ProGAL.proteins.belta
Class PDBFile

java.lang.Object
  java.io.File
      ProGAL.proteins.PDBFile
          ProGAL.proteins.belta.PDBFile

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<java.io.File>

public class PDBFile
extends PDBFile

Quick note: One important feature of this extension of the normal PDBFile is that all indices are shifted so they are consecutive, which is required for betatopologies and secondary structures to make sense and not crash. TODO:

• Fetching secondary structures from other chains than the standard
• Comment and test

Author:

R.Fonseca

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class ProGAL.proteins.PDBFile

PDBFile.AnisouRecord, PDBFile.AtomRecord, PDBFile.EndModelRecord, PDBFile.HelixRecord, PDBFile.HetatmRecord, PDBFile.ModelRecord, PDBFile.OtherRecord, PDBFile.ParentRecord, PDBFile.PDBChain, PDBFile.PDBModel, PDBFile.PDBRecord, PDBFile.RemarkRecord, PDBFile.SheetRecord, PDBFile.TerRecord

Field Summary

Fields inherited from class ProGAL.proteins.PDBFile

name

Fields inherited from class java.io.File

pathSeparator, pathSeparatorChar, separator, separatorChar

Constructor Summary

PDBFile(java.lang.String path)

Method Summary

PDBFile.AtomRecord	getAtom(int res, java.lang.String atomType)
BetaTopology	getBetaTopology()
SecondaryStructure	getSecondaryStructure()
static void	main(java.lang.String[] args)
int	shift(int residueNumber)

Methods inherited from class ProGAL.proteins.PDBFile

downloadPDBFile, getAtomCoords, getAtomCoords, getAtomCoords, getAtomRecords, getAtomRecords, getAtomRecords, getCACoords, getCACoords, getCARecords, getCARecords, getChain, getHetatmRecords, getHetatmRecords, getModels, getRecords, getRemarkRecords, getResolution, getSequence, setIncludeHetatms, setIncludeHydrogens, setStandardChain, setStandardChain, setStandardModel, superposeOnto

Methods inherited from class java.io.File

canExecute, canRead, canWrite, compareTo, createNewFile, createTempFile, createTempFile, delete, deleteOnExit, equals, exists, getAbsoluteFile, getAbsolutePath, getCanonicalFile, getCanonicalPath, getFreeSpace, getName, getParent, getParentFile, getPath, getTotalSpace, getUsableSpace, hashCode, isAbsolute, isDirectory, isFile, isHidden, lastModified, length, list, list, listFiles, listFiles, listFiles, listRoots, mkdir, mkdirs, renameTo, setExecutable, setExecutable, setLastModified, setReadable, setReadable, setReadOnly, setWritable, setWritable, toString, toURI, toURL

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

PDBFile

public PDBFile(java.lang.String path)

Method Detail

shift

public int shift(int residueNumber)

getAtom

public PDBFile.AtomRecord getAtom(int res,
                                  java.lang.String atomType)

Overrides:

getAtom in class PDBFile

getSecondaryStructure

public SecondaryStructure getSecondaryStructure()

getBetaTopology

public BetaTopology getBetaTopology()

main

public static void main(java.lang.String[] args)