Biskit :: ChainSeparator :: ChainSeparator :: Class ChainSeparator

Class ChainSeparator

Open PDB file; give back one chain whenever next() is called. This class is used by the pdb2xplor script.

This class constitutes vintage code. See Biskit.PDBCleaner and Biskit.Mod.TemplateCleaner for a more recent implementation of PDB cleaning.

To Do: The removal of duplicate chains should be transferred to the PDBCleaner so that this class can be retired

Instance Methods

[hide private]

__init__(self, fname, outPath='', chainIdOffset=0, capBreaks=0, chainMask=0, log=None)

str pdbname(self)
Extract pdb code from file name.

_expressionCheck(self, findExpression, findClean)
Check and report if the regular expression 'findExpression' exists in the PDB-file.

_hetatomCheck(self)
Check and report if there are any none-water HETATMs in the PDB-file

_compareSequences(self, seq1, seq2)
Returns identity (0.0 - 1.0) between the two sequences @rtype : float

int _removeDuplicateChains(self, chainMask=None)
Get rid of identical chains by comparing all chains with Blast2seq.

_assign_seg_ids(self)
Assign new segment id to each chain.

list of int _sequentialDist(self, chain, cutoff, atom)
Calculate sequential atom-atom distance, report residues with longer distance than cutoff (chain break positions).

_separateChainBreaks(self)
Separate chains with breaks into 2 chains.

__nCap(self, pep_chain)
Add acetyl capping to N-terminal of peptide chain

__cCap(self, pep_chain)
Add methyle amine capping to C-terminal of peptide chain

extractWaters(self)
Write waters into separate pdb file, called |pdbCode|_waters.pdb.

chain object OR None next(self)
Return next 'clean', non-redundant, non-broken chain from PDB

Method Details

[hide private]

init(self, fname, outPath='', chainIdOffset=0, capBreaks=0, chainMask=0, log=None)
(Constructor)

source code

Parameters:

fname (str) - pdb filename
outPath (str) - path for log file
chainIdOffset (int) - start chain numbering at this offset
capBreaks (0|1) - add ACE and NME to N- and C-term. of chain breaks [0]
chainMask ([1|0]) - chain mask for overriding the default sequence identity [None]
log (object) - LogFile object

pdbname(self)

source code

Extract pdb code from file name.

Returns: str: (assumed) pdb code

_expressionCheck(self, findExpression, findClean)

source code

Check and report if the regular expression 'findExpression' exists in the PDB-file. Use this to locate data in the REMARK section of a pdb file. Prints a warning to stdOut if the regular expression is found.