The Contact Interface of Lahuta¶

Lahuta provides two different API's to access built-in contact types:

• functional and
• object-oriented.

The functional API is more concise and easier to use, but the object-oriented API is more flexible and allows for more customization.

In [2]:

from lahuta import Luni

from lahuta import Luni

In [3]:

luni = Luni('data/2rh1.pdb')
ns = luni.compute_neighbors(radius=4.0, res_dif=4)

luni = Luni('data/2rh1.pdb') ns = luni.compute_neighbors(radius=4.0, res_dif=4)

Functional API¶

Previous notebooks already provide plenty of examples of how to use the functional API to the contact interface

In [4]:

from lahuta.contacts import F

from lahuta.contacts import F

In [5]:

F.polar_hbond_neighbors(ns)

F.polar_hbond_neighbors(ns)

Out[5]:

<Lahuta NeighborPairs class containing 359 atoms and 269 pairs>

Object-Oriented API¶

Atom-Atom Contacts¶

In [6]:

from lahuta.contacts import ( 
    AromaticContacts, 
    IonicContacts, 
    HydrophobicContacts, 
    HBondContacts
)

from lahuta.contacts import ( AromaticContacts, IonicContacts, HydrophobicContacts, HBondContacts )

In [7]:

# aromatic contacts
ac = AromaticContacts(ns)
print (ac.distance) 
ac.compute()
ac.results

# aromatic contacts ac = AromaticContacts(ns) print (ac.distance) ac.compute() ac.results

4.0

Out[7]:

<Lahuta NeighborPairs class containing 66 atoms and 64 pairs>

In [8]:

# hydrophobic contacts
hc = HydrophobicContacts(ns)
hc.compute()
hc.results

# hydrophobic contacts hc = HydrophobicContacts(ns) hc.compute() hc.results

Out[8]:

<Lahuta NeighborPairs class containing 459 atoms and 372 pairs>

Atom-Plane and Plane-Plane Contacts¶

In [9]:

from lahuta.contacts import AtomPlaneContacts, PlanePlaneContacts

# atom-plane contacts
apc = AtomPlaneContacts(ns)

# carbon-pi contacts
apc.carbon_pi() 
apc.cation_pi()

from lahuta.contacts import AtomPlaneContacts, PlanePlaneContacts # atom-plane contacts apc = AtomPlaneContacts(ns) # carbon-pi contacts apc.carbon_pi() apc.cation_pi()

Out[9]:

<Lahuta NeighborPairs class containing 11 atoms and 6 pairs>

In [10]:

# plane-plane contacts
ppc = PlanePlaneContacts(ns)

# plane-plane contacts
results = ppc.compute()
results

# plane-plane contacts ppc = PlanePlaneContacts(ns) # plane-plane contacts results = ppc.compute() results

Out[10]:

<Lahuta NeighborPairs class containing 53 atoms and 50 pairs>

Computing Contacts¶

Both the Functional and Object-Oriented API described earlier offer a lot of flexibility, but they are also verbose and very expressive.
Lahuta implements interfaces that are easier to use and more concise.

Here we describe the LahutaContacts class.

In [11]:

from lahuta.contacts.computer import LahutaContacts

from lahuta.contacts.computer import LahutaContacts

In [12]:

contacts = LahutaContacts()
contacts.compute(ns)
contacts.results

contacts = LahutaContacts() contacts.compute(ns) contacts.results

Out[12]:

{'aromatic_neighbors': <Lahuta NeighborPairs class containing 66 atoms and 64 pairs>,
 'ionic_neighbors': <Lahuta NeighborPairs class containing 37 atoms and 30 pairs>,
 'carbonyl_neighbors': <Lahuta NeighborPairs class containing 14 atoms and 7 pairs>,
 'vdw_neighbors': <Lahuta NeighborPairs class containing 206 atoms and 117 pairs>,
 'hydrophobic_neighbors': <Lahuta NeighborPairs class containing 459 atoms and 372 pairs>,
 'hbond_neighbors': <Lahuta NeighborPairs class containing 0 atoms and 0 pairs>,
 'weak_hbond_neighbors': <Lahuta NeighborPairs class containing 0 atoms and 0 pairs>,
 'polar_hbond_neighbors': <Lahuta NeighborPairs class containing 359 atoms and 269 pairs>,
 'weak_polar_hbond_neighbors': <Lahuta NeighborPairs class containing 306 atoms and 183 pairs>,
 'metalic_neighbors': <Lahuta NeighborPairs class containing 0 atoms and 0 pairs>,
 'donor_pi': <Lahuta NeighborPairs class containing 26 atoms and 14 pairs>,
 'cation_pi': <Lahuta NeighborPairs class containing 11 atoms and 6 pairs>,
 'sulphur_pi': <Lahuta NeighborPairs class containing 20 atoms and 14 pairs>,
 'carbon_pi': <Lahuta NeighborPairs class containing 109 atoms and 71 pairs>,
 'plane_plane_neighbors': <Lahuta NeighborPairs class containing 53 atoms and 50 pairs>}

In [13]:

# Only compute atom-plane contacts
contacts = LahutaContacts(contact_type='atom-plane') 
contacts.compute(ns)
contacts.results

# Only compute atom-plane contacts contacts = LahutaContacts(contact_type='atom-plane') contacts.compute(ns) contacts.results

Out[13]:

{'donor_pi': <Lahuta NeighborPairs class containing 26 atoms and 14 pairs>,
 'cation_pi': <Lahuta NeighborPairs class containing 11 atoms and 6 pairs>,
 'sulphur_pi': <Lahuta NeighborPairs class containing 20 atoms and 14 pairs>,
 'carbon_pi': <Lahuta NeighborPairs class containing 109 atoms and 71 pairs>}

In [14]:

# Remove all built-in contact functions (i.e., we initialize with None)
contacts = LahutaContacts(contact_type=None) 

# Register a custom contact function, which is just a function that does not do anything to the input NeighborPairs object
def custom_contact_func(ns): 
    return ns
contacts.register(custom_contact_func) 
# We can also now register specific built-in contact functions (here we register the hydrophobic and van der Waals contacts)
contacts.register([F.hydrophobic_neighbors, F.vdw_neighbors]) 

contacts.compute(ns)
contacts.results

# Remove all built-in contact functions (i.e., we initialize with None) contacts = LahutaContacts(contact_type=None) # Register a custom contact function, which is just a function that does not do anything to the input NeighborPairs object def custom_contact_func(ns): return ns contacts.register(custom_contact_func) # We can also now register specific built-in contact functions (here we register the hydrophobic and van der Waals contacts) contacts.register([F.hydrophobic_neighbors, F.vdw_neighbors]) contacts.compute(ns) contacts.results

Out[14]:

{'custom_contact_func': <Lahuta NeighborPairs class containing 1778 atoms and 2283 pairs>,
 'hydrophobic_neighbors': <Lahuta NeighborPairs class containing 459 atoms and 372 pairs>,
 'vdw_neighbors': <Lahuta NeighborPairs class containing 206 atoms and 117 pairs>}