org.biojava.bio.structure.io
Class FileParsingParameters

java.lang.Object
  extended by org.biojava.bio.structure.io.FileParsingParameters
All Implemented Interfaces:
Serializable

public class FileParsingParameters
extends Object
implements Serializable

A class that configures parameters that can be sent to the PDB file parsers

Author:
Andreas Prlic
See Also:
Serialized Form

Field Summary
static int ATOM_CA_THRESHOLD
          the maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
static int MAX_ATOMS
          the maximum number of atoms we will add to a structure this protects from memory overflows in the few really big protein structures.
 
Constructor Summary
FileParsingParameters()
           
 
Method Summary
 String[] getAcceptedAtomNames()
          by default the parser will read in all atoms (unless using the CAonly switch).
 int getAtomCaThreshold()
          the maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
 int getMaxAtoms()
          the maximum numbers of atoms to load in a protein structure (prevents memory overflows)
 boolean getStoreEmptySeqRes()
          a flag to detrermine if SEQRES should be stored, even if alignSeqREs is disabled.
 boolean isAlignSeqRes()
          Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
 boolean isHeaderOnly()
          Parse only the PDB file header out of the files
 boolean isLoadChemCompInfo()
          Should the chemical component information be automatically be downloade from the web? If set to false, a limited set of ChemComps is being used.
 boolean isParseCAOnly()
          the flag if only the C-alpha atoms of the structure should be parsed.
 boolean isParseSecStruc()
          is secondary structure assignment being parsed from the file? default is null
 boolean isUpdateRemediatedFiles()
          A flag if local files should be replaced with the latest version of remediated PDB files.
 void setAcceptedAtomNames(String[] fullAtomNames)
          by default the parser will read in all atoms (unless using the CAonly switch).
 void setAlignSeqRes(boolean alignSeqRes)
          define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.
 void setAtomCaThreshold(int atomCaThreshold)
          the maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
 void setDefault()
           
 void setHeaderOnly(boolean headerOnly)
          Parse only the PDB file header out of the files
 void setLoadChemCompInfo(boolean loadChemCompInfo)
          Sets if chemical component defintions should be loaded from the web
 void setMaxAtoms(int maxAtoms)
          the maximum numbers of atoms to load in a protein structure (prevents memory overflows)
 void setParseCAOnly(boolean parseCAOnly)
          the flag if only the C-alpha atoms of the structure should be parsed.
 void setParseSecStruc(boolean parseSecStruc)
          a flag to tell the parser to parse the Author's secondary structure assignment from the file default is set to false, i.e.
 void setStoreEmptySeqRes(boolean storeEmptySeqRes)
           
 void setUpdateRemediatedFiles(boolean updateRemediatedFiles)
          A flag if local files should be replaced with the latest version of remediated PDB files.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

ATOM_CA_THRESHOLD

public static final int ATOM_CA_THRESHOLD
the maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file. If this limit is exceeded also the SEQRES groups will be ignored.

See Also:
Constant Field Values

MAX_ATOMS

public static final int MAX_ATOMS
the maximum number of atoms we will add to a structure this protects from memory overflows in the few really big protein structures.

See Also:
Constant Field Values
Constructor Detail

FileParsingParameters

public FileParsingParameters()
Method Detail

setDefault

public void setDefault()

isParseSecStruc

public boolean isParseSecStruc()
is secondary structure assignment being parsed from the file? default is null

Returns:
boolean if HELIX STRAND and TURN fields are being parsed

setParseSecStruc

public void setParseSecStruc(boolean parseSecStruc)
a flag to tell the parser to parse the Author's secondary structure assignment from the file default is set to false, i.e. do NOT parse.

Parameters:
parseSecStruc - if HELIX STRAND and TURN fields are being parsed

isLoadChemCompInfo

public boolean isLoadChemCompInfo()
Should the chemical component information be automatically be downloade from the web? If set to false, a limited set of ChemComps is being used.

Returns:
flag if the data should be loaded

setLoadChemCompInfo

public void setLoadChemCompInfo(boolean loadChemCompInfo)
Sets if chemical component defintions should be loaded from the web

Parameters:
loadChemCompInfo - flag

isHeaderOnly

public boolean isHeaderOnly()
Parse only the PDB file header out of the files

Returns:
flag

setHeaderOnly

public void setHeaderOnly(boolean headerOnly)
Parse only the PDB file header out of the files

Parameters:
headerOnly - flag

isParseCAOnly

public boolean isParseCAOnly()
the flag if only the C-alpha atoms of the structure should be parsed.

Returns:
the flag

setParseCAOnly

public void setParseCAOnly(boolean parseCAOnly)
the flag if only the C-alpha atoms of the structure should be parsed.

Parameters:
parseCAOnly - boolean flag to enable or disable C-alpha only parsing

isAlignSeqRes

public boolean isAlignSeqRes()
Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.

Returns:
flag if SEQRES - ATOM amino acids alignment is enabled

setAlignSeqRes

public void setAlignSeqRes(boolean alignSeqRes)
define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.

Parameters:
alignSeqRes -

getStoreEmptySeqRes

public boolean getStoreEmptySeqRes()
a flag to detrermine if SEQRES should be stored, even if alignSeqREs is disabled. This will provide access to the sequence in the SEQRES, without linking it up with the ATOMs.

Returns:
flag

setStoreEmptySeqRes

public void setStoreEmptySeqRes(boolean storeEmptySeqRes)

isUpdateRemediatedFiles

public boolean isUpdateRemediatedFiles()
A flag if local files should be replaced with the latest version of remediated PDB files. Default: false


setUpdateRemediatedFiles

public void setUpdateRemediatedFiles(boolean updateRemediatedFiles)
A flag if local files should be replaced with the latest version of remediated PDB files. Default: false

Parameters:
updateRemediatedFiles -

getAcceptedAtomNames

public String[] getAcceptedAtomNames()
by default the parser will read in all atoms (unless using the CAonly switch). This allows to specify a set of atoms to be read. e.g. {" CA ", " CB " }. Returns null if all atoms are accepted.

Returns:
accepted atom names, or null if all atoms are accepted. default null

setAcceptedAtomNames

public void setAcceptedAtomNames(String[] fullAtomNames)
by default the parser will read in all atoms (unless using the CAonly switch). This allows to specify a set of atoms to be read. e.g. {" CA ", " CB " }. Returns null if all atoms are accepted.

Parameters:
accepted - atom names, or null if all atoms are accepted. default null

getMaxAtoms

public int getMaxAtoms()
the maximum numbers of atoms to load in a protein structure (prevents memory overflows)

Returns:
maximum nr of atoms to load, default Integer.MAX_VALUE;

setMaxAtoms

public void setMaxAtoms(int maxAtoms)
the maximum numbers of atoms to load in a protein structure (prevents memory overflows)

Parameters:
maxAtoms - maximun nr of atoms to load

getAtomCaThreshold

public int getAtomCaThreshold()
the maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file. If this limit is exceeded also the SEQRES groups will be ignored.

Returns:
atomCaThreshold.

setAtomCaThreshold

public void setAtomCaThreshold(int atomCaThreshold)
the maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file. If this limit is exceeded also the SEQRES groups will be ignored.

Parameters:
atomCaThreshold - maximum number of atoms for all atom representation.