def get(self, name):
if name.startswith('__'):
return
rcl.init_check('-mute all', strict=False)
this_dir, this_filename = os.path.split(__file__)
pdb_dir = os.path.join(this_dir, 'pdb')
return pyrosetta.pose_from_file(os.path.join(pdb_dir, name + '.pdb'))
def make_atype_charges():
rcl.init_check()
avg_iatype_charge = dict()
atomic_charges = defaultdict(list)
for resn in rif.chem.biochem.aa_name3s:
res = rcl.make_res(resn)
for ia in range(res.natoms()):
iatype = res.atom_type_index(ia + 1)
# if iatype > 100:
# print iatype, resn, res.atom_name(ia+1)
charge = res.atomic_charge(ia + 1)
atomic_charges[iatype].append(charge)
for i, charges in list(atomic_charges.items()):
# print i, rcl.ats()[i].name(), np.mean(charges), np.std(charges)
avg_iatype_charge[rcl.ats()[i].name()] = np.mean(charges)
return avg_iatype_charge
for iat2, atype2 in enumerate(atypes2):
if atypes1 == atypes2 and iat1 > iat2:
continue
jobs.append((iat1, iat2, atype1, atype2, spec))
if multiprocess:
ncpu = multiprocessing.cpu_count() // 2
with ProcessPoolExecutor(ncpu) as executor:
eframes = executor.map(run_make_eframe_for_atoms, jobs)
else:
eframes = list(map(run_make_eframe_for_atoms, jobs))
eframe = pd.concat(eframes)
return eframe
if __name__ == '__main__':
rcl.init_check()
mock_atom = 'mock'
patch_database_with_single_atom_params_files(mock_atom=mock_atom)
spec = EtableSpec(mn=0.0, mx=6, n=64,
label='beta_nov15', map=(square, sqrt))
# print(spec.dists)
# sys.exit(0)
sfunc = rcl.create_score_function(spec.label)
eframe = make_eframes(spec, multiprocess=True)
# atypes1='CH3 Hapo'.split(),
# atypes2='CH3 OOC Nbb Hpol Hapo Haro HNbb'.split())
print('made eframe', eframe.shape)
path = rif.resources.resource_path('rosetta_score_data.h5')
h5path = '/eframes/' + mock_atom + '_dsq' + '/beta_nov15/eframe'
print('save to', path, ':', h5path)
store = pd.HDFStore(path)
def get_pose(pdbdir, fname):
if not rcl.HAVE_PYROSETTA: return None
rcl.init_check(strict=False)
pose = rcl.pose_from_file(join(pdbdir, fname))
return pose
def bigpose(cleanpdbfname):
if not rcl.HAVE_PYROSETTA: return None
rcl.init_check(strict=False)
pose = rcl.pose_from_file(cleanpdbfname)
return pose
def pose(pdbsmallfname):
if not rcl.HAVE_PYROSETTA: return None
rcl.init_check(strict=False)
pose = rcl.pose_from_file(pdbsmallfname)
return pose