Object representation of an I-Sites library peptide fragment.
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attach_structure(self,
pdb_file)
Parse the paradigm's pdb_file and attach structural data to
cluster.representative (source and
structure attributes). |
source code
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float
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city_block(self,
profile,
start=0)
Compute the similarity score of profile matching
self 's profile using the exponential city block metric
(see Baker 1995). |
source code
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float
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cross_entropy(self,
profile,
start=0)
Compute the similarity score of profile matching
self 's profile using the cross entropy method. |
source code
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function
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float
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profile_similarity(self,
profile,
start=0)
Compute the similarity score of profile matching
self 's profile (see Bystroff 2001, 2008). |
source code
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float
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list
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slide_over(self,
target,
mode=Bystroff)
Find profile and structural matches by sliding the fragment over a
specified target chain. |
source code
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list
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slide_over_fast(self,
target,
mode=Bystroff)
Find profile matches only (do not compute RMSD) by sliding the
fragment over a specified target chain. |
source code
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float
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sum_of_odds(self,
profile,
start=0)
Compute the similarity score of profile matching
self 's profile using the log-sum-of-odds method
(Soeding). |
source code
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hmm.ProfileHMM
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__str__ ,
__subclasshook__
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