def dummy(self):
with pymol2.PyMOL() as pymol:
pymol.cmd.load(self.params_file.replace('.params', '.pdb'),
'ligand')
pymol.cmd.fab('ACA', chain='A')
pymol.cmd.alter('resn LIG', 'chain="B"')
pymol.cmd.alter('resn LIG', 'resi="1"')
pymol.cmd.sort()
for atom in pymol.cmd.get_model('resn LIG').atom:
pymol.cmd.translate([random.random() for i in range(3)],
f'resn LIG and name {atom.name}')
dummy = pymol.cmd.get_pdbstr('*')
if self.is_covalent():
dummy = f'LINK SG CYS A 2 {self.covalent_atomname} LIG B 1 1555 1555 1.8\n' + dummy
pyrosetta.init(
extra_options=
'-load_PDB_components false -no_optH true -relax:jump_move true')
pose = pyrosetta.Pose()
params_paths = pyrosetta.rosetta.utility.vector1_string()
params_paths.extend([f"{self.name}.params"])
pyrosetta.generate_nonstandard_residue_set(pose, params_paths)
pyrosetta.rosetta.core.import_pose.pose_from_pdbstring(pose, dummy)
pose.dump_pdb(f'test_{self.name}.0.pdb')
self.do_relax(pose)
pose.dump_pdb(f'test_{self.name}.1.pdb')
#pyrosetta.rosetta.protocols.docking.ConformerSwitchMover().apply(pose)
docking = pyrosetta.rosetta.protocols.docking.DockMCMProtocol().apply(
pose)
pose.dump_pdb(f'test_{self.name}.2.pdb')
def snap_shot(self):
with pymol2.PyMOL() as pymol:
pymol.cmd.bg_color('white')
pymol.cmd.load(f'{self.work_path}/{self.name}/pre_{self.name}.pdb',
'pre')
for k in ('pre', 'min'): #('min1','min2', 'docked'):
pymol.cmd.load(
f'{self.work_path}/{self.name}/{k}_{self.name}.pdb', k)
for hit in self.hits:
pymol.cmd.load(hit.bound_file)
# pymol.cmd.read_pdbstr(Chem.MolToPDBBlock(self.fragmenstein.positioned_mol), 'scaffold')
pymol.cmd.remove('solvent')
pymol.cmd.remove('resn DMS')
pymol.cmd.show('sticks', 'resi 145')
pymol.cmd.show('lines', 'byres resn LIG around 4')
pymol.cmd.zoom('resi 145 or resn LIG')
pymol.cmd.save(
f'{self.work_path}/{self.name}/{self.name}_protein.pse')
def best_hit(self) -> Hit:
#cached.
if self._best_hit is not None:
return self._best_hit
best_d = 99999
best_hit = -1
with pymol2.PyMOL() as pymol:
for hit in self.hits:
pymol.cmd.load(hit.bound_file)
d = min([
pymol.cmd.distance('resi 145 and name SG',
f'resn LIG and name {atom.name}')
for atom in pymol.cmd.get_model('resn LIG').atom
])
if d < best_d:
best_hit = hit
best_d = d
pymol.cmd.delete('*')
print('Best hit', best_hit.name)
self._best_hit = best_hit
return best_hit
def make_fragmenstein(self):
with pymol2.PyMOL() as pymol:
pymol.cmd.load(self.best_hit.bound_file, 'prot')
sg = Chem.MolFromPDBBlock(
pymol.cmd.get_pdbstr('resi 145 and name SG'))
pymol.cmd.save('sg.pdb', 'resi 145 and name SG')
ff = Fragmenstein(self.ori_mol, [h.mol for h in self.hits],
attachment=sg)
ff.make_pse(
f'{self.work_path}/{self.name}/{self.name}_fragmenstein.pse')
Chem.MolToMolFile(
ff.scaffold,
f'{self.work_path}/{self.name}/scaffold.fragmenstein.mol',
kekulize=False)
Chem.MolToMolFile(
ff.chimera,
f'{self.work_path}/{self.name}/chimera.fragmenstein.mol',
kekulize=False)
Chem.MolToMolFile(
ff.positioned_mol,
f'{self.work_path}/{self.name}/{self.name}.fragmenstein.mol',
kekulize=False)
return ff
def load_pose(self):
with pymol2.PyMOL() as pymol:
pymol.cmd.load(self.bound_file)
pymol.cmd.remove('solvent')
pymol.cmd.remove(
'not polymer and not resn LIG'
) # should run it through P Curran\s list of artefacts!
pymol.cmd.alter('resn LIG', 'chain="B"')
pymol.cmd.alter('resn LIG', 'resi="1"')
pymol.cmd.sort()
holo = pymol.cmd.get_pdbstr('*')
if self.is_covalent():
holo = f'LINK SG CYS A 145 {self.covalent_atomname} LIG B 1 1555 1555 1.8\n' + holo
pose = pyrosetta.Pose()
params_paths = pyrosetta.rosetta.utility.vector1_string()
params_paths.extend([self.params_file])
pyrosetta.generate_nonstandard_residue_set(pose, params_paths)
pyrosetta.rosetta.core.import_pose.pose_from_pdbstring(pose, holo)
## Force HIE
r = pose.pdb_info().pdb2pose(res=41, chain='A')
MutateResidue = pyrosetta.rosetta.protocols.simple_moves.MutateResidue
MutateResidue(target=r, new_res='HIS').apply(pose)
return pose