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Update openmmdlsetup.py
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Adjusting to new changes in moval of code
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@talagayev
talagayev authored Aug 9, 2024
1 parent ab4af18 commit fb383eb
Showing 1 changed file with 33 additions and 302 deletions.
335 changes: 33 additions & 302 deletions openmmdl/openmmdl_setup/openmmdlsetup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,9 @@
import webbrowser
import zipfile

from openmmdl.openmmdl_setup.setup_options import SimulationOptionsConfigurator
from openmmdl.openmmdl_setup.configfile_creator import ConfigCreator


if sys.version_info >= (3, 0):
from io import StringIO
Expand All @@ -50,6 +53,8 @@
simulationProcess = None




def saveUploadedFiles():
uploadedFiles.clear()
for key in request.files:
Expand Down Expand Up @@ -1024,88 +1029,17 @@ def downloadPackage():

def configureDefaultOptions():
"""Select default options based on the file format and force field."""
implicitWater = False
session["restart_checkpoint"] = "no"
session["mdtraj_output"] = "mdtraj_pdb_dcd"
session["mdtraj_removal"] = "False"
session["mda_output"] = "mda_pdb_dcd"
session["mda_selection"] = "mda_prot_lig_all"
session["openmmdl_analysis"] = "No"
session["analysis_selection"] = "analysis_all"
session["binding_mode"] = "40"
session["min_transition"] = "1"
session["rmsd_diff"] = "No"
session["pml_generation"] = "True"
session["stable_water"] = "Yes"
session["wc_distance"] = "1.0"
if session["fileType"] == "pdb" and session["waterModel"] == "implicit":
implicitWater = True
session["ensemble"] = "nvt" if implicitWater else "npt"
session["platform"] = "CUDA"
session["precision"] = "mixed"
session["cutoff"] = "2.0" if implicitWater else "1.0"
session["ewaldTol"] = "0.0005"
session["constraintTol"] = "0.000001"
session["hmr"] = True
session["hmrMass"] = "1.5"
session["dt"] = "0.002"
session["sim_length"] = "50"
session["equilibration"] = "equilibration"
session["temperature"] = "300"
session["friction"] = "1.0"
session["pressure"] = "1.0"
session["barostatInterval"] = "25"
session["nonbondedMethod"] = "CutoffNonPeriodic" if implicitWater else "PME"
session["writeDCD"] = True
session["dcdFilename"] = "trajectory.dcd"
session["dcdFrames"] = "1000"
session["pdbInterval_ns"] = "10"
session["writeData"] = True
session["dataFilename"] = "log.txt"
session["dataInterval"] = "1000"
session["dataFields"] = [
"step",
"speed",
"progress",
"potentialEnergy",
"temperature",
]
session["writeCheckpoint"] = True
session["checkpointFilename"] = "checkpoint.chk"
session["checkpointInterval_ns"] = "0.02"
session["writeSimulationXml"] = False
session["systemXmlFilename"] = "system.xml"
session["integratorXmlFilename"] = "integrator.xml"
session["writeFinalState"] = False
session["finalStateFileType"] = "stateXML"
session["finalStateFilename"] = "final_state.xml"
session["constraints"] = "hbonds"
session["rmsd"] = "True"
session["md_postprocessing"] = "True"


def createScript(isInternal=False):

# Initialize the configurator with the session
simulation_configurator = SimulationOptionsConfigurator(session)

simulation_configurator.configure_default_options()

def createScript():
script = []

# If we are creating this script for internal use to run a simulation directly, add extra code at the top
# to set the working directory and redirect stdout to the pipe.

if isInternal:
script.append(
"""
import os
import sys
import time
class PipeOutput(object):
def write(self, string):
output.send(string)
sys.stdout = PipeOutput()
sys.stderr = PipeOutput()
os.chdir(outputDir)"""
)

# Header

script.append(
Expand Down Expand Up @@ -1198,6 +1132,9 @@ def write(self, string):
script.append("prmtop = AmberPrmtopFile(prmtop_file)")
script.append("inpcrd = AmberInpcrdFile(inpcrd_file)")

config_creator = ConfigCreator(session)
config_creator.add_forcefield_and_water_model_configuration(script)

if fileType == "pdb":
script.append(
"""\n############# Forcefield, Water and Membrane Model Selection ###################\n"""
Expand All @@ -1211,244 +1148,38 @@ def write(self, string):
################################## IF CLEANING WAS PERFORMED ##############################################
###########################################################################################################
###########################################################################################################
if fileType == "pdb":
if session["solvent"] == True:
if session["add_membrane"] == True:
script.append(
"""\n############# Membrane Settings ###################\n"""
)
script.append("add_membrane = %s" % session["add_membrane"])
script.append("membrane_lipid_type = '%s'" % session["lipidType"])
script.append("membrane_padding = %s" % session["membrane_padding"])
script.append(
"membrane_ionicstrength = %s" % session["membrane_ionicstrength"]
)
script.append(
"membrane_positive_ion = '%s'" % session["membrane_positive"]
)
script.append(
"membrane_negative_ion = '%s'" % session["membrane_negative"]
)
elif session["add_membrane"] == False:
script.append(
"""\n############# Water Box Settings ###################\n"""
)
script.append("add_membrane = %s" % session["add_membrane"])
if session["water_padding"] == True:
script.append('Water_Box = "Buffer"')
script.append(
"water_padding_distance = %s"
% session["water_padding_distance"]
)
script.append("water_boxShape = '%s'" % session["water_boxShape"])
else:
script.append('Water_Box = "Absolute"')
script.append("water_box_x = %s" % session["box_x"])
script.append("water_box_y = %s" % session["box_y"])
script.append("water_box_z = %s" % session["box_z"])
script.append(
"water_ionicstrength = %s" % session["water_ionicstrength"]
)
script.append("water_positive_ion = '%s'" % session["water_positive"])
script.append("water_negative_ion = '%s'" % session["water_negative"])
else:
if session["solvent"] == False:
script.append("Solvent = %s" % session["solvent"])

################################## IF CLEANING WAS NOT PERFORMED ##########################################
###########################################################################################################
###########################################################################################################

config_creator.add_solvent_configuration(script)


# System configuration
script.append("\n# System Configuration\n")
nonbondedMethod = session["nonbondedMethod"]
script.append("nonbondedMethod = app.%s" % nonbondedMethod)
if nonbondedMethod != "NoCutoff":
script.append("nonbondedCutoff = %s*unit.nanometers" % session["cutoff"])
if nonbondedMethod == "PME":
script.append("ewaldErrorTolerance = %s" % session["ewaldTol"])
hmrOptions = ", hydrogenMass=hydrogenMass" if session["hmr"] else ""
script.append("hmrOptions = '%s'" % hmrOptions)
constraints = session["constraints"]
constraintMethods = {
"none": "None",
"water": "None",
"hbonds": "HBonds",
"allbonds": "AllBonds",
}
if constraints != "none" and constraints != "water":
script.append("constraints = app.%s" % constraintMethods[constraints])
if constraints == "none":
script.append("constraints = %s" % constraintMethods[constraints])
script.append("rigidWater = %s" % ("False" if constraints == "none" else "True"))
if constraints != "none":
script.append("constraintTolerance = %s" % session["constraintTol"])
if session["hmr"]:
script.append("hydrogenMass = %s*unit.amu" % session["hmrMass"])
config_creator.add_system_configuration(script)

# Integration options

script.append("\n# Integration Options\n")
script.append("step_time = %s" % session["dt"])
script.append("dt = %s*unit.picoseconds" % session["dt"])
script.append("temperature = %s*unit.kelvin" % session["temperature"])
script.append("friction = %s/unit.picosecond" % session["friction"])
ensemble = session["ensemble"]
if ensemble == "npt":
script.append("pressure = %s*unit.atmospheres" % session["pressure"])
script.append("barostatInterval = %s" % session["barostatInterval"])
config_creator.add_integration_configuration(script)

# Simulation options

script.append("\n# Simulation Time and Steps Options\n")
script.append("sim_length = %s" % session["sim_length"])
steps = int(float(session["sim_length"])/float(session["dt"]) *1000)
script.append("steps = %s" % steps)

script.append("\n# Frames and Interval Options\n")
script.append("dcdFrames = %s" % session["dcdFrames"])
dcdinterval=int(steps / int(session["dcdFrames"]))
script.append("dcdInterval = %s" % dcdinterval)
script.append("pdbInterval_ns = %s" % session["pdbInterval_ns"])
pdbInterval=int(steps * (float(session["pdbInterval_ns"]) / float(session["sim_length"])))
script.append("pdbInterval = %s" % pdbInterval)

script.append("\n# Restart and Equilibration Options\n")
if session["restart_checkpoint"] == "yes":
script.append("restart_step = %s" % session["restart_step"])

if session["equilibration"] == "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 session["equilibration"] == "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 session["equilibration"] == "None":
script.append("equilibration_stages = None")

script.append("save_box_vectors = False")


script.append("\n# Simulation Options\n")

script.append("platform = Platform.getPlatformByName('%s')" % session["platform"])
if session["platform"] in ("CUDA", "OpenCL"):
script.append("platformProperties = {'Precision': '%s'}" % session["precision"])
if session["writeDCD"]:
if session["restart_checkpoint"] == "yes":
script.append(
"dcdReporter = DCDReporter('%s_%s', dcdInterval)"
% (session["restart_step"], session["dcdFilename"])
)
else:
script.append(
"dcdReporter = DCDReporter('%s', dcdInterval)"
% (session["dcdFilename"])
)
if session["writeData"]:
args = ", ".join("%s=True" % field for field in session["dataFields"])
if session["restart_checkpoint"] == "yes":
script.append(
"dataReporter = StateDataReporter('%s_%s', %s, totalSteps=steps,"
% (
session["restart_step"],
session["dataFilename"],
session["dataInterval"],
)
)
else:
script.append(
"dataReporter = StateDataReporter('%s', %s, totalSteps=steps,"
% (session["dataFilename"], session["dataInterval"])
)
script.append(" %s, separator='\\t')" % args)
if isInternal:
# Create a second reporting sending to stdout so we can display it in the browser.
script.append(
"consoleReporter = StateDataReporter(sys.stdout, %s, totalSteps=steps, %s, separator='\\t')"
% (session["dataInterval"], args)
)
if session["writeCheckpoint"]:
checkpointInterval = int(1000 * float(session["checkpointInterval_ns"]) / float(session["dt"]))
checkpointInterval_10 = checkpointInterval * 10
checkpointInterval_100 = checkpointInterval * 100
script.append("\n# Checkpoint Options\n")
script.append( "checkpointInterval = %s" % checkpointInterval)
if session["restart_checkpoint"] == "yes":
script.append(
"checkpointReporter = CheckpointReporter('%s_%s', %s)"
% (session["restart_step"], session["checkpointFilename"], checkpointInterval)
)
script.append(
"checkpointReporter10 = CheckpointReporter('10x_%s__%s', %s)"
% (session["restart_step"], session["checkpointFilename"], checkpointInterval_10)
)
script.append(
"checkpointReporter100 = CheckpointReporter('100x_%s_%s', %s)"
% (session["restart_step"], session["checkpointFilename"], checkpointInterval_100)
)
else:
script.append(
"checkpointReporter = CheckpointReporter('%s', %s)"
% (session["checkpointFilename"], checkpointInterval)
)
script.append(
"checkpointReporter10 = CheckpointReporter('10x_%s', %s)"
% (session["checkpointFilename"], checkpointInterval_10)
)
script.append(
"checkpointReporter100 = CheckpointReporter('100x_%s', %s)"
% (session["checkpointFilename"], checkpointInterval_100)
)

# Output XML files for system and integrator
config_creator.add_simulation_time_and_steps_configuration(script)

if session["writeSimulationXml"]:
config_creator.add_equilibration_configuration(script)

config_creator.add_simulation_configuration(script)

config_creator.add_checkpoint_configuration(script)


config_creator.add_xml_serialization_configuration(script)

config_creator.add_postprocessing_configuration(script)

config_creator.add_openmmdl_analysis_configuration(script)

def _xml_script_segment(to_serialize, target_file):
if target_file == "":
# if filename is blank, we cannot create the file
return []
return [
f'with open("{target_file}", mode="w") as file:',
f" file.write(XmlSerializer.serialize({to_serialize}))",
]

script.append("\n# Write XML serialized objects\n")
script.extend(_xml_script_segment("system", session["systemXmlFilename"]))
script.extend(
_xml_script_segment("integrator", session["integratorXmlFilename"])
)

# Postprocessing and Cleanup
script.append("\n# Cleaning and Post-Processing Options\n")
script.append("postprocessing = %s" % session["md_postprocessing"])
script.append("old_output = %s" % session["mdtraj_output"])
script.append("old_removal = %s" % session["mdtraj_removal"])
script.append("mda_output = %s" % session["mda_output"])
script.append("mda_selection = %s" % session["mda_selection"])


script.append("\n# OpenMMDL Analysis Options\n")
script.append("openmmdl_analysis = %s" % session["openmmdl_analysis"])
if session["openmmdl_analysis"] == "Yes":
script.append("analysis_selection = %s" % session["analysis_selection"])
script.append("binding_mode = %s" % session["binding_mode"])
script.append("min_transition = %s" % session["min_transition"])
script.append("rmsd_diff = %s" % session["rmsd_diff"])
script.append("pml_generation = %s" % session["pml_generation"])


return "\n".join(script)
Expand Down

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