Merge branch 'master' into bugfix/970

devtools/ci/travis/install.sh

@@ -4,12 +4,12 @@ if [ "$PYTHON_VERSION" = "pypy" ]; then
     export PYENV_ROOT="${HOME}/.pyenv"
     export PATH="${PYENV_ROOT}/bin:${PATH}"
     eval "$(pyenv init -)"
-    pyenv install pypy-4.0.1
-    pyenv global pypy-4.0.1
+    pyenv install pypy2.7-6.0.0
+    pyenv global pypy2.7-6.0.0
 
     pypy -m pip install nose pyflakes==1.0.0 nose-timer lxml
     which pyflakes
-    pypy -m pip install --user git+https://bitbucket.org/pypy/numpy.git@pypy-4.0.1
+    pypy -m pip install numpy
 else # Otherwise, CPython... go through conda
     if [ "$TRAVIS_OS_NAME" = "osx" ]; then
         wget http://repo.continuum.io/miniconda/Miniconda-3.7.0-MacOSX-x86_64.sh -O miniconda.sh;
@@ -38,7 +38,7 @@ else # Otherwise, CPython... go through conda
         conda install -y -n myenv rdkit==2015.09.1 -c omnia
         conda install -y -n myenv boost==1.59.0 -c omnia
         conda install -y -n myenv nglview -c bioconda
-       #conda install -y -n myenv ambertools=17.0 -c http://ambermd.org/downloads/ambertools/conda/
+        conda install -y -n myenv ambertools=18 -c http://ambermd.org/downloads/ambertools/conda/
         conda install -y -n myenv networkx
         conda install -y -n myenv lxml
     else
@@ -48,9 +48,9 @@ else # Otherwise, CPython... go through conda
     fi
     source activate myenv
     pip install pyflakes==1.0.0
-   #if [ -z "$MINIMAL_PACKAGES" ]; then
-   #    pip uninstall parmed -y # from ambertools
-   #fi
+    if [ -z "$MINIMAL_PACKAGES" ]; then
+        pip uninstall parmed -y # from ambertools
+    fi
 
     # DEBUG
     conda list

devtools/ci/travis/runtest.sh

@@ -27,7 +27,7 @@ else
     ./run_scripts.sh
     # Run nose under coverage, since that allows getting the full flexibility of
     # the coverage package without sacrificing nose functionality
-#   test -z "$MINIMAL_PACKAGES" && export AMBERHOME=$HOME/miniconda/envs/myenv
+    test -z "$MINIMAL_PACKAGES" && export AMBERHOME=$HOME/miniconda/envs/myenv
     coverage run --source=parmed --parallel-mode -m \
         nose -vs --with-timer --timer-ok=5s --timer-warning=12s \
              --timer-filter=warning,error .

parmed/modeller/residue.py

@@ -11,7 +11,7 @@
 from parmed.structure import Structure
 from parmed.topologyobjects import Atom, Bond, AtomList, TrackedList
 from parmed.utils.six import iteritems
-from parmed.exceptions import IncompatiblePatchError
+from parmed.exceptions import IncompatiblePatchError, MoleculeError
 import warnings
 
 __all__ = ['PROTEIN', 'NUCLEIC', 'SOLVENT', 'UNKNOWN', 'ResidueTemplate',
@@ -463,8 +463,8 @@ def apply_patch(self, patch, precision=4):
             try:
                 residue.delete_atom(atom_name)
                 modifications_made = True
-            except KeyError as e:
-                raise IncompatiblePatchError(str(e))
+            except (KeyError, MoleculeError) as e:
+                raise IncompatiblePatchError('Atom %s could not be deleted from the patched residue: atoms are %s (exception: %s)' % (atom_name, list(residue._map.keys()), str(e)))
         # Add or replace atoms
         for atom in patch.atoms:
             if atom.name in residue:
@@ -486,8 +486,8 @@ def apply_patch(self, patch, precision=4):
                 # Add bond
                 residue.add_bond(atom1_name, atom2_name, order)
                 modifications_made = True
-            except IndexError as e:
-                raise IncompatiblePatchError('Bond %s-%s could not be added to patched residue: atoms are %s' % (atom1_name, atom2_name, list(residue._map.keys())))
+            except (IndexError, MoleculeError) as e:
+                raise IncompatiblePatchError('Bond %s-%s could not be added to patched residue: atoms are %s (exception: %s)' % (atom1_name, atom2_name, list(residue._map.keys()), str(e)))
         # Delete impropers
         for impr in patch.delete_impropers:
             try:
@@ -512,6 +512,29 @@ def apply_patch(self, patch, precision=4):
 
         return residue
 
+    def patch_is_compatible(self, patch):
+        """Determine whether a specified patch is compatible with this residue.
+
+        Compatibility is determined by whether Residue.Template.apply_patch(patch) raises as
+        exception or not.
+
+        Parameters
+        ----------
+        patch : PatchTemplate
+            The patch to be applied to this residue.
+
+        Returns
+        -------
+        is_compatible : bool
+            True if patch is compatible with the residue; False if not.
+
+        """
+        try:
+            self.apply_patch(patch)
+            return True
+        except IncompatiblePatchError:
+            return False
+
     def to_networkx(self):
         """ Create a NetworkX graph of atoms and bonds
 

parmed/openmm/parameters.py

@@ -23,7 +23,7 @@
 from ..utils.six import add_metaclass, string_types, iteritems
 from ..utils.six.moves import range
 import warnings
-from ..exceptions import ParameterWarning, IncompatiblePatchError
+from ..exceptions import ParameterWarning 
 from itertools import product
 from ..topologyobjects import (DihedralType, ImproperType)
 
@@ -114,6 +114,11 @@ def _remediate_residue_template(cls, params, residue):
         residue : :class:`parmed.modeller.Residue`
             The residue to remediate
 
+        Returns
+        -------
+        missing_parameters : bool
+            If True, the residue template is missing some parameters
+
         """
         # Populate atomic numbers in residue template
         # TODO: This can be removed if the parameter readers are guaranteed to populate this correctly
@@ -198,15 +203,21 @@ def from_parameterset(cls, params, copy=False, remediate_residues=True):
         if hasattr(params, '_improper_key_map'):
             new_params._improper_key_map = new_params._improper_key_map
 
-        # Add only ResidueTemplate instances (no ResidueTemplateContainers)
-        # Maintain original residue ordering
-        remediated_residues = list()
-        for name, residue in iteritems(params.residues):
-            if isinstance(residue, ResidueTemplate):
-                if (not remediate_residues) or cls._remediate_residue_template(new_params, residue):
+        if remediate_residues:
+            # Add only ResidueTemplate instances (no ResidueTemplateContainers)
+            # Maintain original residue ordering
+            remediated_residues = list()
+            for name, residue in iteritems(params.residues):
+                if isinstance(residue, ResidueTemplate):
+                    # Don't discard the residue, but fix it if we need to
+                    cls._remediate_residue_template(new_params, residue)
                     remediated_residues.append(residue)
-        for residue in remediated_residues:
-            new_params.residues[residue.name] = residue
+            for residue in remediated_residues:
+                new_params.residues[residue.name] = residue
+        else:
+            # Don't remediate residues; just copy
+            for name, residue in iteritems(params.residues):
+                new_params.residues[residue.name] = residue
 
         # Only add unique patches
         unique_patches = OrderedDict()
@@ -461,7 +472,7 @@ def _templhasher(residue):
         hash_info = tuple()
         # Sort tuples of atom properties by atom name
         if len(residue.atoms) > 0:
-            hash_info += tuple(sorted( [(atom.name, atom.type, str(atom.charge)) for atom in residue.atoms] ))
+            hash_info += tuple(sorted( [(atom.type, str(atom.charge)) for atom in residue.atoms] ))
         # Sort list of deleted atoms by atom name
         if hasattr(residue, 'delete_atoms') and len(residue.delete_atoms) > 0:
             hash_info += tuple(sorted([atom_name for atom_name in residue.delete_atoms]))
@@ -599,19 +610,16 @@ def _determine_valid_patch_combinations(self, skip_residues):
         for residue in self.residues.values():
             valid_patches_for_residue[residue.name] = list()
 
+        # Create list of residues to check compatibility against
+        residues = [ residue for residue in self.residues.values() if (residue not in skip_residues) ]
+
+        # Check patch compatibilities
         for patch in self.patches.values():
-            for residue in self.residues.values():
-                if residue in skip_residues: continue
-                # Attempt to patch the residue.
-                try:
-                    residue.apply_patch(patch)
-                except IncompatiblePatchError as e:
-                    # Patching failed; continue to next patch
-                    LOGGER.debug('%8s x %8s : %s', patch.name, residue.name, e)
-                    continue
-
-                valid_residues_for_patch[patch.name].append(residue.name)
-                valid_patches_for_residue[residue.name].append(patch.name)
+            residue_compatibilities = [ residue.patch_is_compatible(patch) for residue in residues ]
+            for (residue, is_compatible) in zip(residues, residue_compatibilities):
+                if is_compatible:
+                    valid_residues_for_patch[patch.name].append(residue.name)
+                    valid_patches_for_residue[residue.name].append(patch.name)
 
         return [valid_residues_for_patch, valid_patches_for_residue]
 

test/files/aminont12.lib

@@ -24,17 +24,17 @@
  "NTYR"
  "NVAL"
 !entry.ACE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
- "HH31" "HC" 0 1 131072 1 1 0.112300
+ "H1" "HC" 0 1 131072 1 1 0.112300
  "CH3" "CT" 0 1 131072 2 6 -0.366200
- "HH32" "HC" 0 1 131072 3 1 0.112300
- "HH33" "HC" 0 1 131072 4 1 0.112300
+ "H2" "HC" 0 1 131072 3 1 0.112300
+ "H3" "HC" 0 1 131072 4 1 0.112300
  "C" "C" 0 1 131072 5 6 0.597200
  "O" "O" 0 1 131072 6 8 -0.567900
 !entry.ACE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
- "HH31" "HC" 0 -1 0.0
+ "H1" "HC" 0 -1 0.0
  "CH3" "CT" 0 -1 0.0
- "HH32" "HC" 0 -1 0.0
- "HH33" "HC" 0 -1 0.0
+ "H2" "HC" 0 -1 0.0
+ "H3" "HC" 0 -1 0.0
  "C" "C" 0 -1 0.0
  "O" "O" 0 -1 0.0
 !entry.ACE.unit.boundbox array dbl

test/files/ionsjc.pdb

@@ -0,0 +1,12 @@
+REMARK   1 Test ions from frcmod.ionsjc_tip3p with complete parameters
+CRYST1   22.771   23.117   23.235  90.00  90.00  90.00 P 1           1
+HETATM    1 BR    BR A   1      10.569  16.024  -1.115  1.00  0.00          Br
+HETATM    2 CL    CL A   2       8.569   0.024   7.885  1.00  0.00          Cl
+HETATM    3 CS    CS A   3       2.275  20.986  22.847  1.00  0.00          Cs
+HETATM    4  F     F A   4      -0.725  20.986  18.847  1.00  0.00           F
+HETATM    5  I   IOD A   5      18.711  21.460  16.321  1.00  0.00           I
+HETATM    6  K     K A   6      20.711   6.460  14.321  1.00  0.00           K
+HETATM    7 LI    PI A   7      -4.599  21.150  18.011  1.00  0.00          Li
+HETATM    8 NA    NA A   8      -0.599   8.150   4.011  1.00  0.00          Na
+HETATM    9 RB    RB A   9      23.768   5.391  15.252  1.00  0.00          Rb
+END