Merge pull request #85 from dwhswenson/release-0.6.0

Release 0.6.0

ci/conda-recipe/meta.yaml

@@ -1,7 +1,7 @@
 package:
   name: contact_map
   # add ".dev0" for unreleased versions
-  version: "0.5.1"
+  version: "0.6.0"
 
 source:
   path: ../../

ci/pip-install/testing_requirements.txt

@@ -1,5 +1,5 @@
 pytest
 pytest-cov
-python-coveralls
+coveralls
 codacy-coverage
 autorelease

contact_map/__init__.py

@@ -11,6 +11,8 @@
 
 from .contact_count import ContactCount
 
+from .contact_trajectory import ContactTrajectory, RollingContactFrequency
+
 from .min_dist import NearestAtoms, MinimumDistanceCounter
 
 from .concurrence import (

contact_map/contact_count.py

@@ -16,21 +16,22 @@
 # pandas 0.25 not available on py27; can drop this when we drop py27
 _PD_VERSION = tuple(int(x) for x in pd.__version__.split('.')[:2])
 
-def _colorbar(with_colorbar, cmap_f, norm, min_val):
+
+def _colorbar(with_colorbar, cmap_f, norm, min_val, ax=None):
     if with_colorbar is False:
         return None
     elif with_colorbar is True:
         cbmin = np.floor(min_val)  # [-1.0..0.0] => -1; [0.0..1.0] => 0
         cbmax = 1.0
-        cb = ranged_colorbar(cmap_f, norm, cbmin, cbmax)
+        cb = ranged_colorbar(cmap_f, norm, cbmin, cbmax, ax=ax)
     # leave open other inputs to be parsed later (like tuples)
     return cb
 
 
 # TODO: remove following: this is a monkeypatch for a bug in pandas
 # see: https://github.com/pandas-dev/pandas/issues/29814
 from pandas._libs.sparse import BlockIndex, IntIndex, SparseIndex
-def _patch_from_spmatrix(cls, data):
+def _patch_from_spmatrix(cls, data):  # -no-cov-
     length, ncol = data.shape
 
     if ncol != 1:
@@ -129,7 +130,7 @@ def df(self):
         index = list(range(self.n_x))
         columns = list(range(self.n_y))
 
-        if _PD_VERSION < (0, 25):  # py27 only
+        if _PD_VERSION < (0, 25):  # py27 only  -no-cov-
             mtx = mtx.tocoo()
             return pd.SparseDataFrame(mtx, index=index, columns=columns)
 
@@ -198,18 +199,39 @@ def plot(self, cmap='seismic', vmin=-1.0, vmax=1.0, with_colorbar=True,
         """
         if not HAS_MATPLOTLIB:  # pragma: no cover
             raise RuntimeError("Error importing matplotlib")
+        fig, ax = plt.subplots(**kwargs)
+
+        # Check the number of pixels of the figure
+        self._check_number_of_pixels(fig)
+        self.plot_axes(ax=ax, cmap=cmap, vmin=vmin, vmax=vmax)
+
+        return (fig, ax)
+
+    def plot_axes(self, ax, cmap='seismic', vmin=-1.0, vmax=1.0,
+                  with_colorbar=True):
+        """
+        Plot contact matrix on a matplotlib.axes
+
+        Parameters
+        ----------
+        ax : matplotlib.axes
+           axes to plot the contact matrix on
+        cmap : str
+            color map name, default 'seismic'
+        vmin : float
+            minimum value for color map interpolation; default -1.0
+        vmax : float
+            maximum value for color map interpolation; default 1.0
+        with_colorbar : bool
+            If a colorbar is added to the axes
+        """
+
         norm = matplotlib.colors.Normalize(vmin=vmin, vmax=vmax)
         cmap_f = plt.get_cmap(cmap)
-
-        fig, ax = plt.subplots(**kwargs)
         ax.axis([0, self.n_x, 0, self.n_y])
         ax.set_facecolor(cmap_f(norm(0.0)))
 
         min_val = 0.0
-
-        # Check the number of pixels of the figure
-        self._check_number_of_pixels(fig)
-
         for (pair, value) in self.counter.items():
             if value < min_val:
                 min_val = value
@@ -227,9 +249,7 @@ def plot(self, cmap='seismic', vmin=-1.0, vmax=1.0, with_colorbar=True,
             ax.add_patch(patch_0)
             ax.add_patch(patch_1)
 
-        _colorbar(with_colorbar, cmap_f, norm, min_val)
-
-        return (fig, ax)
+        _colorbar(with_colorbar, cmap_f, norm, min_val, ax=ax)
 
     def most_common(self, obj=None):
         """

contact_map/contact_map.py

@@ -7,6 +7,9 @@
 import itertools
 import pickle
 import json
+
+import warnings
+
 import numpy as np
 import pandas as pd
 import mdtraj as md
@@ -171,6 +174,24 @@ def __init__(self, topology, query, haystack, cutoff, n_neighbors_ignored):
         }
         self._atom_idx_to_residue_idx = self._set_atom_idx_to_residue_idx()
 
+    @classmethod
+    def from_contacts(cls, atom_contacts, residue_contacts, topology,
+                      query=None, haystack=None, cutoff=0.45,
+                      n_neighbors_ignored=2):
+        obj = cls.__new__(cls)
+        super(cls, obj).__init__(topology, query, haystack, cutoff,
+                                 n_neighbors_ignored)
+
+        def get_contact_counter(contact):
+            if isinstance(contact, ContactCount):
+                return contact.counter
+            else:
+                return contact
+
+        obj._atom_contacts = get_contact_counter(atom_contacts)
+        obj._residue_contacts = get_contact_counter(residue_contacts)
+        return obj
+
     def _set_atom_slice(self):
         """ Set atom slice logic """
         if (self._class_use_atom_slice is None and
@@ -675,13 +696,25 @@ def residue_contacts(self):
 class ContactMap(ContactObject):
     """
     Contact map (atomic and residue) for a single frame.
+
+    .. deprecated:: 0.6.0
+        ``ContactMap`` will be removed in Contact Map Explorer 0.7.0 because
+        it is redundant with ``ContactFrequency``. For more, see
+        https://github.com/dwhswenson/contact_map/issues/82.
+
     """
     # Default for use_atom_slice, None tries to be smart
     _class_use_atom_slice = None
 
+    _deprecation_message=(
+        "The ContactMap class will be removed in Contact Map Explorer 0.7. "
+        + "Use ContactFrequency instead. For more, see: "
+        + "https://github.com/dwhswenson/contact_map/issues/82."
+    )
+
     def __init__(self, frame, query=None, haystack=None, cutoff=0.45,
                  n_neighbors_ignored=2):
-
+        warnings.warn(self._deprecation_message, FutureWarning)
         self._frame = frame  # TODO: remove this?
         super(ContactMap, self).__init__(frame.topology, query, haystack,
                                          cutoff, n_neighbors_ignored)
@@ -692,6 +725,19 @@ def __init__(self, frame, query=None, haystack=None, cutoff=0.45,
         (atom_contacts, self._residue_contacts) = contact_maps
         self._atom_contacts = self.convert_atom_contacts(atom_contacts)
 
+    @classmethod
+    def from_dict(cls, dct):
+        warnings.warn(cls._deprecation_message, FutureWarning)
+        return super(ContactMap, cls).from_dict(dct)
+
+    # don't need to add deprecation in from_json because it uses from_dict
+
+    @classmethod
+    def from_file(cls, filename):
+        warnings.warn(cls._deprecation_message, FutureWarning)
+        return super(ContactMap, cls).from_file(filename)
+
+
     def __hash__(self):
         return hash((super(ContactMap, self).__hash__(),
                      tuple(self._atom_contacts.items()),
@@ -746,6 +792,17 @@ def __init__(self, trajectory, query=None, haystack=None, cutoff=0.45,
         contacts = self._build_contact_map(trajectory)
         (self._atom_contacts, self._residue_contacts) = contacts
 
+    @classmethod
+    def from_contacts(cls, atom_contacts, residue_contacts, n_frames,
+                      topology, query=None, haystack=None, cutoff=0.45,
+                      n_neighbors_ignored=2):
+        obj = super(ContactFrequency, cls).from_contacts(
+            atom_contacts, residue_contacts, topology, query, haystack,
+            cutoff, n_neighbors_ignored
+        )
+        obj._n_frames = n_frames
+        return obj
+
     def __hash__(self):
         return hash((super(ContactFrequency, self).__hash__(),
                      tuple(self._atom_contacts.items()),
@@ -923,6 +980,10 @@ def __sub__(self, other):
     def contact_map(self, *args, **kwargs):  #pylint: disable=W0221
         raise NotImplementedError
 
+    @classmethod
+    def from_contacts(self, *args, **kwargs):  #pylint: disable=W0221
+        raise NotImplementedError
+
     @property
     def atom_contacts(self):
         n_x = self.topology.n_atoms