Package install :: Package MoSTBioDat :: Package DataBase :: Package SubStructSearch :: Module SubStructSearch :: Class SubStructSearch
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Class SubStructSearch

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object --+
         |
        SubStructSearch

Substructure search module INPUT: smidict - dict, id:smile dictionary OUTPUT: class object

Instance Methods [hide private]
 
__init__(self, smidict={}, **kwargs)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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writefile(self, smifilepath='db2smi.smi')
write to specified file INPUT: filepath - str, path to file OUTPUT: file
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createfilepath(self, filepath)
create SMILE filepath INPUT: class object OUTPUT: smi filename absolute path
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TanimotoSearch(self, refersmile='', iso=0, coeff=None, fptype='FP2', outfile='TanimotoSearch.txt')
search for substructures with specified Tanimoto coefficient INPUT: refersmile -str, reference SMILE code iso - boolean, create isomeric SMILE, default False coeff - float, Tanimoto coefficient, default None (generally it should be set >0.7) fptype -- the name of the Open Babel fingerprint type.
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calcTanimoto(self, fprefersmi=None, targetsmi='', fptype='FP2')
calculate Tanimoto coefficient INPUT: targetsmi - str, target SMILE code, default empty fprefersmi - pybel.Fingerprint class object, default None fptype -- the name of the Open Babel fingerprint type.
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SmartSearchPyBel(self, smart='', outfile='SmartSearchPyBel.txt')
search for substructures with specified SMART PyBel pattern INPUT: smart - str, reference SMILE code outfile - str, output file path OUTPUT: file
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SmartSearchOE(self, smart='', outfile='SmartSearchOE.txt')
search for substructures with specified SMART OpenEye pattern INPUT: smart - str, reference SMILE code outfile - str, output file path OUTPUT: file
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QuerySearch(self, refersmile='', outfile='QuerySearch.txt', **kwargs)
search for substructures with Query OE pattern INPUT: refersmile -str, reference SMILE code outfile - str, output file path atomatch - int or OE predefined settings, default OEExprOpts_DefaultAtoms bondmatch - int or OE predefined settings, default OEExprOpts_DefaultBonds OUTPUT: file
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MCSearch(self, refersmile='', outfile='MCSearch.txt', **kwargs)
search for maximum common substructure ...
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CliqueSearch(self, refersmile='', outfile='CliqueSearch.txt', **kwargs)
search for common substructure with OE clique detection INPUT: refersmile -str, reference SMILE code outfile - str, output file path atomatch - int or OE predefined settings, default OEExprOpts_DefaultAtoms bondmatch - int or OE predefined settings, default OEExprOpts_DefaultBonds diffnumatoms - int, ignore clique that differ by more than specified atoms number, default 5 uniqueflag - boolean, unique or non-unique substructure searching, default True OUTPUT: file
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RO5Search(self, outfile='RO5Search.txt', **kwargs)
search for Lipinski Rule of Five INPUT: outfile - str, output file path OUTPUT: file
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calcLipinskidesc(self, smile='')
calculate Lipinski descriptors INPUT: smile - str, SMILE code OUTPUT: lipinski descriptors dictionary
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Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, smidict={}, **kwargs)
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

TanimotoSearch(self, refersmile='', iso=0, coeff=None, fptype='FP2', outfile='TanimotoSearch.txt')

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search for substructures with specified Tanimoto coefficient
INPUT:
refersmile -str, reference SMILE code
iso - boolean, create isomeric SMILE, default False
coeff - float, Tanimoto coefficient, default None (generally it should be set >0.7)
fptype -- the name of the Open Babel fingerprint type.
    FP2 -- Indexes linear fragments up to 7 atoms.
    FP3 -- SMARTS patterns specified in the file patterns.txt
    FP4 -- SMARTS patterns specified in the file SMARTS_InteLigand.txt
outfile - str, output file path
OUTPUT:
file

calcTanimoto(self, fprefersmi=None, targetsmi='', fptype='FP2')

source code 

calculate Tanimoto coefficient
INPUT:
targetsmi - str, target SMILE code, default empty
fprefersmi - pybel.Fingerprint class object, default None
fptype -- the name of the Open Babel fingerprint type.
    FP2 -- Indexes linear fragments up to 7 atoms.
    FP3 -- SMARTS patterns specified in the file patterns.txt
    FP4 -- SMARTS patterns specified in the file SMARTS_InteLigand.txt
OUTPUT:
Tanimoto coefficient - float [0-1]

MCSearch(self, refersmile='', outfile='MCSearch.txt', **kwargs)

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search for maximum common substructure 
INPUT:
refersmile -str, reference SMILE code
outfile - str, output file path
atomatch - int or OE predefined settings, default OEExprOpts_DefaultAtoms
bondmatch - int or OE predefined settings, default OEExprOpts_DefaultBonds
searchtype - OE options:
             default OEMCSType_Approximate (faster) 
                     OEMCSType_Exhaustive
scorefunc - OE functions:
            default OEMCSMaxAtoms() -> number of mapped atoms + number of mapped bonds/100
            OEMCSMaxBonds() -> number of mapped bonds + number of mapped atoms/100
            OEMCSMaxAtomsCompleteCycles() -> number of mapped atoms + number of mapped bonds/100
            OEMCSMaxBondsCompleteCycles() -> number of mapped bonds + number of mapped atoms/100 
numatoms - int, minimum atoms number required of subgraph match, default 4
uniqueflag - boolean, unique or non-unique substructure searching, default True
OUTPUT:
file