From 6aa482bd51bb7e12cc102624c3368a5b0cbd0c7c Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 11 Jul 2018 08:42:34 +0200
Subject: [PATCH] Fix secondary struct assignment
---
.../formats/mmcif/secondary-structure.ts | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
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 0c045f605..af127410e 100644
--- a/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
+++ b/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
@@ -37,7 +37,7 @@ type SecondaryStructureEntry = {
key: number
}
type SecondaryStructureMap = Map<string, Map<number, SecondaryStructureEntry>>
-type SecondaryStructureData = { type: SecondaryStructureType[], key: number[], elements: SecondaryStructure.Element[] }
+type SecondaryStructureData = { type: SecondaryStructureType[], key: number[], elements: SecondaryStructure.Element[] }
function addHelices(cat: mmCIF['struct_conf'], map: SecondaryStructureMap, elements: SecondaryStructure.Element[]) {
if (!cat._rowCount) return;
@@ -47,11 +47,11 @@ function addHelices(cat: mmCIF['struct_conf'], map: SecondaryStructureMap, eleme
const { pdbx_PDB_helix_class, conf_type_id, details } = cat;
for (let i = 0, _i = cat._rowCount; i < _i; i++) {
- const type = SecondaryStructureType.create(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.SecondaryStructureMmcif[conf_type_id.value(i)]
+ : SecondaryStructureType.Flag.NA);
const element: SecondaryStructure.Helix = {
kind: 'helix',
@@ -69,6 +69,7 @@ function addHelices(cat: mmCIF['struct_conf'], map: SecondaryStructureMap, eleme
key: elements.length
};
+
elements[elements.length] = element;
const asymId = beg_label_asym_id.value(i)!;
@@ -134,7 +135,7 @@ function assignSecondaryStructureEntry(hierarchy: AtomicHierarchy, entry: Second
const { endSeqNumber, endInsCode, key, type } = entry;
let rI = resStart;
- while (rI < resEnd) {
+ while (rI <= resEnd) {
const seqNumber = label_seq_id.value(rI);
data.type[rI] = type;
data.key[rI] = key;
@@ -149,18 +150,18 @@ function assignSecondaryStructureEntry(hierarchy: AtomicHierarchy, entry: Second
}
function assignSecondaryStructureRanges(hierarchy: AtomicHierarchy, map: SecondaryStructureMap, data: SecondaryStructureData) {
- const { segments: chainSegments, count: chainCount } = hierarchy.chainSegments;
+ const { segments: chainAtomSegments, count: chainCount } = hierarchy.chainSegments;
+ const { segmentMap: residueIndex } = hierarchy.residueSegments;
const { label_asym_id } = hierarchy.chains;
const { label_seq_id, pdbx_PDB_ins_code } = hierarchy.residues;
for (let cI = 0; cI < chainCount; cI++) {
- const resStart = chainSegments[cI], resEnd = chainSegments[cI + 1];
+ const resStart = residueIndex[chainAtomSegments[cI]], resEnd = residueIndex[chainAtomSegments[cI + 1] - 1];
const asymId = label_asym_id.value(cI);
-
if (map.has(asymId)) {
const entries = map.get(asymId)!;
- for (let rI = resStart; rI < resEnd; rI++) {
+ for (let rI = resStart; rI <= resEnd; rI++) {
const seqNumber = label_seq_id.value(rI);
if (entries.has(seqNumber)) {
const entry = entries.get(seqNumber)!;
--
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