Package install :: Package MoSTBioDat :: Package DataBase :: Package ImportData :: Package Data2DB :: Module Smile :: Class Smile
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Class Smile

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object --+
         |
        Smile

Instance Methods [hide private]
 
__init__(self, smile=None)
Operate on SMILE code INPUT: smile - str, SMILE string OUTPUT: class object
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getMol(self)
get Mol object INPUT: class object OUTPUT: molecule object
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Smi2ConnTab(self, mol, aromaticflag=OEAroModelOpenEye)
Create canonical connection table from SMILE INPUT: class object smile - str - SMILE code OUTPUT: connection table - list
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CanSmi(self, mol, iso, kek, verbose)
Create canonical smile (unique or absolute) INPUT: mol - molecule class object iso - boolean, create isomeric SMILE kek - boolean, Kekule aromatic form varbose - boolean, show warnings OUTPUT: smile string
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CanMol(self, mol, kek=0, aromodel=OEAroModelOpenEye, verbose=0)
Create canonical connection table INPUT: mol - molecule class object kek - boolean, Kekule aromatic form aromodel - aromatic OpenEye model, default OEAroModelOpenEye varbose - boolean, show warnings OUPTUT: molecule object
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addCoords(self, mol)
add x,y,z coordinates INPUT: mol - molecule object OUTPUT: molecule object
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getCoords(self, mol)
get x,y,z coordinates INPUT: mol - molecule object OUTPUT: result - dictionary with num,x,y,x atnum q list
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getCoords1(self, mol)
get x,y,z coordinates INPUT: mol - molecule object OUTPUT: result - dictionary with num,x,y,x atnum q list
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getBonds(self, mol)
get bonds INPUT; mol - molecule object OUTPUT: result - dictionary with begatom endatom bondType list
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addH(self, mol, aromaticflag=OEAroModelOpenEye)
add hydrogens INPUT: mol - molecule class object OUTPUT: mol - molecule class object
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getAtoms(self, mol)
get atoms INPUT: mol - molecule class object OUTPUT: atSymQ - dict, atom symbol, charge 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, smile=None)
(Constructor)

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Operate on SMILE code INPUT: smile - str, SMILE string OUTPUT: class object

Overrides: object.__init__