diff --git a/ommprotocol/io.py b/ommprotocol/io.py index 807d31a..05df906 100644 --- a/ommprotocol/io.py +++ b/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): diff --git a/ommprotocol/md.py b/ommprotocol/md.py index 4b66731..d611b8d 100644 --- a/ommprotocol/md.py +++ b/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(): diff --git a/ommprotocol/utils.py b/ommprotocol/utils.py index 70b8b8c..603f6a2 100644 --- a/ommprotocol/utils.py +++ b/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()