From ee43a971b308cad5eff4cb002439b6cc2c5f7ee0 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 22 Jun 2018 16:21:24 -0700
Subject: [PATCH] added model.properties.asymIdSerialMap
---
.../structure/model/formats/mmcif.ts | 26 ++++++++++++++++---
src/mol-model/structure/model/model.ts | 5 ++--
2 files changed, 26 insertions(+), 5 deletions(-)
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index abd3a7a59..6bb1c3566 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -135,7 +135,7 @@ function isHierarchyDataEqual(a: AtomicData, b: AtomicData) {
&& Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
}
-function modResMap(format: mmCIF_Format) {
+function getModifiedResidueNameMap(format: mmCIF_Format) {
const data = format.data.pdbx_struct_mod_residue;
const map = new Map<string, string>();
const comp_id = data.label_comp_id.isDefined ? data.label_comp_id : data.auth_comp_id;
@@ -148,6 +148,24 @@ function modResMap(format: mmCIF_Format) {
return map;
}
+function getAsymIdSerialMap(format: mmCIF_Format) {
+ const data = format.data.struct_asym;
+ const map = new Map<string, number>();
+ let serial = 0
+
+ const id = data.id
+ const count = data._rowCount
+ for (let i = 0; i < count; ++i) {
+ const _id = id.value(i)
+ if (!map.has(_id)) {
+ map.set(_id, serial)
+ serial += 1
+ }
+ }
+
+ return map;
+}
+
function createModel(format: mmCIF_Format, atom_site: AtomSite, previous?: Model): Model {
const hierarchyOffsets = findHierarchyOffsets(atom_site);
const hierarchyData = createHierarchyData(atom_site, hierarchyOffsets);
@@ -176,7 +194,8 @@ function createModel(format: mmCIF_Format, atom_site: AtomSite, previous?: Model
? format.data.entry.id.value(0)
: format.data._name;
- const modifiedResidueNameMap = modResMap(format);
+ const modifiedResidueNameMap = getModifiedResidueNameMap(format);
+ const asymIdSerialMap = getAsymIdSerialMap(format)
return {
id: UUID.create(),
@@ -191,7 +210,8 @@ function createModel(format: mmCIF_Format, atom_site: AtomSite, previous?: Model
coarseConformation: coarse.conformation,
properties: {
secondaryStructure: getSecondaryStructureMmCif(format.data, atomicHierarchy),
- modifiedResidueNameMap
+ modifiedResidueNameMap,
+ asymIdSerialMap
},
symmetry: getSymmetry(format)
};
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 6ade4fe45..48a16e133 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -13,7 +13,7 @@ import { CoarseHierarchy, CoarseConformation } from './properties/coarse'
import { Entities } from './properties/common';
import { SecondaryStructure } from './properties/seconday-structure';
-//import from_gro from './formats/gro'
+// import from_gro from './formats/gro'
import from_mmCIF from './formats/mmcif'
/**
* Interface to the "source data" of the molecule.
@@ -40,6 +40,7 @@ interface Model extends Readonly<{
readonly secondaryStructure: SecondaryStructure,
// maps modified residue name to its parent
readonly modifiedResidueNameMap: Map<string, string>,
+ readonly asymIdSerialMap: Map<string, number>,
[customName: string]: any
},
@@ -54,7 +55,7 @@ interface Model extends Readonly<{
namespace Model {
export function create(format: Format) {
switch (format.kind) {
- //case 'gro': return from_gro(format);
+ // case 'gro': return from_gro(format);
case 'mmCIF': return from_mmCIF(format);
}
}
--
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