New Dihedral and Ramachandran Analysis

package/MDAnalysis/analysis/dihedrals.py

@@ -0,0 +1,105 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import warnings
+import six
+from six.moves import zip
+
+import MDAnalysis as mda
+from MDAnalysis.analysis.base import AnalysisBase
+from MDAnalysis.lib.distances import calc_dihedrals
+
+
+class Ramachandran(AnalysisBase):
+    """Calculate phi and psi dihedral angles of specified residues.
+
+    Note
+    ----
+    Run the analysis with :meth:`Ramachandran.run()`, which stores the results
+    in the array :attr:`Ramachandran.angles`. A axes object can be obtained
+    with :meth: `Ramachandran.run().plot()`.
+
+    If the residue selection is beyond the scope of the protein, then an error
+    will be raised. If the residue selection includes the first or last residue
+    then a warning will be raised, and the final array of angles will not
+    include those residues.
+
+    """
+    def __init__(self, atomgroup, **kwargs):
+        r"""Parameters
+        ----------
+        atomgroup : Atomgroup
+            atoms for residues for which phi and psi are calculated
+        start : int, optional
+            starting frame, default None becomes 0.
+        stop : int, optional
+            Frame index to stop analysis. Default: None becomes
+            n_frames. Iteration stops *before* this frame number,
+            which means that the trajectory would be read until the end.
+        step : int, optional
+            step between frames, default None becomes 1.
+
+        """
+        super(Ramachandran, self).__init__(atomgroup.universe.trajectory, **kwargs)
+        self.atomgroup = atomgroup
+        residues = self.atomgroup.residues
+        protein = self.atomgroup.universe.select_atoms("protein").residues
+
+        if not residues.issubset(protein):
+            raise IndexError("Found atoms outside of protein. Only atoms "
+                             "inside of a 'protein' selection can be used to "
+                             "calculate dihedrals.")
+        elif not residues.isdisjoint(protein[[0, -1]]):
+            warnings.warn("Cannot determine phi and psi angles for the first "
+                          "or last residues")
+            residues = residues.difference(protein[[0, -1]])
+
+        phi_sel = [res.phi_selection() for res in residues]
+        psi_sel = [res.psi_selection() for res in residues]
+        self.ag1 = mda.AtomGroup([atoms[0] for atoms in phi_sel])
+        self.ag2 = mda.AtomGroup([atoms[1] for atoms in phi_sel])
+        self.ag3 = mda.AtomGroup([atoms[2] for atoms in phi_sel])
+        self.ag4 = mda.AtomGroup([atoms[3] for atoms in phi_sel])
+        self.ag5 = mda.AtomGroup([atoms[3] for atoms in psi_sel])
+
+    def _prepare(self):
+        self.angles = []
+
+    def _single_frame(self):
+        phi_angles = calc_dihedrals(self.ag1.positions, self.ag2.positions,
+                                    self.ag3.positions, self.ag4.positions,
+                                    box=self.ag1.dimensions)
+        psi_angles = calc_dihedrals(self.ag2.positions, self.ag3.positions,
+                                    self.ag4.positions, self.ag5.positions,
+                                    box=self.ag1.dimensions)
+        phi_psi = [(phi, psi) for phi, psi in zip(phi_angles, psi_angles)]
+        self.angles.append(phi_psi)
+
+    def _conclude(self):
+        self.angles = np.rad2deg(np.array(self.angles))
+
+
+    def plot(self, ax=None, **kwargs):
+        """Plots data into standard ramachandran plot. Each time step in
+        self.angles is plotted onto the same graph.
+
+        Parameters
+        ----------
+        ax : :class:`matplotlib.axes.Axes`
+              If no `ax` is supplied or set to ``None`` then the plot will
+              be added to the current active axes.
+
+        Returns
+        -------
+        ax : :class:`~matplotlib.axes.Axes`
+             Axes with the plot, either `ax` or the current axes.
+
+        """
+        if ax is None:
+            ax = plt.gca()
+        ax.axis([-180,180,-180,180])
+        ax.axhline(0, color='k', lw=1)
+        ax.axvline(0, color='k', lw=1)
+        ax.set(xticks=range(-180,181,60), yticks=range(-180,181,60),
+               xlabel=r"$\phi$ (deg)", ylabel=r"$\psi$ (deg)")
+        a = self.angles.reshape(np.prod(self.angles.shape[:2]), 2)
+        ax.scatter(a[:,0], a[:,1])

testsuite/MDAnalysisTests/analysis/test_dihedrals.py

@@ -0,0 +1,39 @@
+import numpy as np
+from numpy.testing import assert_almost_equal
+import pytest
+
+import MDAnalysis as mda
+from MDAnalysisTests.datafiles import GRO, XTC, DihedralsArray, GLYDihedralsArray
+from MDAnalysis.analysis import dihedrals
+
+
+class TestRamachandran(object):
+
+    @pytest.fixture()
+    def universe(self):
+        return mda.Universe(GRO, XTC)
+
+    def test_ramachandran(self, universe):
+        rama = dihedrals.Ramachandran(universe.select_atoms("protein")).run()
+        test_rama = np.load(DihedralsArray)
+
+        assert_almost_equal(rama.angles, test_rama, 5,
+                            err_msg="error: dihedral angles should "
+                            "match test values")
+
+    def test_ramachandran_single_frame(self, universe):
+        rama = dihedrals.Ramachandran(universe.select_atoms("protein"),
+                                      start=5, stop=6).run()
+        test_rama = [np.load(DihedralsArray)[5]]
+
+        assert_almost_equal(rama.angles, test_rama, 5,
+                            err_msg="error: dihedral angles should "
+                            "match test values")
+
+    def test_ramachandran_residue_selections(self, universe):
+        rama = dihedrals.Ramachandran(universe.select_atoms("resname GLY")).run()
+        test_rama = np.load(GLYDihedralsArray)
+
+        assert_almost_equal(rama.angles, test_rama, 5,
+                            err_msg="error: dihedral angles should "
+                            "match test values")

testsuite/MDAnalysisTests/datafiles.py

@@ -155,7 +155,8 @@
     "legacy_DCD_NAMD_coords", # frame 0 read in for SiN_tric_namd.dcd using legacy DCD reader
     "legacy_DCD_c36_coords", # frames 1 and 4 read in for tip125_tric_C36.dcd using legacy DCD reader
     "GSD",
-    "GRO_MEMPROT", "XTC_MEMPROT" # YiiP transporter in POPE:POPG lipids with Na+, Cl-, Zn2+ dummy model without water
+    "GRO_MEMPROT", "XTC_MEMPROT", # YiiP transporter in POPE:POPG lipids with Na+, Cl-, Zn2+ dummy model without water
+    "DihedralsArray", "GLYDihedralsArray" # phi and psi angles for testing Ramachandran class
 ]
 
 from pkg_resources import resource_filename
@@ -415,5 +416,8 @@
 
 GSD = resource_filename(__name__, 'data/example.gsd')
 
+DihedralsArray = resource_filename(__name__, 'data/adk_oplsaa_dihedrals.npy')
+GLYDihedralsArray = resource_filename(__name__, 'data/adk_oplsaa_GLY_dihedrals.npy')
+
 # This should be the last line: clean up namespace
 del resource_filename