Class MolReader

java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.molxyz.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 Details

    • haveAtomSerials

      private boolean haveAtomSerials
    • allow2D

      protected boolean allow2D
    • iatom0

      private int iatom0
    • vr

      private V3000Rdr vr
    • atomCount

      private int atomCount
    • atomData

      private String[] atomData
    • bsDeleted

      public javajs.util.BS bsDeleted
    • fixN

      private boolean fixN
      fix charges for RN(=O)(O), =N(O)*, =N
  • Constructor Details

    • MolReader

      public MolReader()
  • Method Details