From dc59cb88dc4666260c7241f031cb7c7d7b5cd9b6 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 5 Jul 2018 14:25:15 +0200
Subject: [PATCH] wip, seconadry structure export, updated sec. struct data
model
---
src/apps/structure-info/model.ts | 14 ++---
.../export/categories/secondary-structure.ts | 5 ++
src/mol-model/structure/export/mmcif.ts | 12 ++++
.../formats/mmcif/secondary-structure.ts | 58 +++++++++++++------
.../model/properties/seconday-structure.ts | 31 +++++++++-
.../structure/structure/properties.ts | 2 +-
6 files changed, 90 insertions(+), 32 deletions(-)
create mode 100644 src/mol-model/structure/export/categories/secondary-structure.ts
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 17f1b6373..a4f8ddf66 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -13,8 +13,6 @@ import { Model, Structure, Element, Unit, Format, StructureProperties } from 'mo
// import { Run, Progress } from 'mol-task'
import { OrderedSet } from 'mol-data/int';
import { openCif, downloadCif } from './helpers';
-import { BitFlags } from 'mol-util';
-import { SecondaryStructureType } from 'mol-model/structure/model/types';
import { UnitRings } from 'mol-model/structure/structure/unit/rings';
import { Vec3 } from 'mol-math/linear-algebra';
@@ -51,21 +49,17 @@ export function residueLabel(model: Model, rI: number) {
export function printSecStructure(model: Model) {
console.log('\nSecondary Structure\n=============');
const { residues } = model.atomicHierarchy;
- const { type, key } = model.properties.secondaryStructure;
+ const { index, elements } = model.properties.secondaryStructure;
const count = residues._rowCount;
let rI = 0;
while (rI < count) {
let start = rI;
- while (rI < count && key[start] === key[rI]) rI++;
+ while (rI < count && index[start] === index[rI]) rI++;
rI--;
- if (BitFlags.has(type[start], SecondaryStructureType.Flag.Beta)) {
- console.log(`Sheet: ${residueLabel(model, start)} - ${residueLabel(model, rI)} (key ${key[start]})`);
- } else if (BitFlags.has(type[start], SecondaryStructureType.Flag.Helix)) {
- console.log(`Helix: ${residueLabel(model, start)} - ${residueLabel(model, rI)} (key ${key[start]})`);
- }
-
+ const e = elements[index[start]];
+ if (e.kind !== 'none') console.log(`${e.kind}: ${residueLabel(model, start)} - ${residueLabel(model, rI)}`);
rI++;
}
}
diff --git a/src/mol-model/structure/export/categories/secondary-structure.ts b/src/mol-model/structure/export/categories/secondary-structure.ts
new file mode 100644
index 000000000..de7200ac1
--- /dev/null
+++ b/src/mol-model/structure/export/categories/secondary-structure.ts
@@ -0,0 +1,5 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index 3a5f900c8..8a33f9851 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -33,17 +33,29 @@ function _entity({ model, structure }: CifExportContext): CifCategory {
}
const Categories = [
+ // Basics
copy_mmCif_category('entry'),
copy_mmCif_category('exptl'),
_entity,
+
+ // Symmetry
copy_mmCif_category('cell'),
copy_mmCif_category('symmetry'),
+
+ // Assemblies
copy_mmCif_category('pdbx_struct_assembly'),
copy_mmCif_category('pdbx_struct_assembly_gen'),
copy_mmCif_category('pdbx_struct_oper_list'),
+
+ // Secondary structure
+ // TODO
+
+ // Misc
// TODO: filter for actual present residues?
copy_mmCif_category('chem_comp'),
copy_mmCif_category('atom_sites'),
+
+ // Atoms
_atom_site
];
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 ed07db38b..69e6f8f42 100644
--- a/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
+++ b/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
@@ -13,13 +13,15 @@ import { Column } from 'mol-data/db';
export function getSecondaryStructureMmCif(data: mmCIF_Database, hierarchy: AtomicHierarchy): SecondaryStructure {
const map: SecondaryStructureMap = new Map();
- addHelices(data.struct_conf, map);
+ const elements: SecondaryStructure.Element[] = [{ kind: 'none' }];
+ addHelices(data.struct_conf, map, elements);
// must add Helices 1st because of 'key' value assignment.
- addSheets(data.struct_sheet_range, map, data.struct_conf._rowCount);
+ addSheets(data.struct_sheet_range, map, data.struct_conf._rowCount, elements);
const secStruct: SecondaryStructureData = {
type: new Int32Array(hierarchy.residues._rowCount) as any,
- key: new Int32Array(hierarchy.residues._rowCount) as any
+ index: new Int32Array(hierarchy.residues._rowCount) as any,
+ elements
};
if (map.size > 0) assignSecondaryStructureRanges(hierarchy, map, secStruct);
@@ -32,34 +34,45 @@ type SecondaryStructureEntry = {
endSeqNumber: number,
endInsCode: string | null,
type: SecondaryStructureType,
- key: number
+ index: number
}
type SecondaryStructureMap = Map<string, Map<number, SecondaryStructureEntry>>
-type SecondaryStructureData = { type: SecondaryStructureType[], key: number[] }
+type SecondaryStructureData = { type: SecondaryStructureType[], index: number[], elements: SecondaryStructure.Element[] }
-function addHelices(cat: mmCIF['struct_conf'], map: SecondaryStructureMap) {
+function addHelices(cat: mmCIF['struct_conf'], map: SecondaryStructureMap, elements: SecondaryStructure.Element[]) {
if (!cat._rowCount) return;
const { beg_label_asym_id, beg_label_seq_id, pdbx_beg_PDB_ins_code } = cat;
const { end_label_seq_id, pdbx_end_PDB_ins_code } = cat;
- const { pdbx_PDB_helix_class, conf_type_id } = cat;
+ const { pdbx_PDB_helix_class, conf_type_id, details } = cat;
for (let i = 0, _i = cat._rowCount; i < _i; i++) {
- const type = pdbx_PDB_helix_class.valueKind(i) === Column.ValueKind.Present
+ const type = SecondaryStructureType.create(pdbx_PDB_helix_class.valueKind(i) === Column.ValueKind.Present
? SecondaryStructureType.SecondaryStructurePdb[pdbx_PDB_helix_class.value(i)]
: conf_type_id.valueKind(i) === Column.ValueKind.Present
? SecondaryStructureType.SecondaryStructureMmcif[conf_type_id.value(i)]
- : SecondaryStructureType.Flag.NA
-
+ : SecondaryStructureType.Flag.NA);
+
+ 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',
+ helix_class: pdbx_PDB_helix_class.value(i),
+ details: details.valueKind(i) === Column.ValueKind.Present ? details.value(i) : void 0
+ };
const entry: SecondaryStructureEntry = {
startSeqNumber: beg_label_seq_id.value(i),
startInsCode: pdbx_beg_PDB_ins_code.value(i),
endSeqNumber: end_label_seq_id.value(i),
endInsCode: pdbx_end_PDB_ins_code.value(i),
- type: SecondaryStructureType.create(type),
- key: i + 1
+ type,
+ index: elements.length
};
+ elements[elements.length] = element;
+
const asymId = beg_label_asym_id.value(i)!;
if (map.has(asymId)) {
map.get(asymId)!.set(entry.startSeqNumber, entry);
@@ -69,7 +82,7 @@ function addHelices(cat: mmCIF['struct_conf'], map: SecondaryStructureMap) {
}
}
-function addSheets(cat: mmCIF['struct_sheet_range'], map: SecondaryStructureMap, sheetCount: number) {
+function addSheets(cat: mmCIF['struct_sheet_range'], map: SecondaryStructureMap, sheetCount: number, elements: SecondaryStructure.Element[]) {
if (!cat._rowCount) return;
const { beg_label_asym_id, beg_label_seq_id, pdbx_beg_PDB_ins_code } = cat;
@@ -88,15 +101,25 @@ function addSheets(cat: mmCIF['struct_sheet_range'], map: SecondaryStructureMap,
sheet_id_key.set(id, key);
}
+ const type = SecondaryStructureType.create(SecondaryStructureType.Flag.Beta | SecondaryStructureType.Flag.BetaSheet);
+ const element: SecondaryStructure.Sheet = {
+ kind: 'sheet',
+ flags: type,
+ sheet_id: id,
+ symmetry: void 0
+ }
const entry: SecondaryStructureEntry = {
startSeqNumber: beg_label_seq_id.value(i),
startInsCode: pdbx_beg_PDB_ins_code.value(i),
endSeqNumber: end_label_seq_id.value(i),
endInsCode: pdbx_end_PDB_ins_code.value(i),
- type: SecondaryStructureType.create(SecondaryStructureType.Flag.Beta | SecondaryStructureType.Flag.BetaSheet),
- key
+ type,
+ index: elements.length
};
+ elements[elements.length] = element;
+
+
const asymId = beg_label_asym_id.value(i)!;
if (map.has(asymId)) {
map.get(asymId)!.set(entry.startSeqNumber, entry);
@@ -110,14 +133,13 @@ function addSheets(cat: mmCIF['struct_sheet_range'], map: SecondaryStructureMap,
function assignSecondaryStructureEntry(hierarchy: AtomicHierarchy, entry: SecondaryStructureEntry, resStart: number, resEnd: number, data: SecondaryStructureData) {
const { label_seq_id, pdbx_PDB_ins_code } = hierarchy.residues;
- const { endSeqNumber, endInsCode, type, key } = entry;
+ const { endSeqNumber, endInsCode, index, type } = entry;
let rI = resStart;
while (rI < resEnd) {
const seqNumber = label_seq_id.value(rI);
-
data.type[rI] = type;
- data.key[rI] = key;
+ data.index[rI] = index;
if ((seqNumber > endSeqNumber) ||
(seqNumber === endSeqNumber && pdbx_PDB_ins_code.value(rI) === endInsCode)) {
diff --git a/src/mol-model/structure/model/properties/seconday-structure.ts b/src/mol-model/structure/model/properties/seconday-structure.ts
index dfde631a3..5ecfb439c 100644
--- a/src/mol-model/structure/model/properties/seconday-structure.ts
+++ b/src/mol-model/structure/model/properties/seconday-structure.ts
@@ -8,10 +8,35 @@ import { SecondaryStructureType } from '../types';
/** Secondary structure "indexed" by residues. */
interface SecondaryStructure {
- // assign flags to each residue
readonly type: ArrayLike<SecondaryStructureType>,
- /** unique value for each "element". This is because single sheet is speficied by multiple records. */
- readonly key: ArrayLike<number>
+
+ /** index into the elements array */
+ readonly index: ArrayLike<number>,
+ /** indexed by key */
+ readonly elements: ReadonlyArray<SecondaryStructure.Element>
+}
+
+namespace SecondaryStructure {
+ export type Element = None | Helix | Sheet
+
+ export interface None {
+ kind: 'none'
+ }
+
+ export interface Helix {
+ kind: 'helix',
+ flags: SecondaryStructureType,
+ type_id: string, // TODO: use aliased type?
+ helix_class: string,
+ details?: string
+ }
+
+ export interface Sheet {
+ kind: 'sheet',
+ flags: SecondaryStructureType,
+ sheet_id: string,
+ symmetry?: string
+ }
}
export { SecondaryStructure }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index d13f5ddd8..7a3e8f789 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -59,7 +59,7 @@ const residue = {
// Properties
secondary_structure_type: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.type[l.unit.residueIndex[l.element]]),
- secondary_structure_key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.key[l.unit.residueIndex[l.element]]),
+ secondary_structure_key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.index[l.unit.residueIndex[l.element]]),
}
const chain = {
--
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