diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index b4c65a89d297e18bb9a37790b3c39f7bbbf33904..75bec96914943b8ef01d6627bc188d49ad823d37 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -240,6 +240,10 @@ export function isNucleic(moleculeType: MoleculeType) {
return moleculeType === MoleculeType.DNA || moleculeType === MoleculeType.RNA || moleculeType === MoleculeType.PNA
}
+export function isProtein(moleculeType: MoleculeType) {
+ return moleculeType === MoleculeType.protein
+}
+
/**
* TODO write script that read CCD and outputs list of ion names
*
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 28869515a8ab573b618a463aaaf92f5b3b84927c..221b858d7af89478519e4273690b10879cbf28f6 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -16,8 +16,7 @@ import StructureElement from './element'
import { ChainIndex, ResidueIndex, ElementIndex } from '../model/indexing';
import { IntMap, SortedArray } from 'mol-data/int';
import { hash2, hashFnv32a } from 'mol-data/util';
-import { getAtomicPolymerElements, getCoarsePolymerElements, getAtomicGapElements, getCoarseGapElements } from './util/polymer';
-import { getNucleotideElements } from './util/nucleotide';
+import { getAtomicPolymerElements, getCoarsePolymerElements, getAtomicGapElements, getCoarseGapElements, getNucleotideElements, getProteinElements } from './util/polymer';
/**
* A building block of a structure that corresponds to an atomic or
@@ -126,7 +125,7 @@ namespace Unit {
* together with a tranformation (rotation and translation)
* that is dynamically applied to the underlying atom set.
*
- * An atom set can be referenced by multiple diffrent units which
+ * An atom set can be referenced by multiple different units which
* makes construction of assemblies and spacegroups very efficient.
*/
export class Atomic implements Base {
@@ -191,6 +190,12 @@ namespace Unit {
return this.props.nucleotideElements.ref;
}
+ get proteinElements() {
+ if (this.props.proteinElements.ref) return this.props.proteinElements.ref;
+ this.props.proteinElements.ref = getProteinElements(this);
+ return this.props.proteinElements.ref;
+ }
+
getResidueIndex(elementIndex: StructureElement.UnitIndex) {
return this.model.atomicHierarchy.residueAtomSegments.index[this.elements[elementIndex]];
}
@@ -215,6 +220,7 @@ namespace Unit {
polymerElements: ValueRef<SortedArray<ElementIndex> | undefined>
gapElements: ValueRef<SortedArray<ElementIndex> | undefined>
nucleotideElements: ValueRef<SortedArray<ElementIndex> | undefined>
+ proteinElements: ValueRef<SortedArray<ElementIndex> | undefined>
}
function AtomicProperties(): AtomicProperties {
@@ -224,7 +230,8 @@ namespace Unit {
rings: ValueRef.create(void 0),
polymerElements: ValueRef.create(void 0),
gapElements: ValueRef.create(void 0),
- nucleotideElements: ValueRef.create(void 0)
+ nucleotideElements: ValueRef.create(void 0),
+ proteinElements: ValueRef.create(void 0),
};
}
diff --git a/src/mol-model/structure/structure/util/nucleotide.ts b/src/mol-model/structure/structure/util/nucleotide.ts
deleted file mode 100644
index 0b77d8301c3bcdd4821a7720dd556fa0cecf4ecf..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/structure/util/nucleotide.ts
+++ /dev/null
@@ -1,31 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Unit, ElementIndex } from 'mol-model/structure';
-import { Segmentation, SortedArray } from 'mol-data/int';
-import { isNucleic } from 'mol-model/structure/model/types';
-
-export function getNucleotideElements(unit: Unit.Atomic) {
- const indices: ElementIndex[] = []
- const { elements, model } = unit
- const { chainAtomSegments, residueAtomSegments } = model.atomicHierarchy
- const { moleculeType, traceElementIndex } = model.atomicHierarchy.derived.residue
- const chainIt = Segmentation.transientSegments(chainAtomSegments, elements)
- const residueIt = Segmentation.transientSegments(residueAtomSegments, elements)
- while (chainIt.hasNext) {
- residueIt.setSegment(chainIt.move());
-
- while (residueIt.hasNext) {
- const { index } = residueIt.move();
-
- if (isNucleic(moleculeType[index])) {
- const elementIndex = traceElementIndex[index]
- indices.push(elementIndex === -1 ? residueAtomSegments.offsets[index] : elementIndex)
- }
- }
- }
- return SortedArray.ofSortedArray<ElementIndex>(indices)
-}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/util/polymer.ts b/src/mol-model/structure/structure/util/polymer.ts
index 951e74807430044b6ef8fd5903cd2dbb22710c0d..ff60719d4811899e5cf2ccbd1f66333fa0e3293d 100644
--- a/src/mol-model/structure/structure/util/polymer.ts
+++ b/src/mol-model/structure/structure/util/polymer.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -7,6 +7,7 @@
import { Unit, ElementIndex } from 'mol-model/structure';
import { Segmentation, OrderedSet, Interval, SortedArray } from 'mol-data/int';
import SortedRanges from 'mol-data/int/sorted-ranges';
+import { isNucleic, isProtein } from 'mol-model/structure/model/types';
export function getAtomicPolymerElements(unit: Unit.Atomic) {
const indices: ElementIndex[] = []
@@ -43,6 +44,8 @@ export function getCoarsePolymerElements(unit: Unit.Spheres | Unit.Gaussians) {
return SortedArray.ofSortedArray<ElementIndex>(indices)
}
+//
+
export function getAtomicGapElements(unit: Unit.Atomic) {
const indices: ElementIndex[] = []
const { elements, model, residueIndex } = unit
@@ -73,4 +76,50 @@ export function getCoarseGapElements(unit: Unit.Spheres | Unit.Gaussians) {
indices.push(elements[start], elements[end - 1])
}
return SortedArray.ofSortedArray<ElementIndex>(indices)
+}
+
+//
+
+export function getNucleotideElements(unit: Unit.Atomic) {
+ const indices: ElementIndex[] = []
+ const { elements, model } = unit
+ const { chainAtomSegments, residueAtomSegments } = model.atomicHierarchy
+ const { moleculeType, traceElementIndex } = model.atomicHierarchy.derived.residue
+ const chainIt = Segmentation.transientSegments(chainAtomSegments, elements)
+ const residueIt = Segmentation.transientSegments(residueAtomSegments, elements)
+ while (chainIt.hasNext) {
+ residueIt.setSegment(chainIt.move());
+
+ while (residueIt.hasNext) {
+ const { index } = residueIt.move();
+
+ if (isNucleic(moleculeType[index])) {
+ const elementIndex = traceElementIndex[index]
+ indices.push(elementIndex === -1 ? residueAtomSegments.offsets[index] : elementIndex)
+ }
+ }
+ }
+ return SortedArray.ofSortedArray<ElementIndex>(indices)
+}
+
+export function getProteinElements(unit: Unit.Atomic) {
+ const indices: ElementIndex[] = []
+ const { elements, model } = unit
+ const { chainAtomSegments, residueAtomSegments } = model.atomicHierarchy
+ const { moleculeType, traceElementIndex } = model.atomicHierarchy.derived.residue
+ const chainIt = Segmentation.transientSegments(chainAtomSegments, elements)
+ const residueIt = Segmentation.transientSegments(residueAtomSegments, elements)
+ while (chainIt.hasNext) {
+ residueIt.setSegment(chainIt.move());
+
+ while (residueIt.hasNext) {
+ const { index } = residueIt.move();
+
+ if (isProtein(moleculeType[index])) {
+ const elementIndex = traceElementIndex[index]
+ indices.push(elementIndex === -1 ? residueAtomSegments.offsets[index] : elementIndex)
+ }
+ }
+ }
+ return SortedArray.ofSortedArray<ElementIndex>(indices)
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/util/nucleotide.ts b/src/mol-repr/structure/visual/util/nucleotide.ts
index 8e8ed71d1e3ad7de88cede0d4e6d5000bb6e77ef..f97703e71dd3bce59823b0439fbba85e35bcacbe 100644
--- a/src/mol-repr/structure/visual/util/nucleotide.ts
+++ b/src/mol-repr/structure/visual/util/nucleotide.ts
@@ -5,7 +5,6 @@
*/
import { Unit, StructureElement, Structure } from 'mol-model/structure';
-import { getNucleotideElements } from 'mol-model/structure/structure/util/nucleotide';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { OrderedSet, Interval } from 'mol-data/int';
import { LocationIterator } from 'mol-geo/util/location-iterator';
@@ -16,7 +15,7 @@ import { getResidueLoci } from './common';
export namespace NucleotideLocationIterator {
export function fromGroup(group: Unit.SymmetryGroup): LocationIterator {
const u = group.units[0]
- const nucleotideElementIndices = Unit.isAtomic(u) ? getNucleotideElements(u) : []
+ const nucleotideElementIndices = Unit.isAtomic(u) ? u.nucleotideElements : []
const groupCount = nucleotideElementIndices.length
const instanceCount = group.units.length
const location = StructureElement.create()