Modules¶

Moves¶

Provides the main Move class which allows definition of moves which alter the positions of subsets of atoms in a context during a BLUES simulation, in order to increase sampling. Also provides functionality for CombinationMove definitions which consist of a combination of other pre-defined moves such as via instances of Move.

Authors: Samuel C. Gill

Contributors: Nathan M. Lim, Kalistyn Burley, David L. Mobley

Move¶

class blues.moves.Move[source]¶

This is the base Move class. Move provides methods for calculating properties and applying the move on the set of atoms being perturbed in the NCMC simulation.

initializeSystem(system, integrator)[source]¶

If the system or integrator needs to be modified to perform the move (ex. adding a force) this method is called during the start of the simulation to change the system or integrator to accomodate that.

Parameters

system (openmm.System) – System to be modified.
integrator (openmm.Integrator) – Integrator to be modified.

Returns

system (openmm.System) – The modified System object.
integrator (openmm.Integrator) – The modified Integrator object.

beforeMove(context)[source]¶

This method is called at the start of the NCMC portion if the context needs to be checked or modified before performing the move at the halfway point.

Parameters: context (openmm.Context) – Context containing the positions to be moved.
Returns: context (openmm.Context) – The same input context, but whose context were changed by this function.

afterMove(context)[source]¶

This method is called at the end of the NCMC portion if the context needs to be checked or modified before performing the move at the halfway point.

Parameters: context (openmm.Context) – Context containing the positions to be moved.
Returns: context (openmm.Context) – The same input context, but whose context were changed by this function.

move(context)[source]¶

This method is called at the end of the NCMC portion if the context needs to be checked or modified before performing the move at the halfway point.

Parameters: context (openmm.Context) – Context containing the positions to be moved.
Returns: context (openmm.Context) – The same input context, but whose context were changed by this function.

RandomLigandRotationMove¶

class blues.moves.RandomLigandRotationMove(structure, resname='LIG', random_state=None)[source]¶

RandomLightRotationMove that provides methods for calculating properties on the object ‘model’ (i.e ligand) being perturbed in the NCMC simulation. Current methods calculate the object’s atomic masses and center of masss. Calculating the object’s center of mass will get the positions and total mass.

Parameters

resname (str) – String specifying the residue name of the ligand.
structure (parmed.Structure) – ParmEd Structure object of the relevant system to be moved.
random_state (integer or numpy.RandomState, optional) – The generator used for random numbers. If an integer is given, it fixes the seed. Defaults to the global numpy random number generator.

structure¶

The structure of the ligand or selected atoms to be rotated.

Type: parmed.Structure

resname¶

The residue name of the ligand or selected atoms to be rotated.

Type: str, default=’LIG’

topology¶

The topology of the ligand or selected atoms to be rotated.

Type: openmm.Topology

atom_indices¶

Atom indicies of the ligand.

Type: list

masses¶

Particle masses of the ligand with units.

Type: list

totalmass¶

Total mass of the ligand.

Type: int

center_of_mass¶

Calculated center of mass of the ligand in XYZ coordinates. This should be updated every iteration.

Type: numpy.array

positions¶

Ligands positions in XYZ coordinates. This should be updated every iteration.

Type: numpy.array

Examples

>>> from blues.move import RandomLigandRotationMove
>>> ligand = RandomLigandRotationMove(structure, 'LIG')
>>> ligand.resname
    'LIG'

getAtomIndices(structure, resname)[source]¶

Get atom indices of a ligand from ParmEd Structure.

Parameters

resname (str) – String specifying the residue name of the ligand.
structure (parmed.Structure) – ParmEd Structure object of the atoms to be moved.

Returns

atom_indices (list of ints) – list of atoms in the coordinate file matching lig_resname

getMasses(topology)[source]¶

Returns a list of masses of the specified ligand atoms.

Parameters

topology (parmed.Topology) – ParmEd topology object containing atoms of the system.

Returns

masses (1xn numpy.array * simtk.unit.dalton) – array of masses of len(self.atom_indices), denoting the masses of the atoms in self.atom_indices
totalmass (float * simtk.unit.dalton) – The sum of the mass found in masses

getCenterOfMass(positions, masses)[source]¶

Returns the calculated center of mass of the ligand as a numpy.array

Parameters

positions (nx3 numpy array * simtk.unit compatible with simtk.unit.nanometers) – ParmEd positions of the atoms to be moved.
masses (numpy.array) – numpy.array of particle masses

Returns

center_of_mass (numpy array * simtk.unit compatible with simtk.unit.nanometers) – 1x3 numpy.array of the center of mass of the given positions

move(context)[source]¶

Function that performs a random rotation about the center of mass of the ligand.

Parameters: context (simtk.openmm.Context object) – Context containing the positions to be moved.
Returns: context (simtk.openmm.Context object) – The same input context, but whose positions were changed by this function.

MoveEngine¶

class blues.moves.MoveEngine(moves, probabilities=None)[source]¶

MoveEngine provides perturbation functions for the context during the NCMC simulation.

Parameters

moves (blues.move object or list of N blues.move objects) – Specifies the possible moves to be performed.
probabilities (list of floats, optional, default=None) – A list of N probabilities, where probabilities[i] corresponds to the probaility of moves[i] being selected to perform its associated move() method. If None, uniform probabilities are assigned.

moves¶

Possible moves to be performed.

Type: blues.move or list of N blues.move objects

probabilities¶

Normalized probabilities for each move.

Type: list of floats

selected_move¶

Selected move to be performed.

Type: blues.move

move_name¶

Name of the selected move to be performed

Type: str

Examples

Load a parmed.Structure, list of moves with probabilities, initialize the MoveEngine class, and select a move from our list.

>>> import parmed
>>> from blues.moves import *
>>> structure = parmed.load_file('tests/data/eqToluene.prmtop', xyz='tests/data/eqToluene.inpcrd')
>>> probabilities = [0.25, 0.75]
>>> moves = [SideChainMove(structure, [111]),RandomLigandRotationMove(structure, 'LIG')]
>>> mover = MoveEngine(moves, probabilities)
>>> mover.moves
[<blues.moves.SideChainMove at 0x7f2eaa168470>,
 <blues.moves.RandomLigandRotationMove at 0x7f2eaaaa51d0>]
>>> mover.selectMove()
>>> mover.selected_move
<blues.moves.RandomLigandRotationMove at 0x7f2eaaaa51d0>

selectMove()[source]¶: Chooses the move which will be selected for a given NCMC iteration

runEngine(context)[source]¶

Selects a random Move object based on its assigned probability and and performs its move() function on a context.

Parameters: context (openmm.Context) – OpenMM context whose positions should be moved.
Returns: context (openmm.Context) – OpenMM context whose positions have been moved.

Under Development¶

WARNING: The following move classes have not been tested. Use at your own risk.

class blues.moves.SideChainMove(structure, residue_list, verbose=False, write_move=False)[source]¶

NOTE: Usage of this class requires a valid OpenEye license.

SideChainMove provides methods for calculating properties needed to rotate a sidechain residue given a parmed.Structure. Calculated properties include: backbone atom indicies, atom pointers and indicies of the residue sidechain, bond pointers and indices for rotatable heavy bonds in the sidechain, and atom indices upstream of selected bond.

The class contains functions to randomly select a bond and angle to be rotated and applies a rotation matrix to the target atoms to update their coordinates on the object ‘model’ (i.e sidechain) being perturbed in the NCMC simulation.

Parameters

structure (parmed.Structure) – The structure of the entire system to be simulated.
residue_list (list of int) – List of the residue numbers of the sidechains to be rotated.
verbose (bool, default=False) – Enable verbosity to print out detailed information of the rotation.
write_move (bool, default=False) – If True, writes a PDB of the system after rotation.

structure¶

The structure of the entire system to be simulated.

Type: parmed.Structure

molecule¶

The OEMolecule containing the sidechain(s) to be rotated.

Type: oechem.OEMolecule

residue_list¶

List containing the residue numbers of the sidechains to be rotated.

Type: list of int

all_atoms¶

List containing the atom indicies of the sidechains to be rotated.

Type: list of int

rot_atoms¶

Dictionary of residues, bonds and atoms to be rotated

Type: dict

rot_bonds¶

Dictionary containing the bond pointers of the rotatable bonds.

Type: dict of oechem.OEBondBase

qry_atoms¶

Dictionary containing all the atom pointers (as OpenEye objects) that make up the given residues.

Type: dict of oechem.OEAtomBase

Examples

>>> from blues.move import SideChainMove
>>> sidechain = SideChainMove(structure, [1])

getBackboneAtoms(molecule)[source]¶

Takes an OpenEye Molecule, finds the backbone atoms and returns the indicies of the backbone atoms.

Parameters: molecule (oechem.OEMolecule) – The OEmolecule of the simulated system.
Returns: backbone_atoms (list of int) – List containing the atom indices of the backbone atoms.

getTargetAtoms(molecule, backbone_atoms, residue_list)[source]¶

Takes an OpenEye molecule and a list of residue numbers then generates a dictionary containing all the atom pointers and indicies for the non-backbone, atoms of those target residues, as well as a list of backbone atoms. Note: The atom indicies start at 0 and are thus -1 from the PDB file indicies

Parameters

molecule (oechem.OEMolecule) – The OEmolecule of the simulated system.
backbone_atoms (list of int) – List containing the atom indices of the backbone atoms.
residue_list (list of int) – List containing the residue numbers of the sidechains to be rotated.

Returns

backbone_atoms (list of int) – List containing the atom indices of the backbone atoms to be rotated.
qry_atoms (dict of oechem.OEAtomBase) – Dictionary containing all the atom pointers (as OpenEye objects) that make up the given residues.

findHeavyRotBonds(pdb_OEMol, qry_atoms)[source]¶

Takes in an OpenEye molecule as well as a dictionary of atom locations (keys) and atom indicies. It loops over the query atoms and identifies any heavy bonds associated with each atom. It stores and returns the bond indicies (keys) and the two atom indicies for each bond in a dictionary Note: atom indicies start at 0, so are offset by 1 compared to pdb)

Parameters

pdb_OEMol (oechem.OEMolecule) – The OEmolecule of the simulated system generated from a PDB file.
qry_atoms (dict of oechem.OEAtomBase) – Dictionary containing all the atom pointers (as OpenEye objects) that make up the given residues.

Returns

rot_bonds (dict of oechem.OEBondBase) – Dictionary containing the bond pointers of the rotatable bonds.

getRotAtoms(rotbonds, molecule, backbone_atoms)[source]¶

Function identifies and stores neighboring, upstream atoms for a given sidechain bond.

Parameters

rot_bonds (dict of oechem.OEBondBase) – Dictionary containing the bond pointers of the rotatable bonds.
molecule (oechem.OEMolecule) – The OEmolecule of the simulated system.
backbone_atoms (list of int) – List containing the atom indices of the backbone atoms.

Returns

rot_atom_dict (dict of oechem.OEAtomBase) – Dictionary containing the atom pointers for a given sidechain bond.

getRotBondAtoms()[source]¶

This function is called on class initialization.

Takes in a PDB filename (as a string) and list of residue numbers. Returns a nested dictionary of rotatable bonds (containing only heavy atoms), that are keyed by residue number, then keyed by bond pointer, containing values of atom indicies [axis1, axis2, atoms to be rotated] Note: The atom indicies start at 0, and are offset by -1 from the PDB file indicies

Returns

rot_atoms (dict) – Dictionary of residues, bonds and atoms to be rotated
rot_bonds (dict of oechem.OEBondBase) – Dictionary containing the bond pointers of the rotatable bonds.
qry_atoms (dict of oechem.OEAtomBase) – Dictionary containing all the atom pointers (as OpenEye objects) that make up the given residues.

chooseBondandTheta()[source]¶

This function is called on class initialization.

Takes a dictionary containing nested dictionary, keyed by res#, then keyed by bond_ptrs, containing a list of atoms to move, randomly selects a bond, and generates a random angle (radians). It returns the atoms associated with the the selected bond, the pointer for the selected bond and the randomly generated angle

Returns

theta_ran
targetatoms
res_choice
bond_choice

rotation_matrix(axis, theta)[source]¶

Function returns the rotation matrix associated with counterclockwise rotation about the given axis by theta radians.

Parameters

axis
theta (float) – The angle of rotation in radians.

move(context, verbose=False)[source]¶

Rotates the target atoms around a selected bond by angle theta and updates the atom coordinates in the parmed structure as well as the ncmc context object

Parameters

context (simtk.openmm.Context object) – Context containing the positions to be moved.
verbose (bool, default=False) – Enable verbosity to print out detailed information of the rotation.

Returns

context (simtk.openmm.Context object) – The same input context, but whose positions were changed by this function.

class blues.moves.SmartDartMove(structure, basis_particles, coord_files, topology=None, dart_radius=Quantity(value=0.2, unit=nanometer), self_dart=False, resname='LIG')[source]¶

WARNING: This class has not been completely tested. Use at your own risk.

Move object that allows center of mass smart darting moves to be performed on a ligand, allowing translations of a ligand between pre-defined regions in space. The SmartDartMove.move() method translates the ligand to the locations of the ligand found in the coord_files. These locations are defined in terms of the basis_particles. These locations are picked with a uniform probability. Based on Smart Darting Monte Carlo [smart-dart]

Parameters

structure (parmed.Structure) – ParmEd Structure object of the relevant system to be moved.
basis_particles (list of 3 ints) – Specifies the 3 indices of the protein whose coordinates will be used to define a new set of basis vectors.
coord_files (list of str) – List containing paths to coordinate files of the whole system for smart darting.
topology (str, optional, default=None) – A path specifying a topology file matching the files in coord_files. Not necessary if the coord_files already contain topologies (ex. PDBs).
dart_radius (simtk.unit float object compatible with simtk.unit.nanometers unit,) – optional, default=0.2*simtk.unit.nanometers The radius of the darting region around each dart.
self_dart (boolean, optional, default=’False’) – When performing the center of mass darting in SmartDartMove.move(),this specifies whether or not to include the darting region where the center of mass currently resides as an option to dart to.
resname (str, optional, default=’LIG’) – String specifying the residue name of the ligand.

References

smart-dart: I. Andricioaei, J. E. Straub, and A. F. Voter, J. Chem. Phys. 114, 6994 (2001). https://doi.org/10.1063/1.1358861

dartsFromParmEd(coord_files, topology=None)[source]¶

Used to setup darts from a generic coordinate file, through MDtraj using the basis_particles to define new basis vectors, which allows dart centers to remain consistant through a simulation. This adds to the self.n_dartboard, which defines the centers used for smart darting.

Parameters

coord_files (list of str) – List containing coordinate files of the whole system for smart darting.
topology (str, optional, default=None) – A path specifying a topology file matching the files in coord_files. Not necessary if the coord_files already contain topologies.

move(context)[source]¶

Function for performing smart darting move with darts that depend on particle positions in the system.

Parameters: context (simtk.openmm.Context object) – Context containing the positions to be moved.
Returns: context (simtk.openmm.Context object) – The same input context, but whose positions were changed by this function.

class blues.moves.CombinationMove(moves)[source]¶

WARNING: This class has not been completely tested. Use at your own risk.

Move object that allows Move object moves to be performed according to the order in move_list. To ensure detailed balance, the moves have an equal chance to be performed in listed or reverse order.

Parameters: moves (list of blues.move.Move)

move(context)[source]¶

Performs the move() functions of the Moves in move_list on a context.

Parameters: context (simtk.openmm.Context object) – Context containing the positions to be moved.
Returns: context (simtk.openmm.Context object) – The same input context, but whose positions were changed by this function.

Simulation¶

Provides classes for setting up and running the BLUES simulation.

SystemFactory : setup and modifying the OpenMM System prior to the simulation.
SimulationFactory : generates the OpenMM Simulations from the System.
BLUESSimulation : runs the NCMC+MD hybrid simulation.
MonteCarloSimulation : runs a pure Monte Carlo simulation.

Authors: Samuel C. Gill Contributors: Nathan M. Lim, Meghan Osato, David L. Mobley

SystemFactory¶

Methods

class blues.simulation.SystemFactory(structure, atom_indices, config=None)[source]¶

SystemFactory contains methods to generate/modify the OpenMM System object required for generating the openmm.Simulation using a given parmed.Structure()

Examples

Load Parmed Structure, select move type, initialize MoveEngine, and generate the openmm.Systems

>>> structure = parmed.load_file('eqToluene.prmtop', xyz='eqToluene.inpcrd')
>>> ligand = RandomLigandRotationMove(structure, 'LIG')
>>> ligand_mover = MoveEngine(ligand)
>>> systems = SystemFactory(structure, ligand.atom_indices, config['system'])

The MD and alchemical Systems are generated and stored as an attribute

>>> systems.md
>>> systems.alch

Freeze atoms in the alchemical system

>>> systems.alch = SystemFactory.freeze_atoms(systems.alch,
                                        freeze_distance=5.0,
                                        freeze_center='LIG'
                                        freeze_solvent='HOH,NA,CL')

Parameters

structure (parmed.Structure) – A chemical structure composed of atoms, bonds, angles, torsions, and other topological features.
atom_indices (list of int) – Atom indicies of the move or designated for which the nonbonded forces (both sterics and electrostatics components) have to be alchemically modified.
config (dict, parameters for generating the openmm.System for the MD) – and NCMC simulation. For complete parameters, see docs for generateSystem and generateAlchSystem

static amber_selection_to_atomidx(structure, selection)[source]¶

Converts AmberMask selection [amber-syntax] to list of atom indices.

Parameters

structure (parmed.Structure()) – Structure of the system, used for atom selection.
selection (str) – AmberMask selection that gets converted to a list of atom indices.

Returns

mask_idx (list of int) – List of atom indices.

References

amber-syntax(1,2,3,4)

Swails, ParmEd Documentation (2015). http://parmed.github.io/ParmEd/html/amber.html#amber-mask-syntax

static atomidx_to_atomlist(structure, mask_idx)[source]¶

Goes through the structure and matches the previously selected atom indices to the atom type.

Parameters

structure (parmed.Structure()) – Structure of the system, used for atom selection.
mask_idx (list of int) – List of atom indices.

Returns

atom_list (list of atoms) – The atoms that were previously selected in mask_idx.

classmethod generateSystem(structure, **kwargs)[source]¶

Construct an OpenMM System representing the topology described by the prmtop file. This function is just a wrapper for parmed Structure.createSystem().

Parameters

structure (parmed.Structure()) – The parmed.Structure of the molecular system to be simulated
nonbondedMethod (cutoff method) – This is the cutoff method. It can be either the NoCutoff, CutoffNonPeriodic, CutoffPeriodic, PME, or Ewald objects from the simtk.openmm.app namespace
nonbondedCutoff (float or distance Quantity) – The nonbonded cutoff must be either a floating point number (interpreted as nanometers) or a Quantity with attached units. This is ignored if nonbondedMethod is NoCutoff.
switchDistance (float or distance Quantity) – The distance at which the switching function is turned on for van der Waals interactions. This is ignored when no cutoff is used, and no switch is used if switchDistance is 0, negative, or greater than the cutoff
constraints (None, app.HBonds, app.HAngles, or app.AllBonds) – Which type of constraints to add to the system (e.g., SHAKE). None means no bonds are constrained. HBonds means bonds with hydrogen are constrained
rigidWater (bool=True) – If True, water is kept rigid regardless of the value of constraints. A value of False is ignored if constraints is not None.
implicitSolvent (None, app.HCT, app.OBC1, app.OBC2, app.GBn, app.GBn2) – The Generalized Born implicit solvent model to use.
implicitSolventKappa (float or 1/distance Quantity = None) – This is the Debye kappa property related to modeling saltwater conditions in GB. It should have units of 1/distance (1/nanometers is assumed if no units present). A value of None means that kappa will be calculated from implicitSolventSaltConc (below)
implicitSolventSaltConc (float or amount/volume Quantity=0 moles/liter) – If implicitSolventKappa is None, the kappa will be computed from the salt concentration. It should have units compatible with mol/L
temperature (float or temperature Quantity = 298.15 kelvin) – This is only used to compute kappa from implicitSolventSaltConc
soluteDielectric (float=1.0) – The dielectric constant of the protein interior used in GB
solventDielectric (float=78.5) – The dielectric constant of the water used in GB
useSASA (bool=False) – If True, use the ACE non-polar solvation model. Otherwise, use no SASA-based nonpolar solvation model.
removeCMMotion (bool=True) – If True, the center-of-mass motion will be removed periodically during the simulation. If False, it will not.
hydrogenMass (float or mass quantity = None) – If not None, hydrogen masses will be changed to this mass and the difference subtracted from the attached heavy atom (hydrogen mass repartitioning)
ewaldErrorTolerance (float=0.0005) – When using PME or Ewald, the Ewald parameters will be calculated from this value
flexibleConstraints (bool=True) – If False, the energies and forces from the constrained degrees of freedom will NOT be computed. If True, they will (but those degrees of freedom will still be constrained).
verbose (bool=False) – If True, the progress of this subroutine will be printed to stdout
splitDihedrals (bool=False) – If True, the dihedrals will be split into two forces – proper and impropers. This is primarily useful for debugging torsion parameter assignments.

Returns

openmm.System – System formatted according to the prmtop file.

Notes

This function calls prune_empty_terms if any Topology lists have changed.

classmethod generateAlchSystem(system, atom_indices, softcore_alpha=0.5, softcore_a=1, softcore_b=1, softcore_c=6, softcore_beta=0.0, softcore_d=1, softcore_e=1, softcore_f=2, annihilate_electrostatics=True, annihilate_sterics=False, disable_alchemical_dispersion_correction=True, alchemical_pme_treatment='direct-space', suppress_warnings=True, **kwargs)[source]¶

Returns the OpenMM System for alchemical perturbations. This function calls openmmtools.alchemy.AbsoluteAlchemicalFactory and openmmtools.alchemy.AlchemicalRegion to generate the System for the NCMC simulation.

Parameters

system (openmm.System) – The OpenMM System object corresponding to the reference system.
atom_indices (list of int) – Atom indicies of the move or designated for which the nonbonded forces (both sterics and electrostatics components) have to be alchemically modified.
annihilate_electrostatics (bool, optional) – If True, electrostatics should be annihilated, rather than decoupled (default is True).
annihilate_sterics (bool, optional) – If True, sterics (Lennard-Jones or Halgren potential) will be annihilated, rather than decoupled (default is False).
softcore_alpha (float, optional) – Alchemical softcore parameter for Lennard-Jones (default is 0.5).
softcore_a, softcore_b, softcore_c (float, optional) – Parameters modifying softcore Lennard-Jones form. Introduced in Eq. 13 of Ref. [TTPham-JChemPhys135-2011] (default is 1).
softcore_beta (float, optional) – Alchemical softcore parameter for electrostatics. Set this to zero to recover standard electrostatic scaling (default is 0.0).
softcore_d, softcore_e, softcore_f (float, optional) – Parameters modifying softcore electrostatics form (default is 1).
disable_alchemical_dispersion_correction (bool, optional, default=True) – If True, the long-range dispersion correction will not be included for the alchemical region to avoid the need to recompute the correction (a CPU operation that takes ~ 0.5 s) every time ‘lambda_sterics’ is changed. If using nonequilibrium protocols, it is recommended that this be set to True since this can lead to enormous (100x) slowdowns if the correction must be recomputed every time step.
alchemical_pme_treatment (str, optional, default = ‘direct-space’) – Controls how alchemical region electrostatics are treated when PME is used. Options are ‘direct-space’, ‘coulomb’, ‘exact’. - ‘direct-space’ only models the direct space contribution - ‘coulomb’ includes switched Coulomb interaction - ‘exact’ includes also the reciprocal space contribution, but it’s only possible to annihilate the charges and the softcore parameters controlling the electrostatics are deactivated. Also, with this method, modifying the global variable lambda_electrostatics is not sufficient to control the charges. The recommended way to change them is through the AlchemicalState class.

Returns

alch_system (alchemical_system) – System to be used for the NCMC simulation.

References

TTPham-JChemPhys135-2011

1. Pham and M. R. Shirts, J. Chem. Phys 135, 034114 (2011). http://dx.doi.org/10.1063/1.3607597

classmethod restrain_positions(structure, system, selection='(@CA,C,N)', weight=5.0, **kwargs)[source]¶

Applies positional restraints to atoms in the openmm.System by the given parmed selection [amber-syntax].

Parameters

system (openmm.System) – The OpenMM System object to be modified.
structure (parmed.Structure()) – Structure of the system, used for atom selection.
selection (str, Default = “(@CA,C,N)”) – AmberMask selection to apply positional restraints to
weight (float, Default = 5.0) – Restraint weight for xyz atom restraints in kcal/(mol A^2)

Returns

system (openmm.System) – Modified with positional restraints applied.

classmethod freeze_atoms(structure, system, freeze_selection=':LIG', **kwargs)[source]¶

Zeroes the masses of atoms from the given parmed selection [amber-syntax]. Massless atoms will be ignored by the integrator and will not change positions.

Parameters

system (openmm.System) – The OpenMM System object to be modified.
structure (parmed.Structure()) – Structure of the system, used for atom selection.
freeze_selection (str, Default = “:LIG”) – AmberMask selection for the center in which to select atoms for zeroing their masses. Defaults to freezing protein backbone atoms.

Returns

system (openmm.System) – The modified system with the selected atoms

classmethod freeze_radius(structure, system, freeze_distance=Quantity(value=5.0, unit=angstrom), freeze_center=':LIG', freeze_solvent=':HOH,NA,CL', **kwargs)[source]¶

Zero the masses of atoms outside the given raidus of the freeze_center parmed selection [amber-syntax]. Massless atoms will be ignored by the integrator and will not change positions.This is intended to freeze the solvent and protein atoms around the ligand binding site.

Parameters

system (openmm.System) – The OpenMM System object to be modified.
structure (parmed.Structure()) – Structure of the system, used for atom selection.
freeze_distance (float, Default = 5.0) – Distance (angstroms) to select atoms for retaining their masses. Atoms outside the set distance will have their masses set to 0.0.
freeze_center (str, Default = “:LIG”) – AmberMask selection for the center in which to select atoms for zeroing their masses. Default: LIG
freeze_solvent (str, Default = “:HOH,NA,CL”) – AmberMask selection in which to select solvent atoms for zeroing their masses.

Returns

system (openmm.System) – Modified system with masses outside the freeze center zeroed.

SimulationFactory¶

Methods

class blues.simulation.SimulationFactory(systems, move_engine, config=None, md_reporters=None, ncmc_reporters=None)[source]¶

SimulationFactory is used to generate the 3 required OpenMM Simulation objects (MD, NCMC, ALCH) required for the BLUES run. This class can take a list of reporters for the MD or NCMC simulation in the arguments md_reporters or ncmc_reporters.

Parameters

systems (blues.simulation.SystemFactory object) – The object containing the MD and alchemical openmm.Systems
move_engine (blues.moves.MoveEngine object) – MoveEngine object which contains the list of moves performed in the NCMC simulation.
config (dict) – Simulation parameters which include: nIter, nstepsNC, nstepsMD, nprop, propLambda, temperature, dt, propSteps, write_move
md_reporters ((optional) list of Reporter objects for the MD openmm.Simulation)
ncmc_reporters ((optional) list of Reporter objects for the NCMC openmm.Simulation)

Examples

Load Parmed Structure from our input files, select the move type, initialize the MoveEngine, and generate the openmm systems.

>>> structure = parmed.load_file('eqToluene.prmtop', xyz='eqToluene.inpcrd')
>>> ligand = RandomLigandRotationMove(structure, 'LIG')
>>> ligand_mover = MoveEngine(ligand)
>>> systems = SystemFactory(structure, ligand.atom_indices, config['system'])

Now, we can generate the Simulations from our openmm Systems using the SimulationFactory class. If a configuration is provided at on initialization, it will call generateSimulationSet() for convenience. Otherwise, the class can be instantiated like a normal python class.

Below is an example of initializing the class like a normal python object.

>>> simulations = SimulationFactory(systems, ligand_mover)
>>> hasattr(simulations, 'md')
False
>>> hasattr(simulations, 'ncmc')
False

Below, we provide a dict for configuring the Simulations and then generate them by calling simulations.generateSimulationSet(). The MD/NCMC simulation objects can be accessed separately as class attributes.

>>> sim_cfg = { 'platform': 'OpenCL',
            'properties' : { 'OpenCLPrecision': 'single',
                             'OpenCLDeviceIndex' : 2},
            'nprop' : 1,
            'propLambda' : 0.3,
            'dt' : 0.001 * unit.picoseconds,
            'friction' : 1 * 1/unit.picoseconds,
            'temperature' : 100 * unit.kelvin,
            'nIter': 1,
            'nstepsMD': 10,
            'nstepsNC': 10,}
>>> simulations.generateSimulationSet(sim_cfg)
>>> hasattr(simulations, 'md')
True
>>> hasattr(simulations, 'ncmc')
True

After generating the Simulations, attach your own reporters by providing the reporters in a list. Be sure to attach to either the MD or NCMC simulation.

>>> from simtk.openmm.app import StateDataReporter
>>> md_reporters = [ StateDataReporter('test.log', 5) ]
>>> ncmc_reporters = [ StateDataReporter('test-ncmc.log', 5) ]
>>> simulations.md = simulations.attachReporters( simulations.md, md_reporters)
>>> simulations.ncmc = simulations.attachReporters( simulations.ncmc, ncmc_reporters)

Alternatively, you can pass the configuration dict and list of reporters upon class initialization. This will do all of the above for convenience.

>>> simulations = SimulationFactory(systems, ligand_mover, sim_cfg,
                                    md_reporters, ncmc_reporters)
>>> print(simulations)
>>> print(simulations.md)
>>> print(simulations.ncmc)
<blues.simulation.SimulationFactory object at 0x7f461b7a8b00>
<simtk.openmm.app.simulation.Simulation object at 0x7f461b7a8780>
<simtk.openmm.app.simulation.Simulation object at 0x7f461b7a87b8>
>>> print(simulations.md.reporters)
>>> print(simulations.ncmc.reporters)
[<simtk.openmm.app.statedatareporter.StateDataReporter object at 0x7f1b4d24cac8>]
[<simtk.openmm.app.statedatareporter.StateDataReporter object at 0x7f1b4d24cb70>]

classmethod addBarostat(system, temperature=Quantity(value=300, unit=kelvin), pressure=Quantity(value=1, unit=atmosphere), frequency=25, **kwargs)[source]¶

Adds a MonteCarloBarostat to the MD system.

Parameters

system (openmm.System) – The OpenMM System object corresponding to the reference system.
temperature (float, default=300) – temperature (Kelvin) to be simulated at.
pressure (int, configional, default=None) – Pressure (atm) for Barostat for NPT simulations.
frequency (int, default=25) – Frequency at which Monte Carlo pressure changes should be attempted (in time steps)

Returns

system (openmm.System) – The OpenMM System with the MonteCarloBarostat attached.

classmethod generateIntegrator(temperature=Quantity(value=300, unit=kelvin), dt=Quantity(value=0.002, unit=picosecond), friction=1, **kwargs)[source]¶

Generates a LangevinIntegrator for the Simulations.

Parameters

temperature (float, default=300) – temperature (Kelvin) to be simulated at.
friction (float, default=1) – friction coefficient which couples to the heat bath, measured in 1/ps
dt (int, configional, default=0.002) – The timestep of the integrator to use (in ps).

Returns

integrator (openmm.LangevinIntegrator) – The LangevinIntegrator object intended for the System.

classmethod generateNCMCIntegrator(nstepsNC=None, alchemical_functions={'lambda_electrostatics': 'step(0.2-lambda) - 1/0.2*lambda*step(0.2-lambda) + 1/0.2*(lambda-0.8)*step(lambda-0.8)', 'lambda_sterics': 'min(1, (1/0.3)*abs(lambda-0.5))'}, splitting='H V R O R V H', temperature=Quantity(value=300, unit=kelvin), dt=Quantity(value=0.002, unit=picosecond), nprop=1, propLambda=0.3, **kwargs)[source]¶

Generates the AlchemicalExternalLangevinIntegrator using openmmtools.

Parameters

nstepsNC (int) – The number of NCMC relaxation steps to use.
alchemical_functions (dict) – default = {‘lambda_sterics’ : ‘min(1, (1/0.3)*abs(lambda-0.5))’, lambda_electrostatics’ : ‘step(0.2-lambda) - 1/0.2*lambda*step(0.2-lambda) + 1/0.2*(lambda-0.8)*step(lambda-0.8)’} key : value pairs such as “global_parameter” : function_of_lambda where function_of_lambda is a Lepton-compatible string that depends on the variable “lambda”.
splitting (string, default: “H V R O R V H”) – Sequence of R, V, O (and optionally V{i}), and { }substeps to be executed each timestep. There is also an H option, which increments the global parameter lambda by 1/nsteps_neq for each step. Forces are only used in V-step. Handle multiple force groups by appending the force group index to V-steps, e.g. “V0” will only use forces from force group 0. “V” will perform a step using all forces. ( will cause metropolization, and must be followed later by a ).
temperature (float, default=300) – temperature (Kelvin) to be simulated at.
dt (int, optional, default=0.002) – The timestep of the integrator to use (in ps).
nprop (int (Default: 1)) – Controls the number of propagation steps to add in the lambda region defined by propLambda
propLambda (float, optional, default=0.3) – The range which additional propogation steps are added, defined by [0.5-propLambda, 0.5+propLambda].

Returns

ncmc_integrator (blues.integrator.AlchemicalExternalLangevinIntegrator) – The NCMC integrator for the alchemical process in the NCMC simulation.

classmethod generateSimFromStruct(structure, system, integrator, platform=None, properties={}, **kwargs)[source]¶

Generate the OpenMM Simulation objects from a given parmed.Structure()

Parameters

structure (parmed.Structure) – ParmEd Structure object of the entire system to be simulated.
system (openmm.System) – The OpenMM System object corresponding to the reference system.
integrator (openmm.Integrator) – The OpenMM Integrator object for the simulation.
platform (str, default = None) – Valid choices: ‘Auto’, ‘OpenCL’, ‘CUDA’ If None is specified, the fastest available platform will be used.

Returns

simulation (openmm.Simulation) – The generated OpenMM Simulation from the parmed.Structure, openmm.System, amd the integrator.

static attachReporters(simulation, reporter_list)[source]¶

Attach the list of reporters to the Simulation object

Parameters

simulation (openmm.Simulation) – The Simulation object to attach reporters to.
reporter_list (list of openmm Reporeters) – The list of reporters to attach to the OpenMM Simulation.

Returns

simulation (openmm.Simulation) – The Simulation object with the reporters attached.

generateSimulationSet(config=None)[source]¶

Generates the 3 OpenMM Simulation objects.

Parameters: config (dict) – Dictionary of parameters for configuring the OpenMM Simulations

BLUESSimulation¶

class blues.simulation.BLUESSimulation(simulations, config=None)[source]¶

BLUESSimulation class provides methods to execute the NCMC+MD simulation.

Parameters

simulations (blues.simulation.SimulationFactory object) – SimulationFactory Object which carries the 3 required OpenMM Simulation objects (MD, NCMC, ALCH) required to run BLUES.
config (dict) – Dictionary of parameters for configuring the OpenMM Simulations If None, will search for configuration parameters on the simulations object.

Examples

Create our SimulationFactory object and run BLUESSimulation

>>> sim_cfg = { 'platform': 'OpenCL',
                'properties' : { 'OpenCLPrecision': 'single',
                                 'OpenCLDeviceIndex' : 2},
                'nprop' : 1,
                'propLambda' : 0.3,
                'dt' : 0.001 * unit.picoseconds,
                'friction' : 1 * 1/unit.picoseconds,
                'temperature' : 100 * unit.kelvin,
                'nIter': 1,
                'nstepsMD': 10,
                'nstepsNC': 10,}
>>> simulations = SimulationFactory(systems, ligand_mover, sim_cfg)
>>> blues = BLUESSimulation(simulations)
>>> blues.run()

classmethod getStateFromContext(context, state_keys)[source]¶

Gets the State information from the given context and list of state_keys to query it with.

Returns the state data as a dict.

Parameters

context (openmm.Context) – Context of the OpenMM Simulation to query.
state_keys (list) – Default: [ positions, velocities, potential_energy, kinetic_energy ] A list that defines what information to get from the context State.

Returns

stateinfo (dict) – Current positions, velocities, energies and box vectors of the context.

classmethod getIntegratorInfo(ncmc_integrator, integrator_keys=['lambda', 'shadow_work', 'protocol_work', 'Eold', 'Enew'])[source]¶

Returns a dict of alchemical/ncmc-swtiching data from querying the the NCMC integrator.

Parameters

ncmc_integrator (openmm.Context.Integrator) – The integrator from the NCMC Context
integrator_keys (list) – list containing strings of the values to get from the integrator. Default = [‘lambda’, ‘shadow_work’, ‘protocol_work’, ‘Eold’, ‘Enew’,’Epert’]

Returns

integrator_info (dict) – Work values and energies from the NCMC integrator.

classmethod setContextFromState(context, state, box=True, positions=True, velocities=True)[source]¶

Update a given Context from the given State.

Parameters

context (openmm.Context) – The Context to be updated from the given State.
state (openmm.State) – The current state (box_vectors, positions, velocities) of the Simulation to update the given context.

Returns

context (openmm.Context) – The updated Context whose box_vectors, positions, and velocities have been updated.

_printSimulationTiming()[source]¶: Prints the simulation timing and related information.

_setStateTable(simkey, stateidx, stateinfo)[source]¶

Updates stateTable (dict) containing: Positions, Velocities, Potential/Kinetic energies of the state before and after a NCMC step or iteration.

Parameters

simkey (str (key: ‘md’, ‘ncmc’, ‘alch’)) – Key corresponding to the simulation.
stateidx (str (key: ‘state0’ or ‘state1’)) – Key corresponding to the state information being stored.
stateinfo (dict) – Dictionary containing the State information.

_syncStatesMDtoNCMC()[source]¶: Retrieves data on the current State of the MD context to replace the box vectors, positions, and velocties in the NCMC context.

_stepNCMC(nstepsNC, moveStep, move_engine=None)[source]¶

Advance the NCMC simulation.

Parameters

nstepsNC (int) – The number of NCMC switching steps to advance by.
moveStep (int) – The step number to perform the chosen move, which should be half the number of nstepsNC.
move_engine (blues.moves.MoveEngine) – The object that executes the chosen move.

_computeAlchemicalCorrection()[source]¶: Computes the alchemical correction term from switching between the NCMC and MD potentials.

_acceptRejectMove(write_move=False)[source]¶

Choose to accept or reject the proposed move based on the acceptance criterion.

Parameters: write_move (bool, default=False) – If True, writes the proposed NCMC move to a PDB file.

_resetSimulations(temperature=None)[source]¶

At the end of each iteration:

Reset the step number in the NCMC context/integrator
Set the velocities to random values chosen from a Boltzmann distribution at a given temperature.

Parameters: temperature (float) – The target temperature for the simulation.

_stepMD(nstepsMD)[source]¶

Advance the MD simulation.

Parameters: nstepsMD (int) – The number of steps to advance the MD simulation.

run(nIter=0, nstepsNC=0, moveStep=0, nstepsMD=0, temperature=300, write_move=False, **config)[source]¶

Executes the BLUES engine to iterate over the actions: Perform NCMC simulation, perform proposed move, accepts/rejects move, then performs the MD simulation from the NCMC state, niter number of times. Note: If the parameters are not given explicitly, will look for the parameters in the provided configuration on the SimulationFactory object.

Parameters

nIter (int, default = None) – Number of iterations of NCMC+MD to perform.
nstepsNC (int) – The number of NCMC switching steps to advance by.
moveStep (int) – The step number to perform the chosen move, which should be half the number of nstepsNC.
nstepsMD (int) – The number of steps to advance the MD simulation.
temperature (float) – The target temperature for the simulation.
write_move (bool, default=False) – If True, writes the proposed NCMC move to a PDB file.

Integrators¶

class blues.integrators.AlchemicalExternalLangevinIntegrator(alchemical_functions, splitting='R V O H O V R', temperature=Quantity(value=298.0, unit=kelvin), collision_rate=Quantity(value=1.0, unit=/picosecond), timestep=Quantity(value=1.0, unit=femtosecond), constraint_tolerance=1e-08, measure_shadow_work=False, measure_heat=True, nsteps_neq=100, nprop=1, prop_lambda=0.3, *args, **kwargs)[source]¶

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
V: Linear “kick” / Constrained “kick”
Deterministic update of velocities, using current forces v <- v + (f/m) dt; where f = force, m = mass
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) – key: value pairs such as “global_parameter” : function_of_lambda where function_of_lambda is a Lepton-compatible string that depends on the variable “lambda”
splitting (string, default: “H V R O V R H”) – Sequence of R, V, O (and optionally V{i}), and { }substeps to be executed each timestep. There is also an H option, which increments the global parameter lambda by 1/nsteps_neq for each step. Forces are only used in V-step. Handle multiple force groups by appending the force group index to V-steps, e.g. “V0” will only use forces from force group 0. “V” will perform a step using all forces.( will cause metropolization, and must be followed later by a ).
temperature (numpy.unit.Quantity compatible with kelvin, default: 298.0*simtk.unit.kelvin) – Fictitious “bath” temperature
collision_rate (numpy.unit.Quantity compatible with 1/picoseconds, default: 91.0/simtk.unit.picoseconds) – Collision rate
timestep (numpy.unit.Quantity compatible with femtoseconds, default: 1.0*simtk.unit.femtoseconds) – Integration timestep
constraint_tolerance (float, default: 1.0e-8) – Tolerance for constraint solver
measure_shadow_work (boolean, default: False) – Accumulate the shadow work performed by the symplectic substeps, in the global shadow_work
measure_heat (boolean, default: True) – Accumulate the heat exchanged with the bath in each step, in the global heat
nsteps_neq (int, default: 100) – Number of steps in nonequilibrium protocol. Default 100
prop_lambda (float (Default = 0.3)) – Defines the region in which to add extra propagation steps during the NCMC simulation from the midpoint 0.5. i.e. A value of 0.3 will add extra steps from lambda 0.2 to 0.8.
nprop (int (Default: 1)) – Controls the number of propagation steps to add in the lambda region defined by prop_lambda.

_kinetic_energy¶

This is 0.5*m*v*v by default, and is the expression used for the kinetic energy

Type: str

Examples

g-BAOAB:
splitting=”R V O H O V R”
VVVR
splitting=”O V R H R V O”
VV
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

reset()[source]¶: Reset all statistics, alchemical parameters, and work.

Utilities¶

Provides a host of utility functions for the BLUES engine.

Authors: Samuel C. Gill Contributors: Nathan M. Lim, David L. Mobley

blues.utils.saveSimulationFrame(simulation, outfname)[source]¶

Extracts a ParmEd structure and writes the frame given an OpenMM Simulation object.

Parameters

simulation (openmm.Simulation) – The OpenMM Simulation to write a frame from.
outfname (str) – The output file name to save the simulation frame from. Supported extensions:
- PDB (.pdb, pdb)
- PDBx/mmCIF (.cif, cif)
- PQR (.pqr, pqr)
- Amber topology file (.prmtop/.parm7, amber)
- CHARMM PSF file (.psf, psf)
- CHARMM coordinate file (.crd, charmmcrd)
- Gromacs topology file (.top, gromacs)
- Gromacs GRO file (.gro, gro)
- Mol2 file (.mol2, mol2)
- Mol3 file (.mol3, mol3)
- Amber ASCII restart (.rst7/.inpcrd/.restrt, rst7)
- Amber NetCDF restart (.ncrst, ncrst)

blues.utils.print_host_info(simulation)[source]¶

Prints hardware related information for the openmm.Simulation

Parameters: simulation (openmm.Simulation) – The OpenMM Simulation to write a frame from.

blues.utils.calculateNCMCSteps(nstepsNC=0, nprop=1, propLambda=0.3, **kwargs)[source]¶

Calculates the number of NCMC switching steps.

Parameters

nstepsNC (int) – The number of NCMC switching steps
nprop (int, default=1) – The number of propagation steps per NCMC switching steps
propLambda (float, default=0.3) – The lambda values in which additional propagation steps will be added or 0.5 +/- propLambda. If 0.3, this will add propgation steps at lambda values 0.2 to 0.8.

blues.utils.check_amber_selection(structure, selection)[source]¶

Given a AmberMask selection (str) for selecting atoms to freeze or restrain, check if it will actually select atoms. If the selection produces None, suggest valid residues or atoms.

Parameters

structure (parmed.Structure) – The structure of the simulated system
selection (str) – The selection string uses Amber selection syntax to select atoms to be restrained/frozen during simulation.
logger (logging.Logger) – Records information or streams to terminal.

blues.utils.parse_unit_quantity(unit_quantity_str)[source]¶

Utility for parsing parameters from the YAML file that require units.

Parameters: unit_quantity_str (str) – A string specifying a quantity and it’s units. i.e. ‘3.024 * daltons’
Returns: unit_quantity (simtk.unit.Quantity) – i.e unit.Quantity(3.024, unit=dalton)

blues.utils.zero_masses(system, atomList=None)[source]¶

Zeroes the masses of specified atoms to constrain certain degrees of freedom.

Parameters

system (penmm.System) – system to zero masses
atomList (list of ints) – atom indicies to zero masses

Returns

system (openmm.System) – The modified system with massless atoms.

blues.utils.atomIndexfromTop(resname, topology)[source]¶

Get atom indices of a ligand from OpenMM Topology.

Parameters

resname (str) – resname that you want to get the atom indicies for (ex. ‘LIG’)
topology (str, optional, default=None) – path of topology file. Include if the topology is not included in the coord_file

Returns

lig_atoms (list of ints) – list of atoms in the coordinate file matching lig_resname

blues.utils.get_data_filename(package_root, relative_path)[source]¶

Get the full path to one of the reference files in testsystems. In the source distribution, these files are in blues/data/, but on installation, they’re moved to somewhere in the user’s python site-packages directory. Adapted from: https://github.com/open-forcefield-group/smarty/blob/master/smarty/utils.py

Parameters

package_root (str) – Name of the included/installed python package
relative_path (str) – Path to the file within the python package

Returns

fn (str) – Full path to file

blues.utils.spreadLambdaProtocol(switching_values, steps, switching_types='auto', kind='cubic', return_tab_function=True)[source]¶

Takes a list of lambda values (either for sterics or electrostatics) and transforms that list to be spread out over a given steps range to be easily compatible with the OpenMM Discrete1DFunction tabulated function.

Parameters

switching_values (list) – A list of lambda values decreasing from 1 to 0.
steps (int) – The number of steps wanted for the tabulated function.
switching_types (str, optional, default=’auto’) – The type of lambda switching the switching_values corresponds to, either ‘auto’, ‘electrostatics’, or ‘sterics’. If ‘electrostatics’ this assumes the inital value immediately decreases from 1. If ‘sterics’ this assumes the inital values stay at 1 for some period. If ‘auto’ this function tries to guess the switching_types based on this, based on typical lambda protocols turning off the electrostatics completely, before turning off sterics.
kind (str, optional, default=’cubic’) – The kind of interpolation that should be performed (using scipy.interpolate.interp1d) to define the lines between the points of switching_values.

Returns

tab_steps (list or simtk.openmm.openmm.Discrete1DFunction) – List of length steps that corresponds to the tabulated-friendly version of the input switching_values. If return-tab_function=True

Examples

>>> from simtk.openmm.openmm import Continuous1DFunction, Discrete1DFunction
>>> sterics = [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.95, 0.8848447462380346,
                0.8428373352131427, 0.7928373352131427, 0.7490146003095886, 0.6934088361682191,
                0.6515123083157823, 0.6088924298371354, 0.5588924298371354, 0.5088924298371353,
                0.4649556683144045, 0.4298606804827029, 0.3798606804827029, 0.35019373288005945,
                0.31648339779024653, 0.2780498882483276, 0.2521302239477468, 0.23139484523965026,
                0.18729812232625365, 0.15427643961733822, 0.12153116162972155,
                0.09632462702545555, 0.06463743549588846, 0.01463743549588846,
                0.0]

>>> statics = [1.0, 0.8519493439593149, 0.7142750443470669,
                0.5385929179832776, 0.3891972949356391, 0.18820309596839535, 0.0,
                0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
                0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
>>> statics_tab = spreadLambdaProtocol(statics, opt['nstepsNC'], switching_types='auto')
>>> sterics_tab = spreadLambdaProtocol(sterics, opt['nstepsNC'], switching_types='sterics')

>>> # Assuming some Context already exists:
>>> context._integrator.addTabulatedFunction( 'sterics_tab', sterics_tab)
>>> context._integrator.addTabulatedFunction( 'electrostatics_tab', statics_tab)

Reporters¶

blues.reporters.addLoggingLevel(levelName, levelNum, methodName=None)[source]¶

Comprehensively adds a new logging level to the logging module and the currently configured logging class.

levelName becomes an attribute of the logging module with the value levelNum. methodName becomes a convenience method for both logging itself and the class returned by logging.getLoggerClass() (usually just logging.Logger). If methodName is not specified, levelName.lower() is used.

To avoid accidental clobberings of existing attributes, this method will raise an AttributeError if the level name is already an attribute of the logging module or if the method name is already present

Parameters

levelName (str) – The new level name to be added to the logging module.
levelNum (int) – The level number indicated for the logging module.
methodName (str, default=None) – The method to call on the logging module for the new level name. For example if provided ‘trace’, you would call logging.trace().

Example

>>> addLoggingLevel('TRACE', logging.DEBUG - 5)
>>> logging.getLogger(__name__).setLevel("TRACE")
>>> logging.getLogger(__name__).trace('that worked')
>>> logging.trace('so did this')
>>> logging.TRACE
5

blues.reporters.init_logger(logger, level=20, stream=True, outfname='blues-20201022-192141')[source]¶

Initialize the Logger module with the given logger_level and outfname.

Parameters

logger (logging.getLogger()) – The root logger object if it has been created already.
level (logging.<LEVEL>) – Valid options for <LEVEL> would be DEBUG, INFO, WARNING, ERROR, CRITICAL.
stream (bool, default = True) – If True, the logger will also stream information to sys.stdout as well as the output file.
outfname (str, default = time.strftime(“blues-%Y%m%d-%H%M%S”)) – The output file path prefix to store the logged data. This will always write to a file with the extension .log.

Returns

logger (logging.getLogger()) – The logging object with additional Handlers added.

class blues.reporters.ReporterConfig(outfname, reporter_config, logger=None)[source]¶

Generates a set of custom/recommended reporters for BLUES simulations from YAML configuration. It can also be called externally without a YAML configuration file.

Parameters

outfname (str,) – Output filename prefix for files generated by the reporters.
reporter_config (dict) – Dict of parameters for the md_reporters or ncmc_reporters. Valid keys for reporters are: state, traj_netcdf, restart, progress, and stream. All reporters except stream are extensions of the parmed.openmm.reporters. More below: - state : State data reporter for OpenMM simulations, but it is a little more generalized. Writes to a .ene file. For full list of parameters see parmed.openmm.reporters.StateDataReporter. - traj_netcdf : Customized AMBER NetCDF (.nc) format reporter - restart : Restart AMBER NetCDF (.rst7) format reporter - progress : Write to a file (.prog), the progress report of how many steps has been done, how fast the simulation is running, and how much time is left (similar to the mdinfo file in Amber). File is overwritten at each reportInterval. For full list of parameters see parmed.openmm.reporters.ProgressReporter - stream : Customized version of openmm.app.StateDataReporter.This will instead stream/print the information to the terminal as opposed to writing to a file. Takes the same parameters as the openmm.app.StateDataReporter
logger (logging.Logger object) – Provide the root logger for printing information.

Examples

This class is intended to be called internally from blues.config.set_Reporters. Below is an example to call this externally.

>>> from blues.reporters import ReporterConfig
>>> import logging
>>> logger = logging.getLogger(__name__)
>>> md_reporters = { "restart": { "reportInterval": 1000 },
                     "state" : { "reportInterval": 250  },
                     "stream": { "progress": true,
                                 "remainingTime": true,
                                 "reportInterval": 250,
                                 "speed": true,
                                 "step": true,
                                 "title": "md",
                                 "totalSteps": 10000},
                     "traj_netcdf": { "reportInterval": 250 }
                    }
>>> md_reporter_cfg = ReporterConfig(outfname='blues-test', md_reporters, logger)
>>> md_reporters_list = md_reporter_cfg.makeReporters()

makeReporters()[source]¶: Returns a list of openmm Reporters based on the configuration at initialization of the class.

class blues.reporters.BLUESHDF5Reporter(file, reportInterval=1, title='NCMC Trajectory', coordinates=True, frame_indices=[], time=False, cell=True, temperature=False, potentialEnergy=False, kineticEnergy=False, velocities=False, atomSubset=None, protocolWork=True, alchemicalLambda=True, parameters=None, environment=True)[source]¶

This is a subclass of the HDF5 class from mdtraj that handles reporting of the trajectory.

HDF5Reporter stores a molecular dynamics trajectory in the HDF5 format. This object supports saving all kinds of information from the simulation – more than any other trajectory format. In addition to all of the options, the topology of the system will also (of course) be stored in the file. All of the information is compressed, so the size of the file is not much different than DCD, despite the added flexibility.

Parameters

file (str, or HDF5TrajectoryFile) – Either an open HDF5TrajecoryFile object to write to, or a string specifying the filename of a new HDF5 file to save the trajectory to.
title (str,) – String to specify the title of the HDF5 tables
frame_indices (list, frame numbers for writing the trajectory)
reportInterval (int) – The interval (in time steps) at which to write frames.
coordinates (bool) – Whether to write the coordinates to the file.
time (bool) – Whether to write the current time to the file.
cell (bool) – Whether to write the current unit cell dimensions to the file.
potentialEnergy (bool) – Whether to write the potential energy to the file.
kineticEnergy (bool) – Whether to write the kinetic energy to the file.
temperature (bool) – Whether to write the instantaneous temperature to the file.
velocities (bool) – Whether to write the velocities to the file.
atomSubset (array_like, default=None) – Only write a subset of the atoms, with these (zero based) indices to the file. If None, all of the atoms will be written to disk.
protocolWork (bool=False,) – Write the protocolWork for the alchemical process in the NCMC simulation
alchemicalLambda (bool=False,) – Write the alchemicalLambda step for the alchemical process in the NCMC simulation.
parameters (dict) – Dict of the simulation parameters. Useful for record keeping.
environment (bool) – True will attempt to export your conda environment to JSON and store the information in the HDF5 file. Useful for record keeping.

Notes

If you use the atomSubset option to write only a subset of the atoms to disk, the kineticEnergy, potentialEnergy, and temperature fields will not change. They will still refer to the energy and temperature of the whole system, and are not “subsetted” to only include the energy of your subsystem.

describeNextReport(simulation)[source]¶

Get information about the next report this object will generate.

Parameters: simulation (app.Simulation) – The simulation to generate a report for
Returns: nsteps, pos, vel, frc, ene (int, bool, bool, bool, bool) – nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

report(simulation, state)[source]¶

Generate a report.

Parameters

simulation (simtk.openmm.app.Simulation) – The Simulation to generate a report for
state (simtk.openmm.State) – The current state of the simulation

class blues.reporters.BLUESStateDataReporter(file, reportInterval=1, frame_indices=[], title='', step=False, time=False, potentialEnergy=False, kineticEnergy=False, totalEnergy=False, temperature=False, volume=False, density=False, progress=False, remainingTime=False, speed=False, elapsedTime=False, separator='\t', systemMass=None, totalSteps=None, protocolWork=False, alchemicalLambda=False, currentIter=False)[source]¶

StateDataReporter outputs information about a simulation, such as energy and temperature, to a file. To use it, create a StateDataReporter, then add it to the Simulation’s list of reporters. The set of data to write is configurable using boolean flags passed to the constructor. By default the data is written in comma-separated-value (CSV) format, but you can specify a different separator to use. Inherited from openmm.app.StateDataReporter

Parameters

file (string or file) – The file to write to, specified as a file name or file-like object (Logger)
reportInterval (int) – The interval (in time steps) at which to write frames
frame_indices (list, frame numbers for writing the trajectory)
title (str,) – Text prefix for each line of the report. Used to distinguish between the NCMC and MD simulation reports.
step (bool=False) – Whether to write the current step index to the file
time (bool=False) – Whether to write the current time to the file
potentialEnergy (bool=False) – Whether to write the potential energy to the file
kineticEnergy (bool=False) – Whether to write the kinetic energy to the file
totalEnergy (bool=False) – Whether to write the total energy to the file
temperature (bool=False) – Whether to write the instantaneous temperature to the file
volume (bool=False) – Whether to write the periodic box volume to the file
density (bool=False) – Whether to write the system density to the file
progress (bool=False) – Whether to write current progress (percent completion) to the file. If this is True, you must also specify totalSteps.
remainingTime (bool=False) – Whether to write an estimate of the remaining clock time until completion to the file. If this is True, you must also specify totalSteps.
speed (bool=False) – Whether to write an estimate of the simulation speed in ns/day to the file
elapsedTime (bool=False) – Whether to write the elapsed time of the simulation in seconds to the file.
separator (string=’,’) – The separator to use between columns in the file
systemMass (mass=None) – The total mass to use for the system when reporting density. If this is None (the default), the system mass is computed by summing the masses of all particles. This parameter is useful when the particle masses do not reflect their actual physical mass, such as when some particles have had their masses set to 0 to immobilize them.
totalSteps (int=None) – The total number of steps that will be included in the simulation. This is required if either progress or remainingTime is set to True, and defines how many steps will indicate 100% completion.
protocolWork (bool=False,) – Write the protocolWork for the alchemical process in the NCMC simulation
alchemicalLambda (bool=False,) – Write the alchemicalLambda step for the alchemical process in the NCMC simulation.

describeNextReport(simulation)[source]¶

Get information about the next report this object will generate.

Parameters: simulation (app.Simulation) – The simulation to generate a report for
Returns: nsteps, pos, vel, frc, ene (int, bool, bool, bool, bool) – nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

report(simulation, state)[source]¶

Generate a report.

Parameters

simulation (Simulation) – The Simulation to generate a report for
state (State) – The current state of the simulation

class blues.reporters.NetCDF4Reporter(file, reportInterval=1, frame_indices=[], crds=True, vels=False, frcs=False, protocolWork=False, alchemicalLambda=False)[source]¶

Class to read or write NetCDF trajectory files Inherited from parmed.openmm.reporters.NetCDFReporter

Parameters

file (str) – Name of the file to write the trajectory to
reportInterval (int) – How frequently to write a frame to the trajectory
frame_indices (list, frame numbers for writing the trajectory) – If this reporter is used for the NCMC simulation, 0.5 will report at the moveStep and -1 will record at the last frame.
crds (bool=True) – Should we write coordinates to this trajectory? (Default True)
vels (bool=False) – Should we write velocities to this trajectory? (Default False)
frcs (bool=False) – Should we write forces to this trajectory? (Default False)
protocolWork (bool=False,) – Write the protocolWork for the alchemical process in the NCMC simulation
alchemicalLambda (bool=False,) – Write the alchemicalLambda step for the alchemical process in the NCMC simulation.

describeNextReport(simulation)[source]¶

Get information about the next report this object will generate.

Parameters: simulation (app.Simulation) – The simulation to generate a report for
Returns: nsteps, pos, vel, frc, ene (int, bool, bool, bool, bool) – nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

report(simulation, state)[source]¶

Generate a report.

Parameters

simulation (app.Simulation) – The Simulation to generate a report for
state (mm.State) – The current state of the simulation

Formats¶

class blues.formats.LoggerFormatter[source]¶

Formats the output of the logger.Logger object. Allows customization for customized logging levels. This will add a custom level ‘REPORT’ to all custom BLUES reporters from the blues.reporters module.

Examples

Below we add a custom level ‘REPORT’ and have the logger module stream the message to sys.stdout without any additional information to our custom reporters from the blues.reporters module

>>> from blues import reporters
>>> from blues.formats import LoggerFormatter
>>> import logging, sys
>>> logger = logging.getLogger(__name__)
>>> reporters.addLoggingLevel('REPORT', logging.WARNING - 5)
>>> fmt = LoggerFormatter(fmt="%(message)s")
>>> stdout_handler = logging.StreamHandler(stream=sys.stdout)
>>> stdout_handler.setFormatter(fmt)
>>> logger.addHandler(stdout_handler)
>>> logger.report('This is a REPORT call')
    This is a REPORT call
>>> logger.info('This is an INFO call')
    INFO: This is an INFO call

format(record)[source]¶

Format the specified record as text.

The record’s attribute dictionary is used as the operand to a string formatting operation which yields the returned string. Before formatting the dictionary, a couple of preparatory steps are carried out. The message attribute of the record is computed using LogRecord.getMessage(). If the formatting string uses the time (as determined by a call to usesTime(), formatTime() is called to format the event time. If there is exception information, it is formatted using formatException() and appended to the message.

class blues.formats.BLUESHDF5TrajectoryFile(filename, mode='r', force_overwrite=True, compression='zlib')[source]¶

Extension of the mdtraj.formats.hdf5.HDF5TrajectoryFile class which handles the writing of the trajectory data to the HDF5 file format. Additional features include writing NCMC related data to the HDF5 file.

Parameters

filename (str) – The filename for the HDF5 file.
mode (str, default=’r’) – The mode to open the HDF5 file in.
force_overwrite (bool, default=True) – If True, overwrite the file if it already exists
compression (str, default=’zlib’) – Valid choices are [‘zlib’, ‘lzo’, ‘bzip2’, ‘blosc’]

write(coordinates, parameters=None, environment=None, time=None, cell_lengths=None, cell_angles=None, velocities=None, kineticEnergy=None, potentialEnergy=None, temperature=None, alchemicalLambda=None, protocolWork=None, title=None)[source]¶

Write one or more frames of data to the file This method saves data that is associated with one or more simulation frames. Note that all of the arguments can either be raw numpy arrays or unitted arrays (with simtk.unit.Quantity). If the arrays are unittted, a unit conversion will be automatically done from the supplied units into the proper units for saving on disk. You won’t have to worry about it.

Furthermore, if you wish to save a single frame of simulation data, you can do so naturally, for instance by supplying a 2d array for the coordinates and a single float for the time. This “shape deficiency” will be recognized, and handled appropriately.

Parameters

coordinates (np.ndarray, shape=(n_frames, n_atoms, 3)) – The cartesian coordinates of the atoms to write. By convention, the lengths should be in units of nanometers.
time (np.ndarray, shape=(n_frames,), optional) – You may optionally specify the simulation time, in picoseconds corresponding to each frame.
cell_lengths (np.ndarray, shape=(n_frames, 3), dtype=float32, optional) – You may optionally specify the unitcell lengths. The length of the periodic box in each frame, in each direction, a, b, c. By convention the lengths should be in units of angstroms.
cell_angles (np.ndarray, shape=(n_frames, 3), dtype=float32, optional) – You may optionally specify the unitcell angles in each frame. Organized analogously to cell_lengths. Gives the alpha, beta and gamma angles respectively. By convention, the angles should be in units of degrees.
velocities (np.ndarray, shape=(n_frames, n_atoms, 3), optional) – You may optionally specify the cartesian components of the velocity for each atom in each frame. By convention, the velocities should be in units of nanometers / picosecond.
kineticEnergy (np.ndarray, shape=(n_frames,), optional) – You may optionally specify the kinetic energy in each frame. By convention the kinetic energies should b in units of kilojoules per mole.
potentialEnergy (np.ndarray, shape=(n_frames,), optional) – You may optionally specify the potential energy in each frame. By convention the kinetic energies should b in units of kilojoules per mole.
temperature (np.ndarray, shape=(n_frames,), optional) – You may optionally specify the temperature in each frame. By convention the temperatures should b in units of Kelvin.
alchemicalLambda (np.ndarray, shape=(n_frames,), optional) – You may optionally specify the alchemicalLambda in each frame. These have no units, but are generally between zero and one.
protocolWork (np.ndarray, shape=(n_frames,), optional) – You may optionally specify the protocolWork in each frame. These are in reduced units of kT but are stored dimensionless
title (str) – Title of the HDF5 trajectory file

class blues.formats.NetCDF4Traj(fname, mode='r')[source]¶

Extension of parmed.amber.netcdffiles.NetCDFTraj to allow proper file flushing. Requires the netcdf4 library (not scipy), install with conda install -c conda-forge netcdf4 .

Parameters

fname (str) – File name for the trajectory file
mode (str, default=’r’) – The mode to open the file in.

flush()[source]¶: Flush buffered data to disc.

classmethod open_new(fname, natom, box, crds=True, vels=False, frcs=False, remd=None, remd_dimension=None, title='', protocolWork=False, alchemicalLambda=False)[source]¶

Opens a new NetCDF file and sets the attributes

Parameters

fname (str) – Name of the new file to open (overwritten)
natom (int) – Number of atoms in the restart
box (bool) – Indicates if cell lengths and angles are written to the NetCDF file
crds (bool, default=True) – Indicates if coordinates are written to the NetCDF file
vels (bool, default=False) – Indicates if velocities are written to the NetCDF file
frcs (bool, default=False) – Indicates if forces are written to the NetCDF file
remd (str, default=None) – ‘T[emperature]’ if replica temperature is written ‘M[ulti]’ if Multi-D REMD information is written None if no REMD information is written
remd_dimension (int, default=None) – If remd above is ‘M[ulti]’, this is how many REMD dimensions exist
title (str, default=’’) – The title of the NetCDF trajectory file
protocolWork (bool, default=False) – Indicates if protocolWork from the NCMC simulation should be written to the NetCDF file
alchemicalLambda (bool, default=False) – Indicates if alchemicalLambda from the NCMC simulation should be written to the NetCDF file

property protocolWork¶: Store the accumulated protocolWork from the NCMC simulation as property.

add_protocolWork(stuff)[source]¶

Adds the time to the current frame of the NetCDF file

Parameters: stuff (float or time-dimension Quantity) – The time to add to the current frame

property alchemicalLambda¶: Store the current alchemicalLambda (0->1.0) from the NCMC simulation as property.

add_alchemicalLambda(stuff)[source]¶

Adds the time to the current frame of the NetCDF file

Parameters: stuff (float or time-dimension Quantity) – The time to add to the current frame