Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…

…to shubham

package/AUTHORS

@@ -217,6 +217,7 @@ Chronological list of authors
   - Egor Marin
   - Shaivi Malik
   - Daniel J. Evans
+  - Mohit Kumar
 
 External code
 -------------

package/CHANGELOG

@@ -13,7 +13,7 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/?? IAlibay, jaclark5
+??/??/?? IAlibay, jaclark5, MohitKumar020291
 
  * 2.6.0
 

package/MDAnalysis/analysis/align.py

@@ -74,7 +74,7 @@
 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 @@
 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 @@
    >>> 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 @@
    >>> 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 @@
    >>> 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 @@
 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)
 

package/pyproject.toml

@@ -76,9 +76,11 @@ extra_formats = [
     "netCDF4>=1.0",
     "h5py>=2.10",
     "chemfiles>=0.10",
+    "parmed",
     "pyedr>=0.7.0",
     "pytng>=0.2.3",
     "gsd>3.0.0",
+    "rdkit>=2020.03.1",
 ]
 analysis = [
     "seaborn",

package/setup.py

@@ -654,6 +654,8 @@ def long_description(readme):
                   'chemfiles>=0.10',  # multiple formats supported by chemfiles
                   'pyedr>=0.7.0',  # EDR files for the EDR AuxReader
                   'gsd>3.0.0', # GSD
+                  'rdkit>=2020.03.1', # RDKit converter
+                  'parmed', # ParmEd converter
                   ],
               'analysis': [
                   'seaborn',  # for annotated heat map and nearest neighbor