From a59f6546c57ec07a473a58491bc0457cac617e5e Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Mon, 1 Jun 2020 18:13:10 -0700
Subject: [PATCH] more comp_id fixes
---
src/cli/structure-info/model.ts | 7 ++++---
src/examples/proteopedia-wrapper/helpers.ts | 2 +-
.../computed/chemistry/util.ts | 2 +-
.../computed/interactions/charged.ts | 4 ++--
.../structure/carbohydrates/compute.ts | 2 +-
.../structure/unit/bonds/intra-compute.ts | 2 +-
.../structure/structure/unit/rings.ts | 2 +-
src/mol-model/structure/util.ts | 21 -------------------
src/mol-plugin-ui/sequence/hetero.ts | 2 +-
.../structure/visual/nucleotide-block-mesh.ts | 2 +-
.../structure/visual/nucleotide-ring-mesh.ts | 2 +-
11 files changed, 14 insertions(+), 34 deletions(-)
diff --git a/src/cli/structure-info/model.ts b/src/cli/structure-info/model.ts
index b7cf39290..87ca5e63a 100644
--- a/src/cli/structure-info/model.ts
+++ b/src/cli/structure-info/model.ts
@@ -39,7 +39,7 @@ export function atomLabel(model: Model, aI: number) {
const { label_asym_id } = chains;
const rI = residueAtomSegments.index[aI];
const cI = chainAtomSegments.index[aI];
- return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)} ${label_atom_id.value(aI)}`;
+ return `${label_asym_id.value(cI)} ${label_comp_id.value(aI)} ${label_seq_id.value(rI)} ${label_atom_id.value(aI)}`;
}
export function residueLabel(model: Model, rI: number) {
@@ -47,8 +47,9 @@ export function residueLabel(model: Model, rI: number) {
const { label_comp_id } = atoms;
const { label_seq_id } = residues;
const { label_asym_id } = chains;
- const cI = chainAtomSegments.index[residueAtomSegments.offsets[rI]];
- return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)}`;
+ const aI = residueAtomSegments.offsets[rI];
+ const cI = chainAtomSegments.index[aI];
+ return `${label_asym_id.value(cI)} ${label_comp_id.value(aI)} ${label_seq_id.value(rI)}`;
}
export function printSecStructure(model: Model) {
diff --git a/src/examples/proteopedia-wrapper/helpers.ts b/src/examples/proteopedia-wrapper/helpers.ts
index 5535a8b76..aad918fd2 100644
--- a/src/examples/proteopedia-wrapper/helpers.ts
+++ b/src/examples/proteopedia-wrapper/helpers.ts
@@ -58,7 +58,7 @@ export namespace ModelInfo {
const entityType = model.entities.data.type.value(eI);
if (entityType !== 'non-polymer' && entityType !== 'branched') continue;
- const comp_id = model.atomicHierarchy.atoms.label_comp_id.value(rI);
+ const comp_id = model.atomicHierarchy.atoms.label_comp_id.value(residueOffsets[rI]);
let lig = hetMap.get(comp_id);
if (!lig) {
diff --git a/src/mol-model-props/computed/chemistry/util.ts b/src/mol-model-props/computed/chemistry/util.ts
index 8a7eaea7d..73f83aab9 100644
--- a/src/mol-model-props/computed/chemistry/util.ts
+++ b/src/mol-model-props/computed/chemistry/util.ts
@@ -27,7 +27,7 @@ export function altLoc(unit: Unit.Atomic, index: StructureElement.UnitIndex) {
}
export function compId(unit: Unit.Atomic, index: StructureElement.UnitIndex) {
- return unit.model.atomicHierarchy.atoms.label_comp_id.value(unit.getResidueIndex(index));
+ return unit.model.atomicHierarchy.atoms.label_comp_id.value(unit.elements[index]);
}
//
diff --git a/src/mol-model-props/computed/interactions/charged.ts b/src/mol-model-props/computed/interactions/charged.ts
index a9735c4c8..e4c0359b9 100644
--- a/src/mol-model-props/computed/interactions/charged.ts
+++ b/src/mol-model-props/computed/interactions/charged.ts
@@ -67,7 +67,7 @@ function addUnitPositiveCharges(structure: Structure, unit: Unit.Atomic, builder
while (residueIt.hasNext) {
const { index: residueIndex, start, end } = residueIt.move();
- const compId = label_comp_id.value(residueIndex);
+ const compId = label_comp_id.value(unit.model.atomicHierarchy.residueAtomSegments.offsets[residueIndex]);
if (PositvelyCharged.includes(compId)) {
builder.startState();
@@ -120,7 +120,7 @@ function addUnitNegativeCharges(structure: Structure, unit: Unit.Atomic, builder
while (residueIt.hasNext) {
const { index: residueIndex, start, end } = residueIt.move();
- const compId = label_comp_id.value(residueIndex);
+ const compId = label_comp_id.value(unit.model.atomicHierarchy.residueAtomSegments.offsets[residueIndex]);
if (NegativelyCharged.includes(compId)) {
builder.startState();
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 478145d03..add42b520 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -168,7 +168,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
while (residueIt.hasNext) {
const { index: residueIndex } = residueIt.move();
- const saccharideComp = getSaccharideComp(label_comp_id.value(residueIndex), model);
+ const saccharideComp = getSaccharideComp(label_comp_id.value(residueAtomSegments.offsets[residueIndex]), model);
if (!saccharideComp) continue;
if (!sugarResidueMap) {
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
index f0899b591..582866cce 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -99,7 +99,7 @@ function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUni
}
const raI = residueIndex[aI];
- const compId = label_comp_id.value(raI);
+ const compId = label_comp_id.value(aI);
if (!props.forceCompute && raI !== lastResidue) {
if (!!component && component.entries.has(compId)) {
diff --git a/src/mol-model/structure/structure/unit/rings.ts b/src/mol-model/structure/structure/unit/rings.ts
index 2bebe086f..ea87703f0 100644
--- a/src/mol-model/structure/structure/unit/rings.ts
+++ b/src/mol-model/structure/structure/unit/rings.ts
@@ -102,7 +102,7 @@ namespace UnitRing {
const { type_symbol, label_comp_id } = unit.model.atomicHierarchy.atoms;
// ignore Proline (can be flat because of bad geometry)
- if (label_comp_id.value(unit.getResidueIndex(ring[0])) === 'PRO') return false;
+ if (label_comp_id.value(unit.elements[ring[0]]) === 'PRO') return false;
let aromaticBondCount = 0;
let hasAromaticRingElement = false;
diff --git a/src/mol-model/structure/util.ts b/src/mol-model/structure/util.ts
index 93d80b88c..317d883fe 100644
--- a/src/mol-model/structure/util.ts
+++ b/src/mol-model/structure/util.ts
@@ -45,27 +45,6 @@ export function getAtomIdForAtomRole(polymerType: PolymerType, atomRole: AtomRol
return EmptyAtomIds;
}
-export function residueLabel(model: Model, rI: number) {
- const { atoms, residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy;
- const { label_comp_id } = atoms;
- const { label_seq_id } = residues;
- const { label_asym_id } = chains;
- const cI = chainAtomSegments.index[residueAtomSegments.offsets[rI]];
- return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)}`;
-}
-
-export function elementLabel(model: Model, index: ElementIndex) {
- const { atoms, residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy;
- const { label_atom_id, label_comp_id } = atoms;
- const { auth_seq_id } = residues;
- const { auth_asym_id } = chains;
-
- const residueIndex = residueAtomSegments.index[index];
- const chainIndex = chainAtomSegments.index[residueIndex];
-
- return `[${label_comp_id.value(residueIndex)}]${auth_seq_id.value(residueIndex)}:${auth_asym_id.value(chainIndex)}.${label_atom_id.value(index)}`;
-}
-
const tmpPositionsVec = Vec3.zero();
export function getPositions(unit: Unit, indices: ArrayLike<number>): NumberArray {
const pos = unit.conformation.position;
diff --git a/src/mol-plugin-ui/sequence/hetero.ts b/src/mol-plugin-ui/sequence/hetero.ts
index b3028fbf2..1265a4963 100644
--- a/src/mol-plugin-ui/sequence/hetero.ts
+++ b/src/mol-plugin-ui/sequence/hetero.ts
@@ -81,7 +81,7 @@ export class HeteroSequenceWrapper extends SequenceWrapper<StructureUnit> {
sequenceIndices.set(index, sequence.length);
residueIndices.set(sequence.length, index);
seqToUnit.set(sequence.length, unit);
- sequence.push(atoms.label_comp_id.value(index));
+ sequence.push(atoms.label_comp_id.value(residueAtomSegments.offsets[index]));
}
}
diff --git a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts b/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
index fbeeb02d5..4ddedf867 100644
--- a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
@@ -75,7 +75,7 @@ function createNucleotideBlockMesh(ctx: VisualContext, unit: Unit, structure: St
const { index: residueIndex } = residueIt.move();
if (isNucleic(moleculeType[residueIndex])) {
- const compId = label_comp_id.value(residueIndex);
+ const compId = label_comp_id.value(residueAtomSegments.offsets[residueIndex]);
let idx1: ElementIndex | -1 = -1, idx2: ElementIndex | -1 = -1, idx3: ElementIndex | -1 = -1, idx4: ElementIndex | -1 = -1, idx5: ElementIndex | -1 = -1, idx6: ElementIndex | -1 = -1;
let width = 4.5, height = 4.5, depth = 2.5 * sizeFactor;
diff --git a/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts b/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts
index b62c69213..5d1cb9eb5 100644
--- a/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts
+++ b/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts
@@ -96,7 +96,7 @@ function createNucleotideRingMesh(ctx: VisualContext, unit: Unit, structure: Str
const { index: residueIndex } = residueIt.move();
if (isNucleic(moleculeType[residueIndex])) {
- const compId = label_comp_id.value(residueIndex);
+ const compId = label_comp_id.value(residueAtomSegments.offsets[residueIndex]);
let idxTrace: ElementIndex | -1 = -1, idxN1: ElementIndex | -1 = -1, idxC2: ElementIndex | -1 = -1, idxN3: ElementIndex | -1 = -1, idxC4: ElementIndex | -1 = -1, idxC5: ElementIndex | -1 = -1, idxC6: ElementIndex | -1 = -1, idxN7: ElementIndex | -1 = -1, idxC8: ElementIndex | -1 = -1, idxN9: ElementIndex | -1 = -1;
--
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