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VeaR/JEllipse | |||||||||
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java.lang.Object pl.krakow.cmuj.bioinformatics.jellipse.PdbFile
public class PdbFile
String operations' implementations are dirty and require more study on regexps, although they work and are quite fast.
Field Summary | |
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private short |
ATOMNAMESTART
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private short |
ATOMNAMESTOP
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private short |
CHAINCOLUMN
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private java.lang.String |
chainsids
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private int |
chainsnum
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private short |
COLUMNWIDTH
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private short |
DISTANCETOTER
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private java.lang.String |
fileContent
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private java.lang.String |
pdbid
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private short |
RESIDUENAMESTART
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private short |
RESIDUENAMESTOP
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private short |
RESIDUENUMBERSTART
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private short |
RESIDUENUMBERSTOP
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private short |
XCOORDSTART
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private short |
XCOORDSTOP
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private short |
YCOORDSTART
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private short |
YCOORDSTOP
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private short |
ZCOORDSTART
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private short |
ZCOORDSTOP
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Constructor Summary | |
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PdbFile(java.lang.String fileContent,
java.lang.String pdbid)
Creates a new instance of PdbFile |
Method Summary | |
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private void |
findChains()
Searches for chains - counts them and collects their one-letter ids. |
Peptide |
getChain(char selectedchainid)
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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private final short COLUMNWIDTH
private final short DISTANCETOTER
private final short ATOMNAMESTART
private final short ATOMNAMESTOP
private final short RESIDUENAMESTART
private final short RESIDUENAMESTOP
private final short CHAINCOLUMN
private final short RESIDUENUMBERSTART
private final short RESIDUENUMBERSTOP
private final short XCOORDSTART
private final short XCOORDSTOP
private final short YCOORDSTART
private final short YCOORDSTOP
private final short ZCOORDSTART
private final short ZCOORDSTOP
private java.lang.String pdbid
private java.lang.String fileContent
private int chainsnum
private java.lang.String chainsids
Constructor Detail |
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public PdbFile(java.lang.String fileContent, java.lang.String pdbid)
Method Detail |
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private void findChains()
public Peptide getChain(char selectedchainid)
public java.lang.String getPdbId()
public int getNumOfChains()
public java.lang.String getChainsIds()
public java.lang.String toString()
toString
in class java.lang.Object
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VeaR/JEllipse | |||||||||
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