Package org.biojava.nbio.structure.io

Class FileConvert

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

    • 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 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​(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

      • 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