Lammps molecule number

.gitignore

@@ -5,6 +5,9 @@ test-output.xml
 # C extensions
 *.so
 
+# Tmp Files
+*.swp
+
 # Packages
 *.egg
 *.egg-info

mbuild/compound.py

@@ -2579,6 +2579,7 @@ def save(
         residues=None,
         combining_rule="lorentz",
         foyer_kwargs=None,
+        parmed_kwargs=None,
         **kwargs,
     ):
         """Save the Compound to a file.
@@ -2623,6 +2624,14 @@ def save(
             `write_mcf`, or `parmed.Structure.save`.
             See `parmed structure documentation
             <https://parmed.github.io/ParmEd/html/structobj/parmed.structure.Structure.html#parmed.structure.Structure.save>`_
+        parmed_kwargs : dict, optional, default=None
+            Keyword arguments to provide to :meth:`mbuild.Compound.to_parmed`
+        **kwargs
+            Depending on the file extension these will be passed to either
+            `write_gsd`, `write_hoomdxml`, `write_lammpsdata`, `write_mcf`, or
+            `parmed.Structure.save`.
+            See https://parmed.github.io/ParmEd/html/structobj/parmed.structure.
+            Structure.html#parmed.structure.Structure.save
 
         Other Parameters
         ----------------
@@ -2677,6 +2686,7 @@ def save(
             residues,
             combining_rule,
             foyer_kwargs,
+            parmed_kwargs,
             **kwargs,
         )
 
@@ -2941,8 +2951,9 @@ def to_parmed(
             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.
+        infer_residues : bool, optional, default=True
+            Attempt to assign residues based on names of children for the level
+            of compound hierarchy without a box definition.
 
         Returns
         -------

mbuild/conversion.py

@@ -935,6 +935,7 @@ def save(
     residues=None,
     combining_rule="lorentz",
     foyer_kwargs=None,
+    parmed_kwargs=None,
     **kwargs,
 ):
     """Save the Compound to a file.
@@ -975,6 +976,8 @@ def save(
         geometric combining rules respectively.
     foyer_kwargs : dict, optional, default=None
         Keyword arguments to provide to `foyer.Forcefield.apply`.
+    parmed_kwargs : dict, optional, default=None
+        Keyword arguments to provide to :meth:`mbuild.Compound.to_parmed`
     **kwargs
         Depending on the file extension these will be passed to either
         `write_gsd`, `write_hoomdxml`, `write_lammpsdata`, `write_mcf`, or
@@ -1047,8 +1050,13 @@ def save(
     if os.path.exists(filename) and not overwrite:
         raise IOError("{0} exists; not overwriting".format(filename))
 
+    if not parmed_kwargs:
+        parmed_kwargs = {}
     structure = compound.to_parmed(
-        box=box, residues=residues, show_ports=show_ports
+        box=box,
+        residues=residues,
+        show_ports=show_ports,
+        **parmed_kwargs,
     )
     # Apply a force field with foyer if specified
     if forcefield_name or forcefield_files:
@@ -1115,7 +1123,7 @@ def to_parmed(
     title="",
     residues=None,
     show_ports=False,
-    infer_residues=False,
+    infer_residues=True,
 ):
     """Create a Parmed Structure from a Compound.
 
@@ -1135,8 +1143,9 @@ def to_parmed(
         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.
+    infer_residues : bool, optional, default=True
+        Attempt to assign residues based on names of children for the level
+        of compound hierarchy without a box definition.
 
     Returns
     -------
@@ -1147,14 +1156,44 @@ def to_parmed(
     --------
     parmed.structure.Structure : Details on the ParmEd Structure object
     """
+
+    def _pull_hierarchical_attrs(
+        compound,
+        target_attr="name",
+        hierarchical_attr="children",
+        target_attr_conditions={"_box": None},
+    ):
+        """List of attributes from children in an obscure hierarchy."""
+        value_list = []
+        if any(
+            [
+                getattr(compound, x) == y
+                for x, y in target_attr_conditions.items()
+            ]
+        ):
+            value_list.append(getattr(compound, target_attr))
+        else:
+            for child in getattr(compound, "children"):
+                value_list.extend(
+                    _pull_hierarchical_attrs(
+                        child,
+                        target_attr=target_attr,
+                        hierarchical_attr=hierarchical_attr,
+                        target_attr_conditions=target_attr_conditions,
+                    )
+                )
+
+        return value_list
+
     structure = pmd.Structure()
     structure.title = title if title else compound.name
     atom_mapping = {}  # For creating bonds below
     guessed_elements = set()
 
-    # Attempt to grab residue names based on names of children
+    # Attempt to grab residue names based on names of children for the first
+    # level of hierarchy without a box definition
     if not residues and infer_residues:
-        residues = list(set([child.name for child in compound.children]))
+        residues = _pull_hierarchical_attrs(compound)
 
     if isinstance(residues, str):
         residues = [residues]