HappyDoc Generated Documentation ./MatchMaker

. / MatchMaker 

Functions   
  align 
align (
        ref,
        match,
        matrix,
        algorithm,
        gapOpen,
        gapExtend,
        ksdsspCache,
        ssMatrix=None,
        ssFraction=None,
        gapOpenHelix=None,
        gapOpenStrand=None,
        gapOpenOther=None,
        computeSS=None,
        )
Exceptions   

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

  cmdMatch 
cmdMatch (
        refSel,
        matchSel,
        pairing=None,
        alg=None,
        ssFraction=None,
        matrix=None,
        gapOpen=None,
        hgap=None,
        sgap=None,
        ogap=None,
        iterate=None,
        gapExtend=None,
        showAlignment=None,
        computeSS=None,
        matHH=None,
        matSS=None,
        matOO=None,
        matHS=None,
        matHO=None,
        matSO=None,
        )
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=None,
        align=None,
        **alignKw,
        )
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 Wed Jul 9 15:48:59 2008 by HappyDoc version 3.1