MDAnalysis 2.5.0__tar.gz → 2.6.1__tar.gz

{MDAnalysis-2.5.0 → MDAnalysis-2.6.1}/AUTHORS

@@ -217,6 +217,10 @@ Chronological list of authors
   - Egor Marin
   - Shaivi Malik
   - Daniel J. Evans
+  - Mohit Kumar
+  - Shubham Kumar
+  - Zaheer Timol
+  - Geongi Moon
 
 External code
 -------------

{MDAnalysis-2.5.0 → MDAnalysis-2.6.1}/CHANGELOG

@@ -13,6 +13,84 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
+28/08/23 IAlibay, hmacdope, pillose, jaclark5, tylerjereddy
+
+ * 2.6.1
+
+Fixes
+  * Fix Atom type guessing error (PR #4168, Issue #4167)
+
+Enhancements
+
+Changes
+  * Reverts PR #4108, builds are now again made using the oldest
+    supported Python version.
+  * NumPy `in1d` replaced with `isin` in preparation for NumPy
+    `2.0` (PR #4255)
+  * Update documentation for SurvivalProbabilty to be more clear
+    (Issue #4247)
+  * Cython DEF statments have been replaced with compile time integer constants
+    as DEF is deprecated as of Cython>=3.0 (Issue #4237, PR #4246)
+
+Deprecations
+
+
+08/15/23 IAlibay, jaclark5, MohitKumar020291, orionarcher, xhgchen,
+         ztimol, orbeckst
+
+ * 2.6.0
+
+Fixes
+  * Fix AtomGroup.center_of_charge(..., unwrap=True) giving
+    inconsistent (but scientifically correct) results on Intel macOS
+    (Issue #4211)
+  * Fix Boltzmann typo in `units.py` (PR #4214, Issue #4213)
+  * Fix deletion of bond/angle/dihedral types (PR #4003, Issue #4001)
+  * CRD, PQR, and PDBQT writers now write BZ2 and GZ files if requested
+    (PR #4163, Issue #4159)
+
+Enhancements
+  * Added a `exclude_same` kwarg to InterRDF (PR #4161)
+  * LAMMPSDump Reader use of `continuous` option to stitch trajectories
+    (Issue #3546)
+
+Changes
+  * Package builds are now made using NumPy 1.25 or higher. This provides
+    backwards runtime compatibility with older NumPy builds within the limit
+    of NEP29 (PR #4108).
+  * Removed `-ffast-math` compiler flag to avoid potentially incorrect
+    floating point results in MDAnalysis *and* other codes when
+    MDAnalysis shared libraries are loaded --- see 
+    https://moyix.blogspot.com/2022/09/someones-been-messing-with-my-subnormals.html
+    (Issues #3821, #4211)
+  * Atom ID representation order updated to match that of associated
+    AtomGroup indices.
+    (PR #4191, Issue #4181)
+  * Package license has been updated to GPLv3+ to better reflect the
+    compatibility of GPLv2+ with Apache and GPLv3 licenced codes (PR #4219).
+  * All new contributions are now made under LGPLv2.1+ (PR #4219).
+  * Support for GSD is now limited to version 3.0.1 and above. Alongside this
+    change, support for schema 1.3 files has been dropped (PR #4153)
+  * Add definition of ts.data['time'] in LAMMPSDump Reader (Issue #3546)
+  * As per NEP29 the minimum supported version has been raised to 1.22. We
+    have opted to pin to a minimum of 1.22.3 to avoid known issues on some
+    platforms.
+  * GSD is no longer a core dependency of MDAnalysis. It must be installed
+    independently if you wish to read HOOMD trajectory files.
+    (PR #4174, Issue #3819)
+
+Deprecations
+  * Incorrectly spelt Boltzmann unit entry will be removed in version 2.8.0
+    (PR #4230, Issue #4229)
+  * The hole2 module is deprecated in favour of the the MDAKit:
+    https://github.com/MDAnalysis/hole2-mdakit (Issue #4179, PR #4200)
+  * MDAnalysis no longer officially supports 32 bit installations (they are
+    no longer tested in our continuous integration pipelines). Note: whilst
+    no code changes have been made to disable 32 bit, although it is known that
+    new versions of most MDAnalysis core dependencies no longer release
+    32 bit compatible versions. (Issue #3858, PR #4176)
+
+
 05/28/23 IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae, 
          ooprathamm, MeetB7, BFedder, v-parmar, MoSchaeffler, jbarnoud, jandom,
          xhgchen, jaclark5, DrDomenicoMarson, AHMED-salah00, schlaicha,
@@ -22,6 +100,7 @@ The rules for this file:
  * 2.5.0
 
 Fixes
+  * Fixed using 'rb' mode inside GSDReader to avoid FutureWarning from GSDFile (Issue #4152)
   * Fixed ChainReader performing transformations correctly across boundaries in the individual trajectories
     (Issue #3657 #4008 PR #3906)
   * Fix the `heavy` distance_type for water bridge analysis where distance
@@ -105,8 +184,6 @@ Changes
       bespoke code to transfer atomic properties from the non-standardized mol
       to the standardized one.
 
-Deprecations
-
 
 03/29/23 richardjgowers, IAlibay
 

{MDAnalysis-2.5.0 → MDAnalysis-2.6.1}/MDAnalysis/analysis/align.py

@@ -74,7 +74,7 @@ In the simplest case, we can simply calculate the C-alpha RMSD between
 two structures, using :func:`rmsd`::
 
    >>> ref = mda.Universe(PDB_small)
-   >>> mobile = mda.Universe(PSF,DCD)
+   >>> mobile = mda.Universe(PSF, DCD)
    >>> rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions)
    28.20178579474479
 
@@ -89,8 +89,8 @@ This has only done a translational superposition. If you want to also do a
 rotational superposition use the superposition keyword. This will calculate a
 minimized RMSD between the reference and mobile structure.
 
-   >>> rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions,
-   >>>      superposition=True)
+   >>> rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions, 
+   ...      superposition=True)
    6.809396586471815
 
 The rotation matrix that superimposes *mobile* on *ref* while
@@ -100,18 +100,21 @@ function ::
    >>> mobile0 = mobile.select_atoms('name CA').positions - mobile.select_atoms('name CA').center_of_mass()
    >>> ref0 = ref.select_atoms('name CA').positions - ref.select_atoms('name CA').center_of_mass()
    >>> R, rmsd = align.rotation_matrix(mobile0, ref0)
-   >>> print rmsd
+   >>> rmsd
    6.809396586471805
-   >>> print R
-   [[ 0.14514539 -0.27259113  0.95111876]
-    [ 0.88652593  0.46267112 -0.00268642]
-    [-0.43932289  0.84358136  0.30881368]]
+   >>> R
+   array([[ 0.14514539, -0.27259113,  0.95111876],
+   ...    [ 0.88652593,  0.46267112, -0.00268642],
+   ...    [-0.43932289,  0.84358136,  0.30881368]])
 
 Putting all this together one can superimpose all of *mobile* onto *ref*::
 
    >>> mobile.atoms.translate(-mobile.select_atoms('name CA').center_of_mass())
+   <AtomGroup with 3341 atoms>
    >>> mobile.atoms.rotate(R)
+   <AtomGroup with 3341 atoms>
    >>> mobile.atoms.translate(ref.select_atoms('name CA').center_of_mass())
+   <AtomGroup with 3341 atoms>
    >>> mobile.atoms.write("mobile_on_ref.pdb")
 
 
@@ -123,6 +126,7 @@ To **fit a single structure** with :func:`alignto`::
    >>> ref = mda.Universe(PSF, PDB_small)
    >>> mobile = mda.Universe(PSF, DCD)     # we use the first frame
    >>> align.alignto(mobile, ref, select="protein and name CA", weights="mass")
+   (21.892591663632704, 6.809396586471809)
 
 This will change *all* coordinates in *mobile* so that the protein
 C-alpha atoms are optimally superimposed (translation and rotation).
@@ -134,6 +138,7 @@ To **fit a whole trajectory** to a reference structure with the
    >>> trj = mda.Universe(PSF, DCD)         # trajectory of change 1AKE->4AKE
    >>> alignment = align.AlignTraj(trj, ref, filename='rmsfit.dcd')
    >>> alignment.run()
+   <MDAnalysis.analysis.align.AlignTraj object at ...> 
 
 It is also possible to align two arbitrary structures by providing a
 mapping between atoms based on a sequence alignment. This allows
@@ -143,9 +148,9 @@ If a alignment was provided as "sequences.aln" one would first produce
 the appropriate MDAnalysis selections with the :func:`fasta2select`
 function and then feed the resulting dictionary to :class:`AlignTraj`::
 
-   >>> seldict = align.fasta2select('sequences.aln')
-   >>> alignment = align.AlignTraj(trj, ref, filename='rmsfit.dcd', select=seldict)
-   >>> alignment.run()
+   >>> seldict = align.fasta2select('sequences.aln') # doctest: +SKIP
+   >>> alignment = align.AlignTraj(trj, ref, filename='rmsfit.dcd', select=seldict) # doctest: +SKIP
+   >>> alignment.run() # doctest: +SKIP
 
 (See the documentation of the functions for this advanced usage.)
 
@@ -222,15 +227,15 @@ def rotation_matrix(a, b, weights=None):
     Parameters
     ----------
     a : array_like
-          coordinates that are to be rotated ("mobile set"); array of N atoms
-          of shape N*3 as generated by, e.g.,
-          :attr:`MDAnalysis.core.groups.AtomGroup.positions`.
+        coordinates that are to be rotated ("mobile set"); array of N atoms
+        of shape N*3 as generated by, e.g.,
+        :attr:`MDAnalysis.core.groups.AtomGroup.positions`.
     b : array_like
-          reference coordinates; array of N atoms of shape N*3 as generated by,
-          e.g., :attr:`MDAnalysis.core.groups.AtomGroup.positions`.
+        reference coordinates; array of N atoms of shape N*3 as generated by,
+        e.g., :attr:`MDAnalysis.core.groups.AtomGroup.positions`.
     weights : array_like (optional)
-          array of floats of size N for doing weighted RMSD fitting (e.g. the
-          masses of the atoms)
+        array of floats of size N for doing weighted RMSD fitting (e.g. the
+        masses of the atoms)
 
     Returns
     -------
@@ -246,10 +251,15 @@ def rotation_matrix(a, b, weights=None):
     :meth:`MDAnalysis.core.groups.AtomGroup.rotate` to generate a rotated
     selection, e.g. ::
 
-    >>> R = rotation_matrix(A.select_atoms('backbone').positions,
-    >>>                     B.select_atoms('backbone').positions)[0]
-    >>> A.atoms.rotate(R)
-    >>> A.atoms.write("rotated.pdb")
+        >>> from MDAnalysisTests.datafiles import TPR, TRR
+        >>> from MDAnalysis.analysis import align
+        >>> A = mda.Universe(TPR,TRR)
+        >>> B = A.copy()
+        >>> R = rotation_matrix(A.select_atoms('backbone').positions,
+        ...                     B.select_atoms('backbone').positions)[0]
+        >>> A.atoms.rotate(R)
+        <AtomGroup with 47681 atoms>
+        >>> A.atoms.write("rotated.pdb")
 
     Notes
     -----
@@ -263,6 +273,7 @@ def rotation_matrix(a, b, weights=None):
     AlignTraj: Fit a whole trajectory.
     """
 
+
     a = np.asarray(a, dtype=np.float64)
     b = np.asarray(b, dtype=np.float64)
 
@@ -1426,7 +1437,7 @@ def get_matching_atoms(ag1, ag2, tol_mass=0.1, strict=False, match_atoms=True):
                 good = ag.residues.resids[match_mask]  # resid for each residue
                 resids = ag.resids                     # resid for each atom
                 # boolean array for all matching atoms
-                ix_good = np.in1d(resids, good)
+                ix_good = np.isin(resids, good)
                 return ag[ix_good]
 
             _ag1 = get_atoms_byres(ag1)

{MDAnalysis-2.5.0 → MDAnalysis-2.6.1}/MDAnalysis/analysis/dielectric.py

@@ -159,7 +159,7 @@ class DielectricConstant(AnalysisBase):
         self.results.fluct = self.results.M2 - self.results.M * self.results.M
 
         self.results.eps = self.results.fluct / (
-              convert(constants["Boltzman_constant"], "kJ/mol", "eV") *
+              convert(constants["Boltzmann_constant"], "kJ/mol", "eV") *
               self.temperature * self.volume * constants["electric_constant"])
 
         self.results.eps_mean = self.results.eps.mean()