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Simpler rate expressions + some reorganization
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,64 +1,16 @@ | ||
| from obj_model import core | ||
|
|
||
| import sympy | ||
| from six import integer_types, string_types, with_metaclass | ||
| #from sympy import S | ||
| #from sympy import core.all_classes as sympy_all_classes | ||
|
|
||
| class SymbolicExpressionAttribute(core.Attribute): | ||
| """ Symbolic Expression to be used in RateLaws """ | ||
| def __init__(self,none=True,default=None,verbose_name='',help='Enter a Sympify-able Expression',primary=False,unique=False): | ||
| if default is not None: | ||
| try: | ||
| default = sympy.S(default) | ||
| except: | ||
| raise ValueError('SymbolicExpressionAttribute must be either None or Sympify-able Expression') | ||
| super(SymbolicExpressionAttribute, self).__init__(default=default,verbose_name=verbose_name,help=help,primary=primary,unique=unique) | ||
| self.none = none | ||
| def clean(self,value): | ||
| if value is None: | ||
| return (value,None) | ||
| if value is '': | ||
| return (value,None) | ||
| if isinstance(value, tuple(sympy.core.all_classes)): | ||
| return (value,None) | ||
| if isinstance(value, string_types+integer_types+(float,)): | ||
| return (sympy.S(value),None) | ||
|
|
||
| class SymbolAttribute(core.Attribute): | ||
| def __init__(self,none=True,default=None,verbose_name='',help='Enter a Sympy Symbol',primary=True,unique=True): | ||
| if default is not None: | ||
| try: | ||
| default = sympy.Symbol(default) | ||
| except: | ||
| raise ValueError('SymbolAttribute must be a Sympy Symbol') | ||
| super(SymbolAttribute, self).__init__(default=default,verbose_name=verbose_name,help=help,primary=primary,unique=unique) | ||
| self.none = none | ||
| def clean(self,value): | ||
| if value is None: | ||
| return (value,None) | ||
| if value is '': | ||
| return (value,None) | ||
| if isinstance(value, tuple(sympy.core.all_classes)): | ||
| return (value,None) | ||
| if isinstance(value, string_types): | ||
| return (sympy.Symbol(value),None) | ||
|
|
||
| class Parameter(core.Model): | ||
| symbol = SymbolAttribute(primary=True) | ||
| symbol = core.StringAttribute(primary=True) | ||
| value = core.FloatAttribute() | ||
|
|
||
| class SymbolicExpression(core.Model): | ||
| class RateExpression(core.Model): | ||
| id = core.StringAttribute(primary=True) | ||
| expr = SymbolicExpressionAttribute() | ||
| params = core.ManyToManyAttribute(Parameter) | ||
|
|
||
| expr = core.StringAttribute() | ||
| parameters = core.ManyToManyAttribute(Parameter,related_name='expressions') | ||
|
|
||
| def main(): | ||
| k1 = Parameter(symbol=sympy.Symbol('k1'),value=1000) | ||
| print( k1, type(k1), k1.symbol, type(k1.symbol), ) | ||
|
|
||
|
|
||
| return | ||
|
|
||
| if __name__ == '__main__': | ||
| main() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| ###### Factory ###### | ||
| class Factory(object): | ||
| def build(self,obj_type,names,instances=True): | ||
| types = dict() | ||
| vec = [] | ||
| for name in names: | ||
| if name not in moltypes: | ||
| types[name] = type(name,(obj_type,),{}) | ||
| if instances==False: | ||
| vec.append( types[name] ) | ||
| if instances==True: | ||
| vec.append( types[name]() ) | ||
| return vec | ||
|
|
||
| ###### Error ###### | ||
| class AddObjectError(Exception): | ||
| def __init__(self,parentobject,currentobject,allowedobjects,methodname='add()'): | ||
| msg = '\nObject of ' + self.to_str(currentobject)+ ' cannot be added to ' + self.to_str(parentobject) + ' using ' + methodname + '. ' | ||
| if (len(allowedobjects)==1 or isinstance(allowedobjects,str)): | ||
| msg = msg + 'Only objects of type' + str(allowedobjects) + 'are allowed.' | ||
| else: | ||
| msg = msg + 'Only objects of type ' + ', '.join(allowedobjects) + ' are allowed.' | ||
| super(AddObjectError, self).__init__(msg) | ||
| @staticmethod | ||
| def to_str(obj): | ||
| msg = str(type(obj)) | ||
| msg = ''.join([ch for ch in msg if ch not in "<>"]) | ||
| return msg |