def testCifMissing(self):
N = 7
cmd.fragment('gly', 'm1')
cmd.alter('all', '(chain, segi, resv, alt) = ("?", ".", 5, "")')
s = cmd.get_str('cif')
self.assertTrue("'?'" in s or '"?"' in s) # chain
self.assertTrue("'.'" in s or '"."' in s) # segi
self.assertTrue(' ? ' in s) # e.g. pdbx_PDB_ins_code
self.assertTrue(' . ' in s) # e.g. label_alt_id
cmd.delete('*')
cmd.set('cif_keepinmemory')
cmd.load(s, 'm2', format='cifstr')
self.assertEqual(['?'], cmd.get_chains())
self.assertEqual(cmd.count_atoms('segi .'), N)
self.assertEqual(cmd.count_atoms('alt ""'), N) # no alt
self.assertEqual(cmd.count_atoms('resi 5'), N) # no ins_code
from pymol.querying import cif_get_array
self.assertEqual(cif_get_array("m2", "_atom_site.type_symbol"),
list('NCCOHHH'))
self.assertEqual(cif_get_array("m2", "_atom_site.id", "i"),
list(range(1, N + 1)))
self.assertEqual(cif_get_array("m2", "_atom_site.auth_asym_id"),
['?'] * N)
self.assertEqual(cif_get_array("m2", "_atom_site.label_asym_id"),
['.'] * N)
self.assertEqual(cif_get_array("m2", "_atom_site.pdbx_pdb_ins_code"),
[None] * N)
self.assertEqual(cif_get_array("m2", "_atom_site.label_alt_id"),
[None] * N)
def testCifMissing(self):
N = 7
cmd.fragment('gly', 'm1')
cmd.alter('all', '(chain, segi, resv, alt) = ("?", ".", 5, "")')
s = cmd.get_str('cif')
self.assertTrue("'?'" in s or '"?"' in s) # chain
self.assertTrue("'.'" in s or '"."' in s) # segi
self.assertTrue(' ? ' in s) # e.g. pdbx_PDB_ins_code
self.assertTrue(' . ' in s) # e.g. label_alt_id
cmd.delete('*')
cmd.set('cif_keepinmemory')
cmd.load(s, 'm2', format='cifstr')
self.assertEqual(['?'], cmd.get_chains())
self.assertEqual(cmd.count_atoms('segi .'), N)
self.assertEqual(cmd.count_atoms('alt ""'), N) # no alt
self.assertEqual(cmd.count_atoms('resi 5'), N) # no ins_code
from pymol.querying import cif_get_array
self.assertEqual(cif_get_array("m2", "_atom_site.type_symbol"), list('NCCOHHH'))
self.assertEqual(cif_get_array("m2", "_atom_site.id", "i"), list(range(1, N + 1)))
self.assertEqual(cif_get_array("m2", "_atom_site.auth_asym_id"), ['?'] * N)
self.assertEqual(cif_get_array("m2", "_atom_site.label_asym_id"), ['.'] * N)
self.assertEqual(cif_get_array("m2", "_atom_site.pdbx_pdb_ins_code"), [None] * N)
self.assertEqual(cif_get_array("m2", "_atom_site.label_alt_id"), [None] * N)
def minimize(selection='all',
forcefield='MMFF94s',
method='Conjugate Gradients',
nsteps0=500,
conv=0.0001,
cutoff=False,
cut_vdw=6.0,
cut_elec=8.0):
mol_string = cmd.get_str('mol', selection)
name = cmd.get_legal_name(selection)
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats('mol', 'mol')
mol = ob.OBMol()
obconversion.ReadString(mol, mol_string)
ff = ob.OBForceField.FindForceField(
forcefield) ## GAFF, MMFF94s, MMFF94, UFF, Ghemical
ff.Setup(mol)
if cutoff == True:
ff.EnableCutOff(True)
ff.SetVDWCutOff(cut_vdw)
ff.SetElectrostaticCutOff(cut_elec)
if method == 'Conjugate Gradients':
ff.ConjugateGradients(nsteps0, conv)
else:
ff.SteepestDescent(nsteps0, conv)
ff.GetCoordinates(mol)
nrg = ff.Energy()
mol_string = obconversion.WriteString(mol)
cmd.delete(name)
if name == 'all':
name = 'all_'
cmd.read_molstr(mol_string, name, state=0, finish=1, discrete=1)
print('#########################################')
print('The Energy of %s is %8.2f %s ' % (name, nrg, ff.GetUnit()))
print('#########################################')
def get_molstr(sele, state):
'''Export the given selection to a molfile string'''
try:
# new in PyMOL 1.8.4
return cmd.get_str('mol', sele, state)
except Exception as e:
print(e)
from chempy import io
model = cmd.get_model(sele, state)
for a in model.atom:
a.symbol = a.symbol.capitalize()
return ''.join(io.mol.toList(model))
def get_molstr(sele, state):
'''Export the given selection to a molfile string'''
try:
# new in PyMOL 1.8.4
return cmd.get_str('mol', sele, state)
except Exception as e:
print(e)
from chempy import io
model = cmd.get_model(sele, state)
for a in model.atom:
a.symbol = a.symbol.capitalize()
return ''.join(io.mol.toList(model))
def conf_search(selection='all',
forcefield='MMFF94s',
method='Weighted',
nsteps1=500,
conformers=25,
lowest_conf=5):
mol_string = cmd.get_str('mol', selection)
name = cmd.get_legal_name(selection)
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats('mol', 'mol')
mol = ob.OBMol()
obconversion.ReadString(mol, mol_string)
ff = ob.OBForceField.FindForceField(
forcefield) ## GAFF, MMFF94s, MMFF94, UFF, Ghemical
ff.Setup(mol)
if method == 'Weighted':
ff.WeightedRotorSearch(conformers, nsteps1)
elif method == 'Random':
ff.RandomRotorSearch(conformers, nsteps1)
else:
ff.SystematicRotorSearch(nsteps1)
if name == 'all':
name = 'all_'
if method in ['Weighted', 'Random']:
ff.GetConformers(mol)
print('##############################################')
print(' Conformer | Energy | RMSD')
nrg_unit = ff.GetUnit()
rmsd = 0
ff.GetCoordinates(mol)
nrg = ff.Energy()
conf_list = []
for i in range(conformers):
mol.SetConformer(i)
ff.Setup(mol)
nrg = ff.Energy()
conf_list.append((nrg, i))
conf_list.sort()
lenght_conf_list = len(conf_list)
if lowest_conf > lenght_conf_list:
lowest_conf = lenght_conf_list
for i in range(lowest_conf):
nrg, orden = conf_list[i]
name_n = '%s%02d' % (name, i)
cmd.delete(name_n)
mol.SetConformer(orden)
mol_string = obconversion.WriteString(mol)
cmd.read_molstr(mol_string, name_n, state=0, finish=1, discrete=1)
if i != 0:
rmsd = cmd.fit(name_n, '%s00' % name, quiet=1)
print('%15s | %10.2f%9s |%6.1f' % (name_n, nrg, nrg_unit, rmsd))
print('##############################################')
else:
ff.GetCoordinates(mol)
nrg = ff.Energy()
mol_string = obconversion.WriteString(mol)
cmd.delete(name)
cmd.read_molstr(mol_string, name, state=0, finish=1, discrete=1)
print('#########################################')
print('The Energy of %s is %8.2f %s ' %
(name, nrg, ff.GetUnit()))
print('#########################################')