Merge branch 'main' into docs

.github/workflows/PR_test.yml

@@ -10,8 +10,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.9]
+        os: [ubuntu-latest, macos-13, windows-latest]
+        python-version: [3.11]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/commit_test.yml

@@ -0,0 +1,40 @@
+name: Test specified commit
+on:
+  workflow_dispatch:
+    inputs:
+      myCommit:
+        description: 'Commit SHA1'
+        required: true
+        default: 'undefined'
+        type: string
+
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.11]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: ${{ inputs.myCommit }}
+
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+      
+      - name: Test with pytest
+        run: |
+          cd tests
+          pytest

README.md

@@ -1,3 +1,23 @@
+
+> [!NOTE]
+> # Announcement:
+>
+> We are pleased to announce a free online workshop about chiLife.
+>
+> This workshop is held online on Wednesday, May 22, 2024 at 6:00am Pacific Time. The workshop will last about 3 hours.
+> 
+> To participate, please register using the online registration form at https://forms.gle/r6VHt1LWKhrsK7Ww7.
+>
+> All registered participants will receive an email with information on how to access the online workshop and materials a few days prior to the workshop. There is no need to install chiLife or Python ahead of time.
+>
+> Please share this announcement with anyone potentially interested in participating.
+> 
+> We look forward to seeing many of you!
+>
+> Best regards,
+> Maxx Tessmer and Stefan Stoll
+>  
+
 # chiLife
 chiLife (or χLife) is a python package for modeling non-canonical amino acid side chain ensembles, primarily site 
 directed spin labels (SDSLs), and using those ensembles to predict experimental results. The goal of chiLife is to provide a 
@@ -127,6 +147,12 @@ traj, de = xl.repack(SL1, SL2, protein=MBP, off_rotamer=True)
 SL1 = xl.SpinLabel.from_trajectory(traj, site=238)
 ```
 
+>Note: if you are creating a SpinLabel object from a label that is unknown to chilife you will have to specify which
+> atoms the spin density primarily resides on. this is done with the ``spin_atoms`` kwarg, e.g.
+> ```python
+> SL1 = xl.SpinLabel.from_trajectory(traj, site=238, spin_atoms=['N1', 'O1'])
+> ```
+
 Off rotamer sampling can be controlled on a per dihedral basis when repacking with chiLife by passing a list of bools to 
 the off_rotamer variable. For example, passing `off_rotamer = [False, False, False, True, True]` will allow for off 
 rotamer sampling of only &chi;<sub>4</sub> and &chi;<sub>5</sub>.
@@ -222,4 +248,4 @@ And when using bifunctional label modeling please cite:
 > Spin Label RX. Appl. Magn. Reson. 1–14.
 
 Note than many rotamer libraries may also have their own references. Please use the ``chilfe.rotlib_info()`` function 
-on the rotamer libraries to check if there is any additional citations that should be referenced when being used. 
+on the rotamer libraries to check if there is any additional citations that should be referenced when being used. 

docs/source/chilife.rst

@@ -1,5 +1,5 @@
-χLife
-======
+chilife Functions
+=================
 
 General Functions
 -----------------

docs/source/conf.py

@@ -29,6 +29,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = ['sphinx.ext.autodoc',
+              'sphinx.ext.autosectionlabel',
               'sphinx_mdinclude',
               'sphinx.ext.coverage',
               'sphinx.ext.napoleon',

docs/source/rotamer_libraries.rst

@@ -64,6 +64,7 @@ conformation is in a given protein environment.
 
 To allow our side chain a little flexibility we can tell chiLife what the mobile dihedrals are.
 
+.. _mobile_dihedrals:
 
 Defining Mobile Dihedrals
 --------------------------
@@ -106,6 +107,8 @@ Now our library can be used to perform accessible volume sampling!
 .. image:: _static/MBP_E278TSP_E322TSP.png
 
 
+.. _spin_atoms:
+
 Defining Spin-atoms and Their Weights
 --------------------------------------
 

pyproject.toml

@@ -7,7 +7,7 @@ authors=[{name = 'Maxx Tessmer', email='mhtessmer@gmail.com'},
          {name = 'Stefan Stoll', email='stst@uw.edu'}]
 keywords=['Spin-label', 'EPR', 'DEER', 'PELDOR', 'Side-chain']
 dynamic = ["version"]
-requires-python = ">= 3.8,<3.12"
+requires-python = ">= 3.8,<3.13"
 dependencies = ['numpy>=1.23.0',
                 'scipy>=1.6.3',
                 'matplotlib>=3.3.4',
@@ -16,15 +16,15 @@ dependencies = ['numpy>=1.23.0',
                 'tqdm>=4.45.0',
                 'pytest>=6.2.2',
                 'memoization>=0.3.1',
-                'argparse>=1.4.0',
                 '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']
+             'Programming Language :: Python :: 3.11',
+             'Programming Language :: Python :: 3.12']
 
 [project.urls]
 homepage = 'https://github.com/StollLab/chiLife'

src/chilife/MolSys.py

@@ -5,7 +5,7 @@
 
 import MDAnalysis
 
-from .protein_utils import sort_pdb
+from .pdb_utils import sort_pdb
 from .Topology import Topology
 import numpy as np
 from numpy.typing import ArrayLike
@@ -62,7 +62,7 @@ def select_atoms(self, selstr):
 
         Returns
         -------
-        atoms : :class:`~AtomGroup`
+        atoms : :class:`~AtomSelection`
             Selected atoms
         """
 
@@ -271,8 +271,6 @@ def __init__(
         self.charges = charges.copy()
         self._fname = name
 
-        self.topology = Topology(bonds) if bonds is not None else None
-
         self.ix = np.arange(len(self.atomids))
         self.mask = np.arange(len(self.atomids))
 
@@ -337,6 +335,7 @@ def __init__(
                                 'around': update_wrapper(partial(within, molsys=self.molsys), within)}
 
         self.atoms = AtomSelection(self, self.mask)
+        self.topology = Topology(self, bonds) if bonds is not None else None
 
     @classmethod
     def from_pdb(cls, file_name, sort_atoms=False):
@@ -410,6 +409,7 @@ def from_arrays(cls,
                     segindices: ArrayLike,
                     segids: ArrayLike = None,
                     trajectory: ArrayLike = None,
+                    **kwargs
                     ) -> MolSys:
         """
         Create a MolSys object from a minimal set of arrays.
@@ -474,10 +474,10 @@ def from_arrays(cls,
 
         occupancies = np.ones(n_atoms)
         bs = np.ones(n_atoms)
-        charges = np.zeros(n_atoms)
+        charges = kwargs.pop('charges', np.zeros(n_atoms))
 
         return cls(atomids, anames, altlocs, resnames, resnums, chains,
-                   trajectory, occupancies, bs, segids, atypes, charges)
+                   trajectory, occupancies, bs, segids, atypes, charges, **kwargs)
 
     @classmethod
     def from_atomsel(cls, atomsel, frames=None):
@@ -488,7 +488,7 @@ def from_atomsel(cls, atomsel, frames=None):
         Parameters
         ----------
         atomsel : :class:`~AtomSelection`, MDAnalysis.AtomGroup
-            The :class:`~AtomSelection` or :class:`~MDAnalysis.AtomGroup` from which to create the new MolSys object.
+            The :class:`~AtomSelection` or MDAnalysis.AtomGroup from which to create the new MolSys object.
         frames : int, Slice, ArrayLike
             Frame index, slice or array of frame indices corresponding to the frames of the atom selection you wish to
             extract into a new :class:`~MolSys` object.
@@ -549,6 +549,7 @@ def copy(self):
     def load_new(self, coordinates):
         """
         Load a new set (trajectory or ensemble) of 3-dimensional coordinates into the MolSys.
+
         Parameters
         ----------
         coordinates : ArrayLike
@@ -566,7 +567,7 @@ def _Atoms(self):
 class Trajectory:
     """
     Object containing and managing 3-dimensional coordinates of :class:`~MolSys` objects, particularly when there are
-    multiple states or time steps
+    multiple states or time steps.
 
     Parameters
     ----------
@@ -991,14 +992,14 @@ def __len__(self):
         return len(self.first_ix)
 
     def __iter__(self):
-        for resnum in self.resnums:
-            mask = self.molsys.resnums == resnum
+        for resnum, segid in zip(self.resnums, self.segids):
+            mask = (self.molsys.resnums == resnum) * (self.molsys.segids == segid)
             yield Residue(self.molsys, mask)
 
 
 class SegmentSelection(MolecularSystemBase):
     """
-    An object containing a group of segements and all their atoms from a :class:`~MolSys` object. Note that if one atom 
+    An object containing a group of segments and all their atoms from a :class:`~MolSys` object. Note that if one atom
     of a segment is present in the AtomSelection used to create the group, all atoms of that segment will be present in
     the SegmentSelection object.
 
@@ -1076,6 +1077,7 @@ def __init__(self, molsys, mask):
         self.resnum = self.resi
         self.chain = molsys.segids[self.index]
         self.segid = molsys.chains[self.index]
+        self.charge = molsys.charges[self.index]
 
     @property
     def position(self):
@@ -1155,14 +1157,14 @@ def psi_selection(self):
 
 class Segment(MolecularSystemBase):
     """
-    An object represeting a single segment of a molecular system.
+    An object representing a single segment of a molecular system.
 
     Parameters
     ----------
-    molsys : :class:`~MolSys`
+    molsys : MolSys
         The :class:`~MolSys` object from which the segment belongs to.
     mask : int
-        An array of atom indices that defines the atoms of the segment
+        An array of atom indices that defines the atoms of the segment.
     """
 
     def __init__(self, molsys, mask):