HappyDoc Generated Documentation ./MatchMaker

. / MatchMaker 

Functions   
  align 
align (
        ref,
        match,
        matrix,
        algorithm,
        gapOpen,
        gapExtend,
        ksdsspCache,
        ssMatrix=defaultSsMatrix,
        ssFraction=defaultSsFraction,
        gapOpenHelix=defaultHGapOpen,
        gapOpenStrand=defaultSGapOpen,
        gapOpenOther=defaultOGapOpen,
        computeSS=defaultComputeSS,
        )
Exceptions   

ValueError( "Unknown sequence alignment algorithm: %s" % algorithm )
ValueError( "Smith-Waterman result not" " a subsequence of original sequence" )

  cmdMatch 
cmdMatch (
        refSel,
        matchSel,
        pairing=defaultPairing,
        alg=defaultAlignAlgorithm,
        ssFraction=defaultSsFraction,
        matrix=defaultMatrix,
        gapOpen=defaultGapOpen,
        hgap=defaultHGapOpen,
        sgap=defaultSGapOpen,
        ogap=defaultOGapOpen,
        iterate=defaultIterateCutoff,
        gapExtend=defaultGapExtend,
        showAlignment=False,
        computeSS=defaultComputeSS,
        matHH=defaultSsMatrix [( 'H', 'H' ) ],
        matSS=defaultSsMatrix [( 'S', 'S' ) ],
        matOO=defaultSsMatrix [( 'O', 'O' ) ],
        matHS=defaultSsMatrix [( 'H', 'S' ) ],
        matHO=defaultSsMatrix [( 'H', 'O' ) ],
        matSO=defaultSsMatrix [( 'S', 'O' ) ],
        )

wrapper for command-line command (friendlier args)

Exceptions   

MidasError( "Specify a single reference" " chain only" )
MidasError("No such matrix name: %s" % str( matrix ) )
MidasError, v
MidasError( "Gap open/extend penalties must be numeric" )
MidasError( "Must use different reference and match" " structures" )
MidasError( "No molecules/chains to match specified" )
MidasError("Different number of reference/match" " chains (%d ref, %d match)" %(len( refs ), len( matches ) ) )
MidasError( "No reference chains specified" )
MidasError( "No reference model specified" )
MidasError( "Specify a single reference" " model only" )

  matrixCompatible 
matrixCompatible ( chain,  matrix )
  match 
match (
        chainPairing,
        matchItems,
        matrix,
        alg,
        gapOpen,
        gapExtend,
        iterate=None,
        showAlignment=False,
        align=align,
        **alignKw,
        )

Superimpose structures based on sequence alignment

chainPairing is the method of pairing chains to match:

CP_SPECIFIC_SPECIFIC
Each reference chain is paired with a specified match chain
CP_SPECIFIC_BEST
Single reference chain is paired with best seq-aligning chain from one or more molecules
CP_BEST
Best seq-aligning pair of chains from reference molecule and match molecule(s) is used
Exceptions   

UserError("No chains in match structure" " %s compatible with %s similarity" " matrix" %( match, matrix ) )
UserError("Reference chain (%s) not" " compatible with %s similarity" " matrix" %( ref.fullName(), matrix ) )
UserError( "Must select at least one reference" " and match item in different models.\n" )
UserError( "Cannot have same molecule" " model provide both reference and" " match chains" )
ValueError( "Unknown sequence alignment algorithm: %s" % alg )
UserError( "Cannot match the same chain" " to multiple reference chains" )
UserError( "Must select at least one reference" " and match item.\n" )
UserError("Reference chain (%s) not compatible" " with %s similarity matrix" %( ref.fullName(), matrix ) )
UserError("Match chain (%s) not" " compatible with %s similarity" " matrix" %( match.fullName(), matrix ) )
ValueError( "No such chain-pairing method" )
LimitationError( smallMolErrMsg )
UserError( "Must select at least one reference" " chain.\n" )
UserError("No chains in reference structure" " %s compatible with %s similarity" " matrix" %( ref, matrix ) )

Classes   
Python files   

ChimeraExtension.py

gui.py


This document was automatically generated Thu Nov 15 14:08:49 2007 by HappyDoc version 3.0.a1