From bf0b37895d5512f83836add8f5890058796d216f Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 23 Jul 2019 15:51:17 -0700
Subject: [PATCH] handle modified base rings (DP, DZ)
---
.../structure/visual/nucleotide-block-mesh.ts | 4 ++++
.../structure/visual/nucleotide-ring-mesh.ts | 12 ++++++++++++
2 files changed, 16 insertions(+)
diff --git a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts b/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
index 36f7dc6f0..55c8dfa68 100644
--- a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
@@ -107,6 +107,10 @@ function createNucleotideBlockMesh(ctx: VisualContext, unit: Unit, structure: St
idx3 = atomicIndex.findAtomOnResidue(residueIndex, 'C4')
idx4 = atomicIndex.findAtomOnResidue(residueIndex, 'C2')
idx5 = atomicIndex.findAtomOnResidue(residueIndex, 'N1')
+ if (idx5 === -1) {
+ // modified ring, e.g. DZ
+ idx5 = atomicIndex.findAtomOnResidue(residueIndex, 'C1')
+ }
idx6 = traceElementIndex[residueIndex]
}
diff --git a/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts b/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts
index 8a1e82017..871fe5364 100644
--- a/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts
+++ b/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts
@@ -122,8 +122,16 @@ function createNucleotideRingMesh(ctx: VisualContext, unit: Unit, structure: Str
idxN3 = atomicIndex.findAtomOnResidue(residueIndex, 'N3')
idxC4 = atomicIndex.findAtomOnResidue(residueIndex, 'C4')
idxC5 = atomicIndex.findAtomOnResidue(residueIndex, 'C5')
+ if (idxC5 === -1) {
+ // modified ring, e.g. DP
+ idxC5 = atomicIndex.findAtomOnResidue(residueIndex, 'N5')
+ }
idxC6 = atomicIndex.findAtomOnResidue(residueIndex, 'C6')
idxN7 = atomicIndex.findAtomOnResidue(residueIndex, 'N7')
+ if (idxN7 === -1) {
+ // modified ring, e.g. DP
+ idxN7 = atomicIndex.findAtomOnResidue(residueIndex, 'C7')
+ }
idxC8 = atomicIndex.findAtomOnResidue(residueIndex, 'C8')
idxN9 = atomicIndex.findAtomOnResidue(residueIndex, 'N9')
@@ -148,6 +156,10 @@ function createNucleotideRingMesh(ctx: VisualContext, unit: Unit, structure: Str
} else if (isPyrimidine) {
idxTrace = traceElementIndex[residueIndex]
idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'N1')
+ if (idxN1 === -1) {
+ // modified ring, e.g. DZ
+ idxN1 = atomicIndex.findAtomOnResidue(residueIndex, 'C1')
+ }
idxC2 = atomicIndex.findAtomOnResidue(residueIndex, 'C2')
idxN3 = atomicIndex.findAtomOnResidue(residueIndex, 'N3')
idxC4 = atomicIndex.findAtomOnResidue(residueIndex, 'C4')
--
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