Molecules and Sites

Molecules are derived from chem2.Molecule and represent collections of sites. Sites are derived from chem2.Site and represent functional substructures of a molecule. A molecule may be related to multiple sites, but a site may be related only to one molecule. Both molecules and sites may be subclassed from their base classes indefinitely many times.

The Molecule object has a site attribute that holds the list of sites. Below is a summary of Molecule attributes and methods.

Attribute	Setter	Getter	Unsetter
`id`	`set_id(id)`	`get_id()`
`sites`	`add_sites(*sites)`	`get_sites(**kwargs)`	`remove_sites(*sites)`

The Site object has a molecule attribute that points to a single molecule. Below is a summary of Site attributes and methods relevant for this section.

Attribute	Setter	Getter	Unsetter
`id`	`set_id(id)`	`get_id()`
`molecule`	`set_molecule(molecule)`	`get_molecule()`	`unset_molecule()`

add_sites() and set_molecule() have the same functionality of setting up relations between sites and molecules. Similarly, remove_sites() and unset_molecule() have the same functionality of removing relations between sites and molecules.

get_sites() can be filtered on attribute and site type.

Site has the allowed_molecule_types class attribute that restricts which molecule types are allowed to have a particular type of site. This can be set when subclassing Site.

Class Attribute	Default	Description
`allowed_molecule_types`	None	Tuple of allowed `Molecule` classes

Creating types & instances



In [1]:

    
from wc_rules.chem2 import Molecule,Site

Below we create the molecule type hierarchy Molecule -> Receptor -> EGFR



In [2]:

    
class Receptor(Molecule):pass
class EGFR(Receptor):pass

Similarly, from Site, we create 2 different types of sites.



In [3]:

    
class LigandBinding(Site):pass
class Dimerize(Site):pass

We create one instance of EGFR molecule, one instance of LigandBinding site and one instance of Dimerize site.



In [4]:

    
Rec = EGFR().set_id('Rec')
L = LigandBinding().set_id('L')
D = Dimerize().set_id('D')

[Rec.get_id(), L.get_id(), D.get_id()]









    Out[4]:





['Rec', 'L', 'D']

The molecule instance named Rec can be type-checked against the EGFR class, the Receptor class and the Molecule class.



In [5]:

    
isinstance(Rec,EGFR) and isinstance(Rec,Receptor) and isinstance(Rec,Molecule)









    Out[5]:





True

Managing molecule-site relations

Function	`Molecule` method	`Site` method
Attach sites to a molecule	`add_sites(*sites)`	`set_molecule(molecule)`
Detach sites from a molecule	`remove_sites(*sites)`	`unset_molecule(molecule)`
Get/Filter the attached sites	`get_sites(**kwargs)`
Get the attached molecule		`get_molecule()`



In [6]:

    
# Adding sites with add_sites()
Rec.add_sites(L,D)
# Getting sites
Rec.get_sites()









    Out[6]:





[<__main__.LigandBinding at 0x2279503fdd8>,
 <__main__.Dimerize at 0x2279503fe48>]



In [7]:

    
# Filter sites by id
Rec.get_sites(id='L')









    Out[7]:





[<__main__.LigandBinding at 0x2279503fdd8>]



In [8]:

    
# Filter sites by site type
Rec.get_sites(site_type=LigandBinding)









    Out[8]:





[<__main__.LigandBinding at 0x2279503fdd8>]



In [9]:

    
# Removing sites with remove_sites()
Rec.remove_sites(L,D)
Rec.get_sites()









    Out[9]:





[]



In [10]:

    
# Adding sites with set_molecule()
L.set_molecule(Rec)
D.set_molecule(Rec)
Rec.get_sites()









    Out[10]:





[<__main__.LigandBinding at 0x2279503fdd8>,
 <__main__.Dimerize at 0x2279503fe48>]



In [11]:

    
# Getting attached molecule
L.get_molecule()









    Out[11]:





<__main__.EGFR at 0x2279503fda0>



In [12]:

    
# Removing sites with unset_molecule()
L.unset_molecule()
D.unset_molecule()
Rec.get_sites()









    Out[12]:





[]



In [13]:

    
# Creating molecule/site instances and setting relations at the same time
Rec = EGFR(id='Rec').add_sites(
    LigandBinding(id='L'),
    Dimerize(id='D'),
)

Rec.get_sites()









    Out[13]:





[<__main__.LigandBinding at 0x2279504f7b8>,
 <__main__.Dimerize at 0x2279504f7f0>]



In [14]:

    
# Defining site types that can only be attached to EGFR
class EGFRSite(Site):
    allowed_molecule_types = (EGFR,) 
    
class IGFR(Molecule):pass

x1 = EGFRSite().set_molecule( IGFR() )
x2 = EGFRSite().set_molecule( EGFR() )
for x in [x1,x2]:
    try:
        x.verify_allowed_molecule_type()
        print('Allowed')
    except:
        print('Not allowed')









    



Not allowed
Allowed