From e8df2a6555e3a7850823ea154dcf0066e85e41d6 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 11 Jul 2018 12:32:56 +0200
Subject: [PATCH] Coarse hierarchy refactor
---
src/mol-geo/representation/structure/visual/util/polymer.ts | 4 ++--
src/mol-model/structure/model/formats/mmcif/ihm.ts | 6 +++---
.../structure/model/properties/coarse/hierarchy.ts | 4 ++--
.../structure/model/properties/utils/coarse-keys.ts | 6 +++---
src/mol-model/structure/structure/structure.ts | 6 +++---
5 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index 6234a27cd..4c80e9466 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -215,10 +215,10 @@ export class CoarsePolymerBackboneIterator<T extends number = number> implements
}
constructor(unit: Unit.Spheres | Unit.Gaussians) {
- const { polymerSegments } = Unit.isSpheres(unit)
+ const { polymerElementSegments } = Unit.isSpheres(unit)
? unit.model.coarseHierarchy.spheres
: unit.model.coarseHierarchy.gaussians
- this.polymerIt = Segmentation.transientSegments(polymerSegments, unit.elements);
+ this.polymerIt = Segmentation.transientSegments(polymerElementSegments, unit.elements);
this.pos = unit.conformation.invariantPosition
this.value = createPolymerBackbonePair(unit)
diff --git a/src/mol-model/structure/model/formats/mmcif/ihm.ts b/src/mol-model/structure/model/formats/mmcif/ihm.ts
index 35d307a4e..04a5b2ec7 100644
--- a/src/mol-model/structure/model/formats/mmcif/ihm.ts
+++ b/src/mol-model/structure/model/formats/mmcif/ihm.ts
@@ -12,7 +12,7 @@ import { getCoarseKeys } from '../../properties/utils/coarse-keys';
import { UUID } from 'mol-util';
import { Segmentation, Interval } from 'mol-data/int';
import { Mat3, Tensor } from 'mol-math/linear-algebra';
-import { ElementIndex } from '../../indexing';
+import { ElementIndex, ChainIndex } from '../../indexing';
export interface IHMData {
model_id: number,
@@ -92,8 +92,8 @@ function getSegments(asym_id: Column<string>, seq_id_begin: Column<number>, seq_
}
return {
- chainSegments: Segmentation.ofOffsets(chainOffsets, Interval.ofBounds(0, asym_id.rowCount)),
- polymerSegments: Segmentation.ofOffsets(polymerOffsets, Interval.ofBounds(0, asym_id.rowCount))
+ chainElementSegments: Segmentation.ofOffsets<ElementIndex, ChainIndex>(chainOffsets, Interval.ofBounds(0, asym_id.rowCount)),
+ polymerElementSegments: Segmentation.ofOffsets(polymerOffsets, Interval.ofBounds(0, asym_id.rowCount))
}
}
diff --git a/src/mol-model/structure/model/properties/coarse/hierarchy.ts b/src/mol-model/structure/model/properties/coarse/hierarchy.ts
index 89e74fcba..f06d3d57a 100644
--- a/src/mol-model/structure/model/properties/coarse/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/coarse/hierarchy.ts
@@ -27,12 +27,12 @@ export interface CoarseElementData {
seq_id_begin: Column<number>,
seq_id_end: Column<number>,
- chainSegments: Segmentation<ElementIndex>,
+ chainElementSegments: Segmentation<ElementIndex, ChainIndex>,
/**
* bonded/connected stretches of polymer chains, i.e. a chain will be
* broken into multiple polymer segments if there are missing residues
*/
- polymerSegments: Segmentation<ElementIndex>
+ polymerElementSegments: Segmentation<ElementIndex>
}
export type CoarseElements = CoarsedElementKeys & CoarseElementData
diff --git a/src/mol-model/structure/model/properties/utils/coarse-keys.ts b/src/mol-model/structure/model/properties/utils/coarse-keys.ts
index ac3b75edf..a20d723bf 100644
--- a/src/mol-model/structure/model/properties/utils/coarse-keys.ts
+++ b/src/mol-model/structure/model/properties/utils/coarse-keys.ts
@@ -52,7 +52,7 @@ function missingEntity(k: string) {
}
export function getCoarseKeys(data: CoarseElementData, entities: Entities): CoarsedElementKeys {
- const { entity_id, asym_id, seq_id_begin, seq_id_end, count, chainSegments } = data;
+ const { entity_id, asym_id, seq_id_begin, seq_id_end, count, chainElementSegments } = data;
const seqMaps = new Map<number, Map<number, number>>();
const chainMaps = new Map<number, Map<string, number>>(), chainCounter = { index: 0 };
@@ -65,8 +65,8 @@ export function getCoarseKeys(data: CoarseElementData, entities: Entities): Coar
if (entityKey[i] < 0) missingEntity(entity_id.value(i));
}
- for (let cI = 0; cI < chainSegments.count; cI++) {
- const start = chainSegments.offsets[cI], end = chainSegments.offsets[cI + 1];
+ for (let cI = 0; cI < chainElementSegments.count; cI++) {
+ const start = chainElementSegments.offsets[cI], end = chainElementSegments.offsets[cI + 1];
const map = getElementSubstructureKeyMap(chainMaps, entityKey[start]);
const key = getElementKey(map, asym_id.value(start), chainCounter);
for (let i = start; i < end; i++) chainKey[i] = key;
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 1be5f7ff6..1e806d8d8 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -149,9 +149,9 @@ namespace Structure {
}
function addCoarseUnits(builder: StructureBuilder, model: Model, elements: CoarseElements, kind: Unit.Kind) {
- const { chainSegments } = elements;
- for (let cI = 0; cI < chainSegments.count; cI++) {
- const elements = SortedArray.ofBounds<ElementIndex>(chainSegments.offsets[cI], chainSegments.offsets[cI + 1]);
+ const { chainElementSegments } = elements;
+ for (let cI = 0; cI < chainElementSegments.count; cI++) {
+ const elements = SortedArray.ofBounds<ElementIndex>(chainElementSegments.offsets[cI], chainElementSegments.offsets[cI + 1]);
builder.addUnit(kind, model, SymmetryOperator.Default, elements);
}
}
--
GitLab