From 82e667e402e872df613c1e7df52ac25313ddba47 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 8 Aug 2019 17:16:47 -0700
Subject: [PATCH] added chemCompType and other mol-script improvements
---
src/mol-model/structure/structure/properties.ts | 15 +++++++++++++--
src/mol-script/language/builder.ts | 17 +++++++++++++----
.../language/symbol-table/structure-query.ts | 2 +-
src/mol-script/runtime/query/table.ts | 14 +++++---------
src/mol-script/script/mol-script/symbols.ts | 1 +
5 files changed, 33 insertions(+), 16 deletions(-)
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index 29c21954a..8826d1019 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -53,19 +53,30 @@ const atom = {
vdw_radius: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : VdwRadius(l.unit.model.atomicHierarchy.atoms.type_symbol.value(l.element))),
}
+function compId(l: StructureElement) {
+ return !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.label_comp_id.value(l.unit.residueIndex[l.element])
+}
+
const residue = {
key: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.residueIndex[l.element]),
group_PDB: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.group_PDB.value(l.unit.residueIndex[l.element])),
- label_comp_id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.label_comp_id.value(l.unit.residueIndex[l.element])),
+ label_comp_id: p(compId),
auth_comp_id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.auth_comp_id.value(l.unit.residueIndex[l.element])),
label_seq_id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.label_seq_id.value(l.unit.residueIndex[l.element])),
auth_seq_id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.element])),
pdbx_PDB_ins_code: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.pdbx_PDB_ins_code.value(l.unit.residueIndex[l.element])),
// Properties
+ isModified: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.modifiedResidues.parentId.has(compId(l))),
+ modifiedParentName: p(l => {
+ if (!Unit.isAtomic(l.unit)) notAtomic()
+ const id = compId(l)
+ return l.unit.model.properties.modifiedResidues.parentId.get(id) || id
+ }),
secondary_structure_type: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.type[l.unit.residueIndex[l.element]]),
secondary_structure_key: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.key[l.unit.residueIndex[l.element]]),
+ chem_comp_type: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.chemicalComponentMap.get(compId(l))!.type),
}
const chain = {
@@ -107,7 +118,7 @@ function eK(l: StructureElement) {
}
const entity = {
- key: eK,
+ key: p(eK),
id: p(l => l.unit.model.entities.data.id.value(eK(l))),
type: p(l => l.unit.model.entities.data.type.value(eK(l))),
diff --git a/src/mol-script/language/builder.ts b/src/mol-script/language/builder.ts
index 8c7efa07d..c114c0ff6 100644
--- a/src/mol-script/language/builder.ts
+++ b/src/mol-script/language/builder.ts
@@ -12,27 +12,36 @@ export namespace MolScriptBuilder {
export const core = SymbolTable.core;
export const struct = SymbolTable.structureQuery;
+ /** Atom-name constructor */
export function atomName(s: string) { return struct.type.atomName([s]); }
+ /** Element-symbol constructor */
export function es(s: string) { return struct.type.elementSymbol([s]); }
+ /** List constructor */
export function list(...xs: Expression[]) { return core.type.list(xs); }
+ /** Set constructor */
export function set(...xs: Expression[]) { return core.type.set(xs); }
+ /** RegEx constructor */
+ export function re(pattern: string, flags?: string) { return core.type.regex([pattern, flags]); }
+ /** Function constructor */
export function fn(x: Expression) { return core.ctrl.fn([x]); }
export function evaluate(x: Expression) { return core.ctrl.eval([x]); }
const _acp = struct.atomProperty.core, _ammp = struct.atomProperty.macromolecular, _atp = struct.atomProperty.topology;
- // atom core property
+ /** atom core property */
export function acp(p: keyof typeof _acp) { return (_acp[p] as MSymbol<any>)() };
- // atom topology property
+ /** atom topology property */
export function atp(p: keyof typeof _atp) { return (_atp[p] as MSymbol<any>)() };
- // atom macromolecular property
+ /** atom macromolecular property */
export function ammp(p: keyof typeof _ammp) { return (_ammp[p] as MSymbol<any>)() };
- // atom property sets
const _aps = struct.atomSet.propertySet
+ /** atom core property set */
export function acpSet(p: keyof typeof _acp) { return _aps([ acp(p) ]) };
+ /** atom topology property set */
export function atpSet(p: keyof typeof _atp) { return _aps([ atp(p) ]) };
+ /** atom macromolecular property set */
export function ammpSet(p: keyof typeof _ammp) { return _aps([ ammp(p) ]) };
}
\ No newline at end of file
diff --git a/src/mol-script/language/symbol-table/structure-query.ts b/src/mol-script/language/symbol-table/structure-query.ts
index 252c1b8ac..c2b04dedc 100644
--- a/src/mol-script/language/symbol-table/structure-query.ts
+++ b/src/mol-script/language/symbol-table/structure-query.ts
@@ -300,9 +300,9 @@ const atomProperty = {
secondaryStructureKey: atomProp(Type.AnyValue, 'Unique value for each secondary structure element.'),
secondaryStructureFlags: atomProp(Types.SecondaryStructureFlags),
-
isModified: atomProp(Type.Bool, 'True if the atom bolongs to modification of a standard residue.'),
modifiedParentName: atomProp(Type.Str, `'3-letter' code of the modifed parent residue.`),
+ chemCompType: atomProp(Type.Str, `Type of the chemical component as defined in mmCIF.`),
}
}
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index eeb4edc18..6ca3a8807 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -301,15 +301,11 @@ const symbols = [
D(MolScript.structureQuery.atomProperty.macromolecular.entityType, atomProp(StructureProperties.entity.type)),
D(MolScript.structureQuery.atomProperty.macromolecular.objectPrimitive, atomProp(StructureProperties.unit.object_primitive)),
- D(MolScript.structureQuery.atomProperty.macromolecular.isModified, (ctx, _) => ctx.element.unit.model.properties.modifiedResidues.parentId.has(StructureProperties.residue.label_comp_id(ctx.element))),
- D(MolScript.structureQuery.atomProperty.macromolecular.modifiedParentName, (ctx, _) => {
- const id = StructureProperties.residue.label_comp_id(ctx.element);
- return ctx.element.unit.model.properties.modifiedResidues.parentId.get(id) || id
- })
-
- // TODO
- // MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureKey
- // MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureFlags
+ D(MolScript.structureQuery.atomProperty.macromolecular.isModified, atomProp(StructureProperties.residue.isModified)),
+ D(MolScript.structureQuery.atomProperty.macromolecular.modifiedParentName, atomProp(StructureProperties.residue.modifiedParentName)),
+ D(MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureKey, atomProp(StructureProperties.residue.secondary_structure_key)),
+ D(MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureFlags, atomProp(StructureProperties.residue.secondary_structure_type)),
+ D(MolScript.structureQuery.atomProperty.macromolecular.chemCompType, atomProp(StructureProperties.residue.chem_comp_type)),
// ============= BOND PROPERTIES ================
];
diff --git a/src/mol-script/script/mol-script/symbols.ts b/src/mol-script/script/mol-script/symbols.ts
index 7c2566ca4..2018030dc 100644
--- a/src/mol-script/script/mol-script/symbols.ts
+++ b/src/mol-script/script/mol-script/symbols.ts
@@ -230,6 +230,7 @@ export const SymbolTable = [
Alias(MolScript.structureQuery.atomProperty.macromolecular.B_iso_or_equiv, 'atom.B_iso_or_equiv', 'atom.bfactor'),
Alias(MolScript.structureQuery.atomProperty.macromolecular.entityType, 'atom.entity-type'),
Alias(MolScript.structureQuery.atomProperty.macromolecular.objectPrimitive, 'atom.object-primitive'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.chemCompType, 'atom.chem-comp-type'),
Alias(MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureKey, 'atom.key.sec-struct'),
--
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