Binding site atom surface area contributions

ligand-buried-surface-areas.py

from credoscript import *

# FETCH PDB ENTRY 3CS9
s = StructureAdaptor().fetch_by_pdb('3cs9')
s.title
>>> 'Human ABL kinase in complex with nilotinib'

# 3CS9 CONTAINS 4 BIOLOGICAL ASSEMBLIES
s.Biomolecules
>>> {1: <Biomolecule(1)>,
>>>  2: <Biomolecule(2)>,
>>>  3: <Biomolecule(3)>,
>>>  4: <Biomolecule(4)>}

# TAKE THE FIRST
b = s[1]

# LIGANDS OF THE FIRST BIOMOLECULE: NILOTINIB
b.Ligands
>>> [<Ligand(A 600 NIL)>]

l = b.Ligands[0]

# GET SOLVENT-ACCESSIBLE SURFACE AREA OF THE LIGAND IN THE APO STATE
l.get_buried_surface_area(projection='ligand', state='apo')
>>> 783.458

# BOUND STATE
l.get_buried_surface_area(projection='ligand', state='bound')
>>> 58.2652

# DELTA: HOW MUCH ASA OF THE LIGAND BECOMES INACCESSIBLE UPON BINDING?
l.get_buried_surface_area(projection='ligand', state='delta')
>>> 725.193

# HOW MUCH OF THAT IS POLAR SURFACE AREA?
l.get_buried_surface_area(Atom.is_polar==True, projection='ligand', state='delta')
>>> 105.689

# SAME AS ABOVE BUT BROKEN DOWN INTO INDIVIDUAL LIGAND ATOMS
l.get_buried_surface_area(Atom.is_polar==True, projection='ligand', state='apo', atom_areas=True)
>>> [(<Atom(O17  )>, 28.4709),
>>>  (<Atom(N14  )>, 8.95594),
>>>  (<Atom(N51  )>, 0.520805),
>>>  (<Atom(N54  )>, 10.0699),
>>>  (<Atom(N31  )>, 12.8868),
>>>  (<Atom(N40  )>, 9.57553),
>>>  (<Atom(N34  )>, 10.3417),
>>>  (<Atom(N44  )>, 24.8668)]