Update imports and tests for OpenMM 7.6

README.md

@@ -265,6 +265,12 @@ See the corresponding directories for information on how to use the provided con
 
 # Changelog
 
+## 0.10.0 Updates for OpenMM 7.6 and AMBER GLYCAM addition
+This release adds support for the AMBER GLYCAM force field supporting glycans and updates imports for OpenMM 7.6.
+
+* [(PR #156)](https://github.com/openmm/openmmforcefields/pull/156) Add support for GLYCAM
+* [(PR #173)](https://github.com/openmm/openmmforcefields/pull/173) Update to OpenMM 7.6 imports
+
 ## 0.9.0 Updates for openforcefield 0.9.0 toolkit
 This release utilizes the new [openforcefield 0.9.0 toolkit](https://open-forcefield-toolkit.readthedocs.io/en/0.9.0/) now distributed through [conda-forge](https://conda-forge.org/).
 

amber/convert_amber.py

@@ -3,10 +3,10 @@
 from __future__ import print_function, division
 from io import StringIO
 import parmed
-from simtk import openmm
-import simtk.openmm.app as app
-import simtk.unit as u
-import simtk
+from parmed.utils.six import iteritems
+from parmed.utils.six.moves import StringIO, zip
+import openmm.app as app
+import openmm.unit as u
 import os
 import sys
 import re
@@ -380,7 +380,7 @@ def convert_yaml(yaml_name, ffxml_dir, ignore=ignore):
         for source_file in source_files:
             if MODE == 'LEAPRC':
                  if os.path.exists(source_file):
-                     _filename = os.path.join('./', source_file)    
+                     _filename = os.path.join('./', source_file)
                  else:
                      _filename = os.path.join(AMBERHOME, 'dat/leap/cmd', source_file)
             elif MODE == 'RECIPE':
@@ -621,7 +621,7 @@ def add_prefix_to_ffxml(ffxml_filename, prefix):
 
 def assert_energies_glyco_protein(prmtop, inpcrd, ffxml, tolerance=1e-1):
     import math
- 
+
     # Get AMBER system
     parm_amber = parmed.load_file(prmtop, inpcrd)
     system_amber = parm_amber.createSystem()
@@ -660,7 +660,7 @@ def compute_potential_components(system, positions, beta=beta):
         system = deepcopy(system)
         for index in range(system.getNumForces()):
             force = system.getForce(index)
-            force.setForceGroup(index) 
+            force.setForceGroup(index)
         integrator = openmm.VerletIntegrator(1.0*u.femtosecond)
         platform = openmm.Platform.getPlatformByName('Reference')
         context = openmm.Context(system, integrator, platform)
@@ -710,7 +710,7 @@ def assert_energies(prmtop, inpcrd, ffxml, system_name='unknown', tolerance=2.5e
     system_omm = parm_omm.createSystem(splitDihedrals=True)
     omm_energies = parmed.openmm.energy_decomposition_system(parm_omm,
                    system_omm, nrg=units, platform='Reference')
-    
+
     # calc rel energies and assert
     energies = []
     rel_energies = []
@@ -1399,9 +1399,9 @@ def modify_glycan_ffxml(input_ffxml_path):
         bond.attrib['type1'] = bond.attrib['class1']
         bond.attrib['type2'] = bond.attrib['class2']
         del bond.attrib['class1']
-        del bond.attrib['class2']        
+        del bond.attrib['class2']
 
-        # Fix prefixes 
+        # Fix prefixes
         types = [bond.get('type1'), bond.get('type2')]
         if any(t in glycam_types for t in types):
             bond.set('type1', replacements[types[0]])
@@ -1446,7 +1446,7 @@ def modify_glycan_ffxml(input_ffxml_path):
             del torsion.attrib['class4']
             if torsion.attrib['type1'] == 'NH' and torsion.attrib['type2'] == 'Cg' and torsion.attrib['type3'] == 'Cg' and torsion.attrib['type4'] == 'Sm':
                 force.remove(torsion)
-                continue      
+                continue
 
             # Fix prefixes
             types = [torsion.get('type1'), torsion.get('type2'), torsion.get('type3'), torsion.get('type4')]
@@ -1465,7 +1465,7 @@ def modify_glycan_ffxml(input_ffxml_path):
         # Change attributes from class to type
         atom.attrib['type'] = atom.attrib['class']
         del atom.attrib['class']
-        
+
         # Fix prefixes
         type = atom.get('type')
         if type in glycam_types:
@@ -1493,7 +1493,7 @@ def modify_glycan_ffxml(input_ffxml_path):
 
     # Add initialization script for setting up GlycamTemplateMatcher
     initialization_script = etree.SubElement(root, 'InitializationScript')
-    initialization_script.text = """ 
+    initialization_script.text = """
 class GlycamTemplateMatcher(object):
   def __init__(self, glycam_residues):
     self.glycam_residues = glycam_residues

charmm/convert_charmm.py

@@ -5,9 +5,9 @@
 from collections import OrderedDict
 import hashlib
 import os
-import simtk.openmm.app as app
-import simtk.openmm as mm
-import simtk.unit as u
+import openmm.app as app
+import openmm as mm
+import openmm.unit as u
 import argparse
 import csv
 import logging

devtools/conda-envs/test_env.yaml

@@ -16,7 +16,7 @@ dependencies:
   - codecov
 
     # Requirements for converted force field installer
-  - openmm >=7.4.2
+  - openmm >=7.6.0
 
     # Requirements for conversion tools
   - pyyaml

openmmforcefields/generators/system_generators.py

@@ -10,7 +10,7 @@
 import logging
 _logger = logging.getLogger("openmmforcefields.system_generators")
 
-from simtk.openmm import app
+from openmm import app
 
 ################################################################################
 # System generator base class
@@ -42,19 +42,19 @@ class SystemGenerator(object):
 
     Parameters
     ----------
-    forcefield : simtk.openmm.app.ForceField
+    forcefield : openmm.app.ForceField
         The ForceField object used to create new System objects.
         New ffxml files can be read in at any time.
     forcefield_kwargs : dict
-        Keyword arguments fed to ``simtk.openmm.app.ForceField.createSystem()`` during System generation.
+        Keyword arguments fed to ``openmm.app.ForceField.createSystem()`` during System generation.
         These keyword arguments can be modified at any time.
     periodic_forcefield_kwargs : dict
-        Keyword arguments fed to ``simtk.openmm.app.ForceField.createSystem()`` during System generation for periodic systems.
+        Keyword arguments fed to ``openmm.app.ForceField.createSystem()`` during System generation for periodic systems.
         These keyword arguments can be modified at any time.
     nonperiodic_forcefield_kwargs : dict
-        Keyword arguments fed to ``simtk.openmm.app.ForceField.createSystem()`` during System generation for non-periodic systems.
+        Keyword arguments fed to ``openmm.app.ForceField.createSystem()`` during System generation for non-periodic systems.
         These keyword arguments can be modified at any time.
-    barostat : simtk.openmm.MonteCarloBarostat
+    barostat : openmm.MonteCarloBarostat
         If not None, this container holds the barostat parameters to use for newly created System objects.
     molecules : openff.toolkit.topology.Molecule or list, optional, default=None
         Can alternatively be an object (such as an OpenEye OEMol or RDKit Mol or SMILES string) that can be used to construct a Molecule.
@@ -85,12 +85,12 @@ def __init__(self, forcefields=None, small_molecule_forcefield='openff-1.0.0', f
             Supported SMIRNOFF force fields include: [`openff-1.0.0`, `smirnoff99Frosst-1.1.0`]
             (See ``SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS`` for a complete list.)
         forcefield_kwargs : dict, optional, default=None
-            Keyword arguments to be passed to ``simtk.openmm.app.ForceField.createSystem()`` during ``System`` object creation.
+            Keyword arguments to be passed to ``openmm.app.ForceField.createSystem()`` during ``System`` object creation.
         nonperiodic_forcefield_kwargs : dict, optional, default={'nonbondedMethod' : NoCutoff}
             Keyword arguments added to forcefield_kwargs when the Topology is non-periodic.
         periodic_forcefield_kwargs : NonbondedMethod, optional, default={'nonbondedMethod' : PME}
             Keyword arguments added to forcefield_kwargs when the Topology is periodic.
-        barostat : simtk.openmm.MonteCarloBarostat, optional, default=None
+        barostat : openmm.MonteCarloBarostat, optional, default=None
             If not None, a new ``MonteCarloBarostat`` with matching parameters (but a different random number seed) will be created and
             added to each newly created ``System``.
         molecules : openff.toolkit.topology.Molecule or list, optional, default=None
@@ -111,12 +111,12 @@ def __init__(self, forcefields=None, small_molecule_forcefield='openff-1.0.0', f
         `Open Force Field Topology <https://open-forcefield-toolkit.readthedocs.io/en/latest/api/generated/openff.toolkit.topology.Topology.html#openff.toolkit.topology.Topology>`_ object:
 
         >>> # Define the keyword arguments to feed to ForceField
-        >>> from simtk import unit
-        >>> from simtk.openmm import app
+        >>> from openmm import unit
+        >>> from openmm import app
         >>> # Define standard OpenMM biopolymer and solvent force fields to use
 
         To initialize the ``SystemGenerator``, we specify the OpenMM force fields, the small molecule force field, and any ``kwargs`` to be fed
-        to the OpenMM ``simtk.openmm.app.ForceField.createSystem()`` method:
+        to the OpenMM ``openmm.app.ForceField.createSystem()`` method:
 
         >>> from openmmforcefields.generators import SystemGenerator
         >>> amber_forcefields = ['amber/protein.ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml']
@@ -173,7 +173,7 @@ def __init__(self, forcefields=None, small_molecule_forcefield='openff-1.0.0', f
 
         # Create OpenMM ForceField object
         forcefields = forcefields if (forcefields is not None) else list()
-        from simtk.openmm import app
+        from openmm import app
         self.forcefield = app.ForceField(*forcefields)
 
         # Cache force fields and settings to use
@@ -244,7 +244,7 @@ def _modify_forces(self, system):
         # Add barostat if requested.
         if self.barostat is not None:
             import numpy as np
-            from simtk import openmm
+            import openmm
             MAXINT = np.iinfo(np.int32).max
 
             # Determine pressure, temperature, and frequency
@@ -304,7 +304,7 @@ def create_system(self, topology, molecules=None):
 
         Returns
         -------
-        system : simtk.openmm.System
+        system : openmm.System
             A system object generated from the topology
 
         """
@@ -363,7 +363,7 @@ def create_system(self, topology, **kwargs):
 
         Returns
         -------
-        system : simtk.openmm.System
+        system : openmm.System
             The System object
 
         """

openmmforcefields/generators/template_generators.py

@@ -131,7 +131,7 @@ def _match_residue(residue, molecule_template):
 
         Parameters
         ----------
-        residue : simtk.openmm.app.topology.Residue
+        residue : openmm.app.topology.Residue
             The residue to check
         molecule_template : openff.toolkit.topology.Molecule
             The Molecule template to compare it to
@@ -218,7 +218,7 @@ def _molecule_has_user_charges(self, molecule):
 
         """
         import numpy as np
-        from simtk import unit
+        from openmm import unit
         zeros = np.zeros([molecule.n_particles])
         if (molecule.partial_charges is None) or (np.allclose(molecule.partial_charges / unit.elementary_charge, zeros)):
             charges_are_zero = True
@@ -244,13 +244,13 @@ def _generate_unique_atom_names(self, molecule):
 
     def generator(self, forcefield, residue):
         """
-        Residue template generator method to register with simtk.openmm.app.ForceField
+        Residue template generator method to register with openmm.app.ForceField
 
         Parameters
         ----------
-        forcefield : simtk.openmm.app.ForceField
+        forcefield : openmm.app.ForceField
             The ForceField object to which residue templates and/or parameters are to be added.
-        residue : simtk.openmm.app.Topology.Residue
+        residue : openmm.app.Topology.Residue
             The residue topology for which a template is to be generated.
 
         Returns
@@ -355,7 +355,7 @@ class GAFFTemplateGenerator(SmallMoleculeTemplateGenerator):
     >>> from openmoltools.forcefield_generators import GAFFTemplateGenerator
     >>> template_generator = GAFFTemplateGenerator(molecules=molecule)
     >>> # Create an OpenMM ForceField
-    >>> from simtk.openmm.app import ForceField
+    >>> from openmm.app import ForceField
     >>> amber_forcefields = ['amber/protein.ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml']
     >>> forcefield = ForceField(*amber_forcefields)
     >>> # Register the template generator
@@ -416,7 +416,7 @@ def __init__(self, molecules=None, forcefield=None, cache=None):
         >>> molecule = Molecule.from_smiles('c1ccccc1')
         >>> from openmoltools.forcefield_generators import GAFFTemplateGenerator
         >>> gaff = GAFFTemplateGenerator(molecules=molecule)
-        >>> from simtk.openmm.app import ForceField
+        >>> from openmm.app import ForceField
         >>> amber_forcefields = ['amber/protein.ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml']
         >>> forcefield = ForceField(*amber_forcefields)
         >>> forcefield.registerTemplateGenerator(gaff)
@@ -462,7 +462,7 @@ def __init__(self, molecules=None, forcefield=None, cache=None):
         # Store user-specified GAFF version
         self._forcefield = forcefield
         import re
-        result = re.match('^gaff-(?P<major_version>\d+)\.(?P<minor_version>\d+)$', forcefield)
+        result = re.match(r'^gaff-(?P<major_version>\d+)\.(?P<minor_version>\d+)$', forcefield)
         if result is None:
             msg = "'forcefield' must be of form 'gaff-X.Y', where X and Y denote major and minor version\n"
             msg += f"Provided 'forcefield' argument was '{forcefield}'\n"
@@ -509,13 +509,13 @@ def gaff_xml_filename(self):
 
     def generator(self, forcefield, residue):
         """
-        Residue template generator method to register with simtk.openmm.app.ForceField
+        Residue template generator method to register with openmm.app.ForceField
 
         Parameters
         ----------
-        forcefield : simtk.openmm.app.ForceField
+        forcefield : openmm.app.ForceField
             The ForceField object to which residue templates and/or parameters are to be added.
-        residue : simtk.openmm.app.Topology.Residue
+        residue : openmm.app.Topology.Residue
             The residue topology for which a template is to be generated.
 
         Returns
@@ -570,7 +570,7 @@ def generate_residue_template(self, molecule, residue_atoms=None):
 
         # Compute net formal charge
         net_charge = molecule.total_charge
-        from simtk import unit
+        from openmm import unit
         if type(net_charge) != unit.Quantity:
             # openforcefield toolkit < 0.7.0 did not return unit-bearing quantity
             net_charge = float(net_charge) * unit.elementary_charge
@@ -621,7 +621,7 @@ def generate_residue_template(self, molecule, residue_atoms=None):
         #       or pure numbers.
         _logger.debug(f'Fixing partial charges...')
         _logger.debug(f'{molecule.partial_charges}')
-        from simtk import unit
+        from openmm import unit
         residue_charge = 0.0 * unit.elementary_charge
         total_charge = unit.sum(molecule.partial_charges)
         sum_of_absolute_charge = unit.sum(abs(molecule.partial_charges))
@@ -889,7 +889,7 @@ class SMIRNOFFTemplateGenerator(SmallMoleculeTemplateGenerator):
     >>> from openmoltools.forcefield_generators import SMIRNOFFTemplateGenerator
     >>> template_generator = SMIRNOFFTemplateGenerator(molecules=molecule)
     >>> # Create an OpenMM ForceField
-    >>> from simtk.openmm.app import ForceField
+    >>> from openmm.app import ForceField
     >>> amber_forcefields = ['amber/protein.ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml']
     >>> forcefield = ForceField(*amber_forcefields)
     >>> # Register the template generator
@@ -947,7 +947,7 @@ def __init__(self, molecules=None, cache=None, forcefield=None):
         >>> molecule = Molecule.from_smiles('c1ccccc1')
         >>> from openmoltools.forcefield_generators import SMIRNOFFTemplateGenerator
         >>> smirnoff = SMIRNOFFTemplateGenerator(molecules=molecule)
-        >>> from simtk.openmm.app import ForceField
+        >>> from openmm.app import ForceField
         >>> amber_forcefields = ['amber/protein.ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml']
         >>> forcefield = ForceField(*amber_forcefields)
 
@@ -1099,7 +1099,7 @@ def get_openmm_system(self, molecule):
 
         Returns
         -------
-        system : simtk.openmm.System or None
+        system : openmm.System or None
             If the Molecule object has already been parameterized by this instance, this molecule is returned.
             Otherwise, None is returned.
         """
@@ -1161,13 +1161,13 @@ def generate_residue_template(self, molecule, residue_atoms=None):
         root = etree.Element("ForceField")
 
         def as_attrib(quantity):
-            """Format simtk.unit.Quantity as XML attribute."""
+            """Format openmm.unit.Quantity as XML attribute."""
             if isinstance(quantity, str):
                 return quantity
             elif isinstance(quantity, float) or isinstance(quantity, int):
                 return str(quantity)
             else:
-                from simtk import unit
+                from openmm import unit
                 return str(quantity.value_in_unit_system(unit.md_unit_system))
 
         # Append unique type names to atoms
@@ -1208,7 +1208,7 @@ def classes(particle_indices):
 
         # Round parameters using strings for ease of comparison
         # DEBUG
-        #from simtk import unit
+        #from openmm import unit
         #def round_quantity(quantity):
         #    NDECIMALS = 3
         #    value = quantity.value_in_unit_system(unit.md_unit_system)
@@ -1288,7 +1288,7 @@ def torsion_tag(particle_indices):
 
         # Create residue definitions
         # TODO: Handle non-Atom particles too (virtual sites)
-        from simtk import unit
+        from openmm import unit
         residues = etree.SubElement(root, "Residues")
         residue = etree.SubElement(residues, "Residue", name=smiles)
         for particle_index, particle in enumerate(molecule.particles):