
}
- else throw `unknown compression method: ${cmpr}`;
}
export async function inflateRaw(runtime: RuntimeContext, file: Uint8Array, buf?: Uint8Array) {
diff --git a/src/servers/volume/common/file.ts b/src/servers/volume/common/file.ts
index 753512601af44476e82b6833e19752416dd97aac..d522224b160e3394acf7f312dd9a0239002089c9 100644
--- a/src/servers/volume/common/file.ts
+++ b/src/servers/volume/common/file.ts
@@ -34,8 +34,9 @@ function makeDir(path: string, root?: string): boolean {
root = (root || '') + dir + '/';
- try { fs.mkdirSync(root); }
- catch (e) {
+ try {
+ fs.mkdirSync(root);
+ } catch (e) {
if (!fs.statSync(root).isDirectory()) throw new Error(e);
}
diff --git a/src/servers/volume/server/local-api.ts b/src/servers/volume/server/local-api.ts
index de87df318ec3e7cf457a92aa932598e2bd7b666b..930aa0c33a3d2b532d770267fe7770aa0151a215 100644
--- a/src/servers/volume/server/local-api.ts
+++ b/src/servers/volume/server/local-api.ts
@@ -104,8 +104,9 @@ function makeDir(path: string, root?: string): boolean {
root = (root || '') + dir + '/';
- try { fs.mkdirSync(root); }
- catch (e) {
+ try {
+ fs.mkdirSync(root);
+ } catch (e) {
if (!fs.statSync(root).isDirectory()) throw new Error(e);
}