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Commit e2a7ca6d authored by David Sehnal's avatar David Sehnal
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wip refactoring custom props

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src/mol-model-props/pdbe/structure-quality-report.ts
+ 108
− 13
View file @ e2a7ca6d
...@@ -36,10 +36,50 @@ export namespace StructureQualityReport { ...@@ -36,10 +36,50 @@ export namespace StructureQualityReport {
{ {
name: 'pdbe_structure_quality_report_issues', name: 'pdbe_structure_quality_report_issues',
instance(ctx) { instance(ctx) {
const prop = get(ctx.firstModel);
if (!prop) return CifWriter.Category.Empty;
let groupCtx: ReportExportContext;
if (ctx.cache.pdbe_structure_quality_report_issues) groupCtx = ctx.cache.pdbe_structure_quality_report_issues;
else {
const exportCtx = prop.data!.getExportContext(ctx.structures[0]);
groupCtx = createExportContext(exportCtx);
ctx.cache.pdbe_structure_quality_report_issues = groupCtx;
}
return { return {
fields: _structure_quality_report_issues_fields, fields: _structure_quality_report_issues_fields,
source: ctx.structures.map(s => IndexedCustomProperty.getCifDataSource(s, StructureQualityReport.getIssueMap(s.model), ctx.cache)) source: [{ data: groupCtx, rowCount: groupCtx.elements.length }]
}; }
// return {
// fields: _structure_quality_report_issues_fields,
// source: ctx.structures.map(s => IndexedCustomProperty.getCifDataSource(s, StructureQualityReport.getIssueMap(s.model), ctx.cache))
// };
}
}, {
name: 'pdbe_structure_quality_report_issue_types',
instance(ctx) {
const prop = get(ctx.firstModel);
if (!prop) return CifWriter.Category.Empty;
let groupCtx: ReportExportContext;
if (ctx.cache.pdbe_structure_quality_report_issues) groupCtx = ctx.cache.pdbe_structure_quality_report_issues;
else {
const exportCtx = prop.data!.getExportContext(ctx.structures[0]);
groupCtx = createExportContext(exportCtx);
ctx.cache.pdbe_structure_quality_report_issues = groupCtx;
}
return {
fields: _structure_quality_report_issue_types_fields,
source: [{ data: groupCtx, rowCount: groupCtx.rows.length }]
}
// return {
// fields: _structure_quality_report_issues_fields,
// source: ctx.structures.map(s => IndexedCustomProperty.getCifDataSource(s, StructureQualityReport.getIssueMap(s.model), ctx.cache))
// };
} }
}] }]
}, },
...@@ -58,13 +98,20 @@ export namespace StructureQualityReport { ...@@ -58,13 +98,20 @@ export namespace StructureQualityReport {
id: Column.Schema.int, id: Column.Schema.int,
...mmCIF_residueId_schema, ...mmCIF_residueId_schema,
pdbx_PDB_model_num: Column.Schema.int, pdbx_PDB_model_num: Column.Schema.int,
issues: Column.Schema.List(',', x => x) issue_group_id: Column.Schema.int
},
pdbe_structure_quality_report_issue_types: {
group_id: Column.Schema.int,
issue_type: Column.Schema.str
} }
} }
function getCifData(model: Model) { function getCifData(model: Model) {
if (model.sourceData.kind !== 'mmCIF') throw new Error('Data format must be mmCIF.'); if (model.sourceData.kind !== 'mmCIF') throw new Error('Data format must be mmCIF.');
return toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.frame.categories.pdbe_structure_quality_report_issues); return {
residues: toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.frame.categories.pdbe_structure_quality_report_issues),
groups: toTable(Schema.pdbe_structure_quality_report_issue_types, model.sourceData.frame.categories.pdbe_structure_quality_report_issue_types),
}
} }
export async function attachFromCifOrApi(model: Model, params: { export async function attachFromCifOrApi(model: Model, params: {
...@@ -77,7 +124,7 @@ export namespace StructureQualityReport { ...@@ -77,7 +124,7 @@ export namespace StructureQualityReport {
let info = PropertyWrapper.tryGetInfoFromCif('pdbe_structure_quality_report', model); let info = PropertyWrapper.tryGetInfoFromCif('pdbe_structure_quality_report', model);
if (info) { if (info) {
const data = getCifData(model); const data = getCifData(model);
issueMap = createIssueMapFromCif(model, data); issueMap = createIssueMapFromCif(model, data.residues, data.groups);
} else if (params.PDBe_apiSourceJson) { } else if (params.PDBe_apiSourceJson) {
const data = await params.PDBe_apiSourceJson(model); const data = await params.PDBe_apiSourceJson(model);
if (!data) return false; if (!data) return false;
...@@ -112,12 +159,39 @@ export namespace StructureQualityReport { ...@@ -112,12 +159,39 @@ export namespace StructureQualityReport {
} }
type ExportCtx = IndexedCustomProperty.ExportCtx<string[]> type ExportCtx = IndexedCustomProperty.ExportCtx<string[]>
const _structure_quality_report_issues_fields: CifField<number, ExportCtx>[] = CifWriter.fields() const _structure_quality_report_issues_fields: CifField<number, ReportExportContext>[] = CifWriter.fields<number, ReportExportContext>()
.index('id') .index('id')
.many(residueIdFields((i, d) => d.elements[i])) .many(residueIdFields((i, d) => d.elements[i], { includeModelNum: true }))
.int('pdbx_PDB_model_num', (i, d) => P.unit.model_num(d.elements[i])) .int('group_id', (i, d) => d.groupId[i])
.str('issues', (i, d) => d.property(i).join(',')) .getFields();
.getFields()
interface ReportExportContext extends ExportCtx {
groupId: number[],
rows: [number, string][]
}
const _structure_quality_report_issue_types_fields: CifField<number, ReportExportContext>[] = CifWriter.fields<number, ReportExportContext>()
.int('group_id', (i, d) => d.rows[i][0])
.str('issue_type', (i, d) => d.rows[i][1])
.getFields();
function createExportContext(ctx: ExportCtx): ReportExportContext {
const groupMap = new Map<string, number>();
const groupId: number[] = [];
const rows: ReportExportContext['rows'] = [];
for (let i = 0; i < ctx.elements.length; i++) {
const issues = ctx.property(i);
const key = issues.join(',');
if (!groupMap.has(key)) {
const idx = groupMap.size + 1;
groupMap.set(key, idx);
for (const issue of issues) {
rows.push([idx, issue]);
}
}
groupId[i] = groupMap.get(key)!;
}
return { ...ctx, groupId, rows };
}
function createIssueMapFromJson(modelData: Model, data: any): StructureQualityReport.IssueMap | undefined { function createIssueMapFromJson(modelData: Model, data: any): StructureQualityReport.IssueMap | undefined {
const ret = new Map<ResidueIndex, string[]>(); const ret = new Map<ResidueIndex, string[]>();
...@@ -143,15 +217,36 @@ function createIssueMapFromJson(modelData: Model, data: any): StructureQualityRe ...@@ -143,15 +217,36 @@ function createIssueMapFromJson(modelData: Model, data: any): StructureQualityRe
return IndexedCustomProperty.fromResidueMap(ret); return IndexedCustomProperty.fromResidueMap(ret);
} }
function createIssueMapFromCif(modelData: Model, data: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issues>): StructureQualityReport.IssueMap | undefined { function createIssueMapFromCif(modelData: Model,
residueData: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issues>,
groupData: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issue_types>): StructureQualityReport.IssueMap | undefined {
const ret = new Map<ResidueIndex, string[]>(); const ret = new Map<ResidueIndex, string[]>();
const { label_entity_id, label_asym_id, auth_seq_id, pdbx_PDB_ins_code, issues, pdbx_PDB_model_num, _rowCount } = data; const { label_entity_id, label_asym_id, auth_seq_id, pdbx_PDB_ins_code, issue_group_id, pdbx_PDB_model_num, _rowCount } = residueData;
const groups = parseIssueTypes(groupData);
for (let i = 0; i < _rowCount; i++) { for (let i = 0; i < _rowCount; i++) {
if (pdbx_PDB_model_num.value(i) !== modelData.modelNum) continue; if (pdbx_PDB_model_num.value(i) !== modelData.modelNum) continue;
const idx = modelData.atomicHierarchy.index.findResidue(label_entity_id.value(i), label_asym_id.value(i), auth_seq_id.value(i), pdbx_PDB_ins_code.value(i)); const idx = modelData.atomicHierarchy.index.findResidue(label_entity_id.value(i), label_asym_id.value(i), auth_seq_id.value(i), pdbx_PDB_ins_code.value(i));
ret.set(idx, issues.value(i)); ret.set(idx, groups.get(issue_group_id.value(i))!);
} }
return IndexedCustomProperty.fromResidueMap(ret); return IndexedCustomProperty.fromResidueMap(ret);
}
function parseIssueTypes(groupData: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issue_types>): Map<number, string[]> {
const ret = new Map<number, string[]>();
const { group_id, issue_type } = groupData;
for (let i = 0; i < groupData._rowCount; i++) {
let group: string[];
const id = group_id.value(i);
if (ret.has(id)) group = ret.get(id)!;
else {
group = [];
ret.set(id, group);
}
group.push(issue_type.value(i));
}
return ret;
} }
\ No newline at end of file
src/mol-model/structure/export/categories/atom_site.ts
+ 34
− 14
View file @ e2a7ca6d
...@@ -74,9 +74,21 @@ function mappedProp<K, D>(loc: (key: K, data: D) => StructureElement, prop: (e: ...@@ -74,9 +74,21 @@ function mappedProp<K, D>(loc: (key: K, data: D) => StructureElement, prop: (e:
return (k: K, d: D) => prop(loc(k, d)); return (k: K, d: D) => prop(loc(k, d));
} }
export function residueIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement, options?: { prefix?: string, postfix?: string }): CifField<K, D>[] { function addModelNum<K, D>(fields: CifWriter.Field.Builder<K, D>, getLocation: (key: K, data: D) => StructureElement, options?: IdFieldsOptions) {
if (options && options.includeModelNum) {
fields.int('pdbx_PDB_model_num', mappedProp(getLocation, P.unit.model_num));
}
}
export interface IdFieldsOptions {
prefix?: string,
postfix?: string,
includeModelNum?: boolean
}
export function residueIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement, options?: IdFieldsOptions): CifField<K, D>[] {
const prefix = options && options.prefix, postfix = options && options.postfix; const prefix = options && options.prefix, postfix = options && options.postfix;
return CifWriter.fields<K, D>() const ret = CifWriter.fields<K, D>()
.str(prepostfixed(prefix, postfix, `label_comp_id`), mappedProp(getLocation, P.residue.label_comp_id)) .str(prepostfixed(prefix, postfix, `label_comp_id`), mappedProp(getLocation, P.residue.label_comp_id))
.int(prepostfixed(prefix, postfix, `label_seq_id`), mappedProp(getLocation, P.residue.label_seq_id), { .int(prepostfixed(prefix, postfix, `label_seq_id`), mappedProp(getLocation, P.residue.label_seq_id), {
encoder: E.deltaRLE, encoder: E.deltaRLE,
...@@ -93,29 +105,35 @@ export function residueIdFields<K, D>(getLocation: (key: K, data: D) => Structur ...@@ -93,29 +105,35 @@ export function residueIdFields<K, D>(getLocation: (key: K, data: D) => Structur
.str(prepostfixed(prefix, postfix, `auth_comp_id`), mappedProp(getLocation, P.residue.auth_comp_id)) .str(prepostfixed(prefix, postfix, `auth_comp_id`), mappedProp(getLocation, P.residue.auth_comp_id))
.int(prepostfixed(prefix, postfix, `auth_seq_id`), mappedProp(getLocation, P.residue.auth_seq_id), { encoder: E.deltaRLE }) .int(prepostfixed(prefix, postfix, `auth_seq_id`), mappedProp(getLocation, P.residue.auth_seq_id), { encoder: E.deltaRLE })
.str(prepostfixed(prefix, postfix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id)) .str(prepostfixed(prefix, postfix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id));
.getFields();
addModelNum(ret, getLocation, options);
return ret.getFields();
} }
export function chainIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement, options?: { prefix?: string, postfix?: string }): CifField<K, D>[] { export function chainIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement, options?: IdFieldsOptions): CifField<K, D>[] {
const prefix = options && options.prefix, postfix = options && options.postfix; const prefix = options && options.prefix, postfix = options && options.postfix;
return CifField.build<K, D>() const ret = CifField.build<K, D>()
.str(prepostfixed(prefix, postfix, `label_asym_id`), mappedProp(getLocation, P.chain.label_asym_id)) .str(prepostfixed(prefix, postfix, `label_asym_id`), mappedProp(getLocation, P.chain.label_asym_id))
.str(prepostfixed(prefix, postfix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id)) .str(prepostfixed(prefix, postfix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id))
.str(prepostfixed(prefix, postfix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id)) .str(prepostfixed(prefix, postfix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id))
.getFields();
addModelNum(ret, getLocation, options);
return ret.getFields();
} }
export function entityIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement, options?: { prefix?: string, postfix?: string }): CifField<K, D>[] { export function entityIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement, options?: IdFieldsOptions): CifField<K, D>[] {
const prefix = options && options.prefix, postfix = options && options.postfix; const prefix = options && options.prefix, postfix = options && options.postfix;
return CifField.build<K, D>() const ret = CifField.build<K, D>()
.str(prepostfixed(prefix, postfix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id)) .str(prepostfixed(prefix, postfix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id))
.getFields();
addModelNum(ret, getLocation, options);
return ret.getFields();
} }
export function atomIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement, options?: { prefix?: string, postfix?: string }): CifField<K, D>[] { export function atomIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement, options?: IdFieldsOptions): CifField<K, D>[] {
const prefix = options && options.prefix, postfix = options && options.postfix; const prefix = options && options.prefix, postfix = options && options.postfix;
return CifWriter.fields<K, D>() const ret = CifWriter.fields<K, D>()
.str(prepostfixed(prefix, postfix, `label_atom_id`), mappedProp(getLocation, P.atom.label_atom_id)) .str(prepostfixed(prefix, postfix, `label_atom_id`), mappedProp(getLocation, P.atom.label_atom_id))
.str(prepostfixed(prefix, postfix, `label_comp_id`), mappedProp(getLocation, P.residue.label_comp_id)) .str(prepostfixed(prefix, postfix, `label_comp_id`), mappedProp(getLocation, P.residue.label_comp_id))
.int(prepostfixed(prefix, postfix, `label_seq_id`), mappedProp(getLocation, P.residue.label_seq_id), { .int(prepostfixed(prefix, postfix, `label_seq_id`), mappedProp(getLocation, P.residue.label_seq_id), {
...@@ -135,6 +153,8 @@ export function atomIdFields<K, D>(getLocation: (key: K, data: D) => StructureEl ...@@ -135,6 +153,8 @@ export function atomIdFields<K, D>(getLocation: (key: K, data: D) => StructureEl
.str(prepostfixed(prefix, postfix, `auth_atom_id`), mappedProp(getLocation, P.atom.auth_atom_id)) .str(prepostfixed(prefix, postfix, `auth_atom_id`), mappedProp(getLocation, P.atom.auth_atom_id))
.str(prepostfixed(prefix, postfix, `auth_comp_id`), mappedProp(getLocation, P.residue.auth_comp_id)) .str(prepostfixed(prefix, postfix, `auth_comp_id`), mappedProp(getLocation, P.residue.auth_comp_id))
.int(prepostfixed(prefix, postfix, `auth_seq_id`), mappedProp(getLocation, P.residue.auth_seq_id), { encoder: E.deltaRLE }) .int(prepostfixed(prefix, postfix, `auth_seq_id`), mappedProp(getLocation, P.residue.auth_seq_id), { encoder: E.deltaRLE })
.str(prepostfixed(prefix, postfix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id)) .str(prepostfixed(prefix, postfix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id));
.getFields();
addModelNum(ret, getLocation, options);
return ret.getFields();
} }
\ No newline at end of file
src/servers/model/test.ts
+ 12
− 12
View file @ e2a7ca6d
...@@ -43,26 +43,26 @@ async function run() { ...@@ -43,26 +43,26 @@ async function run() {
try { try {
// const testFile = '1crn.cif' // const testFile = '1crn.cif'
const testFile = '1cbs_updated.cif' const testFile = '1cbs_updated.cif'
const request = createJob({
entryId: path.join(examplesPath, testFile),
queryName: 'full',
queryParams: { }
});
// const request = createJob({ // const request = createJob({
// entryId: path.join(examplesPath, testFile), // entryId: path.join(examplesPath, testFile),
// queryName: 'atoms', // queryName: 'full',
// queryParams: { // queryParams: { }
// atom_site: { label_comp_id: 'ALA' }
// }
// }); // });
// const request = createJob({ // const request = createJob({
// entryId: path.join(examplesPath, testFile), // entryId: path.join(examplesPath, testFile),
// queryName: 'residueInteraction', // queryName: 'atoms',
// queryParams: { // queryParams: {
// atom_site: { label_comp_id: 'REA' }, // atom_site: { label_comp_id: 'ALA' }
// radius: 5
// } // }
// }); // });
const request = createJob({
entryId: path.join(examplesPath, testFile),
queryName: 'residueInteraction',
queryParams: {
atom_site: { label_comp_id: 'REA' },
radius: 5
}
});
const encoder = await resolveJob(request); const encoder = await resolveJob(request);
const writer = wrapFile(path.join(outPath, testFile)); const writer = wrapFile(path.join(outPath, testFile));
encoder.writeTo(writer); encoder.writeTo(writer);
......
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