Merge branch 'master' into add-37

Author: mattwthompson

.coveragerc

@@ -11,3 +11,5 @@ exclude_lines =
     # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:
+    def __repr__
+    except ImportError

docs/conf.py

@@ -27,6 +27,7 @@
                 'nglview',
                 'oset',
                 'parmed',
+                'parmed.parameters',
                 'parmed.periodic_table',
                 'scipy',
                 'scipy.spatial',

mbuild/box.py

@@ -1,3 +1,5 @@
+from warnings import warn
+
 import numpy as np
 
 
@@ -15,19 +17,25 @@ class Box(object):
 
     """
     def __init__(self, lengths=None, mins=None, maxs=None, angles=None):
-        if lengths is not None:
-            assert mins is None and maxs is None
-            self._mins = np.array([0.0, 0.0, 0.0])
-            self._maxs = np.array(lengths, dtype=np.float)
-            self._lengths = np.array(lengths, dtype=np.float)
-        elif maxs is not None:
-            assert mins is not None and lengths is None
+        if lengths is None:
+            if mins is None or maxs is None:
+                raise ValueError(
+                    "Either provide `lengths` or `mins` and `maxs`. "
+                    "You provided: "
+                    "lengths={} mins={} maxs={}".format(lengths, mins, maxs)
+                )
             self._mins = np.array(mins, dtype=np.float)
             self._maxs = np.array(maxs, dtype=np.float)
             self._lengths = self.maxs - self.mins
         else:
-            raise ValueError("Either provide `lengths` or `mins` and `maxs`."
-                             "You provided: lengths={} mins={} maxs={}".format(lengths, mins, maxs))
+            warn(
+                "Provided `lengths` and `mins` and/or `maxs`. Only `lengths` "
+                "is being used. You provided: "
+                "lengths={} mins={} maxs={}".format(lengths, mins, maxs)
+            )
+            self._mins = np.array([0.0, 0.0, 0.0])
+            self._maxs = np.array(lengths, dtype=np.float)
+            self._lengths = np.array(lengths, dtype=np.float)
         if angles is None:
             angles = np.array([90.0, 90.0, 90.0])
         elif isinstance(angles, (list, np.ndarray)):

mbuild/compound.py

@@ -1153,55 +1153,147 @@ def particles_in_range(
             particle_array = np.array(list(self.particles()))
         return particle_array[idxs]
 
-    def visualize(self, show_ports=False):
-        """Visualize the Compound using nglview.
+    def visualize(self, show_ports=False, 
+            backend='py3dmol', color_scheme={}): # pragma: no cover
+        """Visualize the Compound using py3dmol (default) or nglview.
 
         Allows for visualization of a Compound within a Jupyter Notebook.
 
         Parameters
         ----------
         show_ports : bool, optional, default=False
             Visualize Ports in addition to Particles
+        backend : str, optional, default='py3dmol'
+            Specify the backend package to visualize compounds
+            Currently supported: py3dmol, nglview
+        color_scheme : dict, optional
+            Specify coloring for non-elemental particles
+            keys are strings of the particle names
+            values are strings of the colors
+            i.e. {'_CGBEAD': 'blue'}
 
         """
-        nglview = import_('nglview')
-        from mdtraj.geometry.sasa import _ATOMIC_RADII
+        viz_pkg = {'nglview': self._visualize_nglview,
+                'py3dmol': self._visualize_py3dmol}
         if run_from_ipython():
-            remove_digits = lambda x: ''.join(i for i in x if not i.isdigit()
-                                              or i == '_')
-            for particle in self.particles():
-                particle.name = remove_digits(particle.name).upper()
-                if not particle.name:
-                    particle.name = 'UNK'
-            tmp_dir = tempfile.mkdtemp()
-            self.save(os.path.join(tmp_dir, 'tmp.mol2'),
-                      show_ports=show_ports,
-                      overwrite=True)
-            widget = nglview.show_file(os.path.join(tmp_dir, 'tmp.mol2'))
-            widget.clear()
-            widget.add_ball_and_stick(cylinderOnly=True)
-            elements = set([particle.name for particle in self.particles()])
-            scale = 50.0
-            for element in elements:
-                try:
-                    widget.add_ball_and_stick('_{}'.format(
-                        element.upper()), aspect_ratio=_ATOMIC_RADII[element.title()]**1.5 * scale)
-                except KeyError:
-                    ids = [str(i) for i, particle in enumerate(self.particles())
-                           if particle.name == element]
-                    widget.add_ball_and_stick(
-                        '@{}'.format(
-                            ','.join(ids)),
-                        aspect_ratio=0.17**1.5 * scale,
-                        color='grey')
-            if show_ports:
-                widget.add_ball_and_stick('_VS',
-                                          aspect_ratio=1.0, color='#991f00')
-            return widget
+            if backend.lower() in viz_pkg:
+                return viz_pkg[backend.lower()](show_ports=show_ports, 
+                        color_scheme=color_scheme)
+            else:
+                raise RuntimeError("Unsupported visualization " +
+                        "backend ({}). ".format(backend) +
+                        "Currently supported backends include nglview and py3dmol")
+                        
         else:
             raise RuntimeError('Visualization is only supported in Jupyter '
                                'Notebooks.')
 
+    def _visualize_py3dmol(self, show_ports=False, color_scheme={}):
+        """Visualize the Compound using py3Dmol.
+
+        Allows for visualization of a Compound within a Jupyter Notebook.
+
+        Parameters
+        ----------
+        show_ports : bool, optional, default=False
+            Visualize Ports in addition to Particles
+        color_scheme : dict, optional
+            Specify coloring for non-elemental particles
+            keys are strings of the particle names
+            values are strings of the colors
+            i.e. {'_CGBEAD': 'blue'}
+
+
+        Returns
+        ------
+        view : py3Dmol.view
+
+        """
+        py3Dmol = import_('py3Dmol')
+        remove_digits = lambda x: ''.join(i for i in x if not i.isdigit()
+                                              or i == '_')
+
+        modified_color_scheme = {}
+        for name, color in color_scheme.items():
+            # Py3dmol does some element string conversions, 
+            # first character is as-is, rest of the characters are lowercase
+            new_name = name[0] + name[1:].lower() 
+            modified_color_scheme[new_name] = color
+            modified_color_scheme[name] = color
+
+        for particle in self.particles():
+            particle.name = remove_digits(particle.name).upper()
+            if not particle.name:
+                particle.name = 'UNK'
+        tmp_dir = tempfile.mkdtemp()
+        self.save(os.path.join(tmp_dir, 'tmp.mol2'),
+                  show_ports=show_ports,
+                  overwrite=True)
+
+        view = py3Dmol.view()
+        view.addModel(open(os.path.join(tmp_dir, 'tmp.mol2'), 'r').read(),
+                'mol2', keepH=True)
+        view.setStyle({'stick': {'radius': 0.2,
+                                'color':'grey'},
+                        'sphere': {'scale': 0.3,
+                                    'colorscheme':modified_color_scheme}})
+        if show_ports:
+            for p in self.particles(include_ports=True):
+                if p.port_particle:
+                    view.addSphere({
+                        'center': {'x':p.pos[0], 'y':p.pos[1], 'z':p.pos[2]},
+                        'radius' :0.4,
+                        'color': '0x991f00',
+                        'alpha': 0.9})
+        view.zoomTo()
+        view.show()
+
+        return view
+
+    def _visualize_nglview(self, show_ports=False, color_scheme={}):
+        """Visualize the Compound using nglview.
+
+        Allows for visualization of a Compound within a Jupyter Notebook.
+
+        Parameters
+        ----------
+        show_ports : bool, optional, default=False
+            Visualize Ports in addition to Particles
+            """
+        nglview = import_('nglview')
+        from mdtraj.geometry.sasa import _ATOMIC_RADII
+        remove_digits = lambda x: ''.join(i for i in x if not i.isdigit()
+                                              or i == '_')
+        for particle in self.particles():
+            particle.name = remove_digits(particle.name).upper()
+            if not particle.name:
+                particle.name = 'UNK'
+        tmp_dir = tempfile.mkdtemp()
+        self.save(os.path.join(tmp_dir, 'tmp.mol2'),
+                  show_ports=show_ports,
+                  overwrite=True)
+        widget = nglview.show_file(os.path.join(tmp_dir, 'tmp.mol2'))
+        widget.clear()
+        widget.add_ball_and_stick(cylinderOnly=True)
+        elements = set([particle.name for particle in self.particles()])
+        scale = 50.0
+        for element in elements:
+            try:
+                widget.add_ball_and_stick('_{}'.format(
+                    element.upper()), aspect_ratio=_ATOMIC_RADII[element.title()]**1.5 * scale)
+            except KeyError:
+                ids = [str(i) for i, particle in enumerate(self.particles())
+                       if particle.name == element]
+                widget.add_ball_and_stick(
+                    '@{}'.format(
+                        ','.join(ids)),
+                    aspect_ratio=0.17**1.5 * scale,
+                    color='grey')
+        if show_ports:
+            widget.add_ball_and_stick('_VS',
+                                      aspect_ratio=1.0, color='#991f00')
+        return widget
+
     def update_coordinates(self, filename, update_port_locations=True):
         """Update the coordinates of this Compound from a file.
 
@@ -2112,7 +2204,8 @@ def from_parmed(self, structure, coords_only=False):
         else:
             self.periodicity = np.array([0., 0., 0.])
 
-    def to_parmed(self, box=None, title='', residues=None, show_ports=False):
+    def to_parmed(self, box=None, title='', residues=None, show_ports=False,
+            infer_residues=False):
         """Create a ParmEd Structure from a Compound.
 
         Parameters
@@ -2130,6 +2223,8 @@ def to_parmed(self, box=None, title='', residues=None, show_ports=False):
             checking against Compound.name.
         show_ports : boolean, optional, default=False
             Include all port atoms when converting to a `Structure`.
+        infer_residues : bool, optional, default=False
+            Attempt to assign residues based on names of children.
 
         Returns
         -------
@@ -2146,6 +2241,9 @@ def to_parmed(self, box=None, title='', residues=None, show_ports=False):
         atom_mapping = {}  # For creating bonds below
         guessed_elements = set()
 
+        if not residues and infer_residues:
+            residues = list(set([child.name for child in self.children]))
+
         if isinstance(residues, string_types):
             residues = [residues]
         if isinstance(residues, (list, set)):
@@ -2288,7 +2386,7 @@ def _iterate_children(self, nodes, edges, names_only=False):
             nodes, edges = child._iterate_children(nodes, edges, names_only=names_only)
         return nodes, edges
 
-    def to_intermol(self, molecule_types=None):
+    def to_intermol(self, molecule_types=None): # pragma: no cover
         """Create an InterMol system from a Compound.
 
         Parameters
@@ -2341,7 +2439,7 @@ def to_intermol(self, molecule_types=None):
         return intermol_system
 
     @staticmethod
-    def _add_intermol_molecule_type(intermol_system, parent):
+    def _add_intermol_molecule_type(intermol_system, parent): # pragma: no cover
         """Create a molecule type for the parent and add bonds. """
         from intermol.moleculetype import MoleculeType
         from intermol.forces.bond import Bond as InterMolBond

mbuild/examples/alkane/alkane.py

@@ -3,7 +3,6 @@
 
 from mbuild.lib.moieties import CH2
 from mbuild.lib.moieties import CH3
-from mbuild.lib.recipes import Polymer
 
 
 class Alkane(mb.Compound):

mbuild/examples/alkane_monolayer/alkane_monolayer.py

@@ -6,7 +6,6 @@
 
 from mbuild.lib.surfaces import Betacristobalite
 from mbuild.lib.atoms import H
-from mbuild.lib.recipes import Monolayer
 from mbuild.examples.alkane_monolayer.alkylsilane import AlkylSilane
 
 

mbuild/examples/bilayer/bilayer.py

@@ -7,7 +7,6 @@
 import numpy as np
 
 import mbuild as mb
-from mbuild import clone
 
 class Bilayer(mb.Compound):
     """Create a lipid bilayer and add solvent above and below.
@@ -125,23 +124,25 @@ def create_layer(self, lipid_indices=None, flip_orientation=False):
             current_type = self.lipids[n_type][0]
             for n_this_type, n_this_lipid_type in enumerate(range(n_of_lipid_type)):
                 lipids_placed = n_type + n_this_type
-                new_lipid = clone(current_type)
+                new_lipid = mb.clone(current_type)
                 random_index = lipid_indices[lipids_placed]
                 position = self.pattern[random_index]
 
                 # Zero and space in z-direction
                 particles = list(new_lipid.particles())
                 ref_atom = self.ref_atoms[n_type]
-                new_lipid.translate(-particles[ref_atom].pos + self.spacing)
+                new_lipid.translate(new_lipid, -particles[ref_atom].pos + self.spacing)
 
                 # Move to point on pattern
                 if flip_orientation == True:
+                    # TODO: Function for this?
+                    # E.g., rotate_around_x_keep_com(compound, bool(3))
                     center = new_lipid.center
                     center[2] = 0.0
-                    new_lipid.translate(-center)
-                    new_lipid.rotate(np.pi, [1, 0, 0])
-                    new_lipid.translate(center)
-                new_lipid.translate(position)
+                    new_lipid.translate(new_lipid, -center)
+                    mb.rotate_around_x(new_lipid, np.pi)
+                    new_lipid.translate(new_lipid, center)
+                new_lipid.translate(new_lipid, position)
                 layer.add(new_lipid)
         return layer, lipid_indices
 
@@ -205,4 +206,4 @@ def lipid_box(self):
                                               0.5*np.sqrt(self.apl)])
             return self._lipid_box
 
-# -- ==bilayer== --
+# -- ==bilayer== --

mbuild/examples/lennard_jones/monolj.py

@@ -3,7 +3,6 @@
 
 # -- ==monolj== --
 import mbuild as mb
-from mbuild import clone
 
 
 class MonoLJ(mb.Compound):
@@ -15,7 +14,7 @@ def __init__(self):
         pattern.scale(5)
 
         for pos in pattern:
-            lj_particle = clone(lj_proto)
+            lj_particle = mb.clone(lj_proto)
             lj_particle.translate(pos)
             self.add(lj_particle)
 

mbuild/examples/pmpc/brush.py

@@ -4,7 +4,6 @@
 
 from mbuild.lib.moieties import Silane
 from mbuild.lib.moieties import CH3
-from mbuild.lib.recipes import Polymer
 from mbuild.examples.pmpc.mpc import MPC
 from mbuild.examples.pmpc.initiator import Initiator
 

mbuild/examples/pmpc/pmpc_brush_layer.py

@@ -9,7 +9,6 @@
 import mbuild as mb
 from mbuild.lib.atoms import H
 from mbuild.lib.surfaces import Betacristobalite
-from mbuild.lib.recipes import Monolayer
 from mbuild.examples.pmpc.brush import Brush