Class MdTopReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader

    public class MdTopReader
    extends ForceFieldReader
    A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file

    PDB note: Note that topology format does not include chain designations, chain terminator, chain designator, or element symbol. Chains based on numbering reset just labeled A B C D .... Z a b c d .... z Element symbols based on reasoned guess and properties of hetero groups In principal we could use average atomic mass.

    • Field Detail

      • nAtoms

        private int nAtoms
      • ac

        private int ac
      • atomTypes

        private java.lang.String[] atomTypes
      • group3s

        java.lang.String[] group3s
    • Constructor Detail

      • MdTopReader

        public MdTopReader()
    • Method Detail

      • checkLine

        protected boolean checkLine()
                             throws java.lang.Exception
        Overrides:
        checkLine in class AtomSetCollectionReader
        Returns:
        true if need to read new line
        Throws:
        java.lang.Exception
      • getDataBlock

        private java.lang.String[] getDataBlock()
                                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getPointers

        private void getPointers()
                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getAtomTypes

        private void getAtomTypes()
                           throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getCharges

        private void getCharges()
                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getResiduePointers

        private void getResiduePointers()
                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getResidueLabels

        private void getResidueLabels()
                               throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getAtomNames

        private void getAtomNames()
                           throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getMasses

        private void getMasses()
                        throws java.lang.Exception
        Throws:
        java.lang.Exception