Merge branch 'main' into optimize_json_loading

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
     - id: trailing-whitespace
       exclude: setup.cfg
 - repo: https://github.com/psf/black
-  rev: 23.12.1
+  rev: 24.1.1
   hooks:
     - id: black
       args: [--line-length=80]

mbuild/__init__.py

@@ -1,4 +1,5 @@
 """mBuild: a hierarchical, component based molecule builder."""
+
 from mbuild.box import Box
 from mbuild.coarse_graining import coarse_grain
 from mbuild.compound import *

mbuild/box.py

@@ -1,4 +1,5 @@
 """mBuild box module."""
+
 from warnings import warn
 
 import numpy as np

mbuild/coarse_graining.py

@@ -1,4 +1,5 @@
 """Tools for coarse-grained systems."""
+
 from collections import OrderedDict
 from copy import deepcopy
 

mbuild/compound.py

@@ -1,4 +1,5 @@
 """Module for working with mBuild Compounds."""
+
 __all__ = ["clone", "Compound", "Particle"]
 
 import itertools
@@ -1864,7 +1865,11 @@ def particles_in_range(
         return particle_array[idxs]
 
     def visualize(
-        self, show_ports=False, backend="py3dmol", color_scheme={}
+        self,
+        show_ports=False,
+        backend="py3dmol",
+        color_scheme={},
+        bead_size=0.3,
     ):  # pragma: no cover
         """Visualize the Compound using py3dmol (default) or nglview.
 
@@ -1882,6 +1887,8 @@ def visualize(
             keys are strings of the particle names
             values are strings of the colors
             i.e. {'_CGBEAD': 'blue'}
+        bead_size : float, Optional, default=0.3
+            Size of beads in visualization
         """
         viz_pkg = {
             "nglview": self._visualize_nglview,
@@ -1890,7 +1897,9 @@ def visualize(
         if run_from_ipython():
             if backend.lower() in viz_pkg:
                 return viz_pkg[backend.lower()](
-                    show_ports=show_ports, color_scheme=color_scheme
+                    show_ports=show_ports,
+                    color_scheme=color_scheme,
+                    bead_size=bead_size,
                 )
             else:
                 raise RuntimeError(
@@ -1903,7 +1912,9 @@ def visualize(
                 "Visualization is only supported in Jupyter Notebooks."
             )
 
-    def _visualize_py3dmol(self, show_ports=False, color_scheme={}):
+    def _visualize_py3dmol(
+        self, show_ports=False, color_scheme={}, bead_size=0.3
+    ):
         """Visualize the Compound using py3Dmol.
 
         Allows for visualization of a Compound within a Jupyter Notebook.
@@ -1917,6 +1928,8 @@ def _visualize_py3dmol(self, show_ports=False, color_scheme={}):
             keys are strings of the particle names
             values are strings of the colors
             i.e. {'_CGBEAD': 'blue'}
+        bead_size : float, Optional, default=0.3
+            Size of beads in visualization
 
         Returns
         -------
@@ -1951,15 +1964,20 @@ def _visualize_py3dmol(self, show_ports=False, color_scheme={}):
 
         view.setStyle(
             {
-                "stick": {"radius": 0.2, "color": "grey"},
-                "sphere": {"scale": 0.3, "colorscheme": modified_color_scheme},
+                "stick": {"radius": bead_size * 0.6, "color": "grey"},
+                "sphere": {
+                    "scale": bead_size,
+                    "colorscheme": modified_color_scheme,
+                },
             }
         )
         view.zoomTo()
 
         return view
 
-    def _visualize_nglview(self, show_ports=False, color_scheme={}):
+    def _visualize_nglview(
+        self, show_ports=False, color_scheme={}, bead_size=0.3
+    ):
         """Visualize the Compound using nglview.
 
         Allows for visualization of a Compound within a Jupyter Notebook.

mbuild/conversion.py

@@ -1,4 +1,5 @@
 """Module for handling conversions in mBuild."""
+
 import os
 import sys
 from collections import defaultdict

mbuild/coordinate_transform.py

@@ -1,4 +1,5 @@
 """Coordinate transformation functions."""
+
 from warnings import simplefilter, warn
 
 simplefilter("always", DeprecationWarning)

mbuild/formats/cassandramcf.py

@@ -2,6 +2,7 @@
 
 https://cassandra-mc.readthedocs.io/en/latest/guides/input_files.html#molecular-connectivity-file
 """
+
 from __future__ import division
 
 import warnings

mbuild/formats/gsdwriter.py

@@ -2,6 +2,7 @@
 
 https://gsd.readthedocs.io/en/stable/
 """
+
 import numpy as np
 
 from mbuild.utils.geometry import coord_shift

mbuild/formats/hoomd_forcefield.py

@@ -1,4 +1,5 @@
 """HOOMD v3 forcefield format."""
+
 import itertools
 import operator
 import warnings

mbuild/formats/hoomd_simulation.py

@@ -1,4 +1,5 @@
 """HOOMD simulation format."""
+
 import itertools
 import operator
 import warnings

mbuild/formats/hoomd_snapshot.py

@@ -1,4 +1,5 @@
 """HOOMD snapshot format."""
+
 import operator
 from collections import namedtuple
 

mbuild/formats/hoomdxml.py

@@ -1,4 +1,5 @@
 """HOOMD xml format."""
+
 import operator
 from collections import namedtuple
 from math import radians

mbuild/formats/json_formats.py

@@ -1,4 +1,5 @@
 """JSON format."""
+
 import json
 from collections import OrderedDict
 

mbuild/formats/lammpsdata.py

@@ -1,4 +1,5 @@
 """LAMMPS data format."""
+
 import itertools as it
 from collections import OrderedDict
 from warnings import warn
@@ -708,9 +709,7 @@ def _get_bond_types(
             (
                 round(
                     bond.type.k
-                    * (
-                        sigma_conversion_factor**2 / epsilon_conversion_factor
-                    ),
+                    * (sigma_conversion_factor**2 / epsilon_conversion_factor),
                     bond_precision,
                 ),
                 round(bond.type.req / sigma_conversion_factor, bond_precision),

mbuild/formats/par_writer.py

@@ -1,4 +1,5 @@
 """CHARMM Par format."""
+
 import warnings
 
 __all__ = ["write_par"]

mbuild/formats/protobuf.py

@@ -3,6 +3,7 @@
 A language-agnostic data serialization format developed by Google
 https://developers.google.com/protocol-buffers
 """
+
 import ele
 import numpy as np
 from google.protobuf.text_format import Merge, PrintMessage

mbuild/formats/vasp.py

@@ -1,4 +1,5 @@
 """VASP POSCAR format."""
+
 import warnings
 from itertools import chain
 

mbuild/formats/xyz.py

@@ -1,4 +1,5 @@
 """XYZ format."""
+
 from warnings import warn
 
 import numpy as np

mbuild/lattice.py

@@ -1,4 +1,5 @@
 """mBuild lattice module for working with crystalline systems."""
+
 import itertools as it
 import pathlib
 import warnings
@@ -679,8 +680,8 @@ def populate(self, compound_dict=None, x=1, y=1, z=1):
 
         # if coordinates are below a certain threshold, set to 0
         tolerance = 1e-12
-        ret_lattice.xyz_with_ports[
-            ret_lattice.xyz_with_ports <= tolerance
-        ] = 0.0
+        ret_lattice.xyz_with_ports[ret_lattice.xyz_with_ports <= tolerance] = (
+            0.0
+        )
 
         return ret_lattice

mbuild/lib/atoms/__init__.py

@@ -1,4 +1,5 @@
 """mBuild library of atoms."""
+
 from mbuild.lib.atoms.c3 import C3
 from mbuild.lib.atoms.h import H
 from mbuild.lib.atoms.n4 import N4

mbuild/lib/atoms/c3.py

@@ -1,4 +1,5 @@
 """A tri-valent, planar carbon atom."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/atoms/h.py

@@ -1,4 +1,5 @@
 """An H atom."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/atoms/n4.py

@@ -1,4 +1,5 @@
 """mBuild atom library for tetravalent nitrogen."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/bulk_materials/__init__.py

@@ -1,2 +1,3 @@
 """mBuild bulk materials library."""
+
 from mbuild.lib.bulk_materials.amorphous_silica_bulk import AmorphousSilicaBulk

mbuild/lib/bulk_materials/amorphous_silica_bulk.py

@@ -1,4 +1,5 @@
 """A bulk structure of amorphous silica."""
+
 import mbuild as mb
 
 

mbuild/lib/moieties/__init__.py

@@ -1,4 +1,5 @@
 """mBuild library of common chemical moieties."""
+
 from mbuild.lib.moieties.ch2 import CH2
 from mbuild.lib.moieties.ch3 import CH3
 from mbuild.lib.moieties.ester import Ester

mbuild/lib/moieties/ch2.py

@@ -1,4 +1,5 @@
 """CH2 moiety."""
+
 import mbuild as mb
 
 

mbuild/lib/moieties/ch3.py

@@ -1,4 +1,5 @@
 """mBuild CH3 moiety."""
+
 import mbuild as mb
 
 

mbuild/lib/moieties/ester.py

@@ -1,4 +1,5 @@
 """Ester moiety."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/moieties/h2o.py

@@ -1,4 +1,5 @@
 """A water molecule."""
+
 import mbuild as mb
 
 

mbuild/lib/moieties/peg.py

@@ -1,4 +1,5 @@
 """mBuild polyethylene glycol (PEG) monomer moiety."""
+
 __author__ = "jonestj1"
 
 import mbuild as mb

mbuild/lib/moieties/silane.py

@@ -1,4 +1,5 @@
 """A Silane (Si(OH)2) moiety."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/molecules/__init__.py

@@ -1,4 +1,5 @@
 """Library of molecules for mBuild."""
+
 from mbuild.lib.molecules.ethane import Ethane
 from mbuild.lib.molecules.methane import Methane
 from mbuild.lib.molecules.water import (

mbuild/lib/molecules/ethane.py

@@ -1,4 +1,5 @@
 """An ethane molecule."""
+
 import mbuild as mb
 from mbuild.lib.moieties import CH3
 

mbuild/lib/molecules/methane.py

@@ -1,4 +1,5 @@
 """A methane molecule."""
+
 import mbuild as mb
 
 

mbuild/lib/molecules/water.py

@@ -1,4 +1,5 @@
 """Water molecules with geometries from different models."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/recipes/__init__.py

@@ -1,4 +1,5 @@
 """Library of recipes for mBuild."""
+
 from mbuild.lib.recipes.alkane import Alkane
 from mbuild.lib.recipes.monolayer import Monolayer
 from mbuild.lib.recipes.polymer import Polymer

mbuild/lib/recipes/alkane.py

@@ -1,4 +1,5 @@
 """mBuild recipe for a generic alkane chain."""
+
 import mbuild as mb
 from mbuild.lib.moieties import CH2, CH3
 from mbuild.lib.molecules import Ethane, Methane

mbuild/lib/recipes/monolayer.py

@@ -1,4 +1,5 @@
 """mBuild monolayer recipe."""
+
 from copy import deepcopy
 from warnings import warn
 

mbuild/lib/recipes/polymer.py

@@ -1,4 +1,5 @@
 """Recipe for an mBuild polymer."""
+
 import itertools as it
 
 import numpy as np

mbuild/lib/recipes/silica_interface.py

@@ -1,4 +1,5 @@
 """mBuild recipe for a silica interface."""
+
 import math
 import random
 

mbuild/lib/recipes/tiled_compound.py

@@ -1,4 +1,5 @@
 """Module for creating TiledCompounds."""
+
 __all__ = ["TiledCompound"]
 
 import itertools as it

mbuild/lib/recipes/water_box.py

@@ -1,4 +1,5 @@
 """mBuild recipe for building a water box."""
+
 import itertools
 import math as math
 from collections.abc import Iterable

mbuild/lib/surfaces/__init__.py

@@ -1,3 +1,4 @@
 """mBuild surface library."""
+
 from mbuild.lib.surfaces.amorphous_silica_surface import AmorphousSilicaSurface
 from mbuild.lib.surfaces.betacristobalite import Betacristobalite

mbuild/lib/surfaces/amorphous_silica_surface.py

@@ -1,4 +1,5 @@
 """Amorphous silica surface."""
+
 import mbuild as mb
 
 

mbuild/lib/surfaces/betacristobalite.py

@@ -1,4 +1,5 @@
 """Beta-cristobalite surface."""
+
 import mbuild as mb
 
 

mbuild/packing.py

@@ -2,6 +2,7 @@
 
 http://leandro.iqm.unicamp.br/m3g/packmol/home.shtml
 """
+
 import os
 import sys
 import tempfile