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align
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align (
ref,
match,
matrix,
algorithm,
gapOpen,
gapExtend,
ksdsspCache,
ssMatrix=defaultSsMatrix,
ssFraction=defaultSsFraction,
gapOpenHelix=defaultHGapOpen,
gapOpenStrand=defaultSGapOpen,
gapOpenOther=defaultOGapOpen,
computeSS=defaultComputeSS,
)
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Exceptions
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ValueError( "Unknown sequence alignment algorithm: %s" % algorithm )
ValueError( "Smith-Waterman result not" " a subsequence of original sequence" )
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cmdMatch
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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)
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Exceptions
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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" )
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matrixCompatible
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matrixCompatible ( chain, matrix )
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match
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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
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Exceptions
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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 ) )
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