Class FileConvert


  • public class FileConvert
    extends java.lang.Object
    Methods to convert a structure object into different file formats.
    Since:
    1.4
    Author:
    Andreas Prlic
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.text.DecimalFormat d2  
      static java.text.DecimalFormat d3  
    • Constructor Summary

      Constructors 
      Constructor Description
      FileConvert​(Structure struc)
      Constructs a FileConvert object.
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean doPrintConnections()
      Returns if the Connections should be added default is true;
      static java.lang.String getAtomSiteHeader()  
      void setPrintConnections​(boolean printConnections)
      enable/disable printing of connections connections are sometimes buggy in PDB files so there are some cases where one might turn this off.
      void toDASStructure​(XMLWriter xw)
      Convert a protein Structure to a DAS Structure XML response .
      java.lang.String toMMCIF()  
      static java.lang.String toMMCIF​(Chain chain, boolean writeHeader)  
      static java.lang.String toMMCIF​(Chain chain, java.lang.String authId, java.lang.String asymId, boolean writeHeader)  
      java.lang.String toPDB()
      Convert a structure into a PDB file.
      static java.lang.String toPDB​(Atom a)
      Prints the content of an Atom object as a PDB formatted line.
      static java.lang.String toPDB​(Atom a, java.lang.String chainId)  
      static void toPDB​(Atom a, java.lang.StringBuffer str)  
      static void toPDB​(Atom a, java.lang.StringBuffer str, java.lang.String chainID)
      Print ATOM record in the following syntax
      static java.lang.String toPDB​(Chain chain)
      Convert a Chain object to PDB representation
      static java.lang.String toPDB​(Group g)
      Convert a Group object to PDB representation
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • d3

        public static java.text.DecimalFormat d3
      • d2

        public static java.text.DecimalFormat d2
    • Constructor Detail

      • FileConvert

        public FileConvert​(Structure struc)
        Constructs a FileConvert object.
        Parameters:
        struc - a Structure object
    • Method Detail

      • doPrintConnections

        public boolean doPrintConnections()
        Returns if the Connections should be added default is true;
        Returns:
        if the printConnections flag is set
      • setPrintConnections

        public void setPrintConnections​(boolean printConnections)
        enable/disable printing of connections connections are sometimes buggy in PDB files so there are some cases where one might turn this off.
        Parameters:
        printConnections -
      • toPDB

        public java.lang.String toPDB()
        Convert a structure into a PDB file.
        Returns:
        a String representing a PDB file.
      • toPDB

        public static java.lang.String toPDB​(Atom a)
        Prints the content of an Atom object as a PDB formatted line.
        Parameters:
        a -
        Returns:
      • toPDB

        public static java.lang.String toPDB​(Atom a,
                                             java.lang.String chainId)
      • toPDB

        public static java.lang.String toPDB​(Chain chain)
        Convert a Chain object to PDB representation
        Parameters:
        chain -
        Returns:
      • toPDB

        public static java.lang.String toPDB​(Group g)
        Convert a Group object to PDB representation
        Parameters:
        g -
        Returns:
      • toPDB

        public static void toPDB​(Atom a,
                                 java.lang.StringBuffer str,
                                 java.lang.String chainID)
        Print ATOM record in the following syntax
         ATOM      1  N   ASP A  15     110.964  24.941  59.191  1.00 83.44           N
        
         COLUMNS        DATA TYPE       FIELD         DEFINITION
         ---------------------------------------------------------------------------------
         1 -  6        Record name     "ATOM  "
         7 - 11        Integer         serial        Atom serial number.
         13 - 16        Atom            name          Atom name.
         17             Character       altLoc        Alternate location indicator.
         18 - 20        Residue name    resName       Residue name.
         22             Character       chainID       Chain identifier.
         23 - 26        Integer         resSeq        Residue sequence number.
         27             AChar           iCode         Code for insertion of residues.
         31 - 38        Real(8.3)       x             Orthogonal coordinates for X in
         Angstroms.
         39 - 46        Real(8.3)       y             Orthogonal coordinates for Y in
         Angstroms.
         47 - 54        Real(8.3)       z             Orthogonal coordinates for Z in
         Angstroms.
         55 - 60        Real(6.2)       occupancy     Occupancy.
         61 - 66        Real(6.2)       tempFactor    Temperature factor.
         73 - 76        LString(4)      segID         Segment identifier, left-justified.
         77 - 78        LString(2)      element       Element symbol, right-justified.
         79 - 80        LString(2)      charge        Charge on the atom.
         
        Parameters:
        a -
        str -
        chainID - the chain ID that the Atom will have in the output string
      • toPDB

        public static void toPDB​(Atom a,
                                 java.lang.StringBuffer str)
      • toDASStructure

        public void toDASStructure​(XMLWriter xw)
                            throws java.io.IOException
        Convert a protein Structure to a DAS Structure XML response . Since 5.0, bond (CONECT records) information is not supported anymore.
        Parameters:
        xw - a XMLWriter object
        Throws:
        java.io.IOException - ...
      • toMMCIF

        public java.lang.String toMMCIF()
      • toMMCIF

        public static java.lang.String toMMCIF​(Chain chain,
                                               java.lang.String authId,
                                               java.lang.String asymId,
                                               boolean writeHeader)
      • toMMCIF

        public static java.lang.String toMMCIF​(Chain chain,
                                               boolean writeHeader)
      • getAtomSiteHeader

        public static java.lang.String getAtomSiteHeader()