Speed up json loader (#1163)

* speed up json loader

* include port position when writing, adding test to load back compound with ports

* change name and behavior for include_ports/show_ports

* switch the default back

* fix unit test (update keyword)

mbuild/compound.py

@@ -1953,7 +1953,7 @@ def _visualize_py3dmol(
         tmp_dir = tempfile.mkdtemp()
         cloned.save(
             os.path.join(tmp_dir, "tmp.mol2"),
-            show_ports=show_ports,
+            include_ports=show_ports,
             overwrite=True,
             parmed_kwargs={"infer_residues": False},
         )
@@ -1984,7 +1984,7 @@ def _visualize_nglview(
 
         Parameters
         ----------
-        show_ports : bool, optional, default=False
+        include_ports : bool, optional, default=False
             Visualize Ports in addition to Particles
         """
         nglview = import_("nglview")
@@ -2001,7 +2001,7 @@ def remove_digits(x):
         tmp_dir = tempfile.mkdtemp()
         self.save(
             os.path.join(tmp_dir, "tmp.mol2"),
-            show_ports=show_ports,
+            include_ports=show_ports,
             overwrite=True,
         )
         widget = nglview.show_file(os.path.join(tmp_dir, "tmp.mol2"))
@@ -2930,7 +2930,7 @@ def _energy_minimize_openbabel(
     def save(
         self,
         filename,
-        show_ports=False,
+        include_ports=False,
         forcefield_name=None,
         forcefield_files=None,
         forcefield_debug=False,
@@ -2952,7 +2952,7 @@ def save(
             'hoomdxml', 'gsd', 'gro', 'top', 'lammps', 'lmp', 'mcf', 'pdb', 'xyz',
             'json', 'mol2', 'sdf', 'psf'. See parmed/structure.py for more
             information on savers.
-        show_ports : bool, optional, default=False
+        include_ports : bool, optional, default=False
             Save ports contained within the compound.
         forcefield_files : str, optional, default=None
             Apply a forcefield to the output file using a forcefield provided
@@ -3024,7 +3024,7 @@ def save(
         When saving the compound as a json, only the following arguments are
         used:
         * filename
-        * show_ports
+        * include_ports
 
         See Also
         --------
@@ -3039,7 +3039,7 @@ def save(
         conversion.save(
             self,
             filename,
-            show_ports,
+            include_ports,
             forcefield_name,
             forcefield_files,
             forcefield_debug,
@@ -3232,13 +3232,13 @@ def from_trajectory(
         )
 
     def to_trajectory(
-        self, show_ports=False, chains=None, residues=None, box=None
+        self, include_ports=False, chains=None, residues=None, box=None
     ):
         """Convert to an md.Trajectory and flatten the compound.
 
         Parameters
         ----------
-        show_ports : bool, optional, default=False
+        include_ports : bool, optional, default=False
             Include all port atoms when converting to trajectory.
         chains : mb.Compound or list of mb.Compound
             Chain types to add to the topology
@@ -3261,7 +3261,7 @@ def to_trajectory(
         """
         return conversion.to_trajectory(
             compound=self,
-            show_ports=show_ports,
+            include_ports=include_ports,
             chains=chains,
             residues=residues,
             box=box,
@@ -3323,7 +3323,7 @@ def to_parmed(
         box=None,
         title="",
         residues=None,
-        show_ports=False,
+        include_ports=False,
         infer_residues=False,
         infer_residues_kwargs={},
     ):
@@ -3341,7 +3341,7 @@ def to_parmed(
         residues : str of list of str, optional, default=None
             Labels of residues in the Compound. Residues are assigned by checking
             against Compound.name.
-        show_ports : boolean, optional, default=False
+        include_ports : boolean, optional, default=False
             Include all port atoms when converting to a `Structure`.
         infer_residues : bool, optional, default=True
             Attempt to assign residues based on the number of bonds and particles in
@@ -3364,7 +3364,7 @@ def to_parmed(
             box=box,
             title=title,
             residues=residues,
-            show_ports=show_ports,
+            include_ports=include_ports,
             infer_residues=infer_residues,
             infer_residues_kwargs=infer_residues_kwargs,
         )
@@ -3400,7 +3400,7 @@ def to_pybel(
         box=None,
         title="",
         residues=None,
-        show_ports=False,
+        include_ports=False,
         infer_residues=False,
     ):
         """Create a pybel.Molecule from a Compound.
@@ -3413,7 +3413,7 @@ def to_pybel(
         residues : str of list of str
             Labels of residues in the Compound. Residues are assigned by
             checking against Compound.name.
-        show_ports : boolean, optional, default=False
+        include_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
@@ -3438,7 +3438,7 @@ def to_pybel(
             box=box,
             title=title,
             residues=residues,
-            show_ports=show_ports,
+            include_ports=include_ports,
         )
 
     def to_smiles(self, backend="pybel"):

mbuild/conversion.py

@@ -966,7 +966,7 @@ def from_gmso(
 def save(
     compound,
     filename,
-    show_ports=False,
+    include_ports=False,
     forcefield_name=None,
     forcefield_files=None,
     forcefield_debug=False,
@@ -990,7 +990,7 @@ def save(
         'hoomdxml', 'gsd', 'gro', 'top', 'lammps', 'lmp', 'mcf', 'xyz', 'pdb',
         'sdf', 'mol2', 'psf'. See parmed/structure.py for more information on
         savers.
-    show_ports : bool, optional, default=False
+    include_ports : bool, optional, default=False
         Save ports contained within the compound.
     forcefield_files : str, optional, default=None
         Apply a forcefield to the output file using a forcefield provided by the
@@ -1054,7 +1054,7 @@ def save(
     -----
     When saving the compound as a json, only the following arguments are used:
         - filename
-        - show_ports
+        - include_ports
 
     See Also
     --------
@@ -1068,7 +1068,9 @@ def save(
     extension = os.path.splitext(filename)[-1]
 
     if extension == ".json":
-        compound_to_json(compound, file_path=filename, include_ports=show_ports)
+        compound_to_json(
+            compound, file_path=filename, include_ports=include_ports
+        )
         return
 
     # Savers supported by mbuild.formats
@@ -1098,7 +1100,7 @@ def save(
     structure = compound.to_parmed(
         box=box,
         residues=residues,
-        show_ports=show_ports,
+        include_ports=include_ports,
         **parmed_kwargs,
     )
     # Apply a force field with foyer if specified
@@ -1301,7 +1303,7 @@ def to_parmed(
     box=None,
     title="",
     residues=None,
-    show_ports=False,
+    include_ports=False,
     infer_residues=False,
     infer_residues_kwargs={},
 ):
@@ -1321,7 +1323,7 @@ def to_parmed(
     residues : str of list of str, optional, default=None
         Labels of residues in the Compound. Residues are assigned by checking
         against Compound.name.
-    show_ports : boolean, optional, default=False
+    include_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 the number of bonds and particles in
@@ -1361,7 +1363,7 @@ def to_parmed(
     atom_residue_map = dict()
 
     # Loop through particles and add initialize ParmEd atoms
-    for atom in compound.particles(include_ports=show_ports):
+    for atom in compound.particles(include_ports=include_ports):
         if atom.port_particle:
             current_residue = port_residue
             atom_residue_map[atom] = current_residue
@@ -1458,13 +1460,13 @@ def to_parmed(
 
 
 def to_trajectory(
-    compound, show_ports=False, chains=None, residues=None, box=None
+    compound, include_ports=False, chains=None, residues=None, box=None
 ):
     """Convert to an md.Trajectory and flatten the compound.
 
     Parameters
     ----------
-    show_ports : bool, optional, default=False
+    include_ports : bool, optional, default=False
         Include all port atoms when converting to trajectory.
     chains : mb.Compound or list of mb.Compound
         Chain types to add to the topology
@@ -1485,7 +1487,7 @@ def to_trajectory(
     _to_topology
     """
     md = import_("mdtraj")
-    atom_list = [particle for particle in compound.particles(show_ports)]
+    atom_list = [particle for particle in compound.particles(include_ports)]
 
     top = _to_topology(compound, atom_list, chains, residues)
 
@@ -1650,7 +1652,7 @@ def to_pybel(
     box=None,
     title="",
     residues=None,
-    show_ports=False,
+    include_ports=False,
     infer_residues=False,
 ):
     """Create a pybel.Molecule from a Compound.
@@ -1665,7 +1667,7 @@ def to_pybel(
     residues : str of list of str
         Labels of residues in the Compound. Residues are assigned by checking
         against Compound.name.
-    show_ports : boolean, optional, default=False
+    include_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
@@ -1697,7 +1699,7 @@ def to_pybel(
     compound_residue_map = dict()
     atom_residue_map = dict()
 
-    for i, part in enumerate(compound.particles(include_ports=show_ports)):
+    for i, part in enumerate(compound.particles(include_ports=include_ports)):
         if residues and part.name in residues:
             current_residue = mol.NewResidue()
             current_residue.SetName(part.name)

mbuild/formats/json_formats.py

@@ -6,6 +6,7 @@
 import ele
 
 import mbuild as mb
+from mbuild.bond_graph import BondGraph
 from mbuild.exceptions import MBuildError
 
 
@@ -56,6 +57,7 @@ def compound_from_json(json_file):
                 sub_cmpd = _dict_to_mb(sub_compound)
                 converted_dict[sub_compound["id"]] = sub_cmpd
             sub_cmpd = converted_dict[sub_compound["id"]]
+            sub_cmpd.bond_graph = None
 
             label_str = sub_compound["label"]
             label_list = compound.get("label_list", {})
@@ -64,7 +66,12 @@ def compound_from_json(json_file):
                     parent_compound.labels[key] = list()
                 if sub_compound["id"] in vals:
                     parent_compound.labels[key].append(sub_cmpd)
-            parent_compound.add(sub_cmpd, label=label_str)
+            parent_compound.add(sub_cmpd, check_box_size=False, label=label_str)
+
+        parent.bond_graph = BondGraph()
+        parent.bond_graph.add_nodes_from(
+            [particle for particle in parent.particles()]
+        )
 
         _add_ports(compound_dict, converted_dict)
         _add_bonds(compound_dict, parent, converted_dict)
@@ -152,6 +159,7 @@ def _particle_info(cmpd, include_ports=False):
             else:
                 port_info["anchor"] = None
             port_info["label"] = None
+            port_info["pos"] = port.pos.tolist()
             # Is this the most efficient way?
             for key, val in cmpd.labels.items():
                 if (val == port) and val.port_particle:
@@ -236,15 +244,21 @@ def _add_ports(compound_dict, converted_dict):
             for port in ports:
                 label_str = port["label"]
                 port_to_add = mb.Port(anchor=converted_dict[port["anchor"]])
-                converted_dict[compound["id"]].add(port_to_add, label_str)
+                if port.get("pos", None) is not None:
+                    port_to_add.translate_to(port.get("pos"))
+                converted_dict[compound["id"]].add(
+                    port_to_add, label_str, check_box_size=False
+                )
             # Not necessary to add same port twice
             compound["ports"] = None
         ports = subcompound.get("ports", None)
         if ports:
             for port in ports:
                 label_str = port["label"]
                 port_to_add = mb.Port(anchor=converted_dict[port["anchor"]])
-                converted_dict[subcompound["id"]].add(port_to_add, label_str)
+                converted_dict[subcompound["id"]].add(
+                    port_to_add, label_str, check_box_size=False
+                )
             subcompound["ports"] = None
 
 

mbuild/tests/test_json_formats.py

@@ -121,3 +121,12 @@ def test_float_64_position(self):
         compound_to_json(ethane, "ethane.json", include_ports=True)
         ethane_copy = compound_from_json("ethane.json")
         assert np.allclose(ethane.xyz, ethane_copy.xyz, atol=10**-6)
+
+    def test_compound_with_port(self):
+        ch2 = mb.lib.moieties.CH2()
+        ch2.save("ch2.json", include_ports=True, overwrite=True)
+
+        loaded_ch2 = mb.load("ch2.json")
+        assert len(loaded_ch2.all_ports()) == 2
+        for port in loaded_ch2.all_ports():
+            assert port.separation == 0.07