pl.krakow.cmuj.bioinformatics.jellipse
Class PdbFile

java.lang.Object
  pl.krakow.cmuj.bioinformatics.jellipse.PdbFile

public class PdbFile
extends java.lang.Object

String operations' implementations are dirty and require more study on regexps, although they work and are quite fast.

Field Summary

private short	ATOMNAMESTART
private short	ATOMNAMESTOP
private short	CHAINCOLUMN
private java.lang.String	chainsids
private int	chainsnum
private short	COLUMNWIDTH
private short	DISTANCETOTER
private java.lang.String	fileContent
private java.lang.String	pdbid
private short	RESIDUENAMESTART
private short	RESIDUENAMESTOP
private short	RESIDUENUMBERSTART
private short	RESIDUENUMBERSTOP
private short	XCOORDSTART
private short	XCOORDSTOP
private short	YCOORDSTART
private short	YCOORDSTOP
private short	ZCOORDSTART
private short	ZCOORDSTOP

Constructor Summary

PdbFile(java.lang.String fileContent, java.lang.String pdbid)
Creates a new instance of PdbFile

Method Summary

private void	findChains() Searches for chains - counts them and collects their one-letter ids.
Peptide	getChain(char selectedchainid)
java.lang.String	getChainsIds() Gives chain ids (each is a one-letter).
int	getNumOfChains() Gives the number of chains (mainly separate polypeptides) of which crystallographic data was stored in a pdb file.
java.lang.String	getPdbId() Gives PDB ID in uppercase for this PdbFile object.
java.lang.String	toString() Enables getting whole content of the file stored in the current PdbFile object

Methods inherited from class java.lang.Object

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

Field Detail

COLUMNWIDTH

private final short COLUMNWIDTH

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Constant Field Values

DISTANCETOTER

private final short DISTANCETOTER

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Constant Field Values

ATOMNAMESTART

private final short ATOMNAMESTART

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Constant Field Values

ATOMNAMESTOP

private final short ATOMNAMESTOP

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Constant Field Values

RESIDUENAMESTART

private final short RESIDUENAMESTART

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Constant Field Values

RESIDUENAMESTOP

private final short RESIDUENAMESTOP

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Constant Field Values

CHAINCOLUMN

private final short CHAINCOLUMN

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Constant Field Values

RESIDUENUMBERSTART

private final short RESIDUENUMBERSTART

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Constant Field Values

RESIDUENUMBERSTOP

private final short RESIDUENUMBERSTOP

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Constant Field Values

XCOORDSTART

private final short XCOORDSTART

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Constant Field Values

XCOORDSTOP

private final short XCOORDSTOP

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Constant Field Values

YCOORDSTART

private final short YCOORDSTART

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Constant Field Values

YCOORDSTOP

private final short YCOORDSTOP

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Constant Field Values

ZCOORDSTART

private final short ZCOORDSTART

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Constant Field Values

ZCOORDSTOP

private final short ZCOORDSTOP

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Constant Field Values

pdbid

private java.lang.String pdbid

fileContent

private java.lang.String fileContent

chainsnum

private int chainsnum

chainsids

private java.lang.String chainsids

Constructor Detail

PdbFile

public PdbFile(java.lang.String fileContent,
               java.lang.String pdbid)

Creates a new instance of PdbFile

Method Detail

findChains

private void findChains()

Searches for chains - counts them and collects their one-letter ids. Modifies private values of numofchains and chainids.

getChain

public Peptide getChain(char selectedchainid)

getPdbId

public java.lang.String getPdbId()

Gives PDB ID in uppercase for this PdbFile object.

Returns:

PDB ID - a digit and three uppercased letters

getNumOfChains

public int getNumOfChains()

Gives the number of chains (mainly separate polypeptides) of which crystallographic data was stored in a pdb file.

Returns:

number of marked chains in a pdb file (that means - for the current PdbFile object)

getChainsIds

public java.lang.String getChainsIds()

Gives chain ids (each is a one-letter).

Returns:

ids of chains stored in the current pdb file as concatenated letters

toString

public java.lang.String toString()

Enables getting whole content of the file stored in the current PdbFile object

Overrides:

toString in class java.lang.Object

Returns:

plain pdb file content