Update for new OpenMM Namespace

.github/workflows/CI.yaml

@@ -51,6 +51,7 @@ jobs:
           auto-update-conda: true
           auto-activate-base: false
           show-channel-urls: true
+          mamba-version: "*"
 
       - name: Refine test environment
         shell: bash -l {0}

Yank/analyze.py

@@ -30,7 +30,10 @@
 
 import mpiplus
 import numpy as np
-import simtk.unit as units
+try:
+    import openmm.unit as units
+except ImportError: # OpenMM < 7.6
+    import simtk.unit as units
 import openmmtools as mmtools
 from pymbar import timeseries
 

Yank/commands/analyze.py

@@ -151,7 +151,10 @@ def single_run():
 
 def extract_analyzer_kwargs(args, quantities_as_strings=False):
 
-    import simtk.unit as unit
+    try:
+        import openmm.unit as unit
+    except ImportError: # OpenMM < 7.6
+        import simtk.unit as unit
 
     """Return a dictionary with the keyword arguments to pass to the analyzer."""
     analyzer_kwargs = {}

Yank/commands/platforms.py

@@ -34,7 +34,10 @@
 
 
 def dispatch(args):
-    from simtk import openmm
+    try:
+        import openmm
+    except ImportError: # OpenMM < 7.6
+        from simtk import openmm
     print("Available OpenMM platforms:")
     for platform_index in range(openmm.Platform.getNumPlatforms()):
         print("{0:5d} {1:s}".format(platform_index, openmm.Platform.getPlatform(platform_index).getName()))

Yank/commands/selftest.py

@@ -52,7 +52,10 @@ def dispatch(args):
     import doctest
     import pkgutil
     import subprocess
-    import simtk.openmm as mm
+    try:
+        import openmm as mm
+    except ImportError: # OpenMM < 7.6
+        import simtk.openmm as mm
     from .. import version
     from . import platforms
 

Yank/experiment.py

@@ -32,8 +32,13 @@
 import openmmtools as mmtools
 import openmoltools as moltools
 import yaml
-from simtk import unit, openmm
-from simtk.openmm.app import PDBFile, AmberPrmtopFile
+try:
+    import openmm
+    from openmm import unit
+    from openmm.app import PDBFile, AmberPrmtopFile
+except ImportError: # OpenMM < 7.6
+    from simtk import unit, openmm
+    from simtk.openmm.app import PDBFile, AmberPrmtopFile
 
 from . import utils, pipeline, restraints, schema
 from .yank import AlchemicalPhase, Topography
@@ -2243,7 +2248,7 @@ def _configure_platform(cls, platform_name, platform_precision):
 
         Returns
         -------
-        platform : simtk.openmm.Platform
+        platform : openmm.Platform
            The configured platform.
 
         Raises

Yank/pipeline.py

@@ -33,8 +33,13 @@
 import openmoltools as moltools
 import yaml
 from pdbfixer import PDBFixer
-from simtk import openmm, unit
-from simtk.openmm.app import PDBFile
+try:
+    import openmm
+    from openmm import unit
+    from openmm.app import PDBFile
+except ImportError: # OpenMM < 7.6
+    from simtk import openmm, unit
+    from simtk.openmm.app import PDBFile
 
 
 from . import utils
@@ -175,12 +180,12 @@ def compute_radius_of_gyration(positions):
 
     Parameters
     ----------
-    positions : simtk.unit.Quantity with units compatible with angstrom
+    positions : openmm.unit.Quantity with units compatible with angstrom
        The coordinate set (natoms x 3) for which the radius of gyration is to be computed.
 
     Returns
     -------
-    radius_of_gyration : simtk.unit.Quantity with units compatible with angstrom
+    radius_of_gyration : openmm.unit.Quantity with units compatible with angstrom
        The radius of gyration
 
     """
@@ -209,7 +214,7 @@ def compute_net_charge(system, atom_indices):
 
     Parameters
     ----------
-    system : simtk.openmm.System
+    system : openmm.System
         The system object containing the atoms of interest.
     atom_indices : list of int
         Indices of the atoms of interest.
@@ -245,7 +250,7 @@ def find_alchemical_counterions(system, topography, region_name):
 
     Parameters
     ----------
-    system : simtk.openmm.System
+    system : openmm.System
         The system object containing the atoms of interest.
     topography : yank.Topography
         The topography object holding the indices of the ions and the
@@ -328,7 +333,7 @@ def get_leap_recommended_pbradii(implicit_solvent):
     --------
     >>> get_leap_recommended_pbradii('OBC2')
     'mbondi2'
-    >>> from simtk.openmm.app import HCT
+    >>> from openmm.app import HCT
     >>> get_leap_recommended_pbradii(HCT)
     'mbondi'
 
@@ -347,7 +352,7 @@ def create_system(parameters_file, box_vectors, create_system_args, system_optio
 
     Parameters
     ----------
-    parameters_file : simtk.openmm.app.AmberPrmtopFile or GromacsTopFile
+    parameters_file : openmm.app.AmberPrmtopFile or GromacsTopFile
         The file used to create they system.
     box_vectors : list of Vec3
         The default box vectors of the system will be set to this value.
@@ -358,7 +363,7 @@ def create_system(parameters_file, box_vectors, create_system_args, system_optio
 
     Returns
     -------
-    system : simtk.openmm.System
+    system : openmm.System
         The system created.
 
     """
@@ -432,7 +437,7 @@ def read_system_files(positions_file_path, parameters_file_path, system_options,
 
     Returns
     -------
-    system : simtk.openmm.System
+    system : openmm.System
         The OpenMM System built from the given files.
     topology : openmm.app.Topology
         The OpenMM Topology built from the given files.
@@ -512,7 +517,7 @@ def read_system_files(positions_file_path, parameters_file_path, system_options,
         create_system_args = set(inspect.getargspec(openmm.app.CharmmPsfFile.createSystem).args)
         system_options['params'] = params
         system = create_system(parameters_file, box_vectors, create_system_args, system_options)
-            
+
     # Unsupported file format.
     else:
         raise ValueError('Unsupported format for parameter file {}'.format(parameters_file_extension))

Yank/reports/notebook.py

@@ -16,7 +16,10 @@
 from matplotlib import gridspec
 from pymbar import MBAR
 import seaborn as sns
-from simtk import unit as units
+try:
+    from openmm import unit as units
+except ImportError: # OpenMM < 7.6
+    from simtk import unit as units
 from openmmtools import multistate
 
 from .. import analyze

Yank/restraints.py

@@ -32,7 +32,11 @@
 import mdtraj as md
 import openmmtools as mmtools
 from openmmtools.states import GlobalParameterState
-from simtk import openmm, unit
+try:
+    import openmm
+    from openmm import unit
+except ImportError: # OpenMM < 7.6
+    from simtk import openmm, unit
 
 from . import pipeline
 from .utils import methoddispatch, generate_development_feature
@@ -663,7 +667,7 @@ def _create_restraint_force(self, particles1, particles2):
 
         Returns
         -------
-        force : simtk.openmm.Force
+        force : openmm.Force
            The created restraint force.
 
         """
@@ -798,7 +802,7 @@ def _closest_atom_to_centroid(positions, indices=None, masses=None):
            positions of object to identify atom closes to centroid
         indices : list of int, optional, default=None
            List of atoms indices for which closest atom to centroid is to be computed.
-        masses : simtk.unit.Quantity of natoms with units compatible with amu
+        masses : openmm.unit.Quantity of natoms with units compatible with amu
            Masses of particles used to weight distance calculation, if not None (default: None)
 
         Returns
@@ -871,7 +875,7 @@ class Harmonic(RadiallySymmetricRestraint):
 
     Parameters
     ----------
-    spring_constant : simtk.unit.Quantity, optional
+    spring_constant : openmm.unit.Quantity, optional
         The spring constant K (see energy expression above) in units compatible
         with joule/nanometer**2/mole (default is None).
     restrained_receptor_atoms : iterable of int, int, or str, optional
@@ -958,7 +962,7 @@ def _create_restraint_force(self, particles1, particles2):
 
         Returns
         -------
-        force : simtk.openmm.Force
+        force : openmm.Force
            The created restraint force.
 
         """
@@ -1041,10 +1045,10 @@ class FlatBottom(RadiallySymmetricRestraint):
 
     Parameters
     ----------
-    spring_constant : simtk.unit.Quantity, optional
+    spring_constant : openmm.unit.Quantity, optional
         The spring constant K (see energy expression above) in units compatible
         with joule/nanometer**2/mole (default is None).
-    well_radius : simtk.unit.Quantity, optional
+    well_radius : openmm.unit.Quantity, optional
         The distance r0 (see energy expression above) at which the harmonic
         restraint is imposed in units of distance (default is None).
     restrained_receptor_atoms : iterable of int, int, or str, optional
@@ -1137,7 +1141,7 @@ def _create_restraint_force(self, particles1, particles2):
 
         Returns
         -------
-        force : simtk.openmm.Force
+        force : openmm.Force
            The created restraint force.
 
         """
@@ -1319,22 +1323,22 @@ class BoreschLike(ReceptorLigandRestraint, ABC):
         This can temporarily be left undefined, but ``determine_missing_parameters()``
         must be called before using the Restraint object. The same if a DSL
         expression or Topography region is provided (default is None).
-    K_r : simtk.unit.Quantity, optional
+    K_r : openmm.unit.Quantity, optional
         The spring constant for the restrained distance ``|r3 - l1|`` (units
         compatible with kilocalories_per_mole/angstrom**2).
-    r_aA0 : simtk.unit.Quantity, optional
+    r_aA0 : openmm.unit.Quantity, optional
         The equilibrium distance between r3 and l1 (units of length).
-    K_thetaA, K_thetaB : simtk.unit.Quantity, optional
+    K_thetaA, K_thetaB : openmm.unit.Quantity, optional
         The spring constants for ``angle(r2, r3, l1)`` and ``angle(r3, l1, l2)``
         (units compatible with kilocalories_per_mole/radians**2).
-    theta_A0, theta_B0 : simtk.unit.Quantity, optional
+    theta_A0, theta_B0 : openmm.unit.Quantity, optional
         The equilibrium angles of ``angle(r2, r3, l1)`` and ``angle(r3, l1, l2)``
         (units compatible with radians).
-    K_phiA, K_phiB, K_phiC : simtk.unit.Quantity, optional
+    K_phiA, K_phiB, K_phiC : openmm.unit.Quantity, optional
         The spring constants for ``dihedral(r1, r2, r3, l1)``,
         ``dihedral(r2, r3, l1, l2)`` and ``dihedral(r3,l1,l2,l3)`` (units compatible
         with kilocalories_per_mole/radians**2).
-    phi_A0, phi_B0, phi_C0 : simtk.unit.Quantity, optional
+    phi_A0, phi_B0, phi_C0 : openmm.unit.Quantity, optional
         The equilibrium torsion of ``dihedral(r1,r2,r3,l1)``, ``dihedral(r2,r3,l1,l2)``
         and ``dihedral(r3,l1,l2,l3)`` (units compatible with radians).
 
@@ -1717,7 +1721,7 @@ def _is_collinear(positions, atoms, threshold=0.9):
 
         Parameters
         ----------
-        positions : n_atoms x 3 simtk.unit.Quantity
+        positions : n_atoms x 3 openmm.unit.Quantity
             Reference positions to use for imposing restraints (units of length).
         atoms : iterable of int
             The indices of the atoms to test.
@@ -2019,22 +2023,22 @@ class Boresch(BoreschLike):
         This can temporarily be left undefined, but ``determine_missing_parameters()``
         must be called before using the Restraint object. The same if a DSL
         expression or Topography region is provided (default is None).
-    K_r : simtk.unit.Quantity, optional
+    K_r : openmm.unit.Quantity, optional
         The spring constant for the restrained distance ``|r3 - l1|`` (units
         compatible with kilocalories_per_mole/angstrom**2).
-    r_aA0 : simtk.unit.Quantity, optional
+    r_aA0 : openmm.unit.Quantity, optional
         The equilibrium distance between r3 and l1 (units of length).
-    K_thetaA, K_thetaB : simtk.unit.Quantity, optional
+    K_thetaA, K_thetaB : openmm.unit.Quantity, optional
         The spring constants for ``angle(r2, r3, l1)`` and ``angle(r3, l1, l2)``
         (units compatible with kilocalories_per_mole/radians**2).
-    theta_A0, theta_B0 : simtk.unit.Quantity, optional
+    theta_A0, theta_B0 : openmm.unit.Quantity, optional
         The equilibrium angles of ``angle(r2, r3, l1)`` and ``angle(r3, l1, l2)``
         (units compatible with radians).
-    K_phiA, K_phiB, K_phiC : simtk.unit.Quantity, optional
+    K_phiA, K_phiB, K_phiC : openmm.unit.Quantity, optional
         The spring constants for ``dihedral(r1, r2, r3, l1)``,
         ``dihedral(r2, r3, l1, l2)`` and ``dihedral(r3,l1,l2,l3)`` (units compatible
         with kilocalories_per_mole/radians**2).
-    phi_A0, phi_B0, phi_C0 : simtk.unit.Quantity, optional
+    phi_A0, phi_B0, phi_C0 : openmm.unit.Quantity, optional
         The equilibrium torsion of ``dihedral(r1,r2,r3,l1)``, ``dihedral(r2,r3,l1,l2)``
         and ``dihedral(r3,l1,l2,l3)`` (units compatible with radians).
 
@@ -2291,22 +2295,22 @@ class PeriodicTorsionBoresch(Boresch):
         This can temporarily be left undefined, but ``determine_missing_parameters()``
         must be called before using the Restraint object. The same if a DSL
         expression or Topography region is provided (default is None).
-    K_r : simtk.unit.Quantity, optional
+    K_r : openmm.unit.Quantity, optional
         The spring constant for the restrained distance ``|r3 - l1|`` (units
         compatible with kilocalories_per_mole/angstrom**2).
-    r_aA0 : simtk.unit.Quantity, optional
+    r_aA0 : openmm.unit.Quantity, optional
         The equilibrium distance between r3 and l1 (units of length).
-    K_thetaA, K_thetaB : simtk.unit.Quantity, optional
+    K_thetaA, K_thetaB : openmm.unit.Quantity, optional
         The spring constants for ``angle(r2, r3, l1)`` and ``angle(r3, l1, l2)``
         (units compatible with kilocalories_per_mole/radians**2).
-    theta_A0, theta_B0 : simtk.unit.Quantity, optional
+    theta_A0, theta_B0 : openmm.unit.Quantity, optional
         The equilibrium angles of ``angle(r2, r3, l1)`` and ``angle(r3, l1, l2)``
         (units compatible with radians).
-    K_phiA, K_phiB, K_phiC : simtk.unit.Quantity, optional
+    K_phiA, K_phiB, K_phiC : openmm.unit.Quantity, optional
         The spring constants for ``dihedral(r1, r2, r3, l1)``,
         ``dihedral(r2, r3, l1, l2)`` and ``dihedral(r3,l1,l2,l3)`` (units compatible
         with kilocalories_per_mole/radians**2).
-    phi_A0, phi_B0, phi_C0 : simtk.unit.Quantity, optional
+    phi_A0, phi_B0, phi_C0 : openmm.unit.Quantity, optional
         The equilibrium torsion of ``dihedral(r1,r2,r3,l1)``, ``dihedral(r2,r3,l1,l2)``
         and ``dihedral(r3,l1,l2,l3)`` (units compatible with radians).
 
@@ -2412,9 +2416,9 @@ class RMSD(OpenMM73, ReceptorLigandRestraint):
         If no selection is given, all ligand atoms will be restrained.
         If an empty list is provided, no receptor atoms will be restrained.
         (default is None).
-    K_RMSD : simtk.unit.Quantity, optional, default=0.6*kilocalories_per_mole/angstrom**2
+    K_RMSD : openmm.unit.Quantity, optional, default=0.6*kilocalories_per_mole/angstrom**2
         The spring constant (units compatible with kilocalories_per_mole/angstrom**2).
-    RMSD0 : simtk.unit.Quantity, optional, default=2.0*angstrom
+    RMSD0 : openmm.unit.Quantity, optional, default=2.0*angstrom
         The RMSD at which the restraint becomes nonzero.
     reference_sampler_state : openmmtools.states.SamplerState or None, Optional
         Reference sampler state with coordinates to use as the structure to align the RMSD to.

Yank/schema/validator.py

@@ -8,8 +8,12 @@
 
 import cerberus
 import cerberus.errors
-import simtk.unit as unit
-from simtk.openmm import app
+try:
+    import openmm.unit as unit
+    from openmm import app
+except ImportError: # OpenMM < 7.6
+    import simtk.unit as unit
+    from simtk.openmm import app
 import openmmtools as mmtools
 from openmoltools.utils import unwrap_py2
 

Yank/tests/test_analyze.py

@@ -20,7 +20,10 @@
 import openmmtools as mmtools
 import pymbar
 from pymbar.utils import ParameterError
-from simtk import unit
+try:
+    from openmm import unit
+except ImportError: # OpenMM < 7.6
+    from simtk import unit
 from openmmtools.multistate import (MultiStateReporter, MultiStateSampler,
                                     ReplicaExchangeSampler, SAMSSampler, utils)