From a819835984d4703d1abdba535b70db11c8703d4b Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Wed, 15 Jan 2020 14:58:03 -0500
Subject: [PATCH] add AtomicConformation.xyzDefined & improve getAtomicRanges
---
src/mol-model-formats/structure/mmcif/atomic.ts | 3 ++-
.../structure/model/properties/atomic/conformation.ts | 4 ++++
.../structure/model/properties/utils/atomic-ranges.ts | 4 ++--
3 files changed, 8 insertions(+), 3 deletions(-)
diff --git a/src/mol-model-formats/structure/mmcif/atomic.ts b/src/mol-model-formats/structure/mmcif/atomic.ts
index 85f28233d..9cedc4019 100644
--- a/src/mol-model-formats/structure/mmcif/atomic.ts
+++ b/src/mol-model-formats/structure/mmcif/atomic.ts
@@ -69,8 +69,8 @@ function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, o
const chains = Table.view(atom_site, ChainsSchema, offsets.chains);
// Fix possibly missing auth_/label_ columns
- substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
substUndefinedColumn(atoms, 'label_atom_id', 'auth_atom_id');
+ substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
substUndefinedColumn(residues, 'label_comp_id', 'auth_comp_id');
substUndefinedColumn(chains, 'label_asym_id', 'auth_asym_id');
@@ -83,6 +83,7 @@ function getConformation(atom_site: AtomSite): AtomicConformation {
atomId: atom_site.id,
occupancy: atom_site.occupancy,
B_iso_or_equiv: atom_site.B_iso_or_equiv,
+ xyzDefined: atom_site.Cartn_x.isDefined && atom_site.Cartn_y.isDefined && atom_site.Cartn_z.isDefined,
x: atom_site.Cartn_x.toArray({ array: Float32Array }),
y: atom_site.Cartn_y.toArray({ array: Float32Array }),
z: atom_site.Cartn_z.toArray({ array: Float32Array }),
diff --git a/src/mol-model/structure/model/properties/atomic/conformation.ts b/src/mol-model/structure/model/properties/atomic/conformation.ts
index 984697b02..27dbfcae3 100644
--- a/src/mol-model/structure/model/properties/atomic/conformation.ts
+++ b/src/mol-model/structure/model/properties/atomic/conformation.ts
@@ -34,6 +34,10 @@ export interface AtomicConformation {
// Coordinates. Generally, not to be accessed directly because the coordinate might be
// transformed by an operator. Use Unit.getPosition instead.
+ /**
+ * Are xyz coordinates defined?
+ */
+ xyzDefined: boolean,
/**
* The x coordinate in angstroms specified according to a set of orthogonal Cartesian axes.
*/
diff --git a/src/mol-model/structure/model/properties/utils/atomic-ranges.ts b/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
index 52d414c22..19fc6abe6 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
@@ -70,7 +70,7 @@ export function getAtomicRanges(hierarchy: AtomicHierarchy, entities: Entities,
const riEnd = hierarchy.residueAtomSegments.index[chainSegment.end - 1]
const seqIdStart = label_seq_id.value(riStart)
const seqIdEnd = label_seq_id.value(riEnd)
- if (seqIdStart === 1 && seqIdEnd === maxSeqId && areBackboneConnected(riStart, riEnd, conformation, index, derived)) {
+ if (seqIdStart === 1 && seqIdEnd === maxSeqId && conformation.xyzDefined && areBackboneConnected(riStart, riEnd, conformation, index, derived)) {
cyclicPolymerMap.set(riStart, riEnd)
cyclicPolymerMap.set(riEnd, riStart)
}
@@ -95,7 +95,7 @@ export function getAtomicRanges(hierarchy: AtomicHierarchy, entities: Entities,
} else {
const riStart = hierarchy.residueAtomSegments.index[residueSegment.start]
const riEnd = hierarchy.residueAtomSegments.index[prevEnd - 1]
- if (!areBackboneConnected(riStart, riEnd, conformation, hierarchy.index, derived)) {
+ if (conformation.xyzDefined && !areBackboneConnected(riStart, riEnd, conformation, hierarchy.index, derived)) {
polymerRanges.push(startIndex, prevEnd - 1)
startIndex = residueSegment.start
}
--
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