Class MolReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader
    Direct Known Subclasses:
    JcampdxReader, Mol3DReader

    public class MolReader
    extends AtomSetCollectionReader
    A reader for MDLI mol and sdf files.

    http://www.mdli.com/downloads/public/ctfile/ctfile.jsp

    also: http://www.mdl.com/downloads/public/ctfile/ctfile.pdf simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom, x, y, z) applySymmetryAndSetTrajectory() simple 2D→3D conversion using load "xxx.mol" FILTER "2D" Jmol 14.8.2 adds bond type 15 (quintuple) and 16 (sextuple)

    • Field Detail

      • optimize2D

        private boolean optimize2D
      • haveAtomSerials

        private boolean haveAtomSerials
      • allow2D

        protected boolean allow2D
      • iatom0

        private int iatom0
      • atomCount

        private int atomCount
      • atomData

        private String[] atomData
      • is2D

        private boolean is2D
    • Constructor Detail

      • MolReader

        public MolReader()