org.biojava.bio.structure.io
Class FileConvert

java.lang.Object
  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 - ...