class Analyze:
def __init__(self, protein, ligand, within=7.5):
self.protein = protein
self.ligand = ligand
genASite = GenActiveSite(within=within)
self.asite = genASite(self.protein, self.ligand)
renumberResidues(self.asite)
log(f'nAtoms of asite {self.asite.GetNumAtoms()}')
complex = Chem.CombineMols(self.asite, self.ligand)
self.pmol = PDBComplex()
cont = Chem.MolToPDBBlock(complex).replace('UNL 1', 'MOL 1')
self.pmol.load_pdb(cont, as_string=True)
self.pmol.analyze()
def getPLIPComplexToProteinMap(self):
N = self.protein.GetNumAtoms()
protein_coords = getCoordinates(self.protein)
cpmap = {}
for i in self.pmol.atoms:
atom = self.pmol.get_atom(i)
d = np.linalg.norm(np.tile(np.array(atom.coords), N).reshape(
(N, 3)) - protein_coords,
axis=1)
minidx = d.argmin()
if d[minidx] < 1e-3:
cpmap[atom.idx] = minidx.item()
return cpmap
def getPLIPComplexToLigandMap(self):
N = self.ligand.GetNumAtoms()
ligand_coords = getCoordinates(self.ligand)
clmap = {}
for i in self.pmol.atoms:
atom = self.pmol.get_atom(i)
d = np.linalg.norm(np.tile(np.array(atom.coords), N).reshape(
(N, 3)) - ligand_coords,
axis=1)
minidx = d.argmin()
if d[minidx] < 1e-3:
clmap[atom.idx] = minidx.item()
return clmap
def getPLIPComplexToASiteMap(self):
N = self.asite.GetNumAtoms()
asite_coords = getCoordinates(self.asite)
camap = {}
for i in self.pmol.atoms:
atom = self.pmol.get_atom(i)
d = np.linalg.norm(np.tile(np.array(atom.coords), N).reshape(
(N, 3)) - asite_coords,
axis=1)
minidx = d.argmin()
if d[minidx] < 1e-3:
camap[atom.idx] = minidx.item()
return camap
def interactions(self):
camap = self.getPLIPComplexToASiteMap()
clmap = self.getPLIPComplexToLigandMap()
for bsite, iacts in self.pmol.interaction_sets.items():
for ia in iacts.all_itypes:
iact = Inter(ia)
if not iact.isValid():
continue
aidxs = list(map(lambda x: camap[x], iact.P()))
lidxs = list(map(lambda x: clmap[x], iact.L()))
yield bsite, iact.name, aidxs, lidxs
