Deprecate ContactMap (allowing rename ContactFrequency => ContactMap)

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
@@ -675,13 +678,25 @@ 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 +707,19 @@ 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()),

examples/concurrences.ipynb

@@ -225,6 +225,48 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.7.3"
+  },
+  "toc": {
+   "base_numbering": 1,
+   "nav_menu": {},
+   "number_sections": true,
+   "sideBar": true,
+   "skip_h1_title": true,
+   "title_cell": "Table of Contents",
+   "title_sidebar": "Contents",
+   "toc_cell": false,
+   "toc_position": {},
+   "toc_section_display": true,
+   "toc_window_display": true
+  },
+  "varInspector": {
+   "cols": {
+    "lenName": 16,
+    "lenType": 16,
+    "lenVar": 40
+   },
+   "kernels_config": {
+    "python": {
+     "delete_cmd_postfix": "",
+     "delete_cmd_prefix": "del ",
+     "library": "var_list.py",
+     "varRefreshCmd": "print(var_dic_list())"
+    },
+    "r": {
+     "delete_cmd_postfix": ") ",
+     "delete_cmd_prefix": "rm(",
+     "library": "var_list.r",
+     "varRefreshCmd": "cat(var_dic_list()) "
+    }
+   },
+   "types_to_exclude": [
+    "module",
+    "function",
+    "builtin_function_or_method",
+    "instance",
+    "_Feature"
+   ],
+   "window_display": false
   }
  },
  "nbformat": 4,