fix: simtk namespace is deprecated

ommprotocol/io.py

@@ -34,14 +34,14 @@
 except ImportError:
     from ruamel import yaml
 import jinja2
-from simtk import unit as u
-from simtk.openmm.app import (PDBFile, PDBxFile, ForceField,
-                              PDBReporter, PDBxReporter,
-                              AmberPrmtopFile, AmberInpcrdFile,
-                              CharmmPsfFile, CharmmCrdFile, CharmmParameterSet,
-                              GromacsTopFile, GromacsGroFile,
-                              DesmondDMSFile, CheckpointReporter)
-from simtk.openmm import XmlSerializer, app as openmm_app
+from openmm import unit as u
+from openmm.app import (PDBFile, PDBxFile, ForceField,
+                        PDBReporter, PDBxReporter,
+                        AmberPrmtopFile, AmberInpcrdFile,
+                        CharmmPsfFile, CharmmCrdFile, CharmmParameterSet,
+                        GromacsTopFile, GromacsGroFile,
+                        DesmondDMSFile, CheckpointReporter)
+from openmm import XmlSerializer, app as openmm_app
 import mdtraj
 from mdtraj.reporters import DCDReporter, HDF5Reporter
 import parmed
@@ -267,7 +267,7 @@ def from_amber(cls, path, positions=None, strict=True, **kwargs):
         ----------
         path : str
             Path to *.prmtop or *.top file
-        positions : simtk.unit.Quantity
+        positions : openmm.unit.Quantity
             Atomic positions
 
         Returns
@@ -336,7 +336,7 @@ def from_gromacs(cls, path, positions=None, forcefield=None, strict=True, **kwar
         ---------
         path : str
             Path to a Gromacs TOP file
-        positions : simtk.unit.Quantity
+        positions : openmm.unit.Quantity
             Atomic positions
         forcefield : str, optional
             Root directory for parameter files
@@ -455,7 +455,7 @@ class Positions(MultiFormatLoader):
 
     Returns
     -------
-    positions : simtk.unit.Quantity([atoms,3])
+    positions : openmm.unit.Quantity([atoms,3])
     """
 
     @classmethod
@@ -510,7 +510,7 @@ class Velocities(MultiFormatLoader):
 
     Returns
     -------
-    velocities : simtk.unit.Quantity([atoms,3])
+    velocities : openmm.unit.Quantity([atoms,3])
     """
 
     @classmethod
@@ -540,7 +540,7 @@ class BoxVectors(MultiFormatLoader):
 
     Returns
     -------
-    velocities : simtk.unit.Quantity([atoms,3])
+    velocities : openmm.unit.Quantity([atoms,3])
     """
 
     @classmethod
@@ -597,7 +597,7 @@ def from_csv(cls, path):
 
         Returns
         -------
-        vectors : simtk.unit.Quantity([3, 3], unit=nanometers
+        vectors : openmm.unit.Quantity([3, 3], unit=nanometers
         """
         with open(path) as f:
             fields = [float(x) for x in next(f).split(',')]
@@ -647,9 +647,9 @@ class Restart(MultiFormatLoader, InputContainer):
 
     Returns
     -------
-    positions : simtk.unit.Quantity([atoms,3])
-    velocities : simtk.unit.Quantity([atoms,3])
-    vectors : simtk.unit.Quantity([1,3])
+    positions : openmm.unit.Quantity([atoms,3])
+    velocities : openmm.unit.Quantity([atoms,3])
+    vectors : openmm.unit.Quantity([1,3])
     """
     @classmethod
     def _loaders(cls, ext):

ommprotocol/md.py

@@ -23,9 +23,9 @@
 import logging
 # 3rd party
 import numpy as np
-from simtk import unit as u
-from simtk import openmm as mm
-from simtk.openmm import app
+from openmm import unit as u
+from openmm as mm
+from openmm import app
 from mdtraj import Topology as MDTrajTopology
 # Own
 from .io import REPORTERS, ProgressBarReporter, SerializedReporter, prepare_system_options
@@ -104,9 +104,9 @@ class Stage(object):
 
     Parameters
     ----------
-    handler : simtk.openmm.Topology
+    handler : openmm.Topology
         The topology input file (PRMTOP, PDB)
-    positions : simtk.Quantity, optional
+    positions : openmm.Quantity, optional
         The starting coordinates of this stage. Only needed if
         handler is a PRMTOP file.
     steps : int, optional
@@ -115,10 +115,10 @@ class Stage(object):
         Integration timestep, in fs. Defaults to 1.0.
     forcefields : list of str or file-like, optional
         Forcefields to apply in PDB inputs.
-    velocities : simtk.unit.Quantity, optional
+    velocities : openmm.unit.Quantity, optional
         The initial velocities of this stage. If None, they will be set
         to the requested temperature
-    box_vectors : simtk.unit.Quantity, optional
+    box_vectors : openmm.unit.Quantity, optional
         Replacement periodic box vectors, instead of handler's.
     barostat : bool, optional
         True for NPT @ 1 atmosphere. False for NVT
@@ -180,7 +180,7 @@ class Stage(object):
         kJ/mol. Defaults to 5.0.
     pressure : float, optional
         Barostat pressure, in bar. Defaults to 1.01325.
-    integrator : simtk.openmm.Integrator, optional
+    integrator : openmm.Integrator, optional
         Which integrator to use. Defaults to LangevinIntegrator.
     friction : float, optional
         Friction coefficient for LangevinIntegrator, in 1/ps. Defaults to 1.0.
@@ -515,7 +515,7 @@ def restraint_force(self, indices=None, strength=5.0):
 
         Returns
         -------
-        force : simtk.openmm.CustomExternalForce
+        force : openmm.CustomExternalForce
             A custom force to restrain the selected atoms
         """
         if self.system.usesPeriodicBoundaryConditions():

ommprotocol/utils.py

@@ -66,7 +66,7 @@ def assertinstance(obj, types):
 
 
 def available_platforms():
-    from simtk import openmm as mm
+    import openmm as mm
     names = []
     for i in range(mm.Platform.getNumPlatforms()):
         platform = mm.Platform.getPlatform(i)
@@ -75,7 +75,7 @@ def available_platforms():
 
 
 def available_platforms_properties():
-    from simtk import openmm as mm
+    import openmm as mm
     for i in range(1, mm.Platform.getNumPlatforms()):
         platform = mm.Platform.getPlatform(i)
         name = platform.getName()