1 #!/bin/env python
2 # File: OpenMMUtil.py
3 # Author: Manish Sud <msud@san.rr.com>
4 #
5 # Copyright (C) 2025 Manish Sud. All rights reserved.
6 #
7 # The functionality available in this script is implemented using OpenMM, an
8 # open source molecuar simulation package.
9 #
10 # This file is part of MayaChemTools.
11 #
12 # MayaChemTools is free software; you can redistribute it and/or modify it under
13 # the terms of the GNU Lesser General Public License as published by the Free
14 # Software Foundation; either version 3 of the License, or (at your option) any
15 # later version.
16 #
17 # MayaChemTools is distributed in the hope that it will be useful, but without
18 # any warranty; without even the implied warranty of merchantability of fitness
19 # for a particular purpose. See the GNU Lesser General Public License for more
20 # details.
21 #
22 # You should have received a copy of the GNU Lesser General Public License
23 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
24 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
25 # Boston, MA, 02111-1307, USA.
26 #
27
28 from __future__ import print_function
29
30 import os
31 import sys
32 import re
33 import glob
34 import multiprocessing as mp
35 import numpy as np
36
37 import openmm as mm
38 import openmm.app
39
40 import openmmforcefields as mmff
41 import openmmforcefields.generators
42 import openff as ff
43 import openff.toolkit
44
45 import pdbfixer
46 import mdtraj
47
48 import MiscUtil
49
50 __all__ = ["AddWaterBox", "DoAtomListsOverlap", "DoesAtomListOverlapWithSystemConstraints", "DoesSystemContainWater", "FreezeAtoms", "GetAtoms", "GetFormattedTotalSimulationTime", "InitializeBarostat", "InitializeIntegrator", "InitializeReporters", "InitializeSimulation", "InitializeSystem", "InitializeSystemGenerator", "MergeSmallMoleculeWithMacromolecule", "PerformAnnealing", "ProcessOptionOpenMMRestartParameters", "ProcessOptionOpenMMAtomsSelectionParameters", "ProcessOptionOpenMMAnnealingParameters", "ProcessOptionOpenMMForcefieldParameters", "ProcessOptionOpenMMIntegratorParameters", "ProcessOptionOpenMMPlatformParameters", "ProcessOptionOpenMMOutputParameters", "ProcessOptionOpenMMSimulationParameters", "ProcessOptionOpenMMSystemParameters", "ProcessOptionOpenMMWaterBoxParameters", "ReadPDBFile", "ReadSmallMoleculeFile", "RestraintAtoms", "SetupAnnealingParameters", "SetupIntegratorParameters", "SetupSimulationParameters", "SetupSystemGeneratorForcefieldsParameters", "ValidateAndFreezeRestraintAtoms", "WritePDBFile", "WriteSimulationStatePDBFile"]
51
52 def InitializeSystem(PDBFile, ForcefieldParamsInfo, SystemParamsInfo, WaterBoxAdd = False, WaterBoxParamsInfo = None, SmallMolFile = None, SmallMolID = "LIG"):
53 """Initialize OpenMM system using specified forcefields, system and water box
54 parameters along with a small molecule file and ID.
55
56 The ForcefieldParamsInfo parameter is a dictionary of name and value pairs for
57 system parameters and may be generated by calling the function named
58 ProcessOptionOpenMMForcefieldParameters().
59
60 The SystemParamsInfo parameter is a dictionary of name and value pairs for
61 system parameters and may be generated by calling the function named
62 ProcessOptionOpenMMSystemParameters().
63
64 The WaterBoxParamsInfo parameter is a dictionary of name and value pairs for
65 system parameters and may be generated by calling the function named
66 ProcessOptionOpenMMWaterBoxParameters().
67
68 Arguments:
69 PDBFile (str): PDB file name..
70 ForcefieldParamsInfo (dict): Parameter name and value pairs.
71 SystemParamsInfo (dict): Parameter name and value pairs.
72 WaterBoxAdd (bool): Add water box.
73 WaterBoxParamsInfo (dict): Parameter name and value pairs.
74 SmallMolFile (str): Small molecule file name..
75 SmallMolID (str): Three letter small molecule ID
76
77 Returns:
78 Object: OpenMM system object.
79 Object: OpenMM topology object.
80 Object: OpenMM positions object.
81
82 Examples:
83
84 ... ... ...
85 OptionsInfo["ForcefieldParams"] =
86 OpenMMUtil.ProcessOptionOpenMMForcefieldParameters(
87 "--forcefieldParams", Options["--forcefieldParams"])
88 ... ... ...
89 OptionsInfo["SystemParams"] =
90 OpenMMUtil.ProcessOptionOpenMMSystemParameters("--systemParams",
91 Options["--systemParams"])
92 ... ... ...
93 OptionsInfo["WaterBoxParams"] =
94 OpenMMUtil.ProcessOptionOpenMMWaterBoxParameters(
95 "--waterBoxParams", Options["--waterBoxParams"])
96 ... ... ...
97 System, Topology, Positions = OpenMMUtil.InitializeSystem(
98 OptionsInfo["Infile"], OptionsInfo["ForcefieldParams"],
99 OptionsInfo["SystemParams"], OptionsInfo["WaterBox"],
100 OptionsInfo["WaterBoxParams"], OptionsInfo["SmallMolFile"],
101 OptionsInfo["SmallMolID"])
102
103 """
104
105 # Read PDB file file...
106 MiscUtil.PrintInfo("\nReading PDB file %s..." % PDBFile)
107 PDBHandle = ReadPDBFile(PDBFile)
108
109 ModellerHandle = mm.app.Modeller(PDBHandle.topology, PDBHandle.positions)
110 MiscUtil.PrintInfo("Number of residues: %s; Number of atoms: %s" % (ModellerHandle.topology.getNumResidues(), ModellerHandle.topology.getNumAtoms()))
111
112 # Read small molecule file...
113 SmallMols = None
114 if SmallMolFile is not None:
115 MiscUtil.PrintInfo("\nReading small molecule file %s..." % SmallMolFile)
116 SmallMol = ReadSmallMoleculeFile(SmallMolFile)
117 if SmallMol is None:
118 MiscUtil.PrintError("Failed to read small molecule file: %s" % SmallMolFile)
119 SmallMols = [SmallMol]
120
121 MiscUtil.PrintInfo("\nGenerating macromolecule and small molecule complex...")
122 MergeSmallMoleculeWithMacromolecule(ModellerHandle, SmallMol, SmallMolID)
123 MiscUtil.PrintInfo("Number of residues: %s; Number of atoms: %s" % (ModellerHandle.topology.getNumResidues(), ModellerHandle.topology.getNumAtoms()))
124
125 # Initialize system generator...
126 BiopolymerForcefield = ForcefieldParamsInfo["Biopolymer"]
127 SmallMoleculeForcefield = ForcefieldParamsInfo["SmallMolecule"]
128 WaterForcefield = ForcefieldParamsInfo["Water"]
129 AdditionalForcefiedsList = ForcefieldParamsInfo["AdditionalList"]
130 SystemGeneratorHandle = InitializeSystemGenerator(BiopolymerForcefield, SmallMoleculeForcefield, WaterForcefield, SystemParamsInfo, SmallMols, AdditionalForcefiedsList)
131
132 if WaterBoxAdd:
133 AddWaterBox(ModellerHandle, SystemGeneratorHandle, WaterBoxParamsInfo)
134 MiscUtil.PrintInfo("Number of residues: %s; Number of atoms: %s" % (ModellerHandle.topology.getNumResidues(), ModellerHandle.topology.getNumAtoms()))
135 else:
136 MiscUtil.PrintInfo("\nSkipping addition of a water box...")
137 if DoesSystemContainWater(ModellerHandle.topology):
138 if ForcefieldParamsInfo["ImplicitWater"]:
139 MiscUtil.PrintInfo("Your system contains water molecules during the use of implicit water forcefield. The combination of biopolymer and water forcefields, %s and %s, specified using \"--forcefieldParams\" option may not be valid. You may consider removing water molecules from your system or specify a valid combination of biopolymer and water forcefields for explicit water." % (ForcefieldParamsInfo["Biopolymer"], ForcefieldParamsInfo["Water"]))
140
141 MiscUtil.PrintInfo("\nBuilding system...")
142 SystemHandle = SystemGeneratorHandle.create_system(ModellerHandle.topology, molecules = SmallMols)
143
144 MiscUtil.PrintInfo("Periodic boundary conditions: %s" % ("Yes" if DoesSystemUsesPeriodicBoundaryConditions(SystemHandle) else "No"))
145
146 return (SystemHandle, ModellerHandle.topology, ModellerHandle.positions)
147
148 def InitializeSystemGenerator(BiopolymerForcefield, SmallMoleculeForcefield, WaterForcefield, SystemParamsInfo, SmallMols, AdditionalForcefieldsList = None):
149 """Initialize MMFF system generator using specified forcefields and system parameters
150 along with a list of molecules.
151
152 The SystemParamsInfo parameter is a dictionary of name and value pairs for
153 system parameters and may be generated by calling the function named
154 ProcessOptionOpenMMSystemParameters().
155
156 Arguments:
157 BiopolymerForcefield (str): Biopolymer force field name.
158 SmallMoleculeForcefield (str): Small molecule force field name.
159 WaterForcefield (str): Water force field name.
160 SystemParamsInfo (dict): Parameter name and value pairs.
161 SmallMols (list): List of OpenFF toolkit molecule objects.
162 AdditionalForcefieldsList (list): List of any additional forcefield
163 names
164
165 Returns:
166 Object: MMFF system generator object.
167
168 Examples:
169
170 OptionsInfo["SystemParams"] =
171 OpenMMUtil.ProcessOptionOpenMMSystemParameters("--systemParams",
172 Options["--systemParams"])
173 ... ... ...
174 SystemGeneratorHandle = OpenMMUtil.InitializeSystemGenerator(
175 BiopolymerForcefield, SmallMoleculeForcefield, WaterForcefield,
176 OptionsInfo["SystemParams"], SmallMols, AdditionalForcefiedsList)
177
178 """
179
180 (ForcefieldParams, PeriodicForcefieldParams, NonPeriodicForcefieldParams) = SetupSystemGeneratorForcefieldsParameters(SystemParamsInfo)
181
182 AdditionalForcefieldMsg = ""
183 if AdditionalForcefieldsList is not None:
184 AdditionalForcefieldMsg = "; Additional forcefield(s): %s" % ", ".join(AdditionalForcefieldsList)
185
186 MiscUtil.PrintInfo("\nInitializing system generator (Biopolymer forcefield: %s; Small molecule forcefield: %s; Water forcefield: %s%s)..." % (BiopolymerForcefield, SmallMoleculeForcefield,WaterForcefield, AdditionalForcefieldMsg))
187
188 ForcefieldsList = [BiopolymerForcefield, WaterForcefield]
189 if AdditionalForcefieldsList is not None:
190 ForcefieldsList.extend(AdditionalForcefieldsList)
191
192 SystemGeneratorHandle = mmff.generators.SystemGenerator(forcefields = ForcefieldsList, small_molecule_forcefield = SmallMoleculeForcefield, molecules = SmallMols, forcefield_kwargs = ForcefieldParams, periodic_forcefield_kwargs = PeriodicForcefieldParams, nonperiodic_forcefield_kwargs = NonPeriodicForcefieldParams)
193
194 return SystemGeneratorHandle
195
196 def InitializeIntegrator(ParamsInfo, ConstraintErrorTolerance):
197 """Initialize integrator.
198
199 The ParamsInfo parameter is a dictionary of name and value pairs for
200 integrator parameters and may be generated by calling the function named
201 ProcessOptionOpenMMIntegratorParameters().
202
203 Arguments:
204 ParamsInfo (dict): Parameter name and value pairs.
205 ConstraintErrorTolerance (float): Distance tolerance for
206 constraints as a fraction of the constrained distance.
207
208 Returns:
209 Object: OpenMM integrator object.
210
211 Examples:
212
213 OptionsInfo["IntegratorParams"] =
214 OpenMMUtil.ProcessOptionOpenMMIntegratorParameters(
215 "--integratorParams", Options["--integratorParams"],
216 HydrogenMassRepartioningStatus =
217 OptionsInfo["SystemParams"]["HydrogenMassRepartioning"])
218 ... ... ...
219 Integrator = OpenMMUtil.InitializeIntegrator(
220 OptionsInfo["IntegratorParams"],
221 OptionsInfo["SystemParams"]["ConstraintErrorTolerance"])
222
223 """
224
225 IntegratorParamsInfo = SetupIntegratorParameters(ParamsInfo)
226
227 IntegratorName = IntegratorParamsInfo["Integrator"]
228 RandomSeed = IntegratorParamsInfo["RandomSeed"]
229 StepSize = IntegratorParamsInfo["StepSize"]
230 Temperature = IntegratorParamsInfo["Temperature"]
231 FrictionCoefficient = IntegratorParamsInfo["FrictionCoefficient"]
232
233 MiscUtil.PrintInfo("\nIntializing integrator (Name: %s; StepSize: %s; Temperature: %s)..." % (IntegratorName, StepSize, Temperature))
234
235 if re.match("^LangevinMiddle$", IntegratorName, re.I):
236 Integrator = mm.LangevinMiddleIntegrator(Temperature, FrictionCoefficient, StepSize)
237 elif re.match("^Langevin$", IntegratorName, re.I):
238 Integrator = mm.LangevinIntegrator(Temperature, FrictionCoefficient, StepSize)
239 elif re.match("^NoseHoover$", IntegratorName, re.I):
240 Integrator = mm.NoseHooverIntegrator(Temperature, FrictionCoefficient, StepSize)
241 elif re.match("^Brownian$", IntegratorName, re.I):
242 Integrator = mm.BrownianIntegrator(Temperature, FrictionCoefficient, StepSize)
243 else:
244 MiscUtil.PrintError("The parameter value specified, %s, for parameter name, integrator, for option \"--integratorParams\" is not a valid value. Supported values: LangevinMiddle, Langevin, NoseHoover, or Brownian" % IntegratorName)
245
246 Integrator.setConstraintTolerance(ConstraintErrorTolerance)
247
248 if RandomSeed is not None:
249 if re.match("^(LangevinMiddle|Langevin|Brownian)$", IntegratorName, re.I):
250 MiscUtil.PrintInfo("Setting random number seed for integrator to %s..." % RandomSeed)
251 Integrator.setRandomNumberSeed(RandomSeed)
252 else:
253 MiscUtil.PrintInfo("Skipping setting of random number seed. Not supported for integrator %s..." % IntegratorName)
254
255 return Integrator
256
257 def InitializeBarostat(ParamsInfo):
258 """Initialize barostat.
259
260 The ParamsInfo parameter is a dictionary of name and value pairs for
261 integrator parameters and may be generated by calling the function named
262 ProcessOptionOpenMMIntegratorParameters().
263
264 Arguments:
265 ParamsInfo (dict): Parameter name and value pairs.
266
267 Returns:
268 Object: OpenMM barostat object.
269
270 Examples:
271
272 OptionsInfo["IntegratorParams"] =
273 OpenMMUtil.ProcessOptionOpenMMIntegratorParameters(
274 "--integratorParams", Options["--integratorParams"],
275 HydrogenMassRepartioningStatus =
276 OptionsInfo["SystemParams"]["HydrogenMassRepartioning"])
277 ... ... ...
278 Barostat = OpenMMUtil.InitializeBarostat(
279 OptionsInfo["IntegratorParams"])
280
281 """
282 IntegratorParamsInfo = SetupIntegratorParameters(ParamsInfo)
283
284 BarostatName = IntegratorParamsInfo["Barostat"]
285 if re.match("^MonteCarlo$", BarostatName, re.I):
286 MiscUtil.PrintInfo("\nInitializing Monte Carlo barostat (Pressure: %s)... " % (IntegratorParamsInfo["Pressure"]))
287 Barostat = mm.MonteCarloBarostat(IntegratorParamsInfo["Pressure"], IntegratorParamsInfo["Temperature"], IntegratorParamsInfo["BarostatInterval"])
288 elif re.match("^MonteCarloMembrane$", BarostatName, re.I):
289 MiscUtil.PrintInfo("\nInitializing Monte Carlo membrane barostat (Pressure: %s; SurfaceTension: %s; XYMode: %s; ZMode: %s)... " % (IntegratorParamsInfo["Pressure"], IntegratorParamsInfo["SurfaceTension"], IntegratorParamsInfo["XYModeSpecified"], IntegratorParamsInfo["ZModeSpecified"]))
290 Barostat = mm.MonteCarloMembraneBarostat(IntegratorParamsInfo["Pressure"], IntegratorParamsInfo["SurfaceTension"], IntegratorParamsInfo["Temperature"], IntegratorParamsInfo["XYMode"], IntegratorParamsInfo["ZMode"], IntegratorParamsInfo["BarostatInterval"])
291 else:
292 MiscUtil.PrintError("The parameter value specified, %s, for parameter name, barostat, for option \"--integratorParams\" is not a valid value. Supported values: MonteCarlo or MonteCarloMembrane" % BarostatName)
293
294 if IntegratorParamsInfo["RandomSeed"] is not None:
295 RandomSeed = IntegratorParamsInfo["RandomSeed"]
296 MiscUtil.PrintInfo("Setting random number seed for barostat to %s..." % RandomSeed)
297 Barostat.setRandomNumberSeed(RandomSeed)
298
299 return Barostat
300
301 def InitializeSimulation(System, Integrator, Topology, Positions, PlatformParamsInfo):
302 """Initialize simulation.
303
304 The PlatformParamsInfo parameter is a dictionary of name and value pairs for
305 platform parameters and may be generated by calling the function named
306 ProcessOptionOpenMMPlatformParameters().
307
308 Arguments:
309 System (object): OpenMM system object.
310 Integrator (object): OpenMM integrator object.
311 Topology (object): OpenMM topology object.
312 Positons (object): OpenMM Positions object.
313 PlatformParamsInfo (dict): Parameter name and value pairs.
314
315 Returns:
316 Object: OpenMM simulation object.
317
318 Examples:
319
320 ParamsDefaultInfoOverride = {"Name": Options["--platform"],
321 "Threads": 1}
322 OptionsInfo["PlatformParams"] =
323 OpenMMUtil.ProcessOptionOpenMMPlatformParameters("--platformParams",
324 Options["--platformParams"], ParamsDefaultInfoOverride)
325 ... ... ...
326 Simulation = OpenMMUtil.InitializeSimulation(System, Integrator, Topology,
327 Positions, OptionsInfo["PlatformParams"])
328
329 """
330
331 PlatformName, PlatformProperties, PlatformMsg = SetupPlatformParameters(PlatformParamsInfo)
332 MiscUtil.PrintInfo("\nInitializing simulation (%s)..." % PlatformMsg)
333
334 try:
335 PlatformHandle = mm.Platform.getPlatformByName(PlatformName)
336 except Exception as ErrMsg:
337 MiscUtil.PrintInfo("")
338 MiscUtil.PrintError("Failed to get platform %s:\n%s\n" % (PlatformName, ErrMsg))
339
340 try:
341 SimulationHandle = mm.app.Simulation(Topology, System, Integrator, PlatformHandle, PlatformProperties)
342 except Exception as ErrMsg:
343 MiscUtil.PrintInfo("")
344 MiscUtil.PrintError("Failed to initialize simulation: %s\n" % (ErrMsg))
345
346 SimulationHandle.context.setPositions(Positions)
347
348 return (SimulationHandle)
349
350 def InitializeReporters(OutputParamsInfo, TotalSteps, DataOutAppendStatus):
351 """Initialize reporters for writing data to trajectory, log, and checkpoint
352 files along with reporting to the stdout.
353
354 The OutputParamsInfo parameter is a dictionary of name and value pairs for
355 output parameters and may be generated by calling the function named
356 ProcessOptionOpenMMOutputParameters().
357
358 Arguments:
359 OutputParamsInfo (dict): Parameter name and value pairs.
360 TotalSteps (int): Total number of simulation steps.
361 DataOutAppendStatus (bool): Append data to trajectory and log file.
362
363 Returns:
364 Object: OpenMM trajectory reporter object.
365 Object: OpenMM data log file reporter object.
366 Object: OpenMM stodut reporter object.
367 Object: OpenMM checkpoint reporter object.
368
369 Examples:
370
371 if OptionsInfo["NVTMode"]:
372 ParamsDefaultInfoOverride = {"DataOutType": "Step Speed Progress
373 PotentialEnergy Temperature Time Volume"}
374 else:
375 ParamsDefaultInfoOverride = {"DataOutType": "Step Speed Progress
376 PotentialEnergy Temperature Time Density"}
377 OptionsInfo["OutputParams"] =
378 OpenMMUtil.ProcessOptionOpenMMOutputParameters("--outputParams",
379 Options["--outputParams"], OptionsInfo["OutfilePrefix"],
380 ParamsDefaultInfoOverride)
381 ProcessOutfileNames()
382 ... ... ...
383 (TrajReporter, DataLogReporter, DataStdoutReporter, CheckpointReporter)
384 = OpenMMUtil.InitializeReporters(OptionsInfo["OutputParams"],
385 OptionsInfo["SimulationParams"]["Steps"], OptionsInfo["DataOutAppendMode"])
386
387 """
388
389 (TrajReporter, DataLogReporter, DataStdoutReporter, CheckpointReporter) = [None] * 4
390 if OutputParamsInfo["Traj"]:
391 if re.match("^DCD$", OutputParamsInfo["TrajFormat"], re.I):
392 TrajReporter = mm.app.DCDReporter(OutputParamsInfo["TrajFile"], OutputParamsInfo["TrajSteps"], append = DataOutAppendStatus)
393 elif re.match("^XTC$", OutputParamsInfo["TrajFormat"], re.I):
394 if not DataOutAppendStatus:
395 # Remove existing traj file; otherwise, XTCReporter fails...
396 if os.path.isfile(OutputParamsInfo["TrajFile"]):
397 os.remove(OutputParamsInfo["TrajFile"])
398 TrajReporter = mm.app.XTCReporter(OutputParamsInfo["TrajFile"], OutputParamsInfo["TrajSteps"], append = DataOutAppendStatus)
399 else:
400 MiscUtil.PrintError("The parameter value specified, %s, for parameter name, trajFormat, for option \"--outputParams\" is not a valid value. Supported format: DCD or XTC")
401
402 if OutputParamsInfo["Checkpoint"]:
403 CheckpointReporter = mm.app.CheckpointReporter(OutputParamsInfo["CheckpointFile"], OutputParamsInfo["CheckpointSteps"])
404
405 DataOutTypeStatusMap = OutputParamsInfo["DataOutTypeStatusMap"]
406 if OutputParamsInfo["DataLog"]:
407 DataLogReporter = mm.app.StateDataReporter(OutputParamsInfo["DataLogFile"], OutputParamsInfo["DataLogSteps"], totalSteps = TotalSteps, step = DataOutTypeStatusMap["Step"], time = DataOutTypeStatusMap["Time"], speed = DataOutTypeStatusMap["Speed"], progress = DataOutTypeStatusMap["Progress"], elapsedTime = DataOutTypeStatusMap["ElapsedTime"], remainingTime = DataOutTypeStatusMap["RemainingTime"], potentialEnergy = DataOutTypeStatusMap["PotentialEnergy"], kineticEnergy = DataOutTypeStatusMap["KineticEnergy"], totalEnergy = DataOutTypeStatusMap["TotalEnergy"], temperature = DataOutTypeStatusMap["Temperature"], volume = DataOutTypeStatusMap["Volume"], density = DataOutTypeStatusMap["Density"], separator = OutputParamsInfo["DataOutDelimiter"], append = DataOutAppendStatus)
408
409 if OutputParamsInfo["DataStdout"]:
410 DataStdoutReporter = mm.app.StateDataReporter(sys.stdout, OutputParamsInfo["DataStdoutSteps"], totalSteps = TotalSteps, step = DataOutTypeStatusMap["Step"], time = DataOutTypeStatusMap["Time"], speed = DataOutTypeStatusMap["Speed"], progress = DataOutTypeStatusMap["Progress"], elapsedTime = DataOutTypeStatusMap["ElapsedTime"], remainingTime = DataOutTypeStatusMap["RemainingTime"], potentialEnergy = DataOutTypeStatusMap["PotentialEnergy"], kineticEnergy = DataOutTypeStatusMap["KineticEnergy"], totalEnergy = DataOutTypeStatusMap["TotalEnergy"], temperature = DataOutTypeStatusMap["Temperature"], volume = DataOutTypeStatusMap["Volume"], density = DataOutTypeStatusMap["Density"], separator = OutputParamsInfo["DataOutDelimiter"])
411
412 return (TrajReporter, DataLogReporter, DataStdoutReporter, CheckpointReporter)
413
414 def PerformAnnealing(Simulation, Integrator, Barostat, TemperatureStart, TemperatureEnd, TemperatureChange, SimulationSteps):
415 """Perform annealing by heating or cooling the system from start to end
416 temperature.
417
418 The temperature is increased or decreased from start to end temperature by
419 temperature to perform annealing following by performing simulations for a
420 specified number of steps after each temperature step.
421
422 Arguments:
423 System (object): OpenMM system object.
424 Integrator (object): OpenMM integrator object.
425 Barostat (object): OpenMM integrator object.
426 TemperatureStart (float): Start temperature.
427 TemperatureEnd (float): End temperature.
428 TemperatureChange (int): Temperature step size to heat or cool the
429 system from start to end temperature.
430 SimulationSteps (fint): Number of simulations steps to perform after
431 each temperature step.
432
433 Returns:
434 int: Total number of simulation steps.
435
436 Examples:
437
438 ... ... ...
439 TotalInitialSimulationSteps = OpenMMUtil.PerformAnnealing(Simulation,
440 Integrator, Barostat, InitialStart, InitialEnd, InitialChange, InitialSteps)
441
442 """
443
444 if TemperatureStart < TemperatureEnd:
445 TemperatureRange = np.arange(TemperatureStart, TemperatureEnd, TemperatureChange)
446 else:
447 TemperatureRange = np.arange(TemperatureStart, TemperatureEnd, -TemperatureChange)
448
449 TemperatureRange = TemperatureRange.tolist()
450 TemperatureRange.append(TemperatureEnd)
451
452 TotalSimulationSteps = 0
453 for Temperature in TemperatureRange:
454 Temperature = Temperature * mm.unit.kelvin
455
456 Integrator.setTemperature(Temperature)
457 if Barostat is not None:
458 try:
459 Simulation.context.setParameter(Barostat.Temperature(), Temperature)
460 except Exception as ErrMsg:
461 MiscUtil.PrintInfo("")
462 MiscUtil.PrintError("Failed to set barostat temperature:\n%s\n" % (ErrMsg))
463
464 Simulation.step(SimulationSteps)
465 TotalSimulationSteps += SimulationSteps
466
467 return TotalSimulationSteps
468
469 def AddWaterBox(ModellerHandle, SystemGeneratorHandle, WaterBoxParamsInfo):
470 """Add a water box.
471
472 The WaterBoxParamsInfo parameter is a dictionary of name and value pairs for
473 waterbox parameters and may be generated by calling the function named
474 ProcessOptionOpenMMWaterBoxParameters().
475
476 Arguments:
477 ModellerHandle (object): OpenMM modeller object.
478 SystemGeneratorHandle (object): OpenMM system generator object.
479 WaterBoxParamsInfo (dict): Parameter name and value pairs.
480
481 Returns:
482 None.
483
484 Examples:
485
486 OptionsInfo["WaterBoxParams"] =
487 OpenMMUtil.ProcessOptionOpenMMWaterBoxParameters("--waterBoxParams",
488 Options["--waterBoxParams"])
489 ... ... ...
490 OpenMMUtil.AddWaterBox(ModellerHandle, SystemGeneratorHandle,
491 OptionsInfo["WaterBoxParams"])
492
493 """
494
495 MiscUtil.PrintInfo("\nRemoving any existing waters...")
496 ModellerHandle.deleteWater()
497
498 MiscUtil.PrintInfo("\nAdding a water box...")
499
500 Size, Padding, Shape = [None] * 3
501 if WaterBoxParamsInfo["ModeSize"]:
502 SizeList = WaterBoxParamsInfo["SizeList"]
503 Size = mm.Vec3(SizeList[0], SizeList[1], SizeList[2]) * mm.unit.nanometer
504 elif WaterBoxParamsInfo["ModePadding"]:
505 Padding = WaterBoxParamsInfo["Padding"] * mm.unit.nanometer
506 Shape = WaterBoxParamsInfo["Shape"]
507 else:
508 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, mode, using \"--waterBoxParams\" option is not a valid value. Supported values: Size Padding \n" % (WaterBoxParamsInfo["Mode"]))
509
510 IonicStrength = WaterBoxParamsInfo["IonicStrength"] * mm.unit.molar
511
512 ModellerHandle.addSolvent(SystemGeneratorHandle.forcefield, model = WaterBoxParamsInfo["Model"], boxSize = Size, boxVectors = None, padding = Padding, numAdded = None, boxShape = Shape, positiveIon = WaterBoxParamsInfo["IonPositive"], negativeIon = WaterBoxParamsInfo["IonNegative"], ionicStrength = IonicStrength, neutralize = True)
513
514 def SetupSystemGeneratorForcefieldsParameters(SystemParamsInfo):
515 """Setup forcefied parameters for OpenMM API calls.
516
517 The SystemParamsInfo parameter is a dictionary of name and value pairs for
518 system parameters and may be generated by calling the function named
519 ProcessOptionOpenMMSystemParameters().
520
521 Arguments:
522 SystemParamsInfo (dict): Parameter name and value pairs.
523
524 Returns:
525 dict: Forcefield parameter name and value pairs.
526 dictionary2: Periodic forcefield parameter name and value pairs.
527 dictionary3: Non-periodic parameter name and value pairs.
528
529 Examples:
530
531 OptionsInfo["SystemParams"] =
532 OpenMMUtil.ProcessOptionOpenMMSystemParameters("--systemParams",
533 Options["--systemParams"])
534 ... ... ...
535 (ForcefieldParams, PeriodicForcefieldParams, NonPeriodicForcefieldParams)
536 = SetupSystemGeneratorForcefieldsParameters(OptionsInfo["SystemParams"])
537
538 """
539
540 ForcefieldParams = {"constraints": SystemParamsInfo["Constraints"], "rigidWater": SystemParamsInfo["RigidWater"], "removeCMMotion": SystemParamsInfo["RemoveCMMotion"]}
541 if SystemParamsInfo["HydrogenMassRepartioning"]:
542 ForcefieldParams["hydrogenMass"] = SystemParamsInfo["HydrogenMass"] * mm.unit.amu
543
544 NonbondedCutoff = SystemParamsInfo["NonbondedCutoff"] * mm.unit.nanometers
545 PeriodicForcefieldParams = {"nonbondedMethod": SystemParamsInfo["NonbondedMethodPeriodic"], "nonbondedCutoff": NonbondedCutoff, "ewaldErrorTolerance": SystemParamsInfo["EwaldErrorTolerance"]}
546 NonPeriodicForcefieldParams = {"nonbondedMethod": SystemParamsInfo["NonbondedMethodNonPeriodic"], "nonbondedCutoff" : NonbondedCutoff}
547
548 return (ForcefieldParams, PeriodicForcefieldParams, NonPeriodicForcefieldParams)
549
550 def SetupPlatformParameters(ParamsInfo):
551 """Setup platform parameters for OpenMM calls.
552
553 The ParamsInfo parameter is a dictionary of name and value pairs for
554 platform parameters and may be generated by calling the function named
555 ProcessOptionOpenMMPlatformParameters().
556
557 Arguments:
558 ParamsInfo (dict): Parameter name and value pairs.
559
560 Returns:
561 str: PlatformName.
562 dict: Platform properities parameter name and values pairs.
563 str: Text message describing platform.
564
565 Examples:
566
567 ParamsDefaultInfoOverride = {"Name": Options["--platform"],
568 "Threads": 1}
569 OptionsInfo["PlatformParams"] =
570 OpenMMUtil.ProcessOptionOpenMMPlatformParameters("--platformParams",
571 Options["--platformParams"], ParamsDefaultInfoOverride)
572 ... ... ...
573 PlatformName, PlatformProperties, PlatformMsg =
574 SetupPlatformParameters(PlatformParamsInfo)
575
576 """
577
578 PlatformName = ParamsInfo["Name"]
579 ParamNames = None
580
581 if re.match("^CPU$", PlatformName, re.I):
582 ParamNames = ["Threads"]
583 elif re.match("^CUDA$", PlatformName, re.I):
584 ParamNames = ["DeviceIndex", "DeterministicForces", "Precision", "TempDirectory", "UseBlockingSync", "UseCpuPme"]
585 elif re.match("^OpenCL$", PlatformName, re.I):
586 ParamNames = ["DeviceIndex", "OpenCLPlatformIndex", "Precision", "UseCpuPme"]
587 elif re.match("^Reference$", PlatformName, re.I):
588 ParamNames = None
589 else:
590 MiscUtil.PrintError("The parameter value specified, %s, for parameter name, name, for option \"--platformParams\" is not a valid value. Supported values: CPU, CUDA, OpenCL, or Reference")
591
592 PlatformProperties = None
593 if ParamNames is not None:
594 FirstValue = True
595 for ParamName in ParamNames:
596 ParamValue = ParamsInfo[ParamName]
597 if ParamValue is not None:
598 if FirstValue:
599 FirstValue = False
600 PlatformProperties = {}
601 PlatformProperties[ParamName] = ParamValue
602
603 PlatformMsg = "Platform: %s" % PlatformName
604 if re.match("^CPU$", PlatformName, re.I):
605 Threads = ParamsInfo["Threads"]
606 if Threads is None or Threads == "0":
607 Threads = "auto"
608 PlatformMsg = "Platform: %s; Threads: %s" % (PlatformName, Threads)
609 elif re.match("^(CUDA|OpenCL)$", PlatformName, re.I):
610 DeviceIndex = "auto" if ParamsInfo["DeviceIndex"] is None else ParamsInfo["DeviceIndex"]
611 Precision = "auto" if ParamsInfo["Precision"] is None else ParamsInfo["Precision"]
612 PlatformMsg = "Platform: %s; DeviceIndex: %s; Precision: %s" % (PlatformName, DeviceIndex, Precision)
613
614 return (PlatformName, PlatformProperties, PlatformMsg)
615
616 def SetupAnnealingParameters(ParamsInfo):
617 """Setup annealing parameters for OpenMM API calls.
618
619 The ParamsInfo parameter is a dictionary of name and value pairs for
620 annealing parameters and may be generated by calling the function named
621 ProcessOptionOpenMMAnnealingParameters().
622
623 Arguments:
624 ParamsInfo (dict): Parameter name and value pairs.
625
626 Returns:
627 dict: Integrator parameter name and values pairs.
628
629 Examples:
630
631 OptionsInfo["AnnealingParams"] =
632 OpenMMUtil.ProcessOptionOpenMMAnnealingParameters(
633 "--annealingParams", Options["--annealingParams"],
634 ... ... ...
635 IntegratorParams = SetupIntegratorParameters(
636 OptionsInfo["IntegratorParams"])
637
638 """
639
640 ParamsInfoWithUnits = {}
641
642 ParamsInfoWithUnits["InitialStart"] = ParamsInfo["InitialStart"] * mm.unit.kelvin
643 ParamsInfoWithUnits["InitialEnd"] = ParamsInfo["InitialEnd"] * mm.unit.kelvin
644 ParamsInfoWithUnits["InitialChange"] = ParamsInfo["InitialChange"] * mm.unit.kelvin
645 ParamsInfoWithUnits["InitialSteps"] = ParamsInfo["InitialSteps"]
646
647 ParamsInfoWithUnits["InitialEquilibrationSteps"] = ParamsInfo["InitialEquilibrationSteps"]
648
649 ParamsInfoWithUnits["Cycles"] = ParamsInfo["Cycles"]
650 ParamsInfoWithUnits["CycleStart"] = ParamsInfo["CycleStart"] * mm.unit.kelvin
651 ParamsInfoWithUnits["CycleEnd"] = ParamsInfo["CycleEnd"] * mm.unit.kelvin
652 ParamsInfoWithUnits["CycleChange"] = ParamsInfo["CycleChange"] * mm.unit.kelvin
653 ParamsInfoWithUnits["CycleSteps"] = ParamsInfo["CycleSteps"]
654
655 ParamsInfoWithUnits["CycleEquilibrationSteps"] = ParamsInfo["CycleEquilibrationSteps"]
656
657 ParamsInfoWithUnits["FinalEquilibrationSteps"] = ParamsInfo["FinalEquilibrationSteps"]
658
659 return ParamsInfoWithUnits
660
661 def SetupIntegratorParameters(ParamsInfo):
662 """Setup integrator parameters for OpenMM API calls.
663
664 The ParamsInfo parameter is a dictionary of name and value pairs for
665 integrator parameters and may be generated by calling the function named
666 ProcessOptionOpenMMIntegratorParameters().
667
668 Arguments:
669 ParamsInfo (dict): Parameter name and value pairs.
670
671 Returns:
672 dict: Integrator parameter name and values pairs.
673
674 Examples:
675
676 OptionsInfo["IntegratorParams"] =
677 OpenMMUtil.ProcessOptionOpenMMIntegratorParameters(
678 "--integratorParams", Options["--integratorParams"],
679 HydrogenMassRepartioningStatus =
680 OptionsInfo["SystemParams"]["HydrogenMassRepartioning"])
681 ... ... ...
682 IntegratorParams = SetupIntegratorParameters(
683 OptionsInfo["IntegratorParams"])
684
685 """
686
687 ParamsInfoWithUnits = {}
688
689 ParamsInfoWithUnits["Integrator"] = ParamsInfo["Integrator"]
690
691 ParamsInfoWithUnits["RandomSeed"] = ParamsInfo["RandomSeed"]
692
693 ParamsInfoWithUnits["FrictionCoefficient"] = ParamsInfo["FrictionCoefficient"]/mm.unit.picosecond
694 ParamsInfoWithUnits["StepSize"] = ParamsInfo["StepSize"] * mm.unit.femtoseconds
695 ParamsInfoWithUnits["Temperature"] = ParamsInfo["Temperature"] * mm.unit.kelvin
696
697 ParamsInfoWithUnits["Barostat"] = ParamsInfo["Barostat"]
698
699 ParamsInfoWithUnits["Pressure"] = ParamsInfo["Pressure"] * mm.unit.atmospheres
700 ParamsInfoWithUnits["BarostatInterval"] = ParamsInfo["BarostatInterval"]
701
702 SurfaceTensionInAngstroms = ParamsInfo["SurfaceTension"]
703 SurfaceTension = SurfaceTensionInAngstroms * mm.unit.atmospheres * mm.unit.angstroms
704
705 SurfaceTensionInNanometers = SurfaceTension.value_in_unit(mm.unit.atmospheres * mm.unit.nanometer)
706 ParamsInfoWithUnits["SurfaceTension"] = SurfaceTensionInNanometers * mm.unit.atmospheres * mm.unit.nanometers
707
708 XYMode = ParamsInfo["XYMode"]
709 XYModeSpecified = ""
710 if re.match("^Anisotropic$", XYMode, re.I):
711 XYMode = mm.MonteCarloMembraneBarostat.XYAnisotropic
712 XYModeSpecified = "Anisotropic"
713 elif re.match("^Isotropic$", XYMode, re.I):
714 XYMode = mm.MonteCarloMembraneBarostat.XYIsotropic
715 XYModeSpecified = "Isotropic"
716 else:
717 MiscUtil.PrintError("The parameter value specified, %s, for parameter name, xymode, for option \"--integratorParams\" is not a valid value. Supported values: Anisotropic or Isotropic" % XYMode)
718 ParamsInfoWithUnits["XYMode"] = XYMode
719 ParamsInfoWithUnits["XYModeSpecified"] = XYModeSpecified
720
721 ZMode = ParamsInfo["ZMode"]
722 ZModeSpecified = ""
723 if re.match("^Fixed$", ZMode, re.I):
724 ZMode = mm.MonteCarloMembraneBarostat.ZFixed
725 ZModeSpecified = "Fixed"
726 elif re.match("^Free$", ZMode, re.I):
727 ZMode = mm.MonteCarloMembraneBarostat.ZFree
728 ZModeSpecified = "Free"
729 else:
730 MiscUtil.PrintError("The parameter value specified, %s, for parameter name, zmode, for option \"--integratorParams\" is not a valid value. Supported values: Fixed or Free" % ZMode)
731 ParamsInfoWithUnits["ZMode"] = ZMode
732 ParamsInfoWithUnits["ZModeSpecified"] = ZModeSpecified
733
734 return ParamsInfoWithUnits
735
736 def SetupSimulationParameters(ParamsInfo):
737 """Setup simulation parameters for OpenMM API calls.
738
739 The ParamsInfo parameter is a dictionary of name and value pairs for
740 integrator parameters and may be generated by calling the function named
741 ProcessOptionOpenMSimulationParameters().
742
743 Arguments:
744 ParamsInfo (dict): Parameter name and value pairs.
745
746 Returns:
747 dict: Integrator parameter name and values pairs.
748
749 Examples:
750
751 OptionsInfo["SimulationParams"] =
752 OpenMMUtil.ProcessOptionOpenMMSimulationParameters(
753 "--simulationParams", Options["--simulationParams"])
754 ... ... ...
755 SimulationParams = SetupSimulationParameters(
756 OptionsInfo["SimulationParams"])
757
758 """
759
760 ParamsInfoWithUnits = {}
761
762 ParamsInfoWithUnits["Steps"] = ParamsInfo["Steps"]
763
764 ParamsInfoWithUnits["Minimization"] = ParamsInfo["Minimization"]
765 ParamsInfoWithUnits["MinimizationMaxSteps"] = ParamsInfo["MinimizationMaxSteps"]
766
767 MinimizationToleranceInKcal = ParamsInfo["MinimizationTolerance"]
768 MinimizationTolerance = MinimizationToleranceInKcal * mm.unit.kilocalories_per_mole/mm.unit.angstroms
769
770 MinimizationToleranceInJoules = MinimizationTolerance.value_in_unit(mm.unit.kilojoules_per_mole/mm.unit.nanometer)
771 MinimizationTolerance = MinimizationToleranceInJoules*mm.unit.kilojoules_per_mole/mm.unit.nanometer
772
773 ParamsInfoWithUnits["MinimizationToleranceInKcal"] = MinimizationToleranceInKcal
774 ParamsInfoWithUnits["MinimizationToleranceInJoules"] = MinimizationToleranceInJoules
775 ParamsInfoWithUnits["MinimizationTolerance"] = MinimizationTolerance
776
777 ParamsInfoWithUnits["Equilibration"] = ParamsInfo["Equilibration"]
778 ParamsInfoWithUnits["EquilibrationSteps"] = ParamsInfo["EquilibrationSteps"]
779
780 return ParamsInfoWithUnits
781
782 def ReimageRealignTrajectory(Topology, TrajFile, ReimageFrames = True, RealignFrames = True, Selection = "protein and backbone and name CA"):
783 """Reimage and realign a trajectory file using MDTraj. The trajectory frames
784 are reimaged before realigning to the first frame using the specified atom
785 selection.
786
787 The trajectory file format must a valid format supported by MDTraj. No
788 validation is performed.
789
790 Arguments:
791 Topology (str or object): PDB file name or OpenMM topology object.
792 TrajFile (str): Trajectory file name.
793 ReimageFrames (bool): Reimage trajectory frames.
794 RealignFrames (bool): Realign trajectory frames.
795 Selection (str): MDTraj atom selection for realigning frames.
796
797 Returns:
798 None or object: MDTraj trajectory object.
799 bool: Reimaged status.
800 bool: Realigned status.
801
802 """
803
804 if isinstance(Topology, str):
805 MiscUtil.PrintInfo("Reading trajectory file %s (TopologyFile: %s)..." % (TrajFile, Topology))
806 else:
807 MiscUtil.PrintInfo("Reading trajectory file %s..." % (TrajFile))
808 Topology = mdtraj.Topology.from_openmm(Topology)
809
810 try:
811 Traj = mdtraj.load(TrajFile, top = Topology)
812 except Exception as ErrMsg:
813 MiscUtil.PrintInfo("")
814 MiscUtil.PrintWarning("Failed to read trajectory file: %s" % ErrMsg)
815 MiscUtil.PrintInfo("")
816 return (None, False, False)
817
818 ReimagedStatus, RealignedStatus = [False] * 2
819
820 if ReimageFrames:
821 MiscUtil.PrintInfo("Reimaging frames...")
822 try:
823 Traj.image_molecules(inplace = True)
824 ReimagedStatus = True
825 except Exception as ErrMsg:
826 MiscUtil.PrintInfo("")
827 MiscUtil.PrintWarning("Failed to reimage frames: %s" % ErrMsg)
828 MiscUtil.PrintInfo("")
829 else:
830 MiscUtil.PrintInfo("Skipping reimaging of frames...")
831
832 if RealignFrames:
833 MiscUtil.PrintInfo("Realigning frames to the first frame using selection \"%s\"..." % Selection)
834 try:
835 SelectionAtomIndices = Traj.top.select(Selection)
836 except Exception as ErrMsg:
837 MiscUtil.PrintInfo("")
838 MiscUtil.PrintWarning("Failed to align frames using selection \"%s\": %s" % (Selection, ErrMsg))
839 MiscUtil.PrintInfo("")
840 return (Traj, ReimagedStatus, RealignedStatus)
841
842 if SelectionAtomIndices.size == 0:
843 MiscUtil.PrintInfo("")
844 MiscUtil.PrintWarning("Failed to align frames using selection \"%s\": No matched atoms found" % (Selection))
845 MiscUtil.PrintInfo("")
846 return (Traj, ReimagedStatus, RealignedStatus)
847
848 RealignedStatus = True
849 Traj.superpose(Traj, frame = 0, atom_indices = SelectionAtomIndices)
850 else:
851 MiscUtil.PrintInfo("Skipping realignment of frames to the first frame...")
852
853 return (Traj, ReimagedStatus, RealignedStatus)
854
855 def ValidateAndFreezeRestraintAtoms(FreezeAtomsStatus, FreezeAtomsParamsInfo, RestraintAtomsStatus, RestraintAtomsParamsInfo, RestraintSpringConstantInKcal, SystemParamsInfo, System, Topology, Positions):
856 """Handle freezing and restraining of atoms along with validation of atoms
857 to be frozen/restrained.
858
859 The FreezeAtomsParamsInfo and RestraintAtomsParamsInfo parameters are dictionaries
860 of name and value pairs for system parameters and may be generated by calling the
861 function named ProcessOptionOpenMMAtomsSelectionParameters().
862
863 The SystemParamsInfo parameter is a dictionary of name and value pairs for
864 system parameters and may be generated by calling the function named
865 ProcessOptionOpenMMSystemParameters().
866
867 Arguments:
868 FreezeAtomsStatus (bool): Freeze atoms.
869 FreezeAtomsParamsInfo (dict): Parameter name and value pairs.
870 RestraintAtomsStatus (bool): Restraint atoms.
871 RestraintAtomsParamsInfo (dict): Parameter name and value pairs.
872 RestraintSpringConstantInKcal (float): Restraint spring constant.
873 SystemParamsInfo (dict): Parameter name and value pairs.
874 Topology (object): OpenMM topology object.
875 Positions (object): OpenMM positions object.
876
877 Returns:
878 None or List: OpenMM atom objects.
879 None or List: OpenMM atom objects.
880
881 """
882
883 # Get atoms for freezing...
884 FreezeAtomList = None
885 if FreezeAtomsStatus:
886 FreezeAtomList = GetAtoms(Topology, FreezeAtomsParamsInfo["CAlphaProteinStatus"], FreezeAtomsParamsInfo["ResidueNames"], FreezeAtomsParamsInfo["Negate"])
887 if FreezeAtomList is None:
888 MiscUtil.PrintError("The freeze atoms parameters specified, \"selection, %s, selectionSpec, %s, negate, %s\", using \"--freezeAtomsParams\" option didn't match any atoms in the system. You must specify a valid set of parameters for freezing atoms or disable freezing using \"No\" value for \"--freezeAtoms\" option.." % (FreezeAtomsParamsInfo["Selection"], FreezeAtomsParamsInfo["SelectionSpec"], FreezeAtomsParamsInfo["Negate"]))
889
890 # Get atoms for restraining...
891 RestraintAtomList = None
892 if RestraintAtomsStatus:
893 RestraintAtomList = GetAtoms(Topology, RestraintAtomsParamsInfo["CAlphaProteinStatus"], RestraintAtomsParamsInfo["ResidueNames"], RestraintAtomsParamsInfo["Negate"])
894 if RestraintAtomList is None:
895 MiscUtil.PrintError("The restraint atoms parameters specified, \"selection, %s, selectionSpec, %s, negate, %s\", using \"--restraintAtomsParams\" option didn't match any atoms in the system. You must specify a valid set of parameters for restraining atoms or disable restraining using \"No\" value for \"--restraintAtoms\" option." % (RestraintAtomsParamsInfo["Selection"], RestraintAtomsParamsInfo["SelectionSpec"], RestraintAtomsParamsInfo["Negate"]))
896
897 # Check for atoms to freeze or restraint...
898 if FreezeAtomList is None and RestraintAtomList is None:
899 return (FreezeAtomList, RestraintAtomList)
900
901 # Check for overlap between freeze and restraint atoms...
902 if DoAtomListsOverlap(FreezeAtomList, RestraintAtomList):
903 MiscUtil.PrintError("The atoms specified using \"--freezeAtomsParams\" and \"--restraintAtomsParams\" options appear to overlap. You must specify unique sets of atoms to freeze and restraint.")
904
905 # Check overlap of freeze atoms with system constraints...
906 if DoesAtomListOverlapWithSystemConstraints(System, FreezeAtomList):
907 MiscUtil.PrintError("The atoms specified using \"--freezeAtomsParams\" appear to overlap with atoms being constrained corresponding to the value specified, %s, for paramater name \"constraints\" using \"--systemParams\" option.\n\nYou must specify a unique set of atoms to freeze or turn off system constaints by specifying value, None, for \"constraints\" parameter using option \"--systemsParams\".\n\nIn addtion, you may want specify, no, value for \"rigidWater\" option.\n\nThe atoms are frozen by setting their particle mass to zero. OpenMM doesn't allow to both constraint atoms and set their mass to zero." % (SystemParamsInfo["Constraints"]))
908
909 # Check overlap of restraint atoms with system constraints...
910 if DoesAtomListOverlapWithSystemConstraints(System, RestraintAtomList):
911 MiscUtil.PrintInfo("")
912 MiscUtil.PrintWarning("The atoms specified using \"--restraintAtomsParams\" appear to overlap with atoms being constrained corresponding to the value specified, %s, for paramater name \"constraints\" using \"--systemParams\" option. You may want to specify a unique set of atoms to restraints or turn off system constaints by specifying value, None, for \"constraints\" parameter using option \"--systemsParams\"." % (SystemParamsInfo["Constraints"]))
913
914 # Freeze atoms...
915 if FreezeAtomList is None:
916 MiscUtil.PrintInfo("\nSkipping freezing of atoms...")
917 else:
918 MiscUtil.PrintInfo("\nFreezing atoms (Selection: %s)..." % FreezeAtomsParamsInfo["Selection"])
919 FreezeAtoms(System, FreezeAtomList)
920
921 # Restraint atoms...
922 if RestraintAtomList is None:
923 MiscUtil.PrintInfo("\nSkipping restraining of atoms...")
924 else:
925 MiscUtil.PrintInfo("\nRestraining atoms (Selection: %s)..." % RestraintAtomsParamsInfo["Selection"])
926 RestraintAtoms(System, Positions, RestraintAtomList, RestraintSpringConstantInKcal)
927
928 return (FreezeAtomList, RestraintAtomList)
929
930 def FreezeAtoms(System, AtomList):
931 """Freeze atoms during a simulation. The specified atoms are kept completely
932 fixed by setting their masses to zero. Their positions do not change during
933 local energy minimization and MD simulation, and they do not contribute
934 to the kinetic energy of the system.
935
936 Arguments:
937 System (object): OpenMM system object.
938 AtomList (list): List of OpenMM atom objects.
939
940 Returns:
941 None
942
943 """
944
945 if AtomList is None:
946 return
947
948 for Atom in AtomList:
949 System.setParticleMass(Atom.index, 0*mm.unit.amu)
950
951 def RestraintAtoms(System, Positions, AtomList, SpringConstantInKcal):
952 """Restraint atoms during a simulation. The motion of specified atoms is
953 restricted by adding a harmonic force that binds them to their starting
954 positions. The atoms are not completely fixed unlike freezing of atoms.
955 Their motion, however, is restricted and they are not able to move far away
956 from their starting positions during local energy minimization and MD
957 simulation.
958
959 The SpringConstantInKcal value must be specified in the units of
960 kcal/mol/A*82. It is automatically converted into the units of
961 kjoules/mol/nm**2 for OpenMM API call.
962
963 Arguments:
964 System (object): OpenMM system object.
965 Positions (object): OpenMM positons object object.
966 AtomList (list): List of OpenMM atom object.
967 SpringConstantInKcal (float): Spring constant value.
968
969 Returns:
970 None
971
972 """
973
974 if AtomList is None:
975 return
976
977 SpringConstant = SpringConstantInKcal * mm.unit.kilocalories_per_mole/mm.unit.angstroms**2
978 SpringConstantInKjoules = SpringConstant.value_in_unit(mm.unit.kilojoules_per_mole/mm.unit.nanometer**2)
979
980 MiscUtil.PrintInfo("Restraint spring constant: %.2f kcal/mol/A**2 (%.2f kjoules/mol/nm**2)" % (SpringConstantInKcal, SpringConstantInKjoules))
981
982 if DoesSystemUsesPeriodicBoundaryConditions(System):
983 # For periodic systems...
984 RestraintForce = mm.CustomExternalForce('k*periodicdistance(x, y, z, x0, y0, z0)^2')
985 else:
986 # For non-periodic systems...
987 RestraintForce = mm.CustomExternalForce('k*((x-x0)^2+(y-y0)^2+(z-z0)^2)')
988
989 SpringConstant = SpringConstantInKjoules * mm.unit.kilojoules_per_mole/mm.unit.nanometer**2
990 RestraintForce.addGlobalParameter('k', SpringConstant)
991
992 RestraintForce.addPerParticleParameter('x0')
993 RestraintForce.addPerParticleParameter('y0')
994 RestraintForce.addPerParticleParameter('z0')
995
996 for Atom in AtomList:
997 RestraintForce.addParticle(Atom.index, Positions[Atom.index])
998
999 def GetAtoms(Topology, CAlphaProteinStatus, ResidueNames, Negate):
1000 """Get a list of atoms in the specified residue names. You may set
1001 CAlphaProteinStatus flag to True to only retrieve CAlpha atoms from
1002 the residues. In addition, you may negate residue name match using
1003 Negate flag.
1004
1005 Arguments:
1006 Topology (object): OpenMM topology object.
1007 CAlphaProteinStatus (bool): Get CAlpha atoms only.
1008 ResidueNames (list): List of residue names.
1009 Negate (bool): Negate residue name match.
1010
1011 Returns:
1012 None or List of OpenMM atom objects.
1013
1014 """
1015 AtomList = []
1016 for Chain in Topology.chains():
1017 for Residue in Chain.residues():
1018 if CAlphaProteinStatus:
1019 if Residue.name in ResidueNames:
1020 for Atom in Residue.atoms():
1021 if _MatchName(Atom.name, ["CA"], Negate):
1022 AtomList.append(Atom)
1023 else:
1024 if _MatchName(Residue.name, ResidueNames, Negate):
1025 AtomList.extend(Residue.atoms())
1026
1027 if len(AtomList) == 0:
1028 AtomList = None
1029
1030 return AtomList
1031
1032 def _MatchName(Name, NamesList, Negate = False):
1033 """Match name to the names in a list."""
1034
1035 Status = True if Name in NamesList else False
1036 if Negate:
1037 Status = not Status
1038
1039 return Status
1040
1041 def DoesSystemUsesPeriodicBoundaryConditions(System):
1042 """Check for the use of periodic boundary conditions in a system.
1043
1044 Arguments:
1045 System (object): OpenMM system object.
1046
1047 Returns:
1048 bool : True - Uses periodic boundary conditions; Otherwise, false.
1049
1050 """
1051
1052 try:
1053 Status = True if System.usesPeriodicBoundaryConditions() else False
1054 except Exception:
1055 Status = False
1056
1057 return Status
1058
1059 def DoesAtomListOverlapWithSystemConstraints(System, AtomList):
1060 """Check for the overlap of specified atoms with the atoms involved
1061 in system constraints.
1062
1063 Arguments:
1064 System (object): OpenMM system object.
1065 AtomList (list): List of OpenMM atom objects.
1066
1067 Returns:
1068 bool : True - Overlap with system constraints; Otherwise, false.
1069
1070 """
1071
1072 NumConstraints = System.getNumConstraints()
1073 if NumConstraints == 0:
1074 return False
1075
1076 if AtomList is None:
1077 return False
1078
1079 AtomListIndices = [Atom.index for Atom in AtomList]
1080
1081 for Index in range(NumConstraints):
1082 Particle1Index, Particle2Index, Distance = System.getConstraintParameters(Index)
1083 if Particle1Index in AtomListIndices or Particle2Index in AtomListIndices:
1084 return True
1085
1086 return False
1087
1088 def DoAtomListsOverlap(AtomList1, AtomList2):
1089 """Check for the overlap of atoms in the specified atom lists.
1090
1091 Arguments:
1092 AtomList1 (list): List of OpenMM atom objects.
1093 AtomList2 (list): List of OpenMM atom objects.
1094
1095 Returns:
1096 bool : True - Overlap between atoms lists; Otherwise, false.
1097
1098 """
1099
1100 if AtomList1 is None or AtomList2 is None:
1101 return False
1102
1103 AtomList1Indices = [Atom.index for Atom in AtomList1]
1104
1105 for Atom in AtomList2:
1106 if Atom.index in AtomList1Indices:
1107 return True
1108
1109 return False
1110
1111 def DoesSystemContainWater(Topology, WaterResidueNames = ['HOH']):
1112 """Check for the presence of water residues in a system.
1113
1114 Arguments:
1115 Topology (object): OpenMM modeller topology object.
1116 WaterResidueNames (list): List of water residue names.
1117
1118 Returns:
1119 bool : True - Contains water; Otherwise, false.
1120
1121 """
1122
1123 Status = False
1124 for Residue in Topology.residues():
1125 if Residue.name in WaterResidueNames:
1126 Status = True
1127 break
1128
1129 return Status
1130
1131 def ReadPDBFile(PDBFile):
1132 """Read molecule from a PDB file.
1133
1134 The supported PDB file formats are pdb and cif.
1135
1136 Arguments:
1137 PDBFile (str): Name of PDB file.
1138
1139 Returns:
1140 object: OpenMM PDBFile or PDBFilex object.
1141
1142 """
1143
1144 FileDir, FileName, FileExt = MiscUtil.ParseFileName(PDBFile)
1145 if re.match("^pdb$", FileExt, re.I):
1146 PDBHandle = mm.app.PDBFile(PDBFile)
1147 elif re.match("^cif$", FileExt, re.I):
1148 PDBHandle = mm.app.PDBxFile(PDBFile)
1149 else:
1150 MiscUti.PrintError("Failed to read PDB file. Invalid PDB file format %s...\n" % PDBFile)
1151
1152 return PDBHandle
1153
1154 def WritePDBFile(PDBFile, Topology, Positions, KeepIDs = True):
1155 """Write a PDB file.
1156
1157 The supported PDB file formats are pdb and cif.
1158
1159 Arguments:
1160 PDBFile (str): Name of PDB file.
1161 Topology (object): Topology OpenMM object.
1162 Positions (object): Positions OpenMM object.
1163 KeepIDs (bool): Keep existing residue and chain IDs.
1164
1165 Returns:
1166 None
1167
1168 """
1169
1170 FileDir, FileName, FileExt = MiscUtil.ParseFileName(PDBFile)
1171 if re.match("^pdb$", FileExt, re.I):
1172 mm.app.PDBFile.writeFile(Topology, Positions, PDBFile, KeepIDs)
1173 elif re.match("^cif$", FileExt, re.I):
1174 mm.app.PDBxFile.writeFile(Topology, Positions, PDBFile, KeepIDs)
1175 else:
1176 MiscUti.PrintError("Failed to write PDB file. Invalid PDB file format %s...\n" % PDBFile)
1177
1178 def WriteSimulationStatePDBFile(Simulation, PDBFile, KeepIDs = True):
1179 """Write a PDB file for current simulation state.
1180
1181 The supported PDB file formats are pdb and cif.
1182
1183 Arguments:
1184 Simulation (object): OpenMM simulation object.
1185 PDBFile (str): Name of PDB fil.
1186 KeepIDs (bool): Keep existing residue and chain IDs.
1187
1188 Returns:
1189 None
1190
1191 """
1192
1193 CurrentPositions = Simulation.context.getState(getPositions = True).getPositions()
1194 WritePDBFile(PDBFile, Simulation.topology, CurrentPositions, KeepIDs)
1195
1196 def ReadSmallMoleculeFile(FileName):
1197 """Read small molecule file using OpenFF toolkit.
1198
1199 Arguments:
1200 FileName (str): Small molecule file name.
1201
1202 Returns:
1203 None or OpenFF tookit molecule object.
1204
1205 """
1206
1207 try:
1208 SmallMol = ff.toolkit.Molecule.from_file(FileName)
1209 except Exception as ErrMsg:
1210 SmallMol = None
1211 MiscUtil.PrintInfo("")
1212 MiscUtil.PrintWarning("OpenFF.toolkit.Molecule.from_file() failed: %s" % ErrMsg)
1213 MiscUtil.PrintInfo("")
1214
1215 return SmallMol
1216
1217 def MergeSmallMoleculeWithMacromolecule(ModellerHandle, SmallMol, SmallMolID = "LIG"):
1218 """Merge small molecule with macromolecule data contained in a modeller object and
1219 assign a three letter small molecule residue name to the merged small molecule.
1220
1221 Arguments:
1222 ModellerHandle (object): OpenMM modeller object.
1223 SmallMol (object): OpenFF tookit molecule object.
1224 SmallMolID (str): Three letter residue name for small molecule.
1225
1226 Returns:
1227 None
1228
1229 """
1230
1231 SmallMolToplogy = SmallMol.to_topology()
1232 SmallMolOpenMMTopology = SmallMolToplogy.to_openmm()
1233 SmallMolOpenMMPositions = SmallMolToplogy.get_positions().to_openmm()
1234
1235 # Set small molecule residue name to LIG...
1236 for Chain in SmallMolOpenMMTopology.chains():
1237 for Residue in Chain.residues():
1238 Residue.name = SmallMolID
1239
1240 ModellerHandle.add(SmallMolOpenMMTopology, SmallMolOpenMMPositions)
1241
1242 def GetFormattedTotalSimulationTime(StepSize, Steps):
1243 """Get formatted total simulation time with appropriate time units.
1244 parameter names and values.
1245
1246 Arguments:
1247 StepSize (object): OpenMM quantity object.
1248 Steps (int): Number of steps.
1249
1250 Returns:
1251 str: Total time.
1252
1253 """
1254
1255 TotalTime = StepSize * Steps
1256 TotalTimeValue = TotalTime.value_in_unit(mm.unit.femtoseconds)
1257
1258 if TotalTimeValue < 1e3:
1259 TotalTimeUnits = "fs"
1260 TotalTime = TotalTime.value_in_unit(mm.unit.femtoseconds)
1261 elif TotalTimeValue < 1e6:
1262 TotalTimeUnits = "ps"
1263 TotalTime = TotalTime.value_in_unit(mm.unit.picoseconds)
1264 elif TotalTimeValue < 1e9:
1265 TotalTimeUnits = "ns"
1266 TotalTime = TotalTime.value_in_unit(mm.unit.nanoseconds)
1267 elif TotalTimeValue < 1e12:
1268 TotalTimeUnits = "us"
1269 TotalTime = TotalTime.value_in_unit(mm.unit.microseconds)
1270 else:
1271 TotalTimeUnits = "ms"
1272 TotalTime = TotalTime.value_in_unit(mm.unit.milliseconds)
1273
1274 TotalTime = "%.2f %s" % (TotalTime, TotalTimeUnits)
1275
1276 return TotalTime
1277
1278 def ProcessOptionOpenMMRestartParameters(ParamsOptionName, ParamsOptionValue, OutfilePrefix, ParamsDefaultInfo = None):
1279 """Process parameters for restart option and return a map containing processed
1280 parameter names and values.
1281
1282 ParamsOptionValue is a comma delimited list of parameter name and value pairs
1283 to setup platform.
1284
1285 The supported parameter names along with their default and possible
1286 values are shown below:
1287
1288 finalStateFile, <OutfilePrefix>_FinalState.<chk> [ Possible values:
1289 Valid final state checkpoint or XML filename ]
1290 dataAppend, yes [ Possible values: yes or no]
1291
1292 A brief description of parameters is provided below:
1293
1294 finalStateFile: Final state checkpoint or XML file
1295
1296 dataAppend: Append data to existing trajectory and data log files during the
1297 restart of a simulation using a previously saved final state checkpoint or
1298 XML file.
1299
1300 Arguments:
1301 ParamsOptionName (str): Command line OpenMM restart option name.
1302 ParamsOptionValues (str): Space delimited list of parameter name and value pairs.
1303 OutfilePrefix (str): Prefix for output files.
1304 ParamsDefaultInfo (dict): Default values to override for selected parameters.
1305
1306 Returns:
1307 dictionary: Processed parameter name and value pairs.
1308
1309 """
1310
1311 ParamsInfo = {"FinalStateFile": "auto", "DataAppend": True}
1312
1313 (ValidParamNames, CanonicalParamNamesMap, ParamsOptionValue, ParamsOptionValueWords) = _ValidateAndCanonicalizeParameterNames(ParamsOptionName, ParamsOptionValue, ParamsInfo, ParamsDefaultInfo)
1314
1315 if re.match("^auto$", ParamsOptionValue, re.I):
1316 _ProcessOptionOpenMMRestartParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix)
1317 return ParamsInfo
1318
1319 for Index in range(0, len(ParamsOptionValueWords), 2):
1320 Name = ParamsOptionValueWords[Index].strip()
1321 Value = ParamsOptionValueWords[Index + 1].strip()
1322
1323 ParamName = CanonicalParamNamesMap[Name.lower()]
1324 ParamValue = Value
1325
1326 if re.match("^FinalStateFile$", ParamName, re.I):
1327 if not re.match("^auto$", Value, re.I):
1328 if not os.path.exists(Value):
1329 MiscUtil.PrintError("The file name specified, %s, for parameter name, %s, using option \"%s\" doesn't exist.\n." % (Value, Name, ParamsOptionName))
1330 if not MiscUtil.CheckFileExt(Value, "chk xml"):
1331 MiscUtil.PrintError("The file name specified, %s, for parameter name, %s, using option \"%s\" is not valid file. Supported file formats: chk or xml\n." % (Value, Name, ParamsOptionName))
1332 ParamValue = Value
1333 elif re.match("^DataAppend$", ParamName, re.I):
1334 if not re.match("^(yes|no|true|false)$", Value, re.I):
1335 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: yes or no" % (Value, Name, ParamsOptionName))
1336 ParamValue = True if re.match("^(yes|true)$", Value, re.I) else False
1337 else:
1338 ParamValue = Value
1339
1340 # Set value...
1341 ParamsInfo[ParamName] = ParamValue
1342
1343 # Handle parameters with possible auto values...
1344 _ProcessOptionOpenMMRestartParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix)
1345
1346 return ParamsInfo
1347
1348 def _ProcessOptionOpenMMRestartParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix):
1349 """Process parameters with possible auto values and perform validation.
1350 """
1351
1352 FinalStateFileCheckpointMode = False
1353 FinalStateFileXMLMode = False
1354
1355 ParamName = "FinalStateFile"
1356 FinalStateFile = ParamsInfo[ParamName]
1357 if re.match("^auto$", FinalStateFile, re.I):
1358 FinalStateFile = "%s_FinalState.chk" % OutfilePrefix
1359 FinalStateFileCheckpointMode = True
1360 else:
1361 if MiscUtil.CheckFileExt(FinalStateFile, "chk"):
1362 FinalStateFileCheckpointMode = True
1363 elif MiscUtil.CheckFileExt(FinalStateFile, "xml"):
1364 FinalStateFileXMLMode = True
1365 else:
1366 MiscUtil.PrintError("The file name specified, %s, for parameter name, %s, using option \"%s\ is not valid. Supported file formats: chk or xml\n." % (FinalStateFile, ParamName, ParamsOptionName))
1367
1368 ParamsInfo["FinalStateFile"] = FinalStateFile
1369 ParamsInfo["FinalStateFileCheckpointMode"] = FinalStateFileCheckpointMode
1370 ParamsInfo["FinalStateFileXMLMode"] = FinalStateFileXMLMode
1371
1372 def ProcessOptionOpenMMSystemParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo = None):
1373 """Process parameters for system option and return a map containing processed
1374 parameter names and values.
1375
1376 ParamsOptionValue is a comma delimited list of parameter name and value pairs
1377 to setup platform.
1378
1379 The supported parameter names along with their default and possible
1380 values are shown below:
1381
1382 constraints, BondsInvolvingHydrogens [ Possible values: None,
1383 WaterOnly, BondsInvolvingHydrogens, AllBonds, or
1384 AnglesInvolvingHydrogens ]
1385 constraintErrorTolerance, 0.000001
1386 ewaldErrorTolerance, 0.0005
1387
1388 nonbondedMethodPeriodic, PME [ Possible values: NoCutoff,
1389 CutoffNonPeriodic, or PME ]
1390 nonbondedMethodNonPeriodic, NoCutoff [ Possible values:
1391 NoCutoff or CutoffNonPeriodic]
1392 nonbondedCutoff, 1.0 [ Units: nm ]
1393
1394 hydrogenMassRepartioning, yes [ Possible values: yes or no ]
1395 hydrogenMass, 1.5 [ Units: amu]
1396
1397 removeCMMotion, yes [ Possible values: yes or no ]
1398 rigidWater, auto [ Possible values: yes or no. Default: 'No' for
1399 'None' value of constraints; Otherwise, yes ]
1400
1401 A brief description of parameters is provided below:
1402
1403 constraints: Type of system constraints to use for simulation. These constraints
1404 are different from freezing and restraining of any atoms in the system.
1405
1406 constraintErrorTolerance: Distance tolerance for constraints as a fraction
1407 of the constrained distance.
1408
1409 ewaldErrorTolerance: Ewald error tolerance for a periodic system.
1410
1411 nonbondedMethodPeriodic: Nonbonded method to use during the calculation of
1412 long range interactions for a periodic system.
1413
1414 nonbondedMethodNonPeriodic: Nonbonded method to use during the calculation
1415 of long range interactions for a non-periodic system.
1416
1417 nonbondedCutoff: Cutoff distance to use for long range interactions in both
1418 perioidic non-periodic systems.
1419
1420 hydrogenMassRepartioning: Use hydrogen mass repartioning. It increases the
1421 mass of the hydrogen atoms attached to the heavy atoms and decreasing the
1422 mass of the bonded heavy atom to maintain constant system mass. This allows
1423 the use of larger integration step size (4 fs) during a simulation.
1424
1425 hydrogenMass: Hydrogen mass to use during repartioning.
1426
1427 removeCMMotion: Remove all center of mass motion at every time step.
1428
1429 rigidWater: Keep water rigid during a simulation. This is determined
1430 automatically based on the value of 'constraints' parameter.
1431
1432 Arguments:
1433 ParamsOptionName (str): Command line OpenMM system option name.
1434 ParamsOptionValues (str): Space delimited list of parameter name and value pairs.
1435 ParamsDefaultInfo (dict): Default values to override for selected parameters.
1436
1437 Returns:
1438 dictionary: Processed parameter name and value pairs.
1439
1440 """
1441
1442 ParamsInfo = {"Constraints": "BondsInvolvingHydrogens", "ConstraintErrorTolerance": 0.000001, "EwaldErrorTolerance": 0.0005, "NonbondedMethodPeriodic": "PME", "NonbondedMethodNonPeriodic": "NoCutoff", "NonbondedCutoff": 1.0, "HydrogenMassRepartioning": True, "HydrogenMass": 1.5, "RemoveCMMotion": True, "RigidWater": "auto"}
1443
1444 (ValidParamNames, CanonicalParamNamesMap, ParamsOptionValue, ParamsOptionValueWords) = _ValidateAndCanonicalizeParameterNames(ParamsOptionName, ParamsOptionValue, ParamsInfo, ParamsDefaultInfo)
1445
1446 if re.match("^auto$", ParamsOptionValue, re.I):
1447 _ProcessOptionOpenMMSystemParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
1448 return ParamsInfo
1449
1450 for Index in range(0, len(ParamsOptionValueWords), 2):
1451 Name = ParamsOptionValueWords[Index].strip()
1452 Value = ParamsOptionValueWords[Index + 1].strip()
1453
1454 ParamName = CanonicalParamNamesMap[Name.lower()]
1455 ParamValue = Value
1456
1457 if re.match("^Constraints$", ParamName, re.I):
1458 if not re.match("^auto$", Value, re.I):
1459 if not re.match("^(None|WaterOnly|BondsInvolvingHydrogens|AllBonds|AnglesInvolvingHydrogens)$", Value, re.I):
1460 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: None, WaterOnly, BondsInvolvingHydrogens, AllBonds, or AnglesInvolvingHydrogens." % (Value, Name, ParamsOptionName))
1461 ParamValue = Value
1462 elif re.match("^(ConstraintErrorTolerance|EwaldErrorTolerance|NonbondedCutoff|HydrogenMass)$", ParamName, re.I):
1463 if not MiscUtil.IsFloat(Value):
1464 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a float.\n" % (Value, ParamName, ParamsOptionName))
1465 Value = float(Value)
1466 if Value <= 0:
1467 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
1468 ParamValue = Value
1469 elif re.match("^NonbondedMethodPeriodic$", ParamName, re.I):
1470 if not re.match("^(NoCutoff|CutoffPeriodic|PME)$", Value, re.I):
1471 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: NoCutoff, CutoffPeriodic, or PME" % (Value, Name, ParamsOptionName))
1472 ParamValue = Value
1473 elif re.match("^NonbondedMethodNonPeriodic$", ParamName, re.I):
1474 if not re.match("^(NoCutoff|CutoffNonPeriodic)$", Value, re.I):
1475 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: NoCutoff or CutoffNonPeriodic" % (Value, Name, ParamsOptionName))
1476 ParamValue = Value
1477 elif re.match("^(HydrogenMassRepartioning|removeCMMotion)$", ParamName, re.I):
1478 if not re.match("^(yes|no|true|false)$", Value, re.I):
1479 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: yes or no" % (Value, Name, ParamsOptionName))
1480 ParamValue = True if re.match("^(yes|true)$", Value, re.I) else False
1481 elif re.match("^RigidWater$", ParamName, re.I):
1482 if not re.match("^auto$", Value, re.I):
1483 if not re.match("^(yes|no|true|false)$", Value, re.I):
1484 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: yes or no" % (Value, Name, ParamsOptionName))
1485 ParamValue = True if re.match("^(yes|true)$", Value, re.I) else False
1486 else:
1487 ParamValue = Value
1488
1489 # Set value...
1490 ParamsInfo[ParamName] = ParamValue
1491
1492 # Handle parameters with possible auto values...
1493 _ProcessOptionOpenMMSystemParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
1494
1495 return ParamsInfo
1496
1497 def _ProcessOptionOpenMMSystemParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue):
1498 """Process parameters with possible auto values and perform validation.
1499 """
1500
1501 for ParamName in ["NonbondedMethodPeriodic", "NonbondedMethodNonPeriodic"]:
1502 ParamValue = ParamsInfo[ParamName]
1503 if re.match("^NoCutoff$", ParamValue, re.I):
1504 ParamValue = mm.app.NoCutoff
1505 elif re.match("^CutoffNonPeriodic$", ParamValue, re.I):
1506 ParamValue = mm.app.CutoffNonPeriodic
1507 elif re.match("^CutoffPeriodic$", ParamValue, re.I):
1508 ParamValue = mm.app.CutoffPeriodic
1509 elif re.match("^PME$", ParamValue, re.I):
1510 ParamValue = mm.app.PME
1511 else:
1512 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: NoCutoff, CutoffNonPeriodic, CutoffPeriodic, or PME" % (ParamValue, ParamName, ParamsOptionName))
1513 ParamsInfo[ParamName] = ParamValue
1514
1515 ParamName = "Constraints"
1516 ParamValue = ParamsInfo[ParamName]
1517 ConstraintsValue = None
1518 RigidWaterValue = False
1519 if re.match("^None$", ParamValue, re.I):
1520 ConstraintsValue = None
1521 RigidWaterValue = False
1522 elif re.match("^WaterOnly$", ParamValue, re.I):
1523 ConstraintsValue = None
1524 RigidWaterValue = True
1525 elif re.match("^BondsInvolvingHydrogens$", ParamValue, re.I):
1526 ConstraintsValue = mm.app.HBonds
1527 RigidWaterValue = True
1528 elif re.match("^AllBonds$", ParamValue, re.I):
1529 ConstraintsValue = mm.app.AllBonds
1530 RigidWaterValue = True
1531 elif re.match("^AnglesInvolvingHydrogens$", ParamValue, re.I):
1532 ConstraintsValue = mm.app.HAngles
1533 RigidWaterValue = True
1534 else:
1535 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: None, WaterOnly, BondsInvolvingHydrogens, AllBonds, or AnglesInvolvingHydrogens." % (ParamValue, ParamName, ParamsOptionName))
1536
1537 ParamsInfo[ParamName] = ConstraintsValue
1538
1539 ParamName = "RigidWater"
1540 ParamValue = "%s" % ParamsInfo[ParamName]
1541 if re.match("^auto$", ParamValue, re.I):
1542 ParamsInfo[ParamName] = RigidWaterValue
1543
1544 def ProcessOptionOpenMMIntegratorParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo = None, HydrogenMassRepartioningStatus = False):
1545 """Process parameters for integrator option and return a map containing processed
1546 parameter names and values.
1547
1548 ParamsOptionValue is a comma delimited list of parameter name and value pairs
1549 to setup platform.
1550
1551 The supported parameter names along with their default and possible
1552 values are shown below:
1553
1554 integrator, LangevinMiddle [ Possible values: LangevinMiddle,
1555 Langevin, NoseHoover, Brownian ]
1556
1557 randomSeed, auto [ Possible values: > 0 ]
1558
1559 frictionCoefficient, 1.0 [ Units: 1/ps ]
1560 stepSize, auto [ Units: fs; Default value: 4 fs during yes value of
1561 hydrogen mass repartioning with no freezing/restraining of atoms;
1562 otherwsie, 2 fs ]
1563 temperature, 300.0 [ Units: kelvin ]
1564
1565 barostat, MonteCarlo [ Possible values: MonteCarlo or
1566 MonteCarloMembrane ]
1567 barostatInterval, 25
1568 pressure, 1.0 [ Units: atm ]
1569
1570 Parameters used only for MonteCarloMembraneBarostat with default
1571 values corresponding to Amber forcefields:
1572
1573 surfaceTension, 0.0 [ Units: atm*A. It is automatically converted
1574 into OpenMM default units of atm*nm before its usage. ]
1575 xymode, Isotropic [ Possible values: Anisotropic or Isotropic ]
1576 zmode, Free [ Possible values: Free or Fixed ]
1577
1578 A brief description of parameters is provided below:
1579
1580 integrator: Type of integrator
1581
1582 randomSeed: Random number seed for barostat and integrator. Not supported
1583 NoseHoover integrator.
1584
1585 frictionCoefficient: Friction coefficient for coupling the system to the heat
1586 bath.
1587
1588 stepSize: Simulation time step size.
1589
1590 temperature: Simulation temperature.
1591
1592 barostat: Barostat type.
1593
1594 barostatInterval: Barostat interval step size during NPT simulation for
1595 applying Monte Carlo pressure changes.
1596
1597 pressure: Pressure during NPT simulation.
1598
1599 surfaceTension: Surface tension acting on the system.
1600
1601 xymode: Behavior along X and Y axes. You may allow the X and Y axes
1602 to vary independently of each other or always scale them by the same
1603 amount to keep the ratio of their lengths constant.
1604
1605 zmode: Beahvior along Z axis. You may allow the Z axis to vary
1606 independently of the other axes or keep it fixed.
1607
1608 Arguments:
1609 ParamsOptionName (str): Command line OpenMM integrator option name.
1610 ParamsOptionValues (str): Space delimited list of parameter name and value pairs.
1611 ParamsDefaultInfo (dict): Default values to override for selected parameters.
1612
1613 Returns:
1614 dictionary: Processed parameter name and value pairs.
1615
1616 """
1617
1618 ParamsInfo = {"Integrator": "LangevinMiddle", "RandomSeed": "auto", "FrictionCoefficient": 1.0, "StepSize": "auto", "Temperature": 300.0, "Barostat": "MonteCarlo", "BarostatInterval": 25, "Pressure": 1.0, "SurfaceTension": 0.0, "XYMode": "Isotropic", "ZMode": "Free"}
1619
1620 (ValidParamNames, CanonicalParamNamesMap, ParamsOptionValue, ParamsOptionValueWords) = _ValidateAndCanonicalizeParameterNames(ParamsOptionName, ParamsOptionValue, ParamsInfo, ParamsDefaultInfo)
1621
1622 if re.match("^auto$", ParamsOptionValue, re.I):
1623 _ProcessOptionOpenMMIntegratorParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue, HydrogenMassRepartioningStatus)
1624 return ParamsInfo
1625
1626 for Index in range(0, len(ParamsOptionValueWords), 2):
1627 Name = ParamsOptionValueWords[Index].strip()
1628 Value = ParamsOptionValueWords[Index + 1].strip()
1629
1630 ParamName = CanonicalParamNamesMap[Name.lower()]
1631 ParamValue = Value
1632
1633 if re.match("^Integrator$", ParamName, re.I):
1634 if not re.match("^(LangevinMiddle|Langevin|NoseHoover|Brownian)$", Value, re.I):
1635 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: LangevinMiddle,Langevin, NoseHoover, or Brownian." % (Value, Name, ParamsOptionName))
1636 ParamValue = Value
1637 elif re.match("^(FrictionCoefficient|Pressure)$", ParamName, re.I):
1638 if not MiscUtil.IsFloat(Value):
1639 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a float.\n" % (Value, ParamName, ParamsOptionName))
1640 Value = float(Value)
1641 if Value <= 0:
1642 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
1643 ParamValue = Value
1644 elif re.match("^StepSize$", ParamName, re.I):
1645 if not re.match("^auto$", Value, re.I):
1646 if not MiscUtil.IsFloat(Value):
1647 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a float.\n" % (Value, ParamName, ParamsOptionName))
1648 Value = float(Value)
1649 if Value <= 0:
1650 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
1651 ParamValue = Value
1652 elif re.match("^(Temperature|SurfaceTension)$", ParamName, re.I):
1653 if not MiscUtil.IsFloat(Value):
1654 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a float.\n" % (Value, ParamName, ParamsOptionName))
1655 Value = float(Value)
1656 if Value < 0:
1657 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: >= 0\n" % (ParamValue, ParamName, ParamsOptionName))
1658 ParamValue = Value
1659 elif re.match("^BarostatInterval$", ParamName, re.I):
1660 if not MiscUtil.IsInteger(Value):
1661 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be an integer.\n" % (Value, ParamName, ParamsOptionName))
1662 Value = int(Value)
1663 if Value <= 0:
1664 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
1665 ParamValue = Value
1666 elif re.match("^Barostat$", ParamName, re.I):
1667 if not re.match("^(MonteCarlo|MonteCarloMembrane)$", Value, re.I):
1668 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: MonteCarlo or MonteCarloMembrane" % (Value, Name, ParamsOptionName))
1669 ParamValue = Value
1670 elif re.match("^XYMode$", ParamName, re.I):
1671 if not re.match("^(Anisotropic|Isotropic)$", Value, re.I):
1672 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: Anisotropic or Isotropic" % (Value, Name, ParamsOptionName))
1673 ParamValue = Value
1674 elif re.match("^ZMode$", ParamName, re.I):
1675 if not re.match("^(Free|Fixed)$", Value, re.I):
1676 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: Fixed or Free" % (Value, Name, ParamsOptionName))
1677 ParamValue = Value
1678 elif re.match("^RandomSeed$", ParamName, re.I):
1679 if not re.match("^auto$", Value, re.I):
1680 if not MiscUtil.IsInteger(Value):
1681 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be an integer.\n" % (Value, ParamName, ParamsOptionName))
1682 Value = int(Value)
1683 if Value <= 0:
1684 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
1685 ParamValue = Value
1686 else:
1687 ParamValue = Value
1688
1689 # Set value...
1690 ParamsInfo[ParamName] = ParamValue
1691
1692 # Handle parameters with possible auto values...
1693 _ProcessOptionOpenMMIntegratorParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue, HydrogenMassRepartioningStatus)
1694
1695 return ParamsInfo
1696
1697 def _ProcessOptionOpenMMIntegratorParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue, HydrogenMassRepartioningStatus):
1698 """Process parameters with possible auto values and perform validation.
1699 """
1700
1701 ParamName = "StepSize"
1702 ParamValue = "%s" % ParamsInfo[ParamName]
1703 ParamsInfo["StepSizeSpecified"] = ParamValue
1704 if re.match("^auto$", ParamValue, re.I):
1705 ParamValue = 4.0 if HydrogenMassRepartioningStatus else 2.0
1706 ParamsInfo[ParamName] = ParamValue
1707
1708 ParamName = "RandomSeed"
1709 ParamValue = "%s" % ParamsInfo[ParamName]
1710 ParamsInfo["RandomSeedSpecified"] = ParamValue
1711 if re.match("^auto$", ParamValue, re.I):
1712 ParamsInfo[ParamName] = None
1713
1714 def ProcessOptionOpenMMSimulationParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo = None):
1715 """Process parameters for simulation option and return a map containing processed
1716 parameter names and values.
1717
1718 ParamsOptionValue is a comma delimited list of parameter name and value pairs
1719 to setup platform.
1720
1721 The supported parameter names along with their default and possible
1722 values are shown below:
1723
1724 steps, 1000000 [ Possible values: > 0 ]
1725
1726 minimization, yes [ Possible values: yes or no ]
1727 minimizationMaxSteps, auto [ Possible values: >= 0. The value of
1728 zero implies until the minimization is converged. ]
1729 minimizationTolerance, 0.25 [ Units: kcal/mol/A. The default value
1730 0.25, corresponds to OpenMM default of value of 10.04
1731 kjoules/mol/nm. It is automatically converted into OpenMM
1732 default units before its usage. ]
1733
1734 equilibration, yes [ Possible values: yes or no ]
1735 equilibrationSteps, 1000 [ Possible values: > 0 ]
1736
1737 A brief description of parameters is provided below:
1738
1739 steps: Number of steps for production run.
1740
1741 equilibration: Perform equilibration before the production run.
1742
1743 equilibrationSteps: Number of steps for equilibration.
1744
1745 minimizationMaxSteps: Maximum number of minimization steps. The value
1746 of zero implies until the minimization is converged.
1747
1748 minimizationTolerance: Energy convergence tolerance during minimization.
1749
1750 minimization: Perform minimization before equilibration and production run.
1751
1752 Arguments:
1753 ParamsOptionName (str): Command line OpenMM simulation option name.
1754 ParamsOptionValues (str): Space delimited list of parameter name and value pairs.
1755 ParamsDefaultInfo (dict): Default values to override for selected parameters.
1756
1757 Returns:
1758 dictionary: Processed parameter name and value pairs.
1759
1760 """
1761
1762 ParamsInfo = {"Steps": 1000000, "Minimization": True, "MinimizationMaxSteps": "auto", "MinimizationTolerance": 0.24, "Equilibration": True, "EquilibrationSteps": 1000}
1763
1764 (ValidParamNames, CanonicalParamNamesMap, ParamsOptionValue, ParamsOptionValueWords) = _ValidateAndCanonicalizeParameterNames(ParamsOptionName, ParamsOptionValue, ParamsInfo, ParamsDefaultInfo)
1765
1766 if re.match("^auto$", ParamsOptionValue, re.I):
1767 _ProcessOptionOpenMMSimulationParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
1768 return ParamsInfo
1769
1770 for Index in range(0, len(ParamsOptionValueWords), 2):
1771 Name = ParamsOptionValueWords[Index].strip()
1772 Value = ParamsOptionValueWords[Index + 1].strip()
1773
1774 ParamName = CanonicalParamNamesMap[Name.lower()]
1775 ParamValue = Value
1776
1777 if re.match("^(Steps|EquilibrationSteps)$", ParamName, re.I):
1778 if not MiscUtil.IsInteger(Value):
1779 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be an integer.\n" % (Value, ParamName, ParamsOptionName))
1780 Value = int(Value)
1781 if Value <= 0:
1782 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
1783 ParamValue = Value
1784 elif re.match("^(Minimization|Equilibration)$", ParamName, re.I):
1785 if not re.match("^(yes|no|true|false)$", Value, re.I):
1786 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: yes or no" % (Value, Name, ParamsOptionName))
1787 ParamValue = True if re.match("^(yes|true)$", Value, re.I) else False
1788 elif re.match("^MinimizationMaxSteps$", ParamName, re.I):
1789 if not re.match("^auto$", Value, re.I):
1790 if not MiscUtil.IsInteger(Value):
1791 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be an integer.\n" % (Value, ParamName, ParamsOptionName))
1792 Value = int(Value)
1793 if Value < 0:
1794 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: >= 0\n" % (ParamValue, ParamName, ParamsOptionName))
1795 ParamValue = Value
1796 elif re.match("^MinimizationTolerance$", ParamName, re.I):
1797 if not MiscUtil.IsFloat(Value):
1798 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a float.\n" % (Value, ParamName, ParamsOptionName))
1799 Value = float(Value)
1800 if Value <= 0:
1801 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
1802 ParamValue = Value
1803 else:
1804 ParamValue = Value
1805
1806 # Set value...
1807 ParamsInfo[ParamName] = ParamValue
1808
1809 # Handle parameters with possible auto values...
1810 _ProcessOptionOpenMMSimulationParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
1811
1812 return ParamsInfo
1813
1814 def _ProcessOptionOpenMMSimulationParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue):
1815 """Process parameters with possible auto values and perform validation.
1816 """
1817
1818 ParamName = "MinimizationMaxSteps"
1819 ParamValue = "%s" % ParamsInfo[ParamName]
1820 if re.match("^auto$", ParamValue, re.I):
1821 ParamsInfo[ParamName] = 0
1822
1823 def ProcessOptionOpenMMOutputParameters(ParamsOptionName, ParamsOptionValue, OutfilePrefix, ParamsDefaultInfo = None):
1824 """Process parameters for output option and return a map containing processed
1825 parameter names and values.
1826
1827 ParamsOptionValue is a comma delimited list of parameter name and value pairs
1828 to setup platform.
1829
1830 The supported parameter names along with their default and possible
1831 values are shown below:
1832
1833 checkpoint, no [ Possible values: yes or no ]
1834 checkpointFile, auto [ Default: <OutfilePrefix>.chk ]
1835 checkpointSteps, 10000
1836
1837 dataOutType, auto [ Possible values: A space delimited list of valid
1838 parameter names.
1839 NPT simulation default: Density Step Speed Progress
1840 PotentialEnergy Temperature Time.
1841 NVT simulation default: Step Speed Progress PotentialEnergy
1842 Temperature Time Volumne
1843 Other valid names: ElapsedTime RemainingTime KineticEnergy
1844 TotalEnergy ]
1845
1846 dataLog, yes [ Possible values: yes or no ]
1847 dataLogFile, auto [ Default: <OutfilePrefix>.csv ]
1848 dataLogSteps, 1000
1849
1850 dataStdout, no [ Possible values: yes or no ]
1851 dataStdoutSteps, 1000
1852
1853 minimizationDataSteps, 100
1854 minimizationDataStdout, no [ Possible values: yes or no ]
1855 minimizationDataLog, no [ Possible values: yes or no ]
1856 minimizationDataLogFile, auto [ Default:
1857 <OutfilePrefix>_MinimizationOut.csv ]
1858 minimizationDataOutType, auto [ Possible values: A space delimited
1859 list of valid parameter names. Default: SystemEnergy
1860 RestraintEnergy MaxConstraintError.
1861 Other valid names: RestraintStrength ]
1862
1863 pdbOutFormat, PDB [ Possible values: PDB or CIF ]
1864 pdbOutKeepIDs, yes [ Possible values: yes or no ]
1865
1866 pdbOutMinimized, no [ Possible values: yes or no ]
1867 pdbOutEquilibrated, no [ Possible values: yes or no ]
1868 pdbOutFinal, no [ Possible values: yes or no ]
1869
1870 saveFinalStateCheckpoint, yes [ Possible values: yes or no ]
1871 saveFinalStateCheckpointFile, auto [ Default:
1872 <OutfilePrefix>_FinalState.chk ]
1873 saveFinalStateXML, no [ Possible values: yes or no ]
1874 saveFinalStateXMLFile, auto [ Default:
1875 <OutfilePrefix>_FinalState.xml]
1876
1877 traj, yes [ Possible values: yes or no ]
1878 trajFile, auto [ Default: <OutfilePrefix>.<TrajFormat> ]
1879 trajFormat, DCD [ Possible values: DCD or XTC ]
1880 trajSteps, 10000
1881
1882 xmlSystemOut, no [ Possible values: yes or no ]
1883 xmlSystemFile, auto [ Default: <OutfilePrefix>_System.xml ]
1884 xmlIntegratorOut, no [ Possible values: yes or no ]
1885 xmlIntegratorFile, auto [ Default: <OutfilePrefix>_Integrator.xml ]
1886
1887 A brief description of parameters is provided below:
1888
1889 checkpoint: Write intermediate checkpoint file.
1890 checkpointFile: Intermediate checkpoint file name.
1891 checkpointSteps: Frequency of writing intermediate checkpoint file.
1892
1893 dataOutType: Type of data to write to stdout and log file.
1894
1895 dataLog: Write data to log file.
1896 dataLogFile: Data log file name.
1897 dataLogSteps: Frequency of writing data to log file.
1898
1899 dataStdout: Write data to stdout.
1900 dataStdoutSteps: Frequency of writing data to stdout.
1901
1902 minimizationDataSteps: Frequency of writing data to stdout and log file.
1903 minimizationDataStdout: Write data to stdout.
1904 minimizationDataLog: Write data to log file.
1905 minimizationDataLogFile: Data log fie name.
1906 minimizationDataOutType: Type of data to write to stdout and log file.
1907
1908 pdbOutFormat: Format of output PDB files.
1909 pdbOutKeepIDs: Keep existing chain and residue IDs.
1910
1911 pdbOutMinimized: Write PDB file after minimization.
1912 pdbOutEquilibrated: Write PDB file after equilibration.
1913 pdbOutFinal: Write final PDB file after production run.
1914
1915 saveFinalStateCheckpoint: Save final state checkpoint file.
1916 saveFinalStateCheckpointFile: Name of final state checkpoint file.
1917 saveFinalStateXML: Save final state XML file.
1918 saveFinalStateXMLFile: Name of final state XML file.
1919
1920 traj: Write out trajectory file.
1921 trajFile: Trajectory file name.
1922 trajFormat: Trajectory file format.
1923 trajSteps: Frequency of writing trajectory file.
1924
1925 xmlSystemOut: Write system XML file.
1926 xmlSystemFile: System XML file name.
1927 xmlIntegratorOut: Write integrator XML file.
1928 xmlIntegratorFile: Integrator XML file name.
1929
1930 Arguments:
1931 ParamsOptionName (str): Command line OpenMM system option name.
1932 ParamsOptionValues (str): Space delimited list of parameter name and value pairs.
1933 ParamsDefaultInfo (dict): Default values to override for selected parameters.
1934
1935 Returns:
1936 dictionary: Processed parameter name and value pairs.
1937
1938 """
1939
1940 ParamsInfo = {"Checkpoint": False, "CheckpointFile": "auto", "CheckpointSteps": 10000,
1941 "DataOutType": "auto",
1942 "DataLog": True, "DataLogFile": "auto", "DataLogSteps": 1000,
1943 "DataStdout": False, "DataStdoutSteps": 1000,
1944 "MinimizationDataSteps": 100, "MinimizationDataStdout": False, "MinimizationDataLog": False, "MinimizationDataLogFile": "auto", "MinimizationDataOutType": "auto",
1945 "PDBOutFormat": "PDB", "PDBOutKeepIDs": True, "PDBOutMinimized": False, "PDBOutEquilibrated": False, "PDBOutFinal": False,
1946 "SaveFinalStateCheckpoint": True, "SaveFinalStateCheckpointFile": "auto", "SaveFinalStateXML": False, "SaveFinalStateXMLFile": "auto",
1947 "Traj": True, "TrajFile": "auto", "TrajFormat": "DCD", "TrajSteps": 10000,
1948 "XmlSystemOut": False, "XmlSystemFile": "auto", "XmlIntegratorOut": False, "XmlIntegratorFile": "auto"}
1949
1950 (ValidParamNames, CanonicalParamNamesMap, ParamsOptionValue, ParamsOptionValueWords) = _ValidateAndCanonicalizeParameterNames(ParamsOptionName, ParamsOptionValue, ParamsInfo, ParamsDefaultInfo)
1951
1952 if re.match("^auto$", ParamsOptionValue, re.I):
1953 _ProcessOptionOpenMMOutputParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix)
1954 return ParamsInfo
1955
1956 for Index in range(0, len(ParamsOptionValueWords), 2):
1957 Name = ParamsOptionValueWords[Index].strip()
1958 Value = ParamsOptionValueWords[Index + 1].strip()
1959
1960 ParamName = CanonicalParamNamesMap[Name.lower()]
1961 ParamValue = Value
1962
1963 if re.match("^(Checkpoint|DataLog|DataStdout|MinimizationDataStdout|MinimizationDataLog|PDBOutKeepIDs|SaveFinalStateCheckpoint|SaveFinalStateXML|Traj|XmlSystemOut|XmlIntegratorOut|PDBOutMinimized|PDBOutEquilibrated|PDBOutFinal)$", ParamName, re.I):
1964 if not re.match("^(yes|no|true|false)$", Value, re.I):
1965 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: yes or no" % (Value, Name, ParamsOptionName))
1966 ParamValue = True if re.match("^(yes|true)$", Value, re.I) else False
1967 elif re.match("^(CheckpointFile|SaveFinalStateCheckpointFile)$", ParamName, re.I):
1968 if not re.match("^auto$", Value, re.I):
1969 if not MiscUtil.CheckFileExt(Value, "chk"):
1970 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported file format: chk" % (Value, Name, ParamsOptionName))
1971 ParamValue = Value
1972 elif re.match("^(DataLogFile|MinimizationDataLogFile)$", ParamName, re.I):
1973 if not re.match("^auto$", Value, re.I):
1974 if not MiscUtil.CheckFileExt(Value, "csv"):
1975 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported file formats: csv" % (Value, Name, ParamsOptionName))
1976 ParamValue = Value
1977 elif re.match("^(SaveFinalStateXMLFile|XmlSystemFile|XmlIntegratorFile)$", ParamName, re.I):
1978 if not re.match("^auto$", Value, re.I):
1979 if not MiscUtil.CheckFileExt(Value, "xml"):
1980 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported file format: xml" % (Value, Name, ParamsOptionName))
1981 ParamValue = Value
1982 elif re.match("^TrajFile$", ParamName, re.I):
1983 if not re.match("^auto$", Value, re.I):
1984 if not MiscUtil.CheckFileExt(Value, "dcd xtc"):
1985 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported file formats: dcd xtc" % (Value, Name, ParamsOptionName))
1986 ParamValue = Value
1987 elif re.match("^(CheckpointSteps|DataLogSteps|DataStdoutSteps|MinimizationDataSteps|TrajSteps)$", ParamName, re.I):
1988 if not MiscUtil.IsInteger(Value):
1989 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be an integer.\n" % (Value, ParamName, ParamsOptionName))
1990 Value = int(Value)
1991 if Value <= 0:
1992 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
1993 ParamValue = Value
1994 elif re.match("^DataOutType$", ParamName, re.I):
1995 if not re.match("^auto$", Value, re.I):
1996 ValueTypes = Value.split()
1997 if len(ValueTypes) == 0:
1998 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. It must contain a space delimited list of valid values.\n" % (Value, ParamName, ParamsOptionName))
1999 ValueTypesSpecified = []
2000 for ValueType in ValueTypes:
2001 if not re.match("^(Step|Speed|Progress|PotentialEnergy|Temperature|ElapsedTime|RemainingTime|Time|KineticEnergy|TotalEnergy|Volume|Density)$", ValueType, re.I):
2002 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: Step, Speed, Progress, PotentialEnergy, Temperature, ElapsedTime, RemainingTime, Time, KineticEnergy, TotalEnergy, Volume, or Density" % (ValueType, Name, ParamsOptionName))
2003 if ValueType in ValueTypesSpecified:
2004 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. It has already been specified." % (ValueType, Name, ParamsOptionName))
2005 ValueTypesSpecified.append(ValueType)
2006 ParamsInfo["DataOutTypeList"] = ValueTypes
2007 elif re.match("^MinimizationDataOutType$", ParamName, re.I):
2008 if not re.match("^auto$", Value, re.I):
2009 ValueTypes = Value.split()
2010 if len(ValueTypes) == 0:
2011 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. It must contain a space delimited list of valid values.\n" % (Value, ParamName, ParamsOptionName))
2012 ValueTypesSpecified = []
2013 for ValueType in ValueTypes:
2014 if not re.match("^(SystemEnergy|RestraintEnergy|RestraintStrength|MaxConstraintError)$", ValueType, re.I):
2015 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: SystemEnergy, RestraintEnergy, RestraintStrength, or MaxConstraintError" % (ValueType, Name, ParamsOptionName))
2016 if ValueType in ValueTypesSpecified:
2017 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. It has already been specified." % (ValueType, Name, ParamsOptionName))
2018 ValueTypesSpecified.append(ValueType)
2019 ParamsInfo["MinimizationDataOutTypeList"] = ValueTypes
2020 elif re.match("^PDBOutFormat$", ParamName, re.I):
2021 if not re.match("^(PDB|CIF)$", Value, re.I):
2022 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: PDB or CIF" % (Value, Name, ParamsOptionName))
2023 ParamValue = Value
2024 elif re.match("^TrajFormat$", ParamName, re.I):
2025 if not re.match("^(DCD|XTC)$", Value, re.I):
2026 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: DCD or XTC" % (Value, Name, ParamsOptionName))
2027 ParamValue = Value
2028 else:
2029 ParamValue = Value
2030
2031 # Set value...
2032 ParamsInfo[ParamName] = ParamValue
2033
2034 # Handle parameters with possible auto values...
2035 _ProcessOptionOpenMMOutputParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix)
2036
2037 return ParamsInfo
2038
2039 def _ProcessOptionOpenMMOutputParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix):
2040 """Process parameters with possible auto values and perform validation.
2041 """
2042
2043 # Use comma as a delimiter...
2044 ParamsInfo["DataOutDelimiter"] = ","
2045 ParamsInfo["DataOutfileExt"] = "csv"
2046
2047 ParamName = "TrajFormat"
2048 ParamValue = ParamsInfo[ParamName]
2049 if re.match("^DCD$", ParamValue, re.I):
2050 TrajFileExt = "dcd"
2051 elif re.match("^XTC$", ParamValue, re.I):
2052 TrajFileExt = "xtc"
2053 else:
2054 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: DCD or XTC" % (ParamValue, ParamName, ParamsOptionName))
2055 ParamsInfo["TrajFileExt"] = TrajFileExt
2056
2057 ParamName = "PDBOutFormat"
2058 ParamValue = ParamsInfo[ParamName]
2059 if re.match("^PDB$", ParamValue, re.I):
2060 PDBOutfileExt = "pdb"
2061 elif re.match("^CIF$", ParamValue, re.I):
2062 PDBOutfileExt = "cif"
2063 else:
2064 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: PDB or CIF" % (ParamValue, ParamName, ParamsOptionName))
2065 ParamsInfo["PDBOutfileExt"] = PDBOutfileExt
2066
2067 _ProcessFileNamesOutputPatramaters(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix)
2068 _ProcessDataOutTypeOutputParameter(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix)
2069 _ProcessMinimizationDataOutTypeOutputParameter(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix)
2070
2071 def _ProcessFileNamesOutputPatramaters(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix):
2072 """Process output parameters corresponding to file names."""
2073
2074 OutfileExt = ParamsInfo["DataOutfileExt"]
2075 TrajFileExt = ParamsInfo["TrajFileExt"]
2076 OutfilesSuffixAndExtMap = {"CheckpointFile": ["", "chk"], "DataLogFile": ["", OutfileExt], "MinimizationDataLogFile": ["Minimization", OutfileExt], "SaveFinalStateCheckpointFile": ["FinalState", "chk"], "SaveFinalStateXMLFile": ["FinalState", "xml"], "TrajFile": ["", TrajFileExt], "XmlSystemFile": ["System", "xml"], "XmlIntegratorFile": ["Integrator", "xml"]}
2077 OutfileNames = []
2078 for ParamName in OutfilesSuffixAndExtMap:
2079 ParamValue = ParamsInfo[ParamName]
2080 if re.match("^auto$", ParamValue, re.I):
2081 DataOutfileSuffix, DataOutfileExt = OutfilesSuffixAndExtMap[ParamName]
2082 if len(DataOutfileSuffix):
2083 DataOutfileSuffix = "_%s" % DataOutfileSuffix
2084 ParamValue = "%s%s.%s" % (OutfilePrefix, DataOutfileSuffix, DataOutfileExt)
2085 ParamsInfo[ParamName] = ParamValue
2086 else:
2087 # Check for duplicate output file names...
2088 if ParamValue not in OutfileNames:
2089 OutfileNames.append(ParamValue)
2090 else:
2091 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. It's a duplicate file name." % (ParamValue, ParamName, ParamsOptionName))
2092
2093 # Validate specified traj file extension...
2094 if re.match("^TrajFile$", ParamName, re.I):
2095 TrajFormat = ParamsInfo["TrajFormat"]
2096 if not MiscUtil.CheckFileExt(ParamValue, TrajFileExt):
2097 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. The file extension must match must match the extenstion, %s, corresponding to trajectory format, %s, speecified using \"--trajFormat\" option." % (ParamValue, ParamName, ParamsOptionName, TrajFileExt, TrajFormat))
2098
2099 def _ProcessDataOutTypeOutputParameter(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix):
2100 """Process output parameter corresponding to data out type."""
2101
2102 # Setup data out types...
2103 DataOutTypeStatusMap = {"Step": False, "Speed": False, "Progress": False, "PotentialEnergy": False, "Temperature": False, "ElapsedTime": False, "RemainingTime": False, "Time": False, "KineticEnergy": False, "TotalEnergy": False, "Volume": False, "Density": False}
2104 CanonicalDataOutTypeMap = {}
2105 ValidDataOutTypes = []
2106 for DataOutType in DataOutTypeStatusMap:
2107 ValidDataOutTypes.append(DataOutType)
2108 CanonicalDataOutTypeMap[DataOutType.lower()] = DataOutType
2109
2110 # Process data out types...
2111 ParamName = "DataOutType"
2112 ParamValue = ParamsInfo[ParamName]
2113 DataOutTypeList = []
2114 if re.match("^auto$", ParamValue, re.I):
2115 DataOutTypeList = ["Step", "Speed", "Progress", "PotentialEnergy", "Temperature"]
2116 else:
2117 if "DataOutTypeList" in ParamsInfo:
2118 DataOutTypeList = ParamsInfo["DataOutTypeList"]
2119 else:
2120 DataOutTypeList = ParamsInfo["DataOutType"].split()
2121 ParamsInfo["DataOutTypeList"] = DataOutTypeList
2122
2123 for DataOutType in DataOutTypeList:
2124 CanonicalDataOutType = DataOutType.lower()
2125 if CanonicalDataOutType not in CanonicalDataOutTypeMap:
2126 MiscUtil.PrintError("The parameter value, %s specified for paramaer name, %s, specified using \"%s\" is not a valid name. Supported parameter names: %s" % (DataOutType, ParamName, ParamsOptionName, " ".join(ValidDataOutTypes)))
2127
2128 DataOutType = CanonicalDataOutTypeMap[CanonicalDataOutType]
2129 DataOutTypeStatusMap[DataOutType] = True
2130
2131 ParamsInfo["DataOutTypeList"] = DataOutTypeList
2132 ParamsInfo["DataOutTypeStatusMap"] = DataOutTypeStatusMap
2133
2134 def _ProcessMinimizationDataOutTypeOutputParameter(ParamsInfo, ParamsOptionName, ParamsOptionValue, OutfilePrefix):
2135 """Process output parameter corresponding to minimization data out type."""
2136
2137 # Setup mimimization data out types...
2138 DataOutTypeOpenMMNameMap = {"SystemEnergy": "system energy", "RestraintEnergy": "restraint energy", "RestraintStrength": "restraint strength", "MaxConstraintError": "max constraint error"}
2139
2140 CanonicalDataOutTypeMap = {}
2141 ValidDataOutTypes = []
2142 for DataOutType in DataOutTypeOpenMMNameMap:
2143 ValidDataOutTypes.append(DataOutType)
2144 CanonicalDataOutTypeMap[DataOutType.lower()] = DataOutType
2145
2146 # Process minimization data out types...
2147 ParamName = "MinimizationDataOutType"
2148 ParamValue = ParamsInfo[ParamName]
2149 DataOutTypeList = []
2150 if re.match("^auto$", ParamValue, re.I):
2151 DataOutTypeList = ["SystemEnergy", "RestraintEnergy", "MaxConstraintError"]
2152 else:
2153 if "MinimizationDataOutTypeList" in ParamsInfo:
2154 DataOutTypeList = ParamsInfo["MinimizationDataOutTypeList"]
2155 else:
2156 DataOutTypeList = ParamsInfo["MinimizationDataOutType"].split()
2157 ParamsInfo["MinimizationDataOutTypeList"] = DataOutTypeList
2158
2159 # Set up a list containing OpenMM names for minimization reporter...
2160 DataOutTypeOpenMMNameList = []
2161 for DataOutType in DataOutTypeList:
2162 CanonicalDataOutType = DataOutType.lower()
2163 if CanonicalDataOutType not in CanonicalDataOutTypeMap:
2164 MiscUtil.PrintError("The parameter value, %s specified for paramaer name, %s, specified using \"%s\" is not a valid name. Supported parameter names: %s" % (DataOutType, ParamName, ParamsOptionName, " ".join(ValidDataOutTypes)))
2165
2166 DataOutType = CanonicalDataOutTypeMap[CanonicalDataOutType]
2167
2168 DataOutTypeOpenMMName = DataOutTypeOpenMMNameMap[DataOutType]
2169 DataOutTypeOpenMMNameList.append(DataOutTypeOpenMMName)
2170
2171 ParamsInfo["MinimizationDataOutTypeList"] = DataOutTypeList
2172 ParamsInfo["MinimizationDataOutTypeOpenMMNameList"] = DataOutTypeOpenMMNameList
2173
2174 def ProcessOptionOpenMMAtomsSelectionParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo = None):
2175 """Process parameters for selecting atoms and return a map containing
2176 processed parameter names and values.
2177
2178 ParamsOptionValue is a comma delimited list of parameter name and value pairs
2179 to select atoms.
2180
2181 The supported parameter names along with their default and possible
2182 values are shown below:
2183
2184 selection, none [ Possible values: CAlphaProtein, Ions, Ligand,
2185 Protein, Residues, or Water ]
2186 selectionSpec, auto [ Possible values: A space delimited list of
2187 residue names ]
2188 negate, no [ Possible values: yes or no ]
2189
2190 A brief description of parameters is provided below:
2191
2192 selection: Atom selection to freeze.
2193
2194 selectionSpec: A space delimited list of residue names for selecting atoms.
2195 You must specify its value during 'Ligand' and 'Protein' value for 'selection'.
2196 The default values are automatically set for 'CAlphaProtein', 'Ions', 'Protein',
2197 and 'Water' values of 'selection' as shown below:
2198
2199 CAlphaProtein: List of stadard protein residues from pdbfixer
2200 for selecting CAlpha atoms.
2201 Ions: Li Na K Rb Cs Cl Br F I
2202 Water: HOH
2203 Protein: List of standard protein residues from pdbfixer.
2204
2205 negate: Negate atom selection match to select atoms for freezing.
2206
2207 In addition, you may specify an explicit space delimited list of residue
2208 names using 'selectionSpec' for any 'selection". The specified residue
2209 names are appended to the appropriate default values during the
2210 selection of atoms for freezing.
2211
2212 Arguments:
2213 ParamsOptionName (str): Command line OpenMM selection option name.
2214 ParamsOptionValues (str): Space delimited list of parameter name and value pairs.
2215 ParamsDefaultInfo (dict): Default values to override for selected parameters.
2216
2217 Returns:
2218 dictionary: Processed parameter name and value pairs.
2219
2220 """
2221
2222 ParamsInfo = {"Selection": None, "SelectionSpec": "auto", "Negate": False}
2223
2224 if ParamsOptionValue is None:
2225 return ParamsInfo
2226
2227 (ValidParamNames, CanonicalParamNamesMap, ParamsOptionValue, ParamsOptionValueWords) = _ValidateAndCanonicalizeParameterNames(ParamsOptionName, ParamsOptionValue, ParamsInfo, ParamsDefaultInfo)
2228
2229 if re.match("^auto$", ParamsOptionValue, re.I):
2230 _ProcessOptionOpenMMAtomsSelectionParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
2231 return ParamsInfo
2232
2233 for Index in range(0, len(ParamsOptionValueWords), 2):
2234 Name = ParamsOptionValueWords[Index].strip()
2235 Value = ParamsOptionValueWords[Index + 1].strip()
2236
2237 ParamName = CanonicalParamNamesMap[Name.lower()]
2238 ParamValue = Value
2239
2240 # Set value...
2241 ParamsInfo[ParamName] = ParamValue
2242 if re.match("^Selection$", ParamName, re.I):
2243 if not re.match("^(CAlphaProtein|Ions|Ligand|Protein|Residues|Water)$", Value, re.I):
2244 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: CAlphaProtein, Ions, Ligand, Protein, Residues, or Water" % (Value, Name, ParamsOptionName))
2245 ParamValue = Value
2246 elif re.match("^SelectionSpec$", ParamName, re.I):
2247 if not re.match("^(auto|none)$", Value, re.I):
2248 Values = Value.split()
2249 if len(Values) == 0:
2250 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. It must contain space delimited list of residue names.\n" % (Value, ParamName, ParamsOptionName))
2251 # Set residues list...
2252 ParamsInfo["SelectionSpecList"] = Values
2253 elif re.match("^Negate$", ParamName, re.I):
2254 if not re.match("^(yes|no|true|false)$", Value, re.I):
2255 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: yes or no" % (Value, Name, ParamsOptionName))
2256 ParamValue = True if re.match("^(yes|true)$", Value, re.I) else False
2257 else:
2258 ParamValue = Value
2259
2260 # Set value...
2261 ParamsInfo[ParamName] = ParamValue
2262
2263 # Handle parameters with possible auto values...
2264 _ProcessOptionOpenMMAtomsSelectionParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
2265
2266 return ParamsInfo
2267
2268 def _ProcessOptionOpenMMAtomsSelectionParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue):
2269 """Process parameters with possible auto values and perform validation.
2270 """
2271
2272 SelectionParamName = "Selection"
2273 SelectionParamValue = ParamsInfo[SelectionParamName]
2274
2275 SelectionSpecParamName = "SelectionSpec"
2276 SelectionSpecParamValue = ParamsInfo[SelectionSpecParamName]
2277
2278 SelectionSpecList = None if re.match("^(auto|none)$", SelectionSpecParamValue, re.I) else ParamsInfo["SelectionSpecList"]
2279
2280 ResidueNames = None
2281 if re.match("^(CAlphaProtein|Protein)$", SelectionParamValue, re.I):
2282 ResidueNames = pdbfixer.pdbfixer.proteinResidues
2283 if SelectionSpecList is not None:
2284 ResidueNames.extend(SelectionSpecList)
2285 elif re.match("^Ions$", SelectionParamValue, re.I):
2286 ResidueNames = ["Li", "Na", "K", "Rb", "Cs", "Cl", "Br", "F", "I"]
2287 if SelectionSpecList is not None:
2288 ResidueNames.extend(SelectionSpecList)
2289 elif re.match("^Ligand$", SelectionParamValue, re.I):
2290 if SelectionSpecList is None:
2291 MiscUtil.PrintError("No value specified for parameter name, %s, using \"%s\" option is not a valid value. It must contain a ligand residue name.\n" % (SelectionSpecParamName, ParamsOptionName))
2292 elif len(SelectionSpecList) != 1:
2293 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. It must contain a single ligand residue name.\n" % (SelectionSpecParamValue, SelectionSpecParamName, ParamsOptionName))
2294 ResidueNames = SelectionSpecList
2295 elif re.match("^Residues$", SelectionParamValue, re.I):
2296 if SelectionSpecList is None:
2297 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. It must contain a space delimited list of residue names.\n" % (SelectionSpecParamValue, SelectionSpecParamName, ParamsOptionName))
2298 ResidueNames = SelectionSpecList
2299 elif re.match("^Water$", SelectionParamValue, re.I):
2300 ResidueNames = ["HOH"]
2301 if SelectionSpecList is not None:
2302 ResidueNames.extend(SelectionSpecList)
2303
2304 ParamsInfo["ResidueNames"] = [ResidueName.upper() for ResidueName in ResidueNames]
2305 ParamsInfo["CAlphaProteinStatus"] = True if re.match("^CAlphaProtein$", SelectionParamValue, re.I) else False
2306
2307 def ProcessOptionOpenMMForcefieldParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo = None):
2308 """Process parameters for biopolymer, small molecule, and water forcefields and
2309 return a map containing processed parameter names and values.
2310
2311 ParamsOptionValue is a comma delimited list of parameter name and value pairs
2312 for forcefields.
2313
2314 The supported parameter names along with their default and possible
2315 values are shown below:
2316
2317 biopolymer, amber14-all.xml [ Possible values: Any Valid value ]
2318 smallMolecule, OpenFF_2.2.0 [ Possible values: Any Valid value ]
2319 water, auto [ Possible values: Any Valid value ]
2320
2321 Possible biopolymer forcefield values:
2322
2323 amber14-all.xml, amber99sb.xml, amber99sbildn.xml, amber03.xml,
2324 amber10.xml
2325 charmm36.xml, charmm_polar_2019.xml
2326 amoeba2018.xml
2327
2328 Possible small molecule forcefield values:
2329
2330 openff_2.2.0, openff_2.0.0, openff_1.3.1, openff_1.2.1, openff_1.1.1,
2331 smirnoff99frosst
2332 gaff-2.11, gaff-2.1, gaff-1.81, gaff-1.8, gaff-1.4
2333
2334 The default water forcefield valus is dependent on the type of the
2335 biopolymer forcefield as shown below:
2336
2337 Amber: amber14/tip3pfb.xml
2338 CHARMM: charmm36/water.xml or None for charmm_polar_2019.xml
2339 Amoeba: None (Explicit)
2340
2341 Possible water forcefield values:
2342
2343 amber14/tip3p.xml, amber14/tip3pfb.xml, amber14/spce.xml,
2344 amber14/tip4pew.xml, amber14/tip4pfb.xml,
2345 implicit/obc2.xml, implicit/GBn.xml, implicit/GBn2.xml
2346 charmm36/water.xml, charmm36/tip3p-pme-b.xml,
2347 charmm36/tip3p-pme-f.xml, charmm36/spce.xml,
2348 charmm36/tip4pew.xml, charmm36/tip4p2005.xml,
2349 charmm36/tip5p.xml, charmm36/tip5pew.xml,
2350 implicit/obc2.xml, implicit/GBn.xml, implicit/GBn2.xml
2351 amoeba2018_gk.xml (Implict water), None (Explicit water for amoeba)
2352
2353 You may specify any valid forcefield name supported by OpenMM. No
2354 explicit validation is performed.
2355
2356 Arguments:
2357 ParamsOptionName (str): Command line OpenMM forcefield option name.
2358 ParamsOptionValues (str): Space delimited list of parameter name and value pairs.
2359 ParamsDefaultInfo (dict): Default values to override for selected parameters.
2360
2361 Returns:
2362 dictionary: Processed parameter name and value pairs.
2363
2364 """
2365
2366 ParamsInfo = {"Biopolymer": "amber14-all.xml", "SmallMolecule": "openff-2.2.1", "Water": "auto", "Additional" : "None"}
2367
2368 (ValidParamNames, CanonicalParamNamesMap, ParamsOptionValue, ParamsOptionValueWords) = _ValidateAndCanonicalizeParameterNames(ParamsOptionName, ParamsOptionValue, ParamsInfo, ParamsDefaultInfo)
2369
2370 if re.match("^auto$", ParamsOptionValue, re.I):
2371 _ProcessOptionOpenMMForcefieldParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
2372 return ParamsInfo
2373
2374 for Index in range(0, len(ParamsOptionValueWords), 2):
2375 Name = ParamsOptionValueWords[Index].strip()
2376 Value = ParamsOptionValueWords[Index + 1].strip()
2377
2378 ParamName = CanonicalParamNamesMap[Name.lower()]
2379 ParamValue = Value
2380
2381 # Set value...
2382 ParamsInfo[ParamName] = ParamValue
2383
2384 # Handle parameters with possible auto values...
2385 _ProcessOptionOpenMMForcefieldParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
2386
2387 return ParamsInfo
2388
2389 def _ProcessOptionOpenMMForcefieldParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue):
2390 """Process parameters with possible auto values and perform validation.
2391 """
2392 WaterForcefield = ParamsInfo["Water"]
2393 if re.match("^None$", WaterForcefield, re.I):
2394 WaterForcefield = None
2395 ParamsInfo["Water"] = WaterForcefield
2396 elif re.match("^auto$", WaterForcefield, re.I):
2397 BiopolymerForcefield = ParamsInfo["Biopolymer"]
2398 if re.search("amber", BiopolymerForcefield, re.I):
2399 WaterForcefield = "amber14/tip3pfb.xml"
2400 elif re.search("charmm", BiopolymerForcefield, re.I):
2401 if re.search("charmm_polar_2019", BiopolymerForcefield, re.I):
2402 WaterForcefield = None
2403 else:
2404 WaterForcefield = "charmm36/water.xml"
2405 elif re.search("amoeba", BiopolymerForcefield, re.I):
2406 # Explicit water...
2407 WaterForcefield = None
2408 else:
2409 WaterForcefield = None
2410 ParamsInfo["Water"] = WaterForcefield
2411
2412 # Set status of implicit water forcefield...
2413 BiopolymerForcefield = ParamsInfo["Biopolymer"]
2414 ParamsInfo["ImplicitWater"] = True if _IsImplicitWaterForcefield(BiopolymerForcefield, WaterForcefield) else False
2415
2416 # Process additional forcefields...
2417 ParamName = "Additional"
2418 ParamValue = ParamsInfo[ParamName]
2419 ParamValuesList = None
2420 if not re.match("^None$", ParamValue, re.I):
2421 ParamValuesList = ParamValue.split()
2422 if len(ParamValuesList) == 0:
2423 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. It must contain a space delimited list of valid values.\n" % (ParamValue, ParamName, ParamsOptionName))
2424 ParamsInfo["AdditionalList"] = ParamValuesList
2425
2426 def _IsImplicitWaterForcefield(BiopolymerForcefield, WaterForcefield):
2427 """Check the nature of the water forcefield."""
2428
2429 Status = False
2430 if WaterForcefield is None:
2431 if re.search("charmm_polar_2019", BiopolymerForcefield, re.I):
2432 Status = True
2433 else:
2434 Status = False
2435 else:
2436 if re.search("amber", BiopolymerForcefield, re.I):
2437 if re.search("implicit", WaterForcefield, re.I):
2438 Status = True
2439 elif re.search("charmm", BiopolymerForcefield, re.I):
2440 if re.search("implicit", WaterForcefield, re.I):
2441 Status = True
2442 elif re.search("amoeba", BiopolymerForcefield, re.I):
2443 Status = True
2444
2445 return Status
2446
2447 def ProcessOptionOpenMMAnnealingParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo = None):
2448 """Process parameters for annealing option and return a map containing processed
2449 parameter names and values.
2450
2451 ParamsOptionValue is a comma delimited list of parameter name and value pairs
2452 to setup platform.
2453
2454 The supported parameter names along with their default values for
2455 different platforms are shown below:
2456
2457 threads, 1 [ Possible value: >= 0 or auto. The value of 'auto'
2458 Initial heating parameters:
2459
2460 initialStart, 0.0 [ Units: kelvin ]
2461 initialEnd, 300.0 [ Units: kelvin ]
2462 initialChange, 5.0 [ Units: kelvin ]
2463 initialSteps, 5000
2464
2465 initialEquilibrationSteps, 100000
2466
2467 Heating and cooling cycle parameters:
2468
2469 cycles, 1
2470
2471 cycleStart, auto [ Units: kelvin. The default value is set to
2472 initialEnd ]
2473 cycleEnd, 315.0 [ Units: kelvin ]
2474 cycleChange, 1.0 [ Units: kelvin ]
2475 cycleSteps, 1000
2476
2477 cycleEquilibrationSteps, 100000
2478
2479 Final equilibration parameters:
2480
2481 finalEquilibrationSteps, 200000
2482
2483 A brief description of parameters is provided below:
2484
2485 Initial heating parameters:
2486
2487 initialStart: Start temperature for initial heating.
2488 initialEnd: End temperature for initial heating.
2489 initialChange: Temperature change for increasing temperature
2490 during initial heating.
2491 initialSteps: Number of simulation steps after each
2492 heating step during initial heating
2493
2494 initialEquilibrationSteps: Number of equilibration steps
2495 after the completion of initial heating.
2496
2497 Heating and cooling cycles parameters:
2498
2499 cycles: Number of annealing cycles to perform. Each cycle
2500 consists of a heating and a cooling phase. The heating phase
2501 consists of the following steps: Heat system from start to
2502 end temperature using change size and perform simulation for a
2503 number of steps after each increase in temperature; Perform
2504 equilibration after the completion of heating. The cooling
2505 phase is reverse of the heating phase and cools the system
2506 from end to start temperature.
2507
2508 cycleStart: Start temperature for annealing cycle.
2509 cycleEnd: End temperature for annealing cycle.
2510 cycleChange: Temperature change for increasing or decreasing
2511 temperature during annealing cycle.
2512 cycleSteps: Number of simulation steps after each heating and
2513 cooling step during annealing cycle.
2514
2515 cycleEquilibrationSteps: Number of equilibration steps
2516 after the completion of heating and cooling phase during a
2517 annealing cycle.
2518
2519 Final equilibration parameters:
2520
2521 finalEquilibrationSteps: Number of final equilibration
2522 steps after the completion of annealing cycles.
2523
2524 Arguments:
2525 ParamsOptionName (str): Command line OpenMM annealing option name.
2526 ParamsOptionValues (str): Space delimited list of parameter name and value pairs.
2527 ParamsDefaultInfo (dict): Default values to override for selected parameters.
2528
2529 Returns:
2530 dictionary: Processed parameter name and value pairs.
2531
2532 """
2533
2534 ParamsInfo = {"InitialStart": 0.0, "InitialEnd": 300.0, "InitialChange": 5.0, "InitialSteps": 5000, "InitialEquilibrationSteps": 100000, "Cycles": 1, "CycleStart": "auto", "CycleEnd": 315.0, "CycleChange": 1.0, "CycleSteps": 1000, "CycleEquilibrationSteps": 100000, "FinalEquilibrationSteps": 200000 }
2535
2536 (ValidParamNames, CanonicalParamNamesMap, ParamsOptionValue, ParamsOptionValueWords) = _ValidateAndCanonicalizeParameterNames(ParamsOptionName, ParamsOptionValue, ParamsInfo, ParamsDefaultInfo)
2537
2538 if re.match("^auto$", ParamsOptionValue, re.I):
2539 _ProcessOptionOpenMMAnnealingParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
2540 return ParamsInfo
2541
2542 for Index in range(0, len(ParamsOptionValueWords), 2):
2543 Name = ParamsOptionValueWords[Index].strip()
2544 Value = ParamsOptionValueWords[Index + 1].strip()
2545
2546 ParamName = CanonicalParamNamesMap[Name.lower()]
2547 ParamValue = Value
2548
2549 if re.match("^(InitialStart|InitialEnd|CycleEnd)$", ParamName, re.I):
2550 if not MiscUtil.IsFloat(Value):
2551 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a float.\n" % (Value, ParamName, ParamsOptionName))
2552 Value = float(Value)
2553 if Value < 0:
2554 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
2555 ParamValue = Value
2556 elif re.match("^(InitialChange|CycleChange)$", ParamName, re.I):
2557 if not MiscUtil.IsFloat(Value):
2558 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a float.\n" % (Value, ParamName, ParamsOptionName))
2559 Value = float(Value)
2560 if Value <= 0:
2561 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
2562 ParamValue = Value
2563 elif re.match("^CycleStart$", ParamName, re.I):
2564 if not re.match("^auto$", Value, re.I):
2565 if not MiscUtil.IsFloat(Value):
2566 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a float.\n" % (Value, ParamName, ParamsOptionName))
2567 Value = float(Value)
2568 if Value < 0:
2569 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
2570 ParamValue = Value
2571 elif re.match("^(InitialSteps|InitialEquilibrationSteps|Cycles|CycleSteps|CycleEquilibrationSteps|FinalEquilibrationSteps)$", ParamName, re.I):
2572 if not MiscUtil.IsInteger(Value):
2573 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a integer.\n" % (Value, ParamName, ParamsOptionName))
2574 Value = int(Value)
2575 if Value <= 0:
2576 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
2577 ParamValue = Value
2578 else:
2579 ParamValue = Value
2580
2581 # Set value...
2582 ParamsInfo[ParamName] = ParamValue
2583
2584 # Handle parameters with possible auto values...
2585 _ProcessOptionOpenMMAnnealingParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
2586
2587 return ParamsInfo
2588
2589 def _ProcessOptionOpenMMAnnealingParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue):
2590 """Process parameters with possible auto values and perform validation.
2591 """
2592
2593 ParamName = "CycleStart"
2594 ParamValue = "%s" % ParamsInfo[ParamName]
2595 if re.match("^auto$", ParamValue, re.I):
2596 ParamsInfo[ParamName] = ParamsInfo["InitialEnd"]
2597
2598 if ParamsInfo["InitialStart"] >= ParamsInfo["InitialEnd"]:
2599 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, initialStart, must be less than value, %s, specified for parameter name, initialEnd, using \"%s\" option.\n" % (ParamsInfo["InitialStart"], ParamsInfo["InitialEnd"], ParamsOptionName))
2600
2601 if ParamsInfo["CycleStart"] >= ParamsInfo["CycleEnd"]:
2602 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, cycleStart, must be less than value, %s, specified for parameter name, cycleEnd, using \"%s\" option.\n" % (ParamsInfo["CycleStart"], ParamsInfo["CycleEnd"], ParamsOptionName))
2603
2604 if ParamsInfo["CycleStart"] != ParamsInfo["InitialEnd"]:
2605 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, cycleStart, must be equal to value, %s, specified for parameter name, initialEndEnd, using \"%s\" option.\n" % (ParamsInfo["CycleStart"], ParamsInfo["InitialEnd"], ParamsOptionName))
2606
2607 if ParamsInfo["InitialChange"] >= (ParamsInfo["InitialEnd"] - ParamsInfo["InitialStart"]):
2608 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, initialChange, must be less than value, %s, corresponding to the difference between values specified for parameter names, initialStart and initialEnd, using \"%s\" option.\n" % (ParamsInfo["InitialChange"], (ParamsInfo["InitialEnd"] - ParamsInfo["InitialStart"]), ParamsOptionName))
2609
2610 if ParamsInfo["CycleChange"] >= (ParamsInfo["CycleEnd"] - ParamsInfo["CycleStart"]):
2611 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, cycleChange, must be less than value, %s, corresponding to the difference between values specified for parameter names, cycleStart and cycleEnd, using \"%s\" option.\n" % (ParamsInfo["CycleChange"], (ParamsInfo["CycleEnd"] - ParamsInfo["CycleStart"]), ParamsOptionName))
2612
2613
2614 def ProcessOptionOpenMMPlatformParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo = None):
2615 """Process parameters for platform option and return a map containing processed
2616 parameter names and values.
2617
2618 ParamsOptionValue is a comma delimited list of parameter name and value pairs
2619 to setup platform.
2620
2621 The supported parameter names along with their default values for
2622 different platforms are shown below:
2623
2624 CPU:
2625
2626 threads, 1 [ Possible value: >= 0 or auto. The value of 'auto'
2627 or zero implies the use of all available CPUs for threading. ]
2628
2629 CUDA:
2630
2631 deviceIndex, auto [ Possible values: 0, '0 1' etc. ]
2632 deterministicForces, auto [ Possible values: yes or no ]
2633 precision, single [ Possible values: single, double, or mix ]
2634 tempDirectory, auto [ Possible value: DirName ]
2635 useBlockingSync, auto [ Possible values: yes or no ]
2636 useCpuPme, auto [ Possible values: yes or no ]
2637
2638 OpenCL:
2639
2640 deviceIndex, auto [ Possible values: 0, '0 1' etc. ]
2641 openCLPlatformIndex, auto [ Possible value: Number]
2642 precision, single [ Possible values: single, double, or mix ]
2643 useCpuPme, auto [ Possible values: yes or no ]
2644
2645 A brief description of parameters is provided below:
2646
2647 CPU:
2648
2649 threads: Number of threads to use for simulation.
2650
2651 CUDA:
2652
2653 deviceIndex: Space delimited list of device indices to use for
2654 calculations.
2655 deterministicForces: Generate reproducible results at the cost of a
2656 small decrease in performance.
2657 precision: Number precision to use for calculations.
2658 tempDirectory: Directory name for storing temporary files.
2659 useBlockingSync: Control run-time synchronization between CPU and
2660 GPU.
2661 useCpuPme: Use CPU-based PME implementation.
2662
2663 OpenCL:
2664
2665 deviceIndex: Space delimited list of device indices to use for
2666 simulation.
2667 openCLPlatformIndex: Platform index to use for calculations.
2668 precision: Number precision to use for calculations.
2669 useCpuPme: Use CPU-based PME implementation.
2670
2671 Arguments:
2672 ParamsOptionName (str): Command line OpenMM platform option name.
2673 ParamsOptionValues (str): Space delimited list of parameter name and value pairs.
2674 ParamsDefaultInfo (dict): Default values to override for selected parameters.
2675
2676 Returns:
2677 dictionary: Processed parameter name and value pairs.
2678
2679 """
2680
2681 ParamsInfo = {"Name": "CPU", "Threads": "auto", "DeviceIndex": "auto", "DeterministicForces": "auto", "Precision": "single", "TempDirectory": "auto", "UseBlockingSync": "auto", "UseCpuPme": "auto", "OpenCLPlatformIndex": "auto"}
2682
2683 (ValidParamNames, CanonicalParamNamesMap, ParamsOptionValue, ParamsOptionValueWords) = _ValidateAndCanonicalizeParameterNames(ParamsOptionName, ParamsOptionValue, ParamsInfo, ParamsDefaultInfo)
2684
2685 if re.match("^auto$", ParamsOptionValue, re.I):
2686 _ProcessOptionOpenMMPlatformParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
2687 return ParamsInfo
2688
2689 for Index in range(0, len(ParamsOptionValueWords), 2):
2690 Name = ParamsOptionValueWords[Index].strip()
2691 Value = ParamsOptionValueWords[Index + 1].strip()
2692
2693 ParamName = CanonicalParamNamesMap[Name.lower()]
2694 ParamValue = Value
2695
2696 if re.match("^Name$", ParamName, re.I):
2697 if not re.match("^(CPU|CUDA|OpenCL|Reference)$", Value, re.I):
2698 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: CPU, GPU, OpenCL, or Reference" % (Value, Name, ParamsOptionName))
2699 ParamValue = Value
2700 elif re.match("^Threads$", ParamName, re.I):
2701 if not re.match("^auto$", Value, re.I):
2702 if not MiscUtil.IsInteger(Value):
2703 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be an integer.\n" % (Value, ParamName, ParamsOptionName))
2704 Value = int(Value)
2705 if Value < 0:
2706 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: >=0 \n" % (ParamValue, ParamName, ParamsOptionName))
2707 if Value > mp.cpu_count():
2708 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is greater than number of CPUs, %s, returned by mp.cpu_count().\n" % (ParamValue, ParamName, ParamsOptionName, mp.cpu_count()))
2709 ParamValue = "%s" % Value
2710 elif re.match("^Precision$", ParamName, re.I):
2711 if not re.match("^(Single|Double|Mix)$", Value, re.I):
2712 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: single, double or mix" % (Value, Name, ParamsOptionName))
2713 ParamValue = Value.lower()
2714 elif re.match("^(DeterministicForces|UseBlockingSync|UseCpuPme)$", ParamName, re.I):
2715 if not re.match("^auto$", Value, re.I):
2716 if not re.match("^(yes|no|true|false)$", Value, re.I):
2717 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: yes or no" % (Value, Name, ParamsOptionName))
2718 ParamValue = "true" if re.match("^(yes|true)$", Value, re.I) else "false"
2719 elif re.match("^(DeviceIndex|openCLPlatformIndex)$", ParamName, re.I):
2720 if not re.match("^auto$", Value, re.I):
2721 DeviceIndices = Value.split()
2722 if len(DeviceIndices) == 0:
2723 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. It must contain space delimited list of device indices.\n" % (Value, ParamName, ParamsOptionName))
2724 for DeviceIndex in DeviceIndices:
2725 if not MiscUtil.IsInteger(DeviceIndex):
2726 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be an integer.\n" % (DeviceIndex, ParamName, ParamsOptionName))
2727 ParamValue = ",".join(DeviceIndices)
2728 elif re.match("^TempDirectory$", ParamName, re.I):
2729 if not re.match("^auto$", Value, re.I):
2730 if not os.path.isdir(Value):
2731 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. The specified directory doesn't exists." % (Value, Name, ParamsOptionName))
2732 ParamValue = Value
2733 else:
2734 ParamValue = Value
2735
2736 # Set value...
2737 ParamsInfo[ParamName] = ParamValue
2738
2739 # Handle parameters with possible auto values...
2740 _ProcessOptionOpenMMPlatformParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
2741
2742 return ParamsInfo
2743
2744 def _ProcessOptionOpenMMPlatformParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue):
2745 """Process parameters with possible auto values and perform validation.
2746 """
2747
2748 ParamValueMap = {"cpu": "CPU", "cuda": "CUDA", "opencl": "OpenCL", "reference": "Reference"}
2749 ParamName = "Name"
2750 ParamValue = ParamsInfo[ParamName].lower()
2751 if ParamValue in ParamValueMap:
2752 ParamsInfo[ParamName] = ParamValueMap[ParamValue]
2753
2754 ParamsInfo["Precision"] = ParamsInfo["Precision"].lower()
2755
2756 # Set "auto" values to None and treat all other values as strings...
2757 for ParamName in ParamsInfo:
2758 ParamValue = "%s" % ParamsInfo[ParamName]
2759 if re.match("^auto$", ParamValue, re.I):
2760 ParamsInfo[ParamName] = None
2761 else:
2762 ParamsInfo[ParamName] = ParamValue
2763
2764 def ProcessOptionOpenMMWaterBoxParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo = None):
2765 """Process parameters for adding a water box option and return a map containing
2766 processed parameter names and values.
2767
2768 ParamsOptionValue is a comma delimited list of parameter name and value pairs
2769 for adding a water box.
2770
2771 The supported parameter names along with their default and possible
2772 values are shown below:
2773
2774 model, tip3p [ Possible values: tip3p, spce, tip4pew, tip5p or swm4ndp ]
2775 mode, Padding [ Possible values: Size or Padding ]
2776 size, None [ Possible values: xsize ysize zsize ]
2777 padding, 1.0
2778 shape, cube [ Possible values: cube, dodecahedron, or octahedron ]
2779 ionPositive, Na+ [ Possible values: Li+, Na+, K+, Rb+, or Cs+ ]
2780 ionNegative, Cl- [ Possible values: Cl-, Br-, F-, or I- ]
2781 ionicStrength, 0.0
2782
2783 A brief description of parameters is provided below:
2784
2785 model: Water model to use for adding water box.
2786
2787 mode: Specify the size of the waterbox explicitly or calculate it automatically
2788 for a macromolecule along with adding padding around macromolecule.
2789 Possible values: Size or Padding.
2790
2791 size: A space delimited triplet of values corresponding to water size in
2792 nanometers. It must be specified during 'Size' value of 'mode' parameter.
2793
2794 padding: Padding around macromolecule in nanometers for filling box with
2795 water. It must be specified during 'Padding' value of 'mode' parameter.
2796
2797 ionPositive: Type of positive ion to add during the addition of a water box.
2798
2799 ionNegative: Type of negative ion to add during the addition of a water box.
2800
2801 ionicStrength: Total concentration (molar) of both positive and negative ions
2802 to add excluding he ions added to neutralize the system during the addition
2803 of a water box.
2804
2805 Arguments:
2806 ParamsOptionName (str): Command line OpenMM water box option name.
2807 ParamsOptionValues (str): Space delimited list of parameter name and value pairs.
2808 ParamsDefaultInfo (dict): Default values to override for selected parameters.
2809
2810 Returns:
2811 dictionary: Processed parameter name and value pairs.
2812
2813 """
2814
2815 ParamsInfo = {"Model": "tip3p", "Mode": "Padding", "Size": None, "Padding": 1.0, "Shape": "cube", "IonPositive": "Na+", "IonNegative": "Cl-", "IonicStrength": 0.0}
2816
2817 (ValidParamNames, CanonicalParamNamesMap, ParamsOptionValue, ParamsOptionValueWords) = _ValidateAndCanonicalizeParameterNames(ParamsOptionName, ParamsOptionValue, ParamsInfo, ParamsDefaultInfo)
2818
2819 if re.match("^auto$", ParamsOptionValue, re.I):
2820 _ProcessOptionOpenMMWaterBoxParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
2821 return ParamsInfo
2822
2823 for Index in range(0, len(ParamsOptionValueWords), 2):
2824 Name = ParamsOptionValueWords[Index].strip()
2825 Value = ParamsOptionValueWords[Index + 1].strip()
2826
2827 ParamName = CanonicalParamNamesMap[Name.lower()]
2828 ParamValue = Value
2829
2830 if re.match("^Model$", ParamName, re.I):
2831 if not re.match("^(tip3p|spce|tip4pew|tip5p|swm4ndp)$", Value, re.I):
2832 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: tip3p, spce, tip4pew, tip5p, or swm4ndp" % (Value, Name, ParamsOptionName))
2833 ParamValue = Value.lower()
2834 elif re.match("^Mode$", ParamName, re.I):
2835 if not re.match("^(Padding|Size)$", Value, re.I):
2836 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: Padding or Size" % (Value, Name, ParamsOptionName))
2837 ParamValue = Value
2838 elif re.match("^Size$", ParamName, re.I):
2839 if Value is not None and not re.match("^None$", Value, re.I):
2840 SizeValues = Value.split()
2841 if len(SizeValues) != 3:
2842 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. It must contain 3 float values separated by spaces.\n" % (Value, ParamName, ParamsOptionName))
2843
2844 SizeValueList = []
2845 for SizeValue in SizeValues:
2846 if not MiscUtil.IsFloat(SizeValue):
2847 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a float.\n" % (SizeValue, ParamName, ParamsOptionName))
2848 SizeValue = float(SizeValue)
2849 if SizeValue <= 0:
2850 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (SizeValue, ParamName, ParamsOptionName))
2851 SizeValueList.append(SizeValue)
2852
2853 # Set size values...
2854 ParamsInfo["SizeList"] = SizeValueList
2855
2856 ParamValue = Value
2857 elif re.match("^Padding$", ParamName, re.I):
2858 if not MiscUtil.IsFloat(Value):
2859 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a float.\n" % (Value, ParamName, ParamsOptionName))
2860 Value = float(Value)
2861 if Value <= 0:
2862 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: > 0\n" % (ParamValue, ParamName, ParamsOptionName))
2863 ParamValue = Value
2864 elif re.match("^Shape$", ParamName, re.I):
2865 if not re.match("^(cube|dodecahedron|octahedron)$", Value, re.I):
2866 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: cube, dodecahedron, or octahedron" % (Value, Name, ParamsOptionName))
2867 ParamValue = Value.lower()
2868 elif re.match("^IonPositive$", ParamName, re.I):
2869 ValidValues = "Li+ Na+ K+ Rb+ Cs+"
2870 EscapedValidValuesPattern = "Li\+|Na\+|K\+|Rb\+|Cs\+"
2871 if not re.match("^(%s)$" % EscapedValidValuesPattern, Value):
2872 MiscUtil.PrintError("The value specified, %s, for parameter name, %s, using \"%s\" option is not a valid. Supported value(s): %s" % (ParamValue, ParamName, ParamsOptionName, ValidValues))
2873 ParamValue = Value
2874 elif re.match("^IonNegative$", ParamName, re.I):
2875 ValidValues = "F- Cl- Br- I-"
2876 ValidValuesPattern = "F-|Cl-|Br-|I-"
2877 if not re.match("^(%s)$" % ValidValuesPattern, Value):
2878 MiscUtil.PrintError("The value specified, %s, for parameter name, %s, using \"%s\" option is not a valid. Supported value(s): %s" % (ParamValue, ParamName, ParamsOptionName, ValidValues))
2879 ParamValue = Value
2880 elif re.match("^IonicStrength$", ParamName, re.I):
2881 if not MiscUtil.IsFloat(Value):
2882 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option must be a float.\n" % (Value, ParamName, ParamsOptionName))
2883 Value = float(Value)
2884 if Value < 0:
2885 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: >= 0\n" % (ParamValue, ParamName, ParamsOptionName))
2886 ParamValue = Value
2887 else:
2888 ParamValue = Value
2889
2890 # Set value...
2891 ParamsInfo[ParamName] = ParamValue
2892
2893 # Handle parameters with possible auto values...
2894 _ProcessOptionOpenMMWaterBoxParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue)
2895
2896 return ParamsInfo
2897
2898 def _ProcessOptionOpenMMWaterBoxParameters(ParamsInfo, ParamsOptionName, ParamsOptionValue):
2899 """Process parameters with possible auto values and perform validation.
2900 """
2901
2902 ParamsInfo["ModeSize"] = True if re.match("^Size$", ParamsInfo["Mode"], re.I) else False
2903 ParamsInfo["ModePadding"] = True if re.match("^Padding$", ParamsInfo["Mode"], re.I) else False
2904
2905 if ParamsInfo["ModeSize"]:
2906 ParamName = "Size"
2907 ParamValue = ParamsInfo[ParamName]
2908 if ParamValue is None:
2909 MiscUtil.PrintError("The parameter value, %s, specified for parameter name, %s, using \"%s\" option is not a valid value. Supported values: x y z\n" % (ParamValue, ParamName, ParamsOptionName))
2910 else:
2911 ParamsInfo["SizeList"] = None
2912
2913 def _ValidateAndCanonicalizeParameterNames(ParamsOptionName, ParamsOptionValue, ParamsInfo, ParamsDefaultInfo):
2914 """Validate and canonicalize parameter names."""
2915
2916 # Setup a canonical paramater names...
2917 ValidParamNames = []
2918 CanonicalParamNamesMap = {}
2919 for ParamName in sorted(ParamsInfo):
2920 ValidParamNames.append(ParamName)
2921 CanonicalParamNamesMap[ParamName.lower()] = ParamName
2922
2923 # Update default values...
2924 if ParamsDefaultInfo is not None:
2925 for ParamName in ParamsDefaultInfo:
2926 if ParamName not in ParamsInfo:
2927 MiscUtil.PrintError("The default parameter name, %s, specified using \"%s\" option is not a valid name. Supported parameter names: %s" % (ParamName, ParamsDefaultInfo, " ".join(ValidParamNames)))
2928 ParamsInfo[ParamName] = ParamsDefaultInfo[ParamName]
2929
2930 ParamsOptionValue = ParamsOptionValue.strip()
2931 if not ParamsOptionValue:
2932 MiscUtil.PrintError("No valid parameter name and value pairs specified using \"%s\" option" % ParamsOptionName)
2933
2934 ParamsOptionValueWords = None
2935 if not re.match("^auto$", ParamsOptionValue, re.I):
2936 ParamsOptionValueWords = ParamsOptionValue.split(",")
2937 if len(ParamsOptionValueWords) % 2:
2938 MiscUtil.PrintError("The number of comma delimited paramater names and values, %d, specified using \"%s\" option must be an even number." % (len(ParamsOptionValueWords), ParamsOptionName))
2939
2940 if ParamsOptionValueWords is not None:
2941 for Index in range(0, len(ParamsOptionValueWords), 2):
2942 Name = ParamsOptionValueWords[Index].strip()
2943 CanonicalName = Name.lower()
2944 if not CanonicalName in CanonicalParamNamesMap:
2945 MiscUtil.PrintError("The parameter name, %s, specified using \"%s\" is not a valid name. Supported parameter names: %s" % (Name, ParamsOptionName, " ".join(ValidParamNames)))
2946
2947 return (ValidParamNames, CanonicalParamNamesMap, ParamsOptionValue, ParamsOptionValueWords)
