Merge branch 'main' into rdkit_vis

.github/workflows/CI.yaml

@@ -107,7 +107,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: test
     name: Build Docker Image
-    if: ${{ false }}
+    if: github.event_name != 'pull_request'
 
     steps:
       - name: Set up Docker Buildx

.pre-commit-config.yaml

@@ -10,14 +10,14 @@ ci:
     submodules: false
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
       exclude: setup.cfg
 - repo: https://github.com/psf/black
-  rev: 23.7.0
+  rev: 23.9.1
   hooks:
     - id: black
       args: [--line-length=80]

Dockerfile

@@ -1,4 +1,4 @@
-ARG PY_VERSION=3.8
+ARG PY_VERSION=3.10
 FROM continuumio/miniconda3:4.10.3-alpine AS builder
 
 EXPOSE 8888
@@ -17,6 +17,9 @@ WORKDIR /mbuild
 # Create a group and user
 RUN addgroup -S anaconda && adduser -S anaconda -G anaconda
 
+# install the libarchive package needed by mamba
+RUN apk update && apk add libarchive
+
 RUN conda update conda -yq && \
   conda config --set always_yes yes --set changeps1 no && \
   . /opt/conda/etc/profile.d/conda.sh && \

docs/conf.py

@@ -162,8 +162,8 @@
 # built documents.
 #
 
-version = "0.16.3"
-release = "0.16.3"
+version = "0.16.4"
+release = "0.16.4"
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

docs/docs-env.yml

@@ -19,3 +19,4 @@ dependencies:
     - lxml
     - numpydoc
     - widgetsnbextension
+    - mock

mbuild/__init__.py

@@ -10,4 +10,4 @@
 from mbuild.port import Port
 from mbuild.recipes import recipes
 
-__version__ = "0.16.3"
+__version__ = "0.16.4"

mbuild/compound.py

@@ -2904,7 +2904,9 @@ def save(
         filename : str
             Filesystem path in which to save the trajectory. The extension or
             prefix will be parsed and control the format. Supported extensions:
-            'hoomdxml', 'gsd', 'gro', 'top', 'lammps', 'lmp', 'mcf'
+            '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
             Save ports contained within the compound.
         forcefield_files : str, optional, default=None

mbuild/conversion.py

@@ -986,7 +986,9 @@ def save(
     filename : str
         Filesystem path in which to save the trajectory. The extension or prefix
         will be parsed and control the format. Supported extensions are:
-        'hoomdxml', 'gsd', 'gro', 'top', 'lammps', 'lmp', 'mcf'.
+        '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
         Save ports contained within the compound.
     forcefield_files : str, optional, default=None

mbuild/formats/xyz.py

@@ -44,6 +44,7 @@ def read_xyz(filename, compound=None):
 
     guessed_elements = set()
 
+    compound_list = []
     with open(filename, "r") as xyz_file:
         n_atoms = int(xyz_file.readline())
         xyz_file.readline()
@@ -74,7 +75,7 @@ def read_xyz(filename, compound=None):
                 element = None
 
             particle = mb.Compound(pos=coords[row], name=name, element=element)
-            compound.add(particle)
+            compound_list.append(particle)
 
         # Verify we have read the last line by ensuring the next line in blank
         line = xyz_file.readline().split()
@@ -86,6 +87,8 @@ def read_xyz(filename, compound=None):
             )
             raise MBuildError(msg.format(n_atoms))
 
+    compound.add(compound_list)
+
     return compound
 
 

mbuild/packing.py

@@ -668,6 +668,7 @@ def solvate(
     fix_orientation=False,
     temp_file=None,
     update_port_locations=False,
+    center_solute=True,
 ):
     """Solvate a compound in a box of solvent using PACKMOL.
 
@@ -701,6 +702,8 @@ def solvate(
     update_port_locations : bool, default=False
         After packing, port locations can be updated, but since compounds can be
         rotated, port orientation may be incorrect.
+    center_solute : bool, optional, default=True
+        Move solute center of mass to the center of the `mb.Box` used.
 
     Returns
     -------
@@ -724,8 +727,10 @@ def solvate(
     box_mins = np.asarray(min_tmp) * 10
     box_maxs = np.asarray(max_tmp) * 10
     overlap *= 10
-    center_solute = (box_maxs + box_mins) / 2
-
+    if center_solute:
+        center_solute = (box_maxs + box_mins) / 2
+    else:
+        center_solute = solute.pos * 10
     # Apply edge buffer
     box_maxs = np.subtract(box_maxs, edge * 10)
     box_mins = np.add(box_mins, edge * 10)
@@ -888,9 +893,12 @@ def _create_topology(container, comp_to_add, n_compounds):
     container : mb.Compound
         Compound with added compounds from PACKMOL.
     """
+    container_list = []
     for comp, m_compound in zip(comp_to_add, n_compounds):
         for _ in range(m_compound):
-            container.add(clone(comp))
+            container_list.append(clone(comp))
+
+    container.add(container_list)
     return container
 
 

mbuild/tests/test_compound.py

@@ -310,7 +310,7 @@ def test_show_hierarchy(self, capsys):
         temp_particle.print_hierarchy()
 
         captured = capsys.readouterr()
-        assert captured.out.strip() == "C, 1 particles, 0 bonds, 0 children"
+        assert "C, 1 particles, 0 bonds, 0 children" in captured.out.strip()
 
         temp_particle.print_hierarchy(show_tree=False)
         captured = capsys.readouterr()

mbuild/tests/test_packing.py

@@ -214,9 +214,24 @@ def test_fill_box_multiple(self, ethane, h2o):
 
     def test_solvate(self, ethane, h2o):
         n_solvent = 100
-        solvated = mb.solvate(ethane, h2o, n_solvent=n_solvent, box=[4, 4, 4])
-        assert solvated.n_particles == 8 + n_solvent * 3
-        assert solvated.n_bonds == 7 + n_solvent * 2
+        ethane_pos = ethane.pos
+        solvated1 = mb.solvate(
+            ethane, h2o, n_solvent=n_solvent, box=[4, 4, 4], center_solute=True
+        )
+        solvated2 = mb.solvate(
+            ethane, h2o, n_solvent=n_solvent, box=[4, 4, 4], center_solute=False
+        )
+
+        print(ethane.xyz)
+        print(solvated2.children[0].xyz)
+
+        assert (
+            solvated1.n_particles == solvated2.n_particles == 8 + n_solvent * 3
+        )
+        assert solvated1.n_bonds == solvated2.n_bonds == 7 + n_solvent * 2
+        assert not np.isclose(solvated1.children[0].pos, ethane_pos).all()
+        assert np.isclose(solvated2.children[0].pos, ethane_pos).all()
+
         assert ethane.parent == None
 
     def test_solvate_multiple(self, methane, ethane, h2o):

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.16.3
+current_version = 0.16.4
 commit = True
 tag = True
 message = Bump to version {new_version}

setup.py

@@ -17,7 +17,7 @@
 
 #####################################
 NAME = "mbuild"
-VERSION = "0.16.3"
+VERSION = "0.16.4"
 ISRELEASED = True
 if ISRELEASED:
     __version__ = VERSION