Merge pull request #1001 from ppillot/#999_cif_parsing

#999 cif parsing

src/parser/cif-parser.ts

@@ -25,6 +25,7 @@ const reWhitespace = /\s+/
 const reQuotedWhitespace = /'((?:(?!'\s).)*)'|"((?:(?!"\s).)*)"|(\S+)/g
 const reDoubleQuote = /"/g
 const reTrimQuotes = /^['"]+|['"]+$/g
+const reAtomSymbol = /^\D{1,2}/ // atom symbol in atom_site_label
 
 interface Cif {[k: string]: any}
 
@@ -186,11 +187,20 @@ function parseCore (cif: Cif, structure: Structure, structureBuilder: StructureB
  const c = new Vector3()
  const n = cif.atom_site_type_symbol.length
 
+ const typeSymbolMap: Record<string, string> = {}
+
  for (let i = 0; i < n; ++i) {
  atomStore.growIfFull()
 
  const atomname = cif.atom_site_label[ i ]
- const element = cif.atom_site_type_symbol[ i ]
+ const typeSymbol = cif.atom_site_type_symbol[ i ]
+
+ // typeSymbol can be like `Al2.5+`. Retain element symbol only.
+ let element = typeSymbolMap[typeSymbol]
+ if (!element) {
+ const match = typeSymbol.match(reAtomSymbol)
+ typeSymbolMap[typeSymbol] = element = match?.[0] ?? typeSymbol
+ }
 
  atomStore.atomTypeId[ i ] = atomMap.add(atomname, element)
 
@@ -1072,7 +1082,7 @@ class CifParser extends StructureParser {
  _parseChunkOfLines(0, lines.length, lines)
  })
 
- if (cif.chem_comp && cif.chem_comp_atom) {
+ if (cif.chem_comp && cif.chem_comp_atom && !cif.struct) {
  parseChemComp(cif, s, sb)
  sb.finalize()
  s.finalizeAtoms()