Example09

chilife/chilife.py

@@ -562,6 +562,7 @@ def create_dlibrary(
         resname: str = None,
         dihedrals: ArrayLike = None,
         weights: ArrayLike = None,
+        sort_atoms = True,
         permanent: bool = False,
         default: bool = False,
         force: bool = False,
@@ -649,7 +650,7 @@ def create_dlibrary(
             "residue number"
         )
 
-    struct, spin_atoms = pre_add_library(pdb, spin_atoms, uniform_topology=False)
+    struct, spin_atoms = pre_add_library(pdb, spin_atoms, uniform_topology=False, sort_atoms=sort_atoms)
     res1 = struct.select_atoms(f'resnum {site1}')
     res2 = struct.select_atoms(f'resnum {site2}')
 
@@ -769,6 +770,7 @@ def pre_add_library(
         pdb: str,
         spin_atoms: List[str],
         uniform_topology: bool = True,
+        sort_atoms = True,
 ) -> Tuple[MDAnalysis.Universe, Dict]:
     """Helper function to sort PDBs, save spin atoms, update lists, etc. when adding a SpinLabel or dSpinLabel.
 
@@ -790,27 +792,32 @@ def pre_add_library(
     spin_atoms : dict
         Dictionary of spin atoms and weights if specified.
     """
-    # Sort the PDB for optimal dihedral definitions
-    pdb_lines, bonds = sort_pdb(pdb, uniform_topology=uniform_topology, return_bonds=True)
-    bonds = get_min_topol(pdb_lines, forced_bonds=bonds)
-
-    # Write a temporary file with the sorted atoms
-    if isinstance(pdb_lines[0], list):
-        with tempfile.NamedTemporaryFile(suffix=".pdb", mode="w+", delete=False) as tmpfile:
-            for i, model in enumerate(pdb_lines):
-                tmpfile.write(f"MODEL {i + 1}\n")
-                for atom in model:
-                    tmpfile.write(atom)
-                tmpfile.write("ENDMDL\n")
-    else:
-        with tempfile.NamedTemporaryFile(suffix=".pdb", mode="w+", delete=False) as tmpfile:
-            for line in pdb_lines:
-                tmpfile.write(line)
+    if sort_atoms:
+        # Sort the PDB for optimal dihedral definitions
+        pdb_lines, bonds = sort_pdb(pdb, uniform_topology=uniform_topology, return_bonds=True)
+        bonds = get_min_topol(pdb_lines, forced_bonds=bonds)
+
+        # Write a temporary file with the sorted atoms
+        if isinstance(pdb_lines[0], list):
+            with tempfile.NamedTemporaryFile(suffix=".pdb", mode="w+", delete=False) as tmpfile:
+                for i, model in enumerate(pdb_lines):
+                    tmpfile.write(f"MODEL {i + 1}\n")
+                    for atom in model:
+                        tmpfile.write(atom)
+                    tmpfile.write("ENDMDL\n")
+        else:
+            with tempfile.NamedTemporaryFile(suffix=".pdb", mode="w+", delete=False) as tmpfile:
+                for line in pdb_lines:
+                    tmpfile.write(line)
 
     # Load sorted atom pdb using MDAnalysis and remove tempfile
-    struct = mda.Universe(tmpfile.name, in_memory=True)
-    struct.universe.add_bonds(bonds)
-    os.remove(tmpfile.name)
+        struct = mda.Universe(tmpfile.name, in_memory=True)
+        struct.add_bonds(bonds)
+        os.remove(tmpfile.name)
+    else:
+        struct = mda.Universe(pdb, in_memory=True)
+        bonds = chilife.guess_bonds(struct.atoms.positions, struct.atoms.types)
+        struct.add_bonds(bonds)
 
     # Store spin atoms if provided
     if spin_atoms is not None:

examples/09 - Bifunctional Labels/Exp_Data.txt

@@ -0,0 +1,57 @@
+19.04371135	0
+19.52893153	0
+20.01415171	0
+20.49937088	0
+20.98459106	0
+21.46981124	0.000148602
+21.95503143	0
+22.44025161	0.001277658
+22.9254718	0.001709512
+23.41069198	0.002466733
+23.89591216	0.006279774
+24.38113132	0.011409769
+24.86635151	0.014555304
+25.35157169	0.014929992
+25.83679188	0.01278915
+26.32201206	0.008920883
+26.80723225	0.004488191
+27.29245243	0.001023366
+27.77767261	0
+28.26289177	0
+28.74811196	0
+29.23333214	0.000203712
+29.71855233	0.00051705
+30.20377251	0.000427106
+30.68899269	1.6869E-05
+31.17421288	0
+31.65943306	0
+32.14465222	0
+32.62987241	0
+33.11509259	0
+33.60031278	0
+34.08553296	0
+34.57075314	0
+35.05597333	0
+35.54119351	0
+36.02641267	0
+36.51163286	0
+36.99685304	0
+37.48207322	0
+37.96729341	0
+38.45251359	0
+38.93773378	0
+39.42295396	0
+39.90817312	0
+40.39339331	0
+40.87861349	0
+41.36383367	0
+41.84905386	0
+42.33427404	0
+42.81949423	0
+43.30471441	0
+43.78993357	0
+44.27515376	0
+44.76037394	0
+45.24559412	0
+45.73081431	0
+46.21603449	0

pyproject.toml

@@ -1,6 +1,34 @@
 [project]
 name = "chilife"
-dynamic = ["version"]
+description = 'A package for modeling non-canonical amino acid side chain ensembles.'
+license= {name = 'GNU GPLv3', file = 'LICENSE'}
+authors=[{name = 'Maxx Tessmer', email='[email protected]'},
+         {name = 'Stefan Stoll', email='[email protected]'}]
+keywords=['Spin-label', 'EPR', 'DEER', 'PELDOR', 'Side-chain']
+dynamic = ["version", "readme"]
+requires-python = ">= 3.8,<=3.11"
+dependencies = ['numpy>=1.23.0',
+                'scipy>=1.6.3',
+                'matplotlib>=3.3.4',
+                'numba>=0.57.0',
+                'mdanalysis>=2.0.0',
+                'tqdm>=4.45.0',
+                'pytest>=6.2.2',
+                'memoization>=0.3.1',
+                'argparse>=1.4.0',
+                'setuptools>=53.0.0',
+                'igraph>=0.11.2',
+                'rtoml>=0.9.0']
+
+classifiers=['License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+             'Programming Language :: Python :: 3.8',
+             'Programming Language :: Python :: 3.9',
+             'Programming Language :: Python :: 3.10',
+             'Programming Language :: Python :: 3.11']
+
+[project.urls]
+homepage = 'https://github.com/StollLab/chiLife'
+documentation = "stolllab.github.io/chiLife/"
 
 [tool.setuptools.dynamic]
 version = {attr = "chilife.__version__"}

setup.py

@@ -23,35 +23,11 @@ def __init__(self, *args, **kwargs):
 
 setup(
     name='chilife',
-    python_requires='>=3.8',
     packages=['chilife'],
     package_data={'chilife': ['data/*', 'data/*/*', 'data/*/*/*']},
     scripts=['scripts/update_rotlib.py', 'scripts/oldProteinIC.py'],
-    license='GNU GPLv3',
-    license_files=('LICENSE'),
-    author='Maxx Tessmer',
-    author_email='[email protected]',
-    install_requires=['numpy>=1.23.0',
-                      'scipy>=1.6.3',
-                      'matplotlib>=3.3.4',
-                      'numba>=0.57.0',
-                      'mdanalysis>=2.0.0',
-                      'tqdm>=4.45.0',
-                      'pytest>=6.2.2',
-                      'memoization>=0.3.1',
-                      'argparse>=1.4.0',
-                      'setuptools>=53.0.0',
-                      'igraph>=0.11.2',
-                      'rtoml>=0.9.0'],
-    url='https://github.com/StollLab/chiLife',
     project_urls = {'Source': 'https://github.com/StollLab/chiLife'},
-    keywords=['Spin label', 'EPR', 'DEER', 'PELDOR', 'Side chain'],
-    description='A package for modeling non-canonical amino acid side chain ensembles.',
     long_description=readme,
     long_description_content_type='text/markdown',
-    cmdclass={'install': PostInstall},
-    classifiers=['License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
-                 'Programming Language :: Python :: 3.8',
-                 'Programming Language :: Python :: 3.9',
-                 'Programming Language :: Python :: 3.10',
-                 'Programming Language :: Python :: 3.11'])
+    cmdclass={'install': PostInstall})
+