From 67f3f3fdbb84265f3e1b9d1fe7728e93b519afcd Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 20 Jun 2019 15:42:23 -0700
Subject: [PATCH] improved AtomsQueryParams.unitTest and
StructureProperties.unit
---
.../structure/query/queries/generators.ts | 15 +++++++++++----
src/mol-model/structure/structure/properties.ts | 7 ++++++-
2 files changed, 17 insertions(+), 5 deletions(-)
diff --git a/src/mol-model/structure/query/queries/generators.ts b/src/mol-model/structure/query/queries/generators.ts
index e0984e91a..3afd35b21 100644
--- a/src/mol-model/structure/query/queries/generators.ts
+++ b/src/mol-model/structure/query/queries/generators.ts
@@ -21,6 +21,8 @@ export const none: StructureQuery = ctx => StructureSelection.Sequence(ctx.input
export const all: StructureQuery = ctx => StructureSelection.Singletons(ctx.inputStructure, ctx.inputStructure);
export interface AtomsQueryParams {
+ /** Query to be executed for each unit once */
+ unitTest: QueryPredicate,
/** Query to be executed for each entity once */
entityTest: QueryPredicate,
/** Query to be executed for each chain once */
@@ -39,10 +41,11 @@ function _true(ctx: QueryContextView) { return true; }
function _zero(ctx: QueryContextView) { return 0; }
export function atoms(params?: Partial<AtomsQueryParams>): StructureQuery {
- if (!params || (!params.atomTest && !params.residueTest && !params.chainTest && !params.entityTest && !params.groupBy)) return all;
- if (!!params.atomTest && !params.residueTest && !params.chainTest && !params.entityTest && !params.groupBy) return atomGroupsLinear(params.atomTest);
+ if (!params || (!params.atomTest && !params.residueTest && !params.chainTest && !params.entityTest && !params.unitTest && !params.groupBy)) return all;
+ if (!!params.atomTest && !params.residueTest && !params.chainTest && !params.entityTest && !params.unitTest && !params.groupBy) return atomGroupsLinear(params.atomTest);
const normalized: AtomsQueryParams = {
+ unitTest: params.unitTest || _true,
entityTest: params.entityTest || _true,
chainTest: params.chainTest || _true,
residueTest: params.residueTest || _true,
@@ -79,7 +82,7 @@ function atomGroupsLinear(atomTest: QueryPredicate): StructureQuery {
};
}
-function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: AtomsQueryParams): StructureQuery {
+function atomGroupsSegmented({ unitTest, entityTest, chainTest, residueTest, atomTest }: AtomsQueryParams): StructureQuery {
return ctx => {
const { inputStructure } = ctx;
const { units } = inputStructure;
@@ -88,6 +91,8 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
for (const unit of units) {
l.unit = unit;
+ if (!unitTest(ctx)) continue;
+
const { elements, model } = unit;
builder.beginUnit(unit.id);
@@ -146,7 +151,7 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
};
}
-function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, groupBy }: AtomsQueryParams): StructureQuery {
+function atomGroupsGrouped({ unitTest, entityTest, chainTest, residueTest, atomTest, groupBy }: AtomsQueryParams): StructureQuery {
return ctx => {
const { inputStructure } = ctx;
const { units } = inputStructure;
@@ -155,6 +160,8 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
for (const unit of units) {
l.unit = unit;
+ if (!unitTest(ctx)) continue;
+
const { elements, model } = unit;
if (unit.kind === Unit.Kind.Atomic) {
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index ce4d02dc1..70a449b21 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -111,8 +111,13 @@ const entity = {
}
const unit = {
+ id: StructureElement.property(l => l.unit.id),
operator_name: StructureElement.property(l => l.unit.conformation.operator.name),
- model_num: StructureElement.property(l => l.unit.model.modelNum)
+
+ model_num: StructureElement.property(l => l.unit.model.modelNum),
+ pdbx_struct_assembly_id: StructureElement.property(l => l.unit.conformation.operator.assembly.id),
+ pdbx_struct_oper_list_ids: StructureElement.property(l => l.unit.conformation.operator.assembly.operList),
+ struct_ncs_oper_id: StructureElement.property(l => l.unit.conformation.operator.ncsId),
}
const StructureProperties = {
--
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