def test_ante_error():
ethane = pmd.load_file(get_fn("ethane.mol2"), structure=True)
with temporary_directory() as tmpdir:
with temporary_cd(tmpdir):
with pytest.raises(RuntimeError, match=r"Antechamber failed"):
charges = ante_charges(ethane, "bcc", net_charge=-1)
assert isfile("ante_errorlog.txt")
def ante_atomtyping(molecule, atype_style):
"""Perform atomtyping by calling antechamber
Parameters
----------
molecule : parmed.Structure or mbuild.Compound
Molecular structure to perform atomtyping on
atype_style : str
Style of atomtyping. Options include 'gaff', 'gaff2',
'amber', 'bcc', 'sybyl'.
Returns
-------
typed_molecule : parmed.Structure
The molecule with antechamber atomtyping applied
"""
_check_antechamber(ANTECHAMBER)
# Check valid atomtype name
supported_atomtypes = ['gaff', 'gaff2', 'amber', 'bcc', 'sybyl' ]
if atype_style not in supported_atomtypes:
raise FoyerError( 'Unsupported atomtyping style requested. '
'Please select from {}'.format(supported_atomtypes))
# Check for parmed.Structure. Convert from mbuild.Compound if possible
molecule = _check_structure(molecule)
# Confirm single connected molecule
_check_single_molecule(molecule)
# Get current directory to write any error logs
workdir = os.getcwd()
# Work within a temporary directory
# to clean up after antechamber
with temporary_directory() as tmpdir:
with temporary_cd(tmpdir):
# Save the existing molecule to file
_write_pdb(molecule,'ante_in.pdb')
# Call antechamber
command = ( 'antechamber -i ante_in.pdb -fi pdb '
'-o ante_out.mol2 -fo mol2 ' +
'-at ' + atype_style + ' ' +
'-s 2' )
proc = Popen(command, stdout=PIPE, stderr=PIPE,
universal_newlines=True, shell=True)
out, err = proc.communicate()
# Error handling here
if 'Fatal Error' in err or proc.returncode != 0:
_antechamber_error(out,err,workdir)
# Now read in the mol2 file with atomtyping
typed_molecule = pmd.load_file('ante_out.mol2',structure=True)
# And return it
return typed_molecule
def ante_charges(
molecule, charge_style, net_charge=0.0, multiplicity=1, charge_tol=0.005
):
"""Calculates partial charges by calling antechamber
Parameters
----------
molecule : parmed.Structure or mbuild.Compound
Molecular structure to perform atomtyping on
charge_style : str
Style of partial charges calculation. Options include
'bcc', 'gas', and 'mul'. See antechamber documentation
by running 'antechamber -L' for details.
net_charge : float, optional, default=0.0
Net charge of the molecule
multiplicity : int, optional, default=1
Spin multiplicity, 2S + 1
Returns
-------
molecule : parmed.Structure
The molecule with charges applied
"""
_check_antechamber(ANTECHAMBER)
# Check valid atomtype name
supported_chargetypes = ["bcc", "gas", "mul"]
if charge_style not in supported_chargetypes:
raise FoyerError(
"Unsupported charge style requested. "
"Please select from {}".format(supported_chargetypes)
)
# Check for parmed.Structure. Convert from mbuild.Compound if possible
molecule = _check_structure(molecule)
# Confirm single connected molecule
_check_single_molecule(molecule)
# Get current directory to write any error logs
workdir = os.getcwd()
# Work within a temporary directory
# to clean up after antechamber
with temporary_directory() as tmpdir:
with temporary_cd(tmpdir):
# Save the existing molecule to file
_write_pdb(molecule, "ante_in.pdb")
# Call antechamber
command = (
"antechamber -i ante_in.pdb -fi pdb "
"-o ante_out.mol2 -fo mol2 "
+ "-c "
+ charge_style
+ " "
+ "-nc "
+ str(net_charge)
+ " "
+ "-m "
+ str(multiplicity)
+ " "
+ "-s 2"
)
proc = Popen(
command, stdout=PIPE, stderr=PIPE, universal_newlines=True, shell=True
)
out, err = proc.communicate()
# Error handling here
if "Fatal Error" in err or proc.returncode != 0:
_antechamber_error(out, err, workdir)
# Now read in the mol2 file with atomtyping
charges = pmd.load_file("ante_out.mol2", structure=True)
charge_list = [atom.charge for atom in charges]
if abs(net_charge - sum(charge_list)) > charge_tol:
raise ValueError(
"The sum of charges defined by antechamber"
" is {}, which differs from the desired net charge"
" of {} by a value greater than {}".format(
sum(charge_list), net_charge, charge_tol
)
)
elif abs(net_charge - sum(charge_list)) < charge_tol:
charge_delta = (net_charge - sum(charge_list)) / len(charge_list)
for atom in charges:
atom.charge += charge_delta
# Combine charge information with existing molecule structure
assert len(molecule.atoms) == len(charges.atoms)
for atom_idx in range(len(molecule.atoms)):
assert molecule.atoms[atom_idx].element == charges.atoms[atom_idx].element
molecule.atoms[atom_idx].charge = charges.atoms[atom_idx].charge
return molecule
def ante_charges(molecule, charge_style, net_charge=0.0,
multiplicity=1):
"""Calculates partial charges by calling antechamber
Parameters
----------
molecule : parmed.Structure or mbuild.Compound
Molecular structure to perform atomtyping on
charge_style : str
Style of partial charges calculation. Options include
'bcc', 'gas', and 'mul'. See antechamber documentation
by running 'antechamber -L' for details.
net_charge : float, optional, default=0.0
Net charge of the molecule
multiplicity : int, optional, default=1
Spin multiplicity, 2S + 1
Returns
-------
molecule : parmed.Structure
The molecule with charges applied
"""
_check_antechamber(ANTECHAMBER)
# Check valid atomtype name
supported_chargetypes = ['bcc', 'gas', 'mul']
if charge_style not in supported_chargetypes:
raise FoyerError( 'Unsupported charge style requested. '
'Please select from {}'.format(supported_chargetypes))
# Check for parmed.Structure. Convert from mbuild.Compound if possible
molecule = _check_structure(molecule)
# Confirm single connected molecule
_check_single_molecule(molecule)
# Get current directory to write any error logs
workdir = os.getcwd()
# Work within a temporary directory
# to clean up after antechamber
with temporary_directory() as tmpdir:
with temporary_cd(tmpdir):
# Save the existing molecule to file
_write_pdb(molecule,'ante_in.pdb')
# Call antechamber
command = ( 'antechamber -i ante_in.pdb -fi pdb '
'-o ante_out.mol2 -fo mol2 ' +
'-c ' + charge_style + ' ' +
'-nc ' + str(net_charge) + ' ' +
'-m ' + str(multiplicity) + ' ' +
'-s 2' )
proc = Popen(command, stdout=PIPE, stderr=PIPE,
universal_newlines=True, shell=True)
out, err = proc.communicate()
# Error handling here
if 'Fatal Error' in err or proc.returncode != 0:
_antechamber_error(out,err,workdir)
# Now read in the mol2 file with atomtyping
charges = pmd.load_file('ante_out.mol2',structure=True)
# Combine charge information with existing molecule structure
assert len(molecule.atoms) == len(charges.atoms)
for atom_idx in range(len(molecule.atoms)):
assert molecule.atoms[atom_idx].element == \
charges.atoms[atom_idx].element
molecule.atoms[atom_idx].charge = charges.atoms[atom_idx].charge
return molecule