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

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                                          object --+    
                                                   |    
MoSTBioDat.DataBase.ImportData.Data2DB.DBFile.DBFile --+
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                                                      SDFile

Simple SDF file parser INPUT: dictpath - str - path to dictionary dictfilename - str - dictionary filename dbfile - str - database file path temporary - str - path to temporary dictionary file

format - string format for log handler filter - filter object from logger object datefmt - data/time format path - directory path to log file filename - log file name, default log filemode - mode to open log file, default='a' level - set root logger level to specified level logfilelevel- set level to log file

OUTPUT: dictionary object

Instance Methods [hide private]
 
__init__(self, sdfile=None, **kwargs)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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parseMolOE(self, imolstream, **kwarg)
get SDF fields from molecule using OpenEye INPUT: imolstream - OEChem input object natoms - boolean, get number of atoms nbonds - boolean, get number of bonds coords - boolean, get coords list [ x y z atomic_number q ] boonds - boolean, get bonds list [at1 at2 bondtype] tag - boolean, get all tags if exists
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Smi2ConnTab(self, smile, 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:
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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:
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parseSDFOE(self, **kwarg)
parse ZINC SDF file using OEChem INPUT: oechem - boolean, get oechem number, default True natoms - boolean, get number of atoms, default True nbonds - boolean, get number of bonds, default True chiral- boolean, get chiral flag, default True coords - boolean, get coords list [ x y z symbol q ], default True tag - boolean, get tags if exists, default True overTag - boolean, flag to add or update tags in Property attribute constattr - add constant attribute, default None OUTPUT: result dictionary
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genCanSmi(self)
generate canonical SMILE INPUT: class object OUTPUT: write canonical smile, filename
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genIsoSmi(self)
generate isomeric SMILE INPUT: class object OUTPUT: write isomeric smile, filename
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genAbSmi(self)
generate absolute (isomeric+unique) SMILE INPUT: class object OUTPUT: write absolute smile, filename
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Inherited from MoSTBioDat.DataBase.ImportData.Data2DB.DBFile.DBFile: closeDict, createdict, delAttrDict, delDictKey, findFile, getDict, getLength, insAttrDict, insertDict, openDict, retDict, shoValue, showDict, showDictKey, showPropTag, showPropTagonZINCode

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, sdfile=None, **kwargs)
(Constructor)

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

Overrides: object.__init__
(inherited documentation)

parseMolOE(self, imolstream, **kwarg)

source code 

get SDF fields from molecule using OpenEye INPUT: imolstream - OEChem input object natoms - boolean, get number of atoms nbonds - boolean, get number of bonds coords - boolean, get coords list [ x y z atomic_number q ] boonds - boolean, get bonds list [at1 at2 bondtype] tag - boolean, get all tags if exists

  • str, get specified tag
  • list of strings, get specified tags

OUTPUT: result dictionary