From 1e9bd97121256e7da2617d008bb96e89bbe3a2e1 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 5 Jul 2018 15:29:35 +0200
Subject: [PATCH] mmCIF secondary structure export
---
.../export/categories/secondary-structure.ts | 115 ++++++++++++++++++
src/mol-model/structure/export/mmcif.ts | 4 +-
.../formats/mmcif/secondary-structure.ts | 4 +-
3 files changed, 119 insertions(+), 4 deletions(-)
diff --git a/src/mol-model/structure/export/categories/secondary-structure.ts b/src/mol-model/structure/export/categories/secondary-structure.ts
index de7200ac1..cc27294ab 100644
--- a/src/mol-model/structure/export/categories/secondary-structure.ts
+++ b/src/mol-model/structure/export/categories/secondary-structure.ts
@@ -3,3 +3,118 @@
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
+
+import { Segmentation } from 'mol-data/int';
+import { CifWriter } from 'mol-io/writer/cif';
+import { SecondaryStructure } from '../../model/properties/seconday-structure';
+import { Element, Unit, StructureProperties as P } from '../../structure';
+import { CifExportContext } from '../mmcif';
+
+import CifField = CifWriter.Field
+import CifCategory = CifWriter.Category
+import { Column } from 'mol-data/db';
+
+export function _struct_conf(ctx: CifExportContext): CifCategory {
+ const elements = findElements(ctx, 'helix');
+ return {
+ data: elements,
+ name: 'struct_conf',
+ fields: struct_conf_fields,
+ rowCount: elements.length
+ };
+}
+
+export function _struct_sheet_range(ctx: CifExportContext): CifCategory {
+ const elements = findElements(ctx, 'sheet');
+ return {
+ data: elements,
+ name: 'struct_sheet_range',
+ fields: struct_sheet_range_fields,
+ rowCount: elements.length
+ };
+}
+
+const struct_conf_fields: CifField[] = [
+ CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('conf_type_id', (i, data) => data[i].element.type_id),
+ CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('conf_type_id', (i, data, idx) => `${data[i].element.type_id}${idx + 1}`),
+ ...residueIdFields('beg_', e => e.start),
+ ...residueIdFields('end_', e => e.end),
+ CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('pdbx_PDB_helix_class', (i, data) => data[i].element.helix_class),
+ CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('details', (i, data) => data[i].element.details || '', {
+ valueKind: (i, d) => !!d[i].element.details ? Column.ValueKind.Present : Column.ValueKind.Unknown
+ }),
+ CifField.int<number, SSElement<SecondaryStructure.Helix>[]>('pdbx_PDB_helix_class', (i, data) => data[i].length)
+];
+
+const struct_sheet_range_fields: CifField[] = [
+ CifField.index('id'),
+ CifField.str<number, SSElement<SecondaryStructure.Sheet>[]>('sheet_id', (i, data) => data[i].element.sheet_id),
+ ...residueIdFields('beg_', e => e.start),
+ ...residueIdFields('end_', e => e.end),
+ CifField.str('symmetry', (i, data) => '', { valueKind: (i, d) => Column.ValueKind.Unknown })
+];
+
+function residueIdFields(prefix: string, loc: (e: SSElement<any>) => Element.Location): CifField<number, SSElement<SecondaryStructure.Helix>[]>[] {
+ return [
+ CifField.str(`${prefix}label_comp_id`, (i, d) => P.residue.label_comp_id(loc(d[i]))),
+ CifField.int(`${prefix}label_seq_id`, (i, d) => P.residue.label_seq_id(loc(d[i]))),
+ CifField.str(`pdbx_${prefix}PDB_ins_code`, (i, d) => P.residue.pdbx_PDB_ins_code(loc(d[i]))),
+ CifField.str(`${prefix}label_asym_id`, (i, d) => P.chain.label_asym_id(loc(d[i]))),
+ CifField.str(`${prefix}_entity_id`, (i, d) => P.chain.label_entity_id(loc(d[i]))),
+ CifField.str(`${prefix}auth_comp_id`, (i, d) => P.residue.auth_comp_id(loc(d[i]))),
+ CifField.int(`${prefix}auth_seq_id`, (i, d) => P.residue.auth_seq_id(loc(d[i]))),
+ CifField.str(`${prefix}auth_asym_id`, (i, d) => P.chain.auth_asym_id(loc(d[i])))
+ ];
+}
+
+interface SSElement<T extends SecondaryStructure.Element> {
+ start: Element.Location,
+ end: Element.Location,
+ length: number,
+ element: T
+}
+
+function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContext, kind: SecondaryStructure.Element['kind']) {
+ const { index, elements } = ctx.model.properties.secondaryStructure;
+
+ const ssElements: SSElement<any>[] = [];
+
+ for (const unit of ctx.structure.units) {
+ // currently can only support this for "identity" operators.
+ if (!Unit.isAtomic(unit) || !unit.conformation.operator.isIdentity) continue;
+
+ const segs = unit.model.atomicHierarchy.residueSegments;
+ const residues = Segmentation.transientSegments(segs, unit.elements);
+
+ let current: Segmentation.Segment<Element>, move = true;
+ while (residues.hasNext) {
+ if (move) current = residues.move();
+
+ const start = current!.index;
+ const startIdx = index[start];
+ const element = elements[startIdx];
+ if (element.kind !== kind) {
+ move = true;
+ continue;
+ }
+
+ let prev = start;
+ while (residues.hasNext) {
+ prev = current!.index;
+ current = residues.move();
+ if (startIdx !== index[current.index]) {
+ move = false;
+ ssElements[ssElements.length] = {
+ start: Element.Location(unit, segs.segments[start]),
+ end: Element.Location(unit, segs.segments[prev]),
+ length: prev - start + 1,
+ element
+ }
+ break;
+ }
+ }
+ }
+ }
+
+ return ssElements as SSElement<T>[];
+}
\ 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 8a33f9851..c783b552e 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -17,6 +17,7 @@ export interface CifExportContext {
}
import CifCategory = CifWriter.Category
+import { _struct_conf, _struct_sheet_range } from './categories/secondary-structure';
function copy_mmCif_category(name: keyof mmCIF_Schema) {
return ({ model }: CifExportContext) => {
@@ -48,7 +49,8 @@ const Categories = [
copy_mmCif_category('pdbx_struct_oper_list'),
// Secondary structure
- // TODO
+ _struct_conf,
+ _struct_sheet_range,
// Misc
// TODO: filter for actual present residues?
diff --git a/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts b/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
index 69e6f8f42..15ff80bb2 100644
--- a/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
+++ b/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
@@ -56,9 +56,7 @@ function addHelices(cat: mmCIF['struct_conf'], map: SecondaryStructureMap, eleme
const element: SecondaryStructure.Helix = {
kind: 'helix',
flags: type,
- type_id: pdbx_PDB_helix_class.valueKind(i) === Column.ValueKind.Present
- ? pdbx_PDB_helix_class.value(i) : conf_type_id.valueKind(i) === Column.ValueKind.Present
- ? conf_type_id.value(i) : 'HELIX_P',
+ type_id: conf_type_id.valueKind(i) === Column.ValueKind.Present ? conf_type_id.value(i) : 'HELIX_P',
helix_class: pdbx_PDB_helix_class.value(i),
details: details.valueKind(i) === Column.ValueKind.Present ? details.value(i) : void 0
};
--
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