diff --git a/src/mol-model/structure/export/categories/atom_site.ts b/src/mol-model/structure/export/categories/atom_site.ts
index 661e00dbd300a3501f240061c6ebae620e6f6175..271f9f287c46a7573bdf2f9cae0b758df1e92077 100644
--- a/src/mol-model/structure/export/categories/atom_site.ts
+++ b/src/mol-model/structure/export/categories/atom_site.ts
@@ -59,4 +59,26 @@ export const _atom_site: CifCategory<CifExportContext> = {
keys: () => structure.elementLocations()
};
}
+}
+
+export function residueIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement): CifField<K, D>[] {
+ return [
+ CifField.str('label_comp_id', (k, d) => P.residue.label_comp_id(getLocation(k, d))),
+ CifField.int('label_seq_id', (k, d) => P.residue.label_seq_id(getLocation(k, d)), {
+ encoder: E.deltaRLE,
+ valueKind: (k, d) => {
+ const e = getLocation(k, d);
+ const m = e.unit.model;
+ return m.atomicHierarchy.residues.label_seq_id.valueKind(m.atomicHierarchy.residueAtomSegments.index[e.element]);
+ }
+ }),
+ CifField.str('pdbx_PDB_ins_code', (k, d) => P.residue.pdbx_PDB_ins_code(getLocation(k, d))),
+
+ CifField.str('label_asym_id', (k, d) => P.chain.label_asym_id(getLocation(k, d))),
+ CifField.str('label_entity_id', (k, d) => P.chain.label_entity_id(getLocation(k, d))),
+
+ CifField.str('auth_comp_id', (k, d) => P.residue.auth_comp_id(getLocation(k, d))),
+ CifField.int('auth_seq_id', (k, d) => P.residue.auth_seq_id(getLocation(k, d)), { encoder: E.deltaRLE }),
+ CifField.str('auth_asym_id', (k, d) => P.chain.auth_asym_id(getLocation(k, d))),
+ ]
}
\ No newline at end of file
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index f8c9d7dcb661acc99d891efe430faeddf59c8b48..e0a071af7fd5ee59cf9093910c5513cdf909f1e6 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -98,8 +98,10 @@ export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structure: S
encoder.writeCategory(cat, ctx);
}
for (const customProp of model.customProperties.all) {
+ const prefix = customProp.cifExport.prefix;
const cats = customProp.cifExport.categories;
for (const cat of cats) {
+ if (cat.name.indexOf(prefix) !== 0) throw new Error(`Custom category '${cat.name}' name must start with prefix '${prefix}.'`);
encoder.writeCategory(cat, ctx);
}
}
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts b/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
index 2785d960372256cf9352a9946d4e3228ec87012b..4b7491f960e8341b148b5bbd256bc74086c41e31 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
@@ -22,6 +22,7 @@ export namespace ComponentBond {
isStatic: true,
name: 'chem_comp_bond',
cifExport: {
+ prefix: '',
categories: [{
name: 'chem_comp_bond',
instance(ctx) {
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts b/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
index 933705171012573a68167af9657cfa80e7460fd1..371ac04a16b8410f2b256703813aa044e9a4d0a8 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
@@ -27,6 +27,7 @@ export namespace StructConn {
isStatic: true,
name: 'struct_conn',
cifExport: {
+ prefix: '',
categories: [{
name: 'struct_conn',
instance(ctx) {
diff --git a/src/mol-model/structure/model/properties/custom/descriptor.ts b/src/mol-model/structure/model/properties/custom/descriptor.ts
index fd60c265dc356c5f86a44dbf370aa915794b5633..d83a32cca4e9278304637a41f7ab9f3247ffc004 100644
--- a/src/mol-model/structure/model/properties/custom/descriptor.ts
+++ b/src/mol-model/structure/model/properties/custom/descriptor.ts
@@ -13,6 +13,8 @@ interface ModelPropertyDescriptor<Symbols extends { [name: string]: QuerySymbolR
readonly name: string,
cifExport: {
+ // Prefix enforced during export.
+ prefix: string,
categories: CifWriter.Category<CifExportContext>[]
},
diff --git a/src/perf-tests/mol-script.ts b/src/perf-tests/mol-script.ts
index 0329847e96a45993edd765f51830b29dedba7cae..f05a1d8f26b6bf547b502804da0e9321700e7c6d 100644
--- a/src/perf-tests/mol-script.ts
+++ b/src/perf-tests/mol-script.ts
@@ -46,7 +46,7 @@ console.log(result);
const CustomProp = ModelPropertyDescriptor({
name: 'test_prop',
isStatic: true,
- cifExport: { categories: [ ]},
+ cifExport: { prefix: '', categories: [ ]},
symbols: {
residueIndex: QuerySymbolRuntime.Dynamic(CustomPropSymbol('custom.test-prop', 'residue-index', Type.Num), ctx => {
const e = ctx.element;
diff --git a/src/servers/model/properties.ts b/src/servers/model/properties.ts
index eafa41955940a0efc940e872b67bf8ab2fb1ac58..093b01d89afa7f14e410f3c1a97d4c840e5fbc91 100644
--- a/src/servers/model/properties.ts
+++ b/src/servers/model/properties.ts
@@ -7,13 +7,14 @@
import { Model } from 'mol-model/structure';
import { StructureQualityReport } from './properties/structure-quality-report';
-import { SymmetryAnnotation } from './properties/rcsb/symmetry';
+// import { SymmetryAnnotation } from './properties/rcsb/symmetry';
export function attachModelProperties(model: Model): Promise<any>[] {
// return a list of promises that start attaching the props in parallel
// (if there are downloads etc.)
return [
StructureQualityReport.attachFromPDBeApi(model),
- SymmetryAnnotation.attachFromRCSB(model)
+ // removed for now because of schema validation error
+ // SymmetryAnnotation.attachFromRCSB(model)
];
}
\ No newline at end of file
diff --git a/src/servers/model/properties/rcsb/symmetry.ts b/src/servers/model/properties/rcsb/symmetry.ts
index e34934c8d5e374ea45c1dfc8ed26ca8e75f872b1..c58f09ca9cc005b83642b3028d9336ddce7c57ff 100644
--- a/src/servers/model/properties/rcsb/symmetry.ts
+++ b/src/servers/model/properties/rcsb/symmetry.ts
@@ -32,9 +32,9 @@ function getCategory(name: keyof SymmetryAnnotation.Schema) {
function createDatabase(assemblies: ReadonlyArray<RcsbSymmetry.Assemblies>): SymmetryAnnotation.Database {
const Schema = SymmetryAnnotation.Schema
- const featureRows: Table.Row<typeof Schema.symmetry_annotation_feature>[] = []
- const clusterRows: Table.Row<typeof Schema.symmetry_annotation_cluster>[] = []
- const axisRows: Table.Row<typeof Schema.symmetry_annotation_axis>[] = []
+ const featureRows: Table.Row<typeof Schema.rcsb_symmetry_annotation_feature>[] = []
+ const clusterRows: Table.Row<typeof Schema.rcsb_symmetry_annotation_cluster>[] = []
+ const axisRows: Table.Row<typeof Schema.rcsb_symmetry_annotation_axis>[] = []
let id = 0
for (let i = 0, il = assemblies.length; i < il; ++i) {
@@ -83,9 +83,9 @@ function createDatabase(assemblies: ReadonlyArray<RcsbSymmetry.Assemblies>): Sym
}
return _Database.ofTables('symmetry_annotation', Schema, {
- symmetry_annotation_feature: Table.ofRows(Schema.symmetry_annotation_feature, featureRows),
- symmetry_annotation_cluster: Table.ofRows(Schema.symmetry_annotation_cluster, clusterRows),
- symmetry_annotation_axis: Table.ofRows(Schema.symmetry_annotation_axis, axisRows)
+ symmetry_annotation_feature: Table.ofRows(Schema.rcsb_symmetry_annotation_feature, featureRows),
+ symmetry_annotation_cluster: Table.ofRows(Schema.rcsb_symmetry_annotation_cluster, clusterRows),
+ symmetry_annotation_axis: Table.ofRows(Schema.rcsb_symmetry_annotation_axis, axisRows)
})
}
@@ -93,10 +93,11 @@ const _Descriptor: ModelPropertyDescriptor = {
isStatic: true,
name: 'symmetry_annotation',
cifExport: {
+ prefix: 'rcsb',
categories: [
- getCategory('symmetry_annotation_feature'),
- getCategory('symmetry_annotation_cluster'),
- getCategory('symmetry_annotation_axis')
+ getCategory('rcsb_symmetry_annotation_feature'),
+ getCategory('rcsb_symmetry_annotation_cluster'),
+ getCategory('rcsb_symmetry_annotation_axis')
]
}
}
@@ -105,7 +106,7 @@ const client = new GraphQLClient('http://rest-experimental.rcsb.org/graphql')
export namespace SymmetryAnnotation {
export const Schema = {
- symmetry_annotation_feature: {
+ rcsb_symmetry_annotation_feature: {
id: int,
assembly_id: str,
source: str,
@@ -113,12 +114,12 @@ export namespace SymmetryAnnotation {
stoichiometry_value: List(',', x => x),
stoichiometry_description: str
},
- symmetry_annotation_cluster: {
+ rcsb_symmetry_annotation_cluster: {
feature_id: int,
avg_rmsd: float,
members: List(',', x => x)
},
- symmetry_annotation_axis: {
+ rcsb_symmetry_annotation_axis: {
feature_id: int,
order: int,
start: Vector(3),
diff --git a/src/servers/model/properties/structure-quality-report.ts b/src/servers/model/properties/structure-quality-report.ts
index 0b75f6d7d7b86d0ed293f918a1635ffc233d4962..b65a1d959befcda3a52354f0b6fe9162e251163d 100644
--- a/src/servers/model/properties/structure-quality-report.ts
+++ b/src/servers/model/properties/structure-quality-report.ts
@@ -4,11 +4,12 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { ResidueIndex, ModelPropertyDescriptor, Model, Structure, Unit, StructureElement, StructureProperties as P } from 'mol-model/structure';
+import { ResidueIndex, ModelPropertyDescriptor, Model, Structure, Unit, StructureElement } from 'mol-model/structure';
import fetch from 'node-fetch';
import { CifWriter } from 'mol-io/writer/cif';
import CifField = CifWriter.Field;
import { Segmentation } from 'mol-data/int';
+import { residueIdFields } from 'mol-model/structure/export/categories/atom_site';
type IssueMap = Map<ResidueIndex, string[]>
@@ -16,8 +17,9 @@ const _Descriptor: ModelPropertyDescriptor = {
isStatic: true,
name: 'structure_quality_report',
cifExport: {
+ prefix: 'pdbe',
categories: [{
- name: 'structure_quality_report',
+ name: 'pdbe_structure_quality_report',
instance(ctx) {
const issues = StructureQualityReport.get(ctx.model);
if (!issues) return CifWriter.Category.Empty;
@@ -36,16 +38,8 @@ const _Descriptor: ModelPropertyDescriptor = {
type ExportCtx = { model: Model, residueIndex: ArrayLike<ResidueIndex>, residues: StructureElement[], issues: IssueMap };
const _structure_quality_report_fields: CifField<ResidueIndex, ExportCtx>[] = [
- CifField.str<ResidueIndex, ExportCtx>('label_comp_id', (i, d) => P.residue.label_comp_id(d.residues[i])),
- CifField.int<ResidueIndex, ExportCtx>('label_seq_id', (i, d) => P.residue.label_seq_id(d.residues[i])),
- CifField.str<ResidueIndex, ExportCtx>('pdbx_PDB_ins_code', (i, d) => P.residue.pdbx_PDB_ins_code(d.residues[i])),
- CifField.str<ResidueIndex, ExportCtx>('label_asym_id', (i, d) => P.chain.label_asym_id(d.residues[i])),
- CifField.str<ResidueIndex, ExportCtx>('label_entity_id', (i, d) => P.entity.id(d.residues[i])),
-
- CifField.str<ResidueIndex, ExportCtx>('auth_comp_id', (i, d) => P.residue.auth_comp_id(d.residues[i])),
- CifField.int<ResidueIndex, ExportCtx>('auth_seq_id', (i, d) => P.residue.auth_seq_id(d.residues[i])),
- CifField.str<ResidueIndex, ExportCtx>('auth_asym_id', (i, d) => P.chain.auth_asym_id(d.residues[i])),
-
+ CifField.index('id'),
+ ...residueIdFields<ResidueIndex, ExportCtx>((k, d) => d.residues[k]),
CifField.str<ResidueIndex, ExportCtx>('issues', (i, d) => d.issues.get(d.residueIndex[d.residues[i].element])!.join(','))
];