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 Summary

Fields

Modifier and Type	Field and Description
static DecimalFormat	d2
static DecimalFormat	d3

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
boolean	doPrintConnections() Returns if the Connections should be added default is true;
static String	getAtomSiteHeader()
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	toMMCIF()
static String	toMMCIF(Chain chain, boolean writeHeader)
static String	toMMCIF(Chain chain, String authId, String asymId, boolean writeHeader)
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 String	toPDB(Atom a, String chainId)
static void	toPDB(Atom a, StringBuffer str)
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.
static String	toPDB(Chain chain) Convert a Chain object to PDB representation
static String	toPDB(Group g) Convert a Group object to PDB representation

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

d3

public static DecimalFormat d3

d2

public static DecimalFormat d2

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(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()

toMMCIF

public static String toMMCIF(Chain chain,
                             String authId,
                             String asymId,
                             boolean writeHeader)

toMMCIF

public static String toMMCIF(Chain chain,
                             boolean writeHeader)

getAtomSiteHeader

public static String getAtomSiteHeader()