def test_raise_OSError(self):
with mock.patch("HPC_Drug.auxiliary_functions.path.which",
side_effect=OSError,
autospec=True):
with mock.patch(
"HPC_Drug.auxiliary_functions.path.absolute_filepath",
side_effect=FileNotFoundError,
autospec=True):
with self.assertRaises(OSError):
path.absolute_programpath(program="test")
def _plumed_partial_tempering(self, scaling_value, input_file, output_file):
"""
private
Creates the scaled topology files with plumed
"""
plumed = path.absolute_programpath(program = "plumed")
command = [plumed, "partial_tempering", f"{scaling_value}"]
print(f"Running Plumed, with scaling value {scaling_value}")
with open(input_file, "r") as input_file_handle:
with open(output_file, "w") as output_file_handle:
r = subprocess.run(command,
shell = False,
stdin = input_file_handle,
stdout= output_file_handle,
stderr= subprocess.PIPE)
print(r.stderr)
if r.returncode != 0:
raise RuntimeError(f"Plumed failure\n{r.stderr}")
def __init__(self,
Protein,
solvent_box,
MD_program_path='orac',
number_of_cores_per_node=64,
number_of_replicas=8):
self.Protein = Protein
self.solvent_box = solvent_box
self.MD_program_path = path.absolute_programpath(
program=MD_program_path)
self.number_of_cores_per_node = number_of_cores_per_node
self.orac_in_file = f"HREM.in"
#dummy useless value
self.kind_of_processor = 'skylake'
#an instance of orient.Orient class
self.orient = orient.Orient(self.Protein,
self.Protein.get_ligand_list())
self.BATTERIES = self._get_BATTERIES()
self.replicas = number_of_replicas
def test_use_which(self):
with mock.patch("HPC_Drug.auxiliary_functions.path.which",
return_value="test_output",
autospec=True) as mocked_function:
output = path.absolute_programpath(program="test")
mocked_function.assert_called_once_with(program="test")
self.assertEqual(output, "test_output")
def __init__(self, Protein=None, MD_program_path='gmx'):
self.Protein = Protein
self.output_gro_file = os.getcwd(
) + f"{self.Protein.protein_id}_gromacs.gro"
self.output_pdb_file = os.getcwd(
) + f"{self.Protein.protein_id}_gromacs.pdb"
self.mdp_file = os.getcwd() + f"/{self.Protein.protein_id}_gromacs.mdp"
self.MD_program_path = path.absolute_programpath(
program=MD_program_path)
self.command_string = []
self.template = []
def __init__(self, Protein, solvent_pdb=None, MD_program_path='orac'):
"""
Protein :: HPC_Drug.structures.protein.Protein instance
solvent_pdb :: string, it is the pdb file that contains the coordinates of a solvent molecule
it is needed if there has to be added a solvent box around the protein
default HPC_Drug.lib "water.pdb"
MD_program_path :: string, the absolute path to the orac executable
dafault will look for an executable called orac in the PATH and the working directory (in this order)
"""
self.Protein = Protein
self.orac_in_file = os.getcwd() + f"/{self.Protein.protein_id}_orac.in"
self.solvent_pdb = solvent_pdb
#if no path is given searches the standard water.pdb inside lib module
if self.solvent_pdb == None:
with importlib_resources.path('HPC_Drug.lib',
'water.pdb') as _path:
self.solvent_pdb = str(_path.resolve())
self.MD_program_path = path.absolute_programpath(
program=MD_program_path)
self.output_pdb_file = os.getcwd(
) + f"/{self.Protein.protein_id}_orac.pdb"
#an instance of orient.Orient class
self.orient = orient.Orient(self.Protein,
self.Protein.get_ligand_list())
self.template = []
#some values that are needed many times are calculated in the constructor
#The box sizes (lx, ly, lz)
#the structure is rotated in its tensor of inertia ref
self.box = self._create_selfbox()
def get_topology(Protein, program_path, tool="primadorac", ph=7.0):
"""
uses the right tool to get
the topology of a given organic ligand (.itp .tpg .prm etc...)
in order to use it in a MD run
returns the updated protein
Protein :: HPC_Drug.structures.protein.Protein instance
with a valid Protein._ligands (Protein.get_ligand_list())
value (if it is None or [] will return the protein untouched)
program_path :: string, the absolute path to the tool's executable
tool :: string, default primadorac, the tool to use to get the
topology (.itp .tpg .prm etc...)
ph :: float, default 7.0, the ph at which the ligand shall be added the missing hydrogens
return Protein
"""
if Protein.get_ligand_list() == None or Protein.get_ligand_list() == []:
return Protein
program_path = path.absolute_programpath(program=program_path)
if tool == "primadorac":
primadorac_obj = primadorac.Primadorac(Protein=Protein,
primadorac_path=program_path,
ph=ph)
Protein = primadorac_obj.execute()
else:
raise NotImplementedError(f"{tool} is not an implemented tool")
return Protein
def _refine_input(self, input_variables = None):
"""Makes the needed casts from string, defines some None to default ecc"""
# Protein_model must be an integer
if input_variables['Protein_model'] != None:
input_variables['Protein_model'] = int(input_variables['Protein_model'])
#default is zero
elif input_variables['Protein_model'] == None:
input_variables['Protein_model'] = 0
#The standard chain is 'A'
if input_variables['Protein_chain'] == None:
input_variables['Protein_chain'] = 'A'
#need it uppercase
else:
input_variables['Protein_chain'] = input_variables['Protein_chain'].upper().strip()
#ph must be a float
if input_variables['ph'] != None:
input_variables['ph'] = float(input_variables['ph'])
#sets primadorac as the default ligand elaboration program and tries to guess where the executable is
if input_variables['ligand_elaboration_program'] == None:
input_variables['ligand_elaboration_program'] = 'primadorac'
if input_variables['ligand_elaboration_program_path'] == None:
input_variables['ligand_elaboration_program_path'] = program_path.absolute_programpath(program = '~/ORAC/trunk/tools/primadorac/primadorac.bash')
else:
input_variables['ligand_elaboration_program_path'] = program_path.absolute_programpath(program = input_variables['ligand_elaboration_program_path'])
#absolute path of the program path
input_variables['MD_program_path'] = program_path.absolute_programpath(program = input_variables['MD_program_path'])
if input_variables['MD_program'] == None:
input_variables['MD_program'] = 'gromacs'
if input_variables['MD_program'] == 'orac':
if input_variables['protein_tpg_file'] == None:
with importlib_resources.path('HPC_Drug.lib', 'amber99sb-ildn.tpg') as path:
input_variables['protein_tpg_file'] = str(path.resolve())
if input_variables['protein_prm_file'] == None:
with importlib_resources.path('HPC_Drug.lib', 'amber99sb-ildn.prm') as path:
input_variables['protein_prm_file'] = str(path.resolve())
if input_variables['solvent_pdb'] == None:
with importlib_resources.path('HPC_Drug.lib', 'water.pdb') as path:
input_variables['solvent_pdb'] = str(path.resolve())
elif input_variables['MD_program'] == 'gromacs':
if input_variables['protein_tpg_file'] == None:
input_variables['protein_tpg_file'] = 'amber99sb-ildn'
if input_variables['solvent_pdb'] == None:
input_variables['solvent_pdb'] = 'spce'
#set a default for processor (skylake)
if input_variables['kind_of_processor'] == None:
input_variables['kind_of_processor'] = 'skylake'
else:
#in this way I don't have to worry about strange input formats
input_variables['kind_of_processor'] = input_variables['kind_of_processor'].lower().strip()
#the number of cores per node is usually 64
if input_variables['number_of_cores_per_node'] == None:
input_variables['number_of_cores_per_node'] = 64
else:
#cast string to integer
input_variables['number_of_cores_per_node'] = int(input_variables['number_of_cores_per_node'].strip())
if input_variables['residue_substitution'] == None:
input_variables['residue_substitution'] = 'standard'
if input_variables['use_gpu'] == None:
input_variables['use_gpu'] = 'auto'
if input_variables['gpu_per_node'] is None:
input_variables['gpu_per_node'] = 1
else:
input_variables['gpu_per_node'] = int(input_variables['gpu_per_node'])
if input_variables['number_of_hrem_replicas_per_battery_bound'] is None:
input_variables['number_of_hrem_replicas_per_battery_bound'] = 8
elif input_variables['number_of_hrem_replicas_per_battery_bound'] == 0 or input_variables['number_of_hrem_replicas_per_battery_bound'] == 1:
raise ValueError("The number of bound HREM replicas must be greater than 1")
else:
input_variables['number_of_hrem_replicas_per_battery_bound'] = int(input_variables['number_of_hrem_replicas_per_battery_bound'].strip())
if input_variables['number_of_hrem_replicas_per_battery_unbound'] is None:
input_variables['number_of_hrem_replicas_per_battery_unbound'] = 8
elif input_variables['number_of_hrem_replicas_per_battery_unbound'] == 0 or input_variables['number_of_hrem_replicas_per_battery_unbound'] == 1:
raise ValueError("The number of bound HREM replicas must be greater than 1")
else:
input_variables['number_of_hrem_replicas_per_battery_unbound'] = int(input_variables['number_of_hrem_replicas_per_battery_unbound'].strip())
for i in ('bound_batteries', 'unbound_batteries', 'n_steps_bound_hrem', 'n_steps_unbound_hrem'):
if input_variables[i] == 'auto':
input_variables[i] = None
elif input_variables[i] is not None:
input_variables[i] = int(input_variables[i])
for i in ('timestep_bound_hrem', 'timestep_unbound_hrem'):
if input_variables[i] == 'auto':
input_variables[i] = None
elif input_variables[i] is not None:
input_variables[i] = float(input_variables[i])
for i in ('constraints_bound_hrem', 'constraints_unbound_hrem'):
if input_variables[i] == 'auto':
input_variables[i] = None
if input_variables['box_borders'] is not None:
input_variables['box_borders'] = float(input_variables['box_borders'])
if input_variables['repairing_method'].lower() == 'none':
input_variables['repairing_method'] = False
return input_variables
"The number of alchemical transformations to do, a good default is 200 protein ligand and 400 ligand only, default=200"
)
parser.add_argument(
'--constrains',
action="store",
default=None,
type=str,
choices=['none', 'h-bonds', 'all-bonds'],
help=
"how to constraints vibrations, same syntax as gromacs mdp file default=all-bonds"
)
parsed_input = parser.parse_args()
parsed_input.program_path = path.absolute_programpath(
parsed_input.program_path)
if parsed_input.hrem_type == "protein-ligand":
creation = False
elif parsed_input.hrem_type == "only-ligand":
creation = True
# From comma separated list to list of int
parsed_input.pbc_atoms = parsed_input.pbc_atoms.split(',')
for i, atom in enumerate(parsed_input.pbc_atoms):
parsed_input.pbc_atoms[i] = int(atom)
fsdam_obj = fsdam.FSDAMInputPreprocessing(