added chemCompType and other mol-script improvements

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))),

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

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.`),
     }
 }
 

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 ================
 ];

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'),