Package install :: Package MoSTBioDat :: Package DataBase :: Package ImportData :: Package Data2DB :: Module PDBFile :: Class Molecule
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Class Molecule

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object --+
         |
        Molecule

Molecule class INPUT: modelid - int, model id chainid - int, chain id molid - int, molecule id molname - str, molecule name molatnum - int, molecule atom number molinscode - str, molecule insertion code molfragnum - int, molecule fragment number molcoords - dict, molecule coordinates dictionary OUTPUT: class object

Instance Methods [hide private]
 
__init__(self, modelid, chainid, molid, molname, molatnum, molinscode, molfragnum, molsecstruct, molatoms, molhetflag)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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getmodelid(self)
get model id INPUT: class object OUTPUT: model id
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setmodelid(self, id)
set model id INPUT: class object id - int, model id OUTPUT: model id
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getchainid(self)
get chain id INPUT: class object OUTPUT: chain id
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getmolname(self)
get molecule name INPUT: class object OUTPUT: molecule name
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getmolid(self)
get molecule id INPUT: class object OUTPUT: molecule id
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getmolatnum(self)
get molecule atom number INPUT: class object OUTPUT: molecule atom number
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getmolatoms(self)
get molecule atoms INPUT: class object OUTPUT: dictionary 'atom id': atom class object
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getmolinscode(self)
get molecule insertion code INPUT: class object OUTPUT: molecule insertion code, str, default space
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getmolfragnum(self)
get molecule fragment number INPUT: class object OUTPUT: molecule fragment number, int, default 0
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getmolsecstruct(self)
get molecule secondary structure INPUT: class object OUTPUT: molecule secondary structure, int, default 0
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getisosmi(self)
get isomeric SMILE code INPUT: class object OUTPUT: isomeric SMILE code
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getype(self)
get molecule type INPUT: class object OUTPUT: char - P - polymer, S - polymer segment, M - non polymer, W - water, I - ion, A - atom
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getsymq(self)
get symbol and charge dictionary with list in canonical order INPUT: class object OUTPUT: symbol and charge dictionary
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getbonds(self)
get bonds dictionary with list in canonical order INPUT: class object OUTPUT: bonds dictionary
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getcoords(self)
get coordinates dictionary with list in canonical order INPUT: class object OUTPUT: coordinates dictionary
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getmw(self)
get molecule weight INPUT: class object OUTPUT: molecular weight
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getmq(self)
get molecule charge INPUT: class object OUTPUT: molecular net charge
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getformul(self)
get molecule formula INPUT: class object OUTPUT: molecule formula
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gethetflag(self)
get molecule heteroflag INPUT: class object OUTPUT: boolean
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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, modelid, chainid, molid, molname, molatnum, molinscode, molfragnum, molsecstruct, molatoms, molhetflag)
(Constructor)

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

Overrides: object.__init__
(inherited documentation)