Sites, Bonds and Overlaps

Sites and Bonds

Bonds are derived from chem2.Bond and indicate binding interactions between sites. By default, a bond may only have two sites and a site may only have one bond.

The Bond object has a sites attribute which holds the pair of sites as a list. The following methods are available to Bond objects.

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

Bonds have internal class attributes that dictate bond behavior. These include:

Class Attribute	Default Value	Description
`allowed_site_types`	None	Tuple of allowed site classes
`n_max_sites`	2	Maximum number of sites per bond

For the purpose of managing bonds, Site objects have the bond instance attribute and the allowed_to_bind class attribute.

Instance Attribute	Setter	Getter	Unsetter
`bond`	`set_bond(bond)`	`get_bond()`	`unset_bond()`

Class Attribute	Default Value	Description
`allowed_to_bind`	True	Boolean controlling whether site can have a bond

Managing Site-Bond Relations

Function	`Site` method	`Bond` method
Attach sites to a bond	`set_bond(bond)`	`add_sites(*sites)`
Detach sites from a bond	`unset_bond()`	`remove_sites(*sites)`
Get/Filter the attached sites		`get_sites(**kwargs)`
Get the attached bond	`get_molecule()`



In [1]:

    
from wc_rules.chem2 import Molecule,Site,Bond



In [2]:

    
# creating sites to use for bond
class LigandBinding(Site):pass
class ReceptorBinding(Site):pass
s1,s2 = LigandBinding(id='s1'), ReceptorBinding(id='s2')



In [3]:

    
# Attaching sites to a bond using add_sites()
bnd = Bond(id='bnd').add_sites(s1,s2)
# Getting sites attached to a bond
bnd.get_sites()









    Out[3]:





[<__main__.LigandBinding at 0x1b2a5cc15f8>,
 <__main__.ReceptorBinding at 0x1b2a5cc1630>]



In [4]:

    
# Filtering attached sites by id
bnd.get_sites(id='s1')









    Out[4]:





[<__main__.LigandBinding at 0x1b2a5cc15f8>]



In [5]:

    
# Removing attached sites using remove_sites()
bnd.remove_sites(s1,s2)
bnd.get_sites()









    Out[5]:





[]



In [6]:

    
# Attaching sites to a bond using set_bond()
bnd = Bond(id='bnd')
s1.set_bond(bnd)
s2.set_bond(bnd)
bnd.get_sites()









    Out[6]:





[<__main__.LigandBinding at 0x1b2a5cc15f8>,
 <__main__.ReceptorBinding at 0x1b2a5cc1630>]



In [7]:

    
# Getting bond attached to sites
[s1.get_bond().get_id(), s2.get_bond().get_id()]









    Out[7]:





['bnd', 'bnd']



In [8]:

    
# Removing bond from sites using remove_bond()
s1.unset_bond()
s2.unset_bond()
bnd.get_sites()









    Out[8]:





[]



In [9]:

    
# Subclassing bonds to increase the number of allowed sites
class TetramerBond(Bond):
    n_max_sites = 4
    
bnd1 = TetramerBond().add_sites( Site(), Site(), Site(), Site() )
bnd2 = Bond().add_sites( Site(), Site(), Site(), Site() )
for x in [bnd1,bnd2]:
    try:
        x.verify_maximum_number_of_sites()
        print('Allowed.')
    except:
        print('Not allowed.')









    



Allowed.
Not allowed.

Sites and Overlaps

Overlaps are groups of sites that can only have one bond at a time. They are used to reflect groups of sites that spatially overlap with each other.

The Overlap object has a sites attribute which holds a list of sites.

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

Site objects have the instance attribute overlaps, which holds a list of overlaps.

Attribute	Setter	Getter	Unsetter
`overlaps`	`add_overlaps(*overlaps)`	`get_overlaps(**kwargs)`	`remove_overlaps(*overlap)`



In [10]:

    
# Creating sites to use in overlaps
s1,s2,s3 = Site(id='s1'), Site(id='s2'), Site(id='s3')



In [11]:

    
# Adding overlaps using add_sites()
from wc_rules.chem2 import Overlap
olp1 = Overlap(id='olp1').add_sites(s1,s2)
# Getting overlapping sites
olp1.get_sites()









    Out[11]:





[<wc_rules.chem2.Site at 0x1b2a5cd9390>,
 <wc_rules.chem2.Site at 0x1b2a5cd93c8>]



In [12]:

    
# Filtering overlapping sites
olp1.get_sites(id='s1')









    Out[12]:





[<wc_rules.chem2.Site at 0x1b2a5cd9390>]



In [13]:

    
# Remove overlaps using remove_sites()
olp1.remove_sites(s1,s2)
olp1.get_sites()









    Out[13]:





[]



In [14]:

    
# Add overlaps using add_overlaps()
s1.add_overlaps(olp1)
s2.add_overlaps(olp1)
olp1.get_sites()









    Out[14]:





[<wc_rules.chem2.Site at 0x1b2a5cd9390>,
 <wc_rules.chem2.Site at 0x1b2a5cd93c8>]



In [15]:

    
# Get overlaps from site
s1.get_overlaps()









    Out[15]:





[<wc_rules.chem2.Overlap at 0x1b2a5cd95c0>]



In [16]:

    
# Remove overlaps using remove_overlaps()
s1.remove_overlaps(olp1)
s2.remove_overlaps(olp1)
olp1.get_sites()









    Out[16]:





[]



In [17]:

    
# An overlap may have many sites
olp1 = Overlap(id='s1').add_sites(s1,s2,s3)
olp1.get_sites()









    Out[17]:





[<wc_rules.chem2.Site at 0x1b2a5cd9390>,
 <wc_rules.chem2.Site at 0x1b2a5cd93c8>,
 <wc_rules.chem2.Site at 0x1b2a5cd9400>]



In [18]:

    
# A site may have many overlaps
olp1.remove_sites(s1,s2,s3)
olp1 = Overlap(id='s1').add_sites(s1,s2)
olp2 = Overlap(id='s1').add_sites(s1,s3)
s1.get_overlaps()









    Out[18]:





[<wc_rules.chem2.Overlap at 0x1b2a5cf2438>,
 <wc_rules.chem2.Overlap at 0x1b2a5cf2470>]