fixes merge conflicts

Author: Meg Osato

README.md

@@ -13,10 +13,12 @@ Latest release:
 ## Citations
 #### Publication
 - [Gill, S; Lim, N. M.; Grinaway, P.; Rustenburg, A. S.; Fass, J.; Ross, G.; Chodera, J. D.; Mobley, D. L. “Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo”](https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b11820) - Journal of Physical Chemistry B. February 27, 2018
+- [Burley, K. H., Gill, S. C., Lim, N. M., & Mobley, D. L. "Enhancing Sidechain Rotamer Sampling Using Non-Equilibrium Candidate Monte Carlo"](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.8b01018) - Journal of Chemical Theory and Computation. January 24, 2019
 
 #### Preprints
 - [BLUES v1](https://chemrxiv.org/articles/Binding_Modes_of_Ligands_Using_Enhanced_Sampling_BLUES_Rapid_Decorrelation_of_Ligand_Binding_Modes_Using_Nonequilibrium_Candidate_Monte_Carlo/5406907) - ChemRxiv September 19, 2017
 - [BLUES v2](https://doi.org/10.26434/chemrxiv.5406907.v2) - ChemRxiv September 25, 2017
+- [Sampling alternate conformations of bound ligands](https://chemrxiv.org/articles/Sampling_Conformational_Changes_of_Bound_Ligands_Using_Nonequilibrium_Candidate_Monte_Carlo/10003412) - ChemRxiv October 23, 2019
 
 ## Manifest
 * `blues/` -  Source code and example scripts for BLUES toolkit

blues/example.py

@@ -61,6 +61,65 @@ def sidechain_example(yaml_file):
         for value in dihedraldata:
             output.write("%s\n" % str(value)[1:-1])
 
+def rotbondmove_example(yaml_file):
+    # Parse a YAML configuration, return as Dict
+    cfg = Settings(yaml_file).asDict()
+    structure = cfg['Structure']
+
+    #Select move type
+    prmtop = cfg['structure']['filename']
+    inpcrd = cfg['structure']['xyz']
+    dihedral_atoms = cfg['rotbond_info']['dihedral_atoms']
+    alch_list = cfg['rotbond_info']['alch_list']
+    ligand = RandomRotatableBondMove(structure, prmtop, inpcrd, dihedral_atoms, alch_list, 'LIG')
+
+    #Iniitialize object that selects movestep
+    ligand_mover = MoveEngine(ligand)
+
+    #Generate the openmm.Systems outside SimulationFactory to allow modifications
+    systems = SystemFactory(structure, ligand.atom_indices, cfg['system'])
+
+    #Freeze atoms in the alchemical system to speed up alchemical calculation
+    systems.alch = systems.freeze_radius(structure, systems.alch, **cfg['freeze'])
+
+    #Generate the OpenMM Simulations
+    simulations = SimulationFactory(systems, ligand_mover, cfg['simulation'], cfg['md_reporters'],
+                                    cfg['ncmc_reporters'])
+
+    # Run BLUES Simulation
+    blues = BLUESSimulation(simulations, cfg['simulation'])
+    blues.run()
+
+def rotbondlfipmove_cuda(yaml_file):
+    # Parse a YAML configuration, return as Dict
+    cfg = Settings(yaml_file).asDict()
+    structure = cfg['Structure']
+
+    #Select move type
+    prmtop = cfg['structure']['filename']
+    inpcrd = cfg['structure']['xyz']
+    dihedral_atoms = cfg['rotbond_info']['dihedral_atoms']
+    alch_list = cfg['rotbond_info']['alch_list']
+    ligand = RandomRotatableBondFlipMove(structure, prmtop, inpcrd, dihedral_atoms, alch_list, 'LIG')
+
+    #Iniitialize object that selects movestep
+    ligand_mover = MoveEngine(ligand)
+
+    #Generate the openmm.Systems outside SimulationFactory to allow modifications
+    systems = SystemFactory(structure, ligand.atom_indices, cfg['system'])
+
+    #Freeze atoms in the alchemical system to speed up alchemical calculation
+    systems.alch = systems.freeze_radius(structure, systems.alch, **cfg['freeze'])
+
+    #Generate the OpenMM Simulations
+    simulations = SimulationFactory(systems, ligand_mover, cfg['simulation'], cfg['md_reporters'],
+                                    cfg['ncmc_reporters'])
+
+    # Run BLUES Simulation
+    blues = BLUESSimulation(simulations, cfg['simulation'])
+    blues.run()
 
 ligrot_example(get_data_filename('blues', '../examples/rotmove_cuda.yml'))
 #sidechain_example(get_data_filename('blues', '../examples/sidechain_cuda.yml'))
+#rotbondmove_example(get_data_filename('blues', '../examples/rotbondmove_cuda.yaml'))
+#rotbondflipmove_example(get_data_filename('blues', '../examples/rotbondmove_cuda.yaml'))

blues/integrators.py

@@ -11,16 +11,13 @@ class AlchemicalExternalLangevinIntegrator(AlchemicalNonequilibriumLangevinInteg
     """Allows nonequilibrium switching based on force parameters specified in alchemical_functions.
     A variable named lambda is switched from 0 to 1 linearly throughout the nsteps of the protocol.
     The functions can use this to create more complex protocols for other global parameters.
-
     As opposed to `openmmtools.integrators.AlchemicalNonequilibriumLangevinIntegrator`,
     which this inherits from, the AlchemicalExternalLangevinIntegrator integrator also takes
     into account work done outside the nonequilibrium switching portion(between integration steps).
     For example if a molecule is rotated between integration steps, this integrator would
     correctly account for the work caused by that rotation.
-
     Propagator is based on Langevin splitting, as described below.
     One way to divide the Langevin system is into three parts which can each be solved "exactly:"
-
     - R: Linear "drift" / Constrained "drift"
         Deterministic update of *positions*, using current velocities
         ``x <- x + v dt``
@@ -30,18 +27,15 @@ class AlchemicalExternalLangevinIntegrator(AlchemicalNonequilibriumLangevinInteg
     - O: Ornstein-Uhlenbeck
         Stochastic update of velocities, simulating interaction with a heat bath
         ``v <- av + b sqrt(kT/m) R`` where:
-
         - a = e^(-gamma dt)
         - b = sqrt(1 - e^(-2gamma dt))
         - R is i.i.d. standard normal
-
     We can then construct integrators by solving each part for a certain timestep in sequence.
     (We can further split up the V step by force group, evaluating cheap but fast-fluctuating
     forces more frequently than expensive but slow-fluctuating forces. Since forces are only
     evaluated in the V step, we represent this by including in our "alphabet" V0, V1, ...)
     When the system contains holonomic constraints, these steps are confined to the constraint
     manifold.
-
     Parameters
     ----------
     alchemical_functions : dict of strings
@@ -71,12 +65,10 @@ class AlchemicalExternalLangevinIntegrator(AlchemicalNonequilibriumLangevinInteg
     nprop : int (Default: 1)
         Controls the number of propagation steps to add in the lambda
         region defined by `prop_lambda`.
-
     Attributes
     ----------
     _kinetic_energy : str
         This is 0.5*m*v*v by default, and is the expression used for the kinetic energy
-
     Examples
     --------
     - g-BAOAB:
@@ -87,14 +79,10 @@ class AlchemicalExternalLangevinIntegrator(AlchemicalNonequilibriumLangevinInteg
         splitting="V R H R V"
     - An NCMC algorithm with Metropolized integrator:
         splitting="O { V R H R V } O"
-
-
     References
     ----------
     [Nilmeier, et al. 2011] Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation
-
     [Leimkuhler and Matthews, 2015] Molecular dynamics: with deterministic and stochastic numerical methods, Chapter 7
-
     """
 
     def __init__(self,
@@ -124,6 +112,10 @@ def __init__(self,
             nsteps_neq=nsteps_neq)
 
         self._prop_lambda = self._get_prop_lambda(prop_lambda)
+        frame = inspect.currentframe()
+        args, _, _, values = inspect.getargvalues(frame)
+        inputs = dict([(i, values[i]) for i in args if i is not 'self'])
+        self.int_kwargs = inputs
 
         # add some global variables relevant to the integrator
         kB = openmm.unit.BOLTZMANN_CONSTANT_kB * openmm.unit.AVOGADRO_CONSTANT_NA
@@ -206,4 +198,6 @@ def reset(self):
         self.setGlobalVariableByName("perturbed_pe", 0.0)
         self.setGlobalVariableByName("unperturbed_pe", 0.0)
         self.setGlobalVariableByName("prop", 1)
-        super(AlchemicalExternalLangevinIntegrator, self).reset()
+        #super(AlchemicalExternalLangevinIntegrator, self).reset()
+
+