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

Constructors

Constructor and Description
FileConvert(Structure struc) Constructs a FileConvert object.

Method Summary

Methods

Modifier and Type	Method and Description
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 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.

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 - ...