From c91b826f245e1126bbd612918a9852311f76a1bc Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 11 Oct 2018 15:06:10 +0200
Subject: [PATCH] added pdbx_nonpoly_scheme category to mmCIF schema and export
---
data/mmcif-field-names.csv | 11 +++++++++++
src/mol-io/reader/cif/schema/mmcif.ts | 12 ++++++++++++
.../structure/export/categories/misc.ts | 10 ++++++++++
.../structure/export/categories/utils.ts | 17 +++++++++++++++++
src/mol-model/structure/export/mmcif.ts | 18 +++---------------
5 files changed, 53 insertions(+), 15 deletions(-)
diff --git a/data/mmcif-field-names.csv b/data/mmcif-field-names.csv
index 45602d31e..fba153c63 100644
--- a/data/mmcif-field-names.csv
+++ b/data/mmcif-field-names.csv
@@ -123,6 +123,17 @@ pdbx_entity_descriptor.type
pdbx_entity_descriptor.program
pdbx_entity_descriptor.program_version
+pdbx_nonpoly_scheme.asym_id
+pdbx_nonpoly_scheme.entity_id
+pdbx_nonpoly_scheme.mon_id
+pdbx_nonpoly_scheme.ndb_seq_num
+pdbx_nonpoly_scheme.pdb_seq_num
+pdbx_nonpoly_scheme.auth_seq_num
+pdbx_nonpoly_scheme.pdb_mon_id
+pdbx_nonpoly_scheme.auth_mon_id
+pdbx_nonpoly_scheme.pdb_strand_id
+pdbx_nonpoly_scheme.pdb_ins_code
+
entry.id
exptl.entry_id
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index b0799e894..d2565a478 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -1950,6 +1950,18 @@ export const mmCIF_Schema = {
*/
ordinal: int,
},
+ pdbx_nonpoly_scheme: {
+ asym_id: str,
+ entity_id: str,
+ mon_id: str,
+ ndb_seq_num: int,
+ pdb_seq_num: int,
+ auth_seq_num: int,
+ pdb_mon_id: str,
+ auth_mon_id: str,
+ pdb_strand_id: str,
+ pdb_ins_code: str
+ },
/**
* Data items in the IHM_STARTING_MODEL_DETAILS category records the
* details about structural models used as starting inputs in
diff --git a/src/mol-model/structure/export/categories/misc.ts b/src/mol-model/structure/export/categories/misc.ts
index 39d3d40f2..bd4772a45 100644
--- a/src/mol-model/structure/export/categories/misc.ts
+++ b/src/mol-model/structure/export/categories/misc.ts
@@ -32,4 +32,14 @@ export const _pdbx_chem_comp_identifier: CifCategory<CifExportContext> = {
const indices = Column.indicesOf(comp_id, id => names.has(id));
return CifCategory.ofTable(pdbx_chem_comp_identifier, indices);
}
+}
+
+export const _pdbx_nonpoly_scheme: CifCategory<CifExportContext> = {
+ name: 'pdbx_nonpoly_scheme',
+ instance({ firstModel, structures, cache }) {
+ const pdbx_nonpoly_scheme = getModelMmCifCategory(firstModel, 'pdbx_nonpoly_scheme');
+ if (!pdbx_nonpoly_scheme) return CifCategory.Empty;
+ // TODO: filter?
+ return CifCategory.ofTable(pdbx_nonpoly_scheme);
+ }
}
\ No newline at end of file
diff --git a/src/mol-model/structure/export/categories/utils.ts b/src/mol-model/structure/export/categories/utils.ts
index be0276c94..d33f72fac 100644
--- a/src/mol-model/structure/export/categories/utils.ts
+++ b/src/mol-model/structure/export/categories/utils.ts
@@ -11,6 +11,8 @@ import { Structure } from '../../structure';
import { EntityIndex } from '../../model/indexing';
import { UniqueArray } from 'mol-data/generic';
import { sortArray } from 'mol-data/util';
+import { CifWriter } from 'mol-io/writer/cif';
+import { CifExportContext } from '../mmcif';
export function getModelMmCifCategory<K extends keyof mmCIF_Schema>(model: Model, name: K): mmCIF_Database[K] | undefined {
if (model.sourceData.kind !== 'mmCIF') return;
@@ -39,4 +41,19 @@ export function getUniqueEntityIndicesFromStructures(structures: Structure[]): R
}
sortArray(ret.array);
return ret.array;
+}
+
+export function copy_mmCif_category(name: keyof mmCIF_Schema, condition?: (model: Model) => boolean): CifWriter.Category<CifExportContext> {
+ return {
+ name,
+ instance({ structures }) {
+ const model = structures[0].model;
+ if (model.sourceData.kind !== 'mmCIF') return CifWriter.Category.Empty;
+ if (condition && !condition(model)) return CifWriter.Category.Empty;
+
+ const table = model.sourceData.data[name];
+ if (!table || !table._rowCount) return CifWriter.Category.Empty;
+ return CifWriter.Category.ofTable(table);
+ }
+ };
}
\ 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 40dd6985c..5ed7dd4a4 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -12,9 +12,9 @@ import { _atom_site } from './categories/atom_site';
import CifCategory = CifWriter.Category
import { _struct_conf, _struct_sheet_range } from './categories/secondary-structure';
import { _pdbx_struct_mod_residue } from './categories/modified-residues';
-import { _chem_comp, _pdbx_chem_comp_identifier } from './categories/misc';
+import { _chem_comp, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './categories/misc';
import { Model } from '../model';
-import { getUniqueEntityIndicesFromStructures } from './categories/utils';
+import { getUniqueEntityIndicesFromStructures, copy_mmCif_category } from './categories/utils';
import { _struct_asym, _entity_poly, _entity_poly_seq } from './categories/sequence';
import { ModelPropertyDescriptor } from '../model/properties/custom';
@@ -35,19 +35,6 @@ export namespace CifExportContext {
}
}
-function copy_mmCif_category(name: keyof mmCIF_Schema): CifCategory<CifExportContext> {
- return {
- name,
- instance({ structures }) {
- const model = structures[0].model;
- if (model.sourceData.kind !== 'mmCIF') return CifCategory.Empty;
- const table = model.sourceData.data[name];
- if (!table || !table._rowCount) return CifCategory.Empty;
- return CifCategory.ofTable(table);
- }
- };
-}
-
const _entity: CifCategory<CifExportContext> = {
name: 'entity',
instance({ structures }) {
@@ -91,6 +78,7 @@ const Categories = [
_pdbx_chem_comp_identifier,
copy_mmCif_category('atom_sites'),
+ _pdbx_nonpoly_scheme,
_pdbx_struct_mod_residue,
// Atoms
--
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