Use JAX for relaxation

.github/workflows/test_and_deploy.yml

@@ -32,7 +32,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04, windows-2019, macos-11]
-    
+
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v3
@@ -86,7 +86,7 @@ jobs:
           auto-update-conda: true
           python-version: '3.11'
       - name: Installing dependencies
-        run: conda install -c conda-forge sphinx cython numpy numpydoc biotite
+        run: conda install -c conda-forge sphinx numpy numpydoc biotite
       - name: Building documentation
         run: sphinx-build ./doc ./build/doc
       - name: Zipping documentation

.gitignore

@@ -19,14 +19,8 @@ htmlcov
 # Ignore all compiled python files (e.g. from running the unit tests)
 *.pyc
 *.pyo
-*.py{}
 *.py-e
 
-# Ignore files created via Cython
-*.c
-*.so
-*.pyd
-
 # Ignore potential directory created during install
 *.egg-info
 
@@ -42,5 +36,6 @@ htmlcov
 *.code-workspace
 .vscode/*
 
-# Ignore fuse_hidden files on Linux systems
+# Ignore OS specific files
 *.fuse_hidden*
+.DS_Store

doc/cli.rst

@@ -22,7 +22,7 @@ Structure input and output
 
 ``--infile``/``-i`` and ``-outfile``/``-o`` define the paths of the input or
 output structure file, respectively.
-*Hydride* supports the *PDB*, *PDBx/mmCIF*, *MMTF*, *MOL* and *SDF*
+*Hydride* supports the *PDB*, *PDBx/mmCIF*, *BinaryCIF*, *MOL* and *SDF*
 format.
 By default, the format is determined from the file extension, but it can also
 be explicitly provided via the ``--informat``/``-I`` or
@@ -38,8 +38,6 @@ used is specified with ``--model``/``-m``. By default, the first model is used.
 
 The addition of hydrogen atoms requires complete information about the
 bonds between atoms.
-Currently, this information can only be read from *PDB*, *MMTF*, *MOL* and
-*SDF* files.
 If bond information is absent, *Hydride* automatically connects
 atoms based on the molecule/residue name and the atom names.
 However, the automatic bond detection only works for molecules in the
@@ -97,7 +95,7 @@ libraries by providing a path to a corresponding structure file via
 Analogous to the input and output file parameters, the file format can be
 specified with ``--fragformat``/``-f``.
 Note that the file must contain proper bond information and correct formal
-charges, so effectively a *MMTF*, *MOL* and *SDF* must be supplied.
+charges.
 
 By default, *Hydride* does not consider periodic boundary conditions,
 as they appear e.g. in MD simulations.

doc/conf.py

@@ -4,40 +4,31 @@
 
 __author__ = "Patrick Kunzmann"
 
-try:
-    import numpy as np
-    import pyximport
-    pyximport.install(
-        build_in_temp=False,
-        setup_args={"include_dirs":np.get_include()},
-        language_level=3
-    )
-except ImportError:
-    pass
-
-from os.path import realpath, dirname, join, isdir, isfile, basename
-from os import listdir, makedirs
 import sys
+from os.path import dirname, join, realpath
 
 doc_path = dirname(realpath(__file__))
 # Include hydride/src in PYTHONPATH
 # in order to import the 'hydride' package
 package_path = join(dirname(doc_path), "src")
 sys.path.insert(0, package_path)
-import hydride
+import hydride  # noqa: E402
+
 # Include gecos/doc in PYTHONPATH
 # in order to import modules for plot genaration etc.
 sys.path.insert(0, doc_path)
 
 
 #### General ####
 
-extensions = ["sphinx.ext.autodoc",
-              "sphinx.ext.autosummary",
-              "sphinx.ext.doctest",
-              "sphinx.ext.mathjax",
-              "sphinx.ext.viewcode",
-              "numpydoc"]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "numpydoc",
+]
 
 templates_path = ["templates"]
 source_suffix = [".rst"]
@@ -62,25 +53,26 @@
 
 html_theme = "alabaster"
 html_static_path = ["static"]
-html_css_files = [
-    "hydride.css",
-    "fonts.css"
-]
+html_css_files = ["hydride.css", "fonts.css"]
 html_favicon = "static/assets/hydride_icon_32p.png"
 htmlhelp_basename = "HydrideDoc"
-html_sidebars = {"**": ["about.html",
-                        "navigation.html",
-                        "relations.html",
-                        "searchbox.html",
-                        "donate.html"]}
+html_sidebars = {
+    "**": [
+        "about.html",
+        "navigation.html",
+        "relations.html",
+        "searchbox.html",
+        "donate.html",
+    ]
+}
 html_theme_options = {
-    "description"   : "Adding hydrogen atoms to molecular models",
-    "logo"          : "assets/hydride_logo.png",
-    "logo_name"     : "false",
-    "github_user"   : "biotite-dev",
-    "github_repo"   : "hydride",
-    "github_type"   : "star",
-    "github_banner" : "true",
-    "page_width"    : "85%",
-    "fixed_sidebar" : "true"
+    "description": "Adding hydrogen atoms to molecular models",
+    "logo": "assets/hydride_logo.png",
+    "logo_name": "false",
+    "github_user": "biotite-dev",
+    "github_repo": "hydride",
+    "github_type": "star",
+    "github_banner": "true",
+    "page_width": "85%",
+    "fixed_sidebar": "true",
 }

doc/figure_scripts/api.py

@@ -5,13 +5,12 @@
 """
 
 import tempfile
+import ammolite
 import biotite.structure as struc
-import biotite.structure.io.mol as mol
 import biotite.structure.info as info
-import ammolite
+import biotite.structure.io.mol as mol
 from util import COLORS, init_pymol_parameters
 
-
 ZOOM = 1.5
 PNG_SIZE = (400, 400)
 
@@ -63,7 +62,7 @@ def color_atoms(pymol_object, atom_array):
 
 print("\nEND OF SNIPPET\n")
 pymol_heavy = ammolite.PyMOLObject.from_structure(molecule, "heavy")
-#pymol_heavy.orient()
+# pymol_heavy.orient()
 pymol_heavy.zoom(buffer=ZOOM)
 color_atoms(pymol_heavy, molecule)
 ammolite.cmd.png("api_01.png", *PNG_SIZE)
@@ -168,9 +167,10 @@ def color_atoms(pymol_object, atom_array):
 
 
 print("\nEND OF SNIPPET\n", end="")
-import matplotlib.pyplot as plt
 import matplotlib as mpl
-plt.rcParams['axes.prop_cycle'] = mpl.cycler(color=[COLORS["N"]])
+import matplotlib.pyplot as plt
+
+plt.rcParams["axes.prop_cycle"] = mpl.cycler(color=[COLORS["N"]])
 
 
 ########################################################################
@@ -201,6 +201,7 @@ def color_atoms(pymol_object, atom_array):
 fig.savefig("api_04.png")
 
 import biotite.structure.info as info
+
 molecule = info.residue("ASP")
 
 
@@ -229,4 +230,4 @@ def color_atoms(pymol_object, atom_array):
 
 #
 #
-########################################################################
+########################################################################

doc/figure_scripts/cover_structure.py

@@ -1,24 +1,14 @@
-import numpy as np
-import pyximport
-pyximport.install(
-    build_in_temp=False,
-    setup_args={"include_dirs":np.get_include()},
-    language_level=3
-)
-
-from os.path import join
-import numpy as np
-import biotite.structure as struc
-import biotite.structure.io.mmtf as mmtf
-import biotite.database.rcsb as rcsb
-import hydride
 import ammolite
+import biotite.database.rcsb as rcsb
+import biotite.structure as struc
+import biotite.structure.io.pdbx as pdbx
+import numpy as np
 from util import COLORS, init_pymol_parameters
+import hydride
 
-
-mmtf_file = mmtf.MMTFFile.read(rcsb.fetch("1bna", "mmtf"))
-heavy_atoms = mmtf.get_structure(
-    mmtf_file, model=1, include_bonds=True, extra_fields=["charge"]
+pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch("1bna", "bcif"))
+heavy_atoms = pdbx.get_structure(
+    pdbx_file, model=1, include_bonds=True, extra_fields=["charge"]
 )
 heavy_atoms = heavy_atoms[heavy_atoms.res_name != "HOH"]
 
@@ -43,9 +33,7 @@
 pymol_all.zoom(buffer=1.0)
 ammolite.cmd.rotate("z", 90)
 
-for pymol_object, atoms in zip(
-    (pymol_heavy, pymol_all), (heavy_atoms, all_atoms)
-):
+for pymol_object, atoms in zip((pymol_heavy, pymol_all), (heavy_atoms, all_atoms)):
     for element in ("H", "C", "N", "O", "P"):
         pymol_object.color(COLORS[element], atoms.element == element)
 
@@ -56,9 +44,8 @@
 pymol_heavy.disable()
 pymol_all.enable()
 for i, (_, atom_i, atom_j) in enumerate(bonds):
-    color = COLORS["N"] if all_atoms.element[atom_j] == "N"\
-            else COLORS["O"]
+    color = COLORS["N"] if all_atoms.element[atom_j] == "N" else COLORS["O"]
     pymol_all.distance(str(i), atom_i, atom_j, show_label=False)
     ammolite.cmd.set_color(f"bond_color_{i}", list(color))
     ammolite.cmd.color(f"bond_color_{i}", str(i))
-ammolite.cmd.png("cover_hydrogenated.png", 400, 800)
+ammolite.cmd.png("cover_hydrogenated.png", 400, 800)

doc/figure_scripts/fragments.py

@@ -1,13 +1,10 @@
-import time
-from os.path import join, abspath, dirname
-import numpy as np
-from sklearn.decomposition import PCA
+from os.path import abspath, dirname, join
+import ammolite
 import biotite.structure as struc
 import biotite.structure.io.mol as mol
-import ammolite
+import numpy as np
 from util import COLORS, init_pymol_parameters
 
-
 PNG_SIZE = (300, 300)
 ZOOM = 3.5
 MOL_DIR = dirname(abspath(__file__))
@@ -20,17 +17,18 @@ def load_and_orient(mol_name):
     molecule.coord -= struc.centroid(molecule)
     return molecule
 
-benzene  = load_and_orient("benzene")
+
+benzene = load_and_orient("benzene")
 butylene = load_and_orient("isobutylene")
-toluene  = load_and_orient("toluene")
+toluene = load_and_orient("toluene")
 benzene_heavy, butylene_heavy, toluene_heavy = [
     atoms[atoms.element != "H"] for atoms in (benzene, butylene, toluene)
 ]
 
 
 init_pymol_parameters()
 
-center = struc.array([struc.Atom([0,0,0], atom_name="C", element="C")])
+center = struc.array([struc.Atom([0, 0, 0], atom_name="C", element="C")])
 center.bonds = struc.BondList(1)
 CENTER = ammolite.PyMOLObject.from_structure(center, "center_")
 ammolite.cmd.disable("center_")
@@ -41,7 +39,9 @@ def load_and_orient(mol_name):
 ammolite.cmd.png("toluene.png", *PNG_SIZE)
 ammolite.cmd.disable("toluene")
 
-pymol_toluene_heavy = ammolite.PyMOLObject.from_structure(toluene_heavy, "toluene_heavy")
+pymol_toluene_heavy = ammolite.PyMOLObject.from_structure(
+    toluene_heavy, "toluene_heavy"
+)
 CENTER.zoom(buffer=ZOOM)
 pymol_toluene_heavy.color(COLORS["O"])
 ammolite.cmd.png("toluene_heavy.png", *PNG_SIZE)
@@ -70,7 +70,7 @@ def visualize_fragments(molecule, mol_name, color):
             fragment = molecule[np.append(bonded_i, [i])]
             fragment_name = f"{mol_name}_frag_{frag_num:02d}"
             frag_num += 1
-            
+
             pymol_fragment = ammolite.PyMOLObject.from_structure(
                 fragment, fragment_name
             )
@@ -80,6 +80,7 @@ def visualize_fragments(molecule, mol_name, color):
             ammolite.cmd.png(f"{fragment_name}.png", *PNG_SIZE)
             ammolite.cmd.disable(fragment_name)
 
-visualize_fragments(toluene_heavy, "toluene",  COLORS["O"])
-visualize_fragments(benzene,       "benzene",  COLORS["N"])
-visualize_fragments(butylene,      "butylene", COLORS["N"])
+
+visualize_fragments(toluene_heavy, "toluene", COLORS["O"])
+visualize_fragments(benzene, "benzene", COLORS["N"])
+visualize_fragments(butylene, "butylene", COLORS["N"])

doc/figure_scripts/rotation_freedom.py

@@ -1,13 +1,10 @@
-import time
-from os.path import join, abspath, dirname
-import numpy as np
-from sklearn.decomposition import PCA
+from os.path import abspath, dirname, join
+import ammolite
 import biotite.structure as struc
 import biotite.structure.io.mol as mol
-import ammolite
+import numpy as np
 from util import COLORS, init_pymol_parameters
 
-
 PNG_SIZE = (300, 300)
 ZOOM = 1.0
 MOL_DIR = dirname(abspath(__file__))
@@ -20,14 +17,15 @@ def load_and_orient(mol_name):
     molecule.coord -= struc.centroid(molecule)
     return molecule
 
-propane  = load_and_orient("propane")
+
+propane = load_and_orient("propane")
 
 
 ammolite.launch_interactive_pymol()
 
 init_pymol_parameters()
 
-center = struc.array([struc.Atom([0,0,0], atom_name="C", element="C")])
+center = struc.array([struc.Atom([0, 0, 0], atom_name="C", element="C")])
 center.bonds = struc.BondList(1)
 CENTER = ammolite.PyMOLObject.from_structure(center, "center_")
 ammolite.cmd.disable("center_")
@@ -37,12 +35,10 @@ def load_and_orient(mol_name):
     bonded_i = all_bonds[carbon_i]
     bonded_i = bonded_i[bonded_i != -1]
     fragment = propane[np.append(bonded_i, [carbon_i])]
-
-    pymol_fragment = ammolite.PyMOLObject.from_structure(
-        fragment, name, delete=False
-    )
+
+    pymol_fragment = ammolite.PyMOLObject.from_structure(fragment, name, delete=False)
     CENTER.zoom(buffer=ZOOM)
     pymol_fragment.color(COLORS["C"], fragment.element != "H")
     pymol_fragment.color(COLORS["N"], -1)
-    #ammolite.cmd.png(f"{name}.png", *PNG_SIZE)
-    #ammolite.cmd.disable(name)
+    # ammolite.cmd.png(f"{name}.png", *PNG_SIZE)
+    # ammolite.cmd.disable(name)