org.biojava.bio.structure.io
Class FileConvert

java.lang.Object
  extended by org.biojava.bio.structure.io.FileConvert

public class FileConvert
extends Object

Methods to convert a structure object into different file formats.

Since:
1.4
Author:
Andreas Prlic

Constructor Summary
FileConvert(Structure struc)
          Constructs a FileConvert object.
 
Method Summary
 boolean doPrintConnections()
          returns if the Connections should be added default is true;
 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 .
 String toPDB()
          Convert a structure into a PDB file.
static String toPDB(Atom a)
          Prints the content of an Atom object as a PDB formatted line.
static void toPDB(Atom a, StringBuffer str)
          print ATOM record in the following syntax
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

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 void toPDB(Atom a,
                         StringBuffer str)
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.


toDASStructure

public void toDASStructure(XMLWriter xw)
                    throws IOException
convert a protein Structure to a DAS Structure XML response .

Parameters:
xw - a XMLWriter object
Throws:
IOException - ...