Package org.biojava.nbio.structure.io

Class FileConvert

java.lang.Object
org.biojava.nbio.structure.io.FileConvert
public class FileConvert extends Object
Methods to convert a structure object into different file formats.
Since:
1.4
Author:
Andreas Prlic

  • Field Details

  • Constructor Details

    • FileConvert

      public FileConvert(Structure struc)
      Constructs a FileConvert object.
      Parameters:
      struc - a Structure object

  • Method Details

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

    • toPDB

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

    • toPDB

      public static String toPDB(Atom a, String chainId)

    • toPDB

      public static String toPDB(Chain chain)
      Convert a Chain object to PDB representation
      Parameters:
      chain -
      Returns:

    • toPDB

      public static String toPDB(Group g)
      Convert a Group object to PDB representation
      Parameters:
      g -
      Returns:

    • toPDB

      public static void toPDB(Atom a, StringBuffer str, 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, StringBuffer str)

    • toDASStructure

      public void toDASStructure(XMLWriter xw) throws 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:
      IOException - ...

    • toMMCIF

      public String toMMCIF()
      Convert this structure to its CIF representation.
      Returns:
      a String representing this structure as CIF

    • toMMCIF

      public static String toMMCIF(Chain chain)
      Convert a chain to its CIF representation.
      Parameters:
      chain - data
      Returns:
      a String representing this chain as CIF