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Update configfile_creator.py
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Adjusted code for easier config parser
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@talagayev
talagayev authored Aug 27, 2024
1 parent fd1f111 commit 38c1535
Showing 1 changed file with 29 additions and 50 deletions.
79 changes: 29 additions & 50 deletions openmmdl/openmmdl_setup/configfile_creator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,16 +74,16 @@ def add_pdb_input_files_configuration(self, script):
"""############# Ligand and Protein Data ###################"""
)
if self.session["pdbType"] == "pdb":
script.append('input_file_type = "pdb"')
script.append('protein = "%s"' % self.uploadedFiles["file"][0][1])
script.append('input_file_type = pdb')
script.append('protein = %s' % self.uploadedFiles["file"][0][1])
if self.session["sdfFile"] != "":
script.append("ligand = '%s'" % self.session["sdfFile"])
script.append('ligand_name = "UNK"')
script.append("ligand = %s" % self.session["sdfFile"])
script.append('ligand_name = UNK')
script.append(
"minimization = %s" % self.session["ligandMinimization"]
)
script.append(
"smallMoleculeForceField = '%s'"
"smallMoleculeForceField = %s"
% self.session["smallMoleculeForceField"]
)
script.append(
Expand All @@ -107,12 +107,12 @@ def add_amber_file_configuration(self, script):

# amber_files related variables
if self.session["has_files"] == "yes":
script.append('input_file_type = "amber"')
script.append('input_file_type = amber')
script.append(
"prmtop_file = '%s'" % self.uploadedFiles["prmtopFile"][0][1]
"prmtop_file = %s" % self.uploadedFiles["prmtopFile"][0][1]
)
script.append(
'inpcrd_file = "%s"' % self.uploadedFiles["inpcrdFile"][0][1]
'inpcrd_file = %s' % self.uploadedFiles["inpcrdFile"][0][1]
)

# ligand related variables
Expand All @@ -121,10 +121,10 @@ def add_amber_file_configuration(self, script):

elif self.session["has_files"] == "no":
script.append(
"prmtop_file = 'system.%s.prmtop'" % self.session["water_ff"]
"prmtop_file = system.%s.prmtop" % self.session["water_ff"]
)
script.append(
"inpcrd_file = 'system.%s.inpcrd' " % self.session["water_ff"]
"inpcrd_file = system.%s.inpcrd " % self.session["water_ff"]
)

# ligand related variables
Expand Down Expand Up @@ -158,9 +158,9 @@ def add_forcefield_and_water_model_configuration(self, script):
script.append(
"""\n############# Forcefield, Water and Membrane Model Selection ###################\n"""
)
script.append("forcefield = '%s'" % self.session["forcefield"])
script.append("forcefield = %s" % self.session["forcefield"])
if self.session["waterModel"] != "None":
script.append("water = '%s'" % self.session["waterModel"])
script.append("water = %s" % self.session["waterModel"])
else:
script.append("water = %s" % self.session["waterModel"])

Expand All @@ -181,7 +181,7 @@ def add_solvent_configuration(self, script):
)
script.append("add_membrane = %s" % self.session["add_membrane"])
script.append(
"membrane_lipid_type = '%s'" % self.session["lipidType"]
"membrane_lipid_type = %s" % self.session["lipidType"]
)
script.append(
"membrane_padding = %s" % self.session["membrane_padding"]
Expand All @@ -191,11 +191,11 @@ def add_solvent_configuration(self, script):
% self.session["membrane_ionicstrength"]
)
script.append(
"membrane_positive_ion = '%s'"
"membrane_positive_ion = %s"
% self.session["membrane_positive"]
)
script.append(
"membrane_negative_ion = '%s'"
"membrane_negative_ion = %s"
% self.session["membrane_negative"]
)
else:
Expand All @@ -204,27 +204,27 @@ def add_solvent_configuration(self, script):
)
script.append("add_membrane = %s" % self.session["add_membrane"])
if self.session["water_padding"]:
script.append('Water_Box = "Buffer"')
script.append('Water_Box = Buffer')
script.append(
"water_padding_distance = %s"
% self.session["water_padding_distance"]
)
script.append(
"water_boxShape = '%s'" % self.session["water_boxShape"]
"water_boxShape = %s" % self.session["water_boxShape"]
)
else:
script.append('Water_Box = "Absolute"')
script.append('Water_Box = Absolute')
script.append("water_box_x = %s" % self.session["box_x"])
script.append("water_box_y = %s" % self.session["box_y"])
script.append("water_box_z = %s" % self.session["box_z"])
script.append(
"water_ionicstrength = %s" % self.session["water_ionicstrength"]
)
script.append(
"water_positive_ion = '%s'" % self.session["water_positive"]
"water_positive_ion = %s" % self.session["water_positive"]
)
script.append(
"water_negative_ion = '%s'" % self.session["water_negative"]
"water_negative_ion = %s" % self.session["water_negative"]
)
else:
script.append("Solvent = %s" % self.session["solvent"])
Expand Down Expand Up @@ -332,33 +332,13 @@ def add_equilibration_configuration(self, script):
Args:
script (list): A list of strings representing the configuration script being built.
"""
equilibration_type = self.session["equilibration"]
preparation_type = self.session["equilibration"]
script.append("\n# Equilibration & Minimization Configuration\n")

if equilibration_type == "equilibration":
script.append(
"""equilibration_stages = [
{'EOM': 'minimize', 'n_steps': 10000, 'temperature': 300*unit.kelvin, 'ensemble': None, 'restraint_selection': 'protein and not type H', 'force_constant': 100*unit.kilocalories_per_mole/unit.angstrom**2, 'collision_rate': 2/unit.picoseconds, 'timestep': 1*unit.femtoseconds},
{'EOM': 'MD_interpolate', 'n_steps': 100000, 'temperature': 100*unit.kelvin, 'temperature_end': 300*unit.kelvin, 'ensemble': 'NVT', 'restraint_selection': 'protein and not type H', 'force_constant': 100*unit.kilocalories_per_mole/unit.angstrom**2, 'collision_rate': 10/unit.picoseconds, 'timestep': 1*unit.femtoseconds},
{'EOM': 'MD', 'n_steps': 100000, 'temperature': 300, 'ensemble': 'NPT', 'restraint_selection': 'protein and not type H', 'force_constant': 100*unit.kilocalories_per_mole/unit.angstrom**2, 'collision_rate': 10/unit.picoseconds, 'timestep': 1*unit.femtoseconds},
{'EOM': 'MD', 'n_steps': 250000, 'temperature': 300*unit.kelvin, 'ensemble': 'NPT', 'restraint_selection': 'protein and not type H', 'force_constant': 10*unit.kilocalories_per_mole/unit.angstrom**2, 'collision_rate': 2/unit.picoseconds, 'timestep': 1*unit.femtoseconds},
{'EOM': 'minimize', 'n_steps': 10000, 'temperature': 300*unit.kelvin, 'ensemble': None, 'restraint_selection': 'protein and backbone', 'force_constant': 10*unit.kilocalories_per_mole/unit.angstrom**2, 'collision_rate': 2/unit.picoseconds, 'timestep': 1*unit.femtoseconds},
{'EOM': 'MD', 'n_steps': 100000, 'temperature': 300*unit.kelvin, 'ensemble': 'NPT', 'restraint_selection': 'protein and backbone', 'force_constant': 10*unit.kilocalories_per_mole/unit.angstrom**2, 'collision_rate': 2/unit.picoseconds, 'timestep': 1*unit.femtoseconds},
{'EOM': 'MD', 'n_steps': 100000, 'temperature': 300*unit.kelvin, 'ensemble': 'NPT', 'restraint_selection': 'protein and backbone', 'force_constant': 1*unit.kilocalories_per_mole/unit.angstrom**2, 'collision_rate': 2/unit.picoseconds, 'timestep': 1*unit.femtoseconds},
{'EOM': 'MD', 'n_steps': 100000, 'temperature': 300*unit.kelvin, 'ensemble': 'NPT', 'restraint_selection': 'protein and backbone', 'force_constant': 0.1*unit.kilocalories_per_mole/unit.angstrom**2, 'collision_rate': 2/unit.picoseconds, 'timestep': 1*unit.femtoseconds},
{'EOM': 'MD', 'n_steps': 2500000, 'temperature': 300*unit.kelvin, 'ensemble': 'NPT', 'restraint_selection': None, 'force_constant': 0*unit.kilocalories_per_mole/unit.angstrom**2, 'collision_rate': 2/unit.picoseconds, 'timestep': 2*unit.femtoseconds},
]
"""
)
elif equilibration_type == "minimization":
script.append(
"""equilibration_stages = [
{'EOM': 'minimize', 'n_steps': 10000, 'temperature': 300*unit.kelvin, 'ensemble': None, 'restraint_selection': 'protein and not type H', 'force_constant': 100*unit.kilocalories_per_mole/unit.angstrom**2, 'collision_rate': 2/unit.picoseconds, 'timestep': 1*unit.femtoseconds},
]
"""
)
elif equilibration_type == "None":
script.append("equilibration_stages = None")
if preparation_type == "equilibration":
script.append("preparation_type = equilibration")
elif preparation_type == "minimization":
script.append("preparation_type = minimization")

def add_simulation_configuration(self, script):
"""
Expand All @@ -371,21 +351,20 @@ def add_simulation_configuration(self, script):
script.append("\n# Simulation Configuration\n")

script.append(
"platform = Platform.getPlatformByName('%s')" % self.session["platform"]
"platform = '%s'" % self.session["platform"]
)
if self.session["platform"] in ("CUDA", "OpenCL"):
script.append(
"platformProperties = {'Precision': '%s'}" % self.session["precision"]
)
if self.session["writeDCD"]:
if self.session["restart_step"] == "":
if self.session["restart_checkpoint"] and self.session["restart_step"] != "":
script.append(
"dcdReporter = DCDReporter('%s_%s', dcdInterval)"
"dcd_name = '%s_%s'"
% (self.session["restart_step"], self.session["dcdFilename"])
)
else:
script.append(
"dcdReporter = DCDReporter('%s', dcdInterval)"
script.append("dcd_name = '%s'"
% (self.session["dcdFilename"])
)
if self.session["writeData"]:
Expand Down

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