Contact trajectories

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_map.py

@@ -174,6 +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
@@ -774,6 +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()),
@@ -951,6 +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