Addition of Protein and Residue interaction types

CHANGELOG.md

@@ -21,6 +21,7 @@ The rules for this file:
 talagayev, NDoering99
 
 ### Added
+- Addition of two `protein` and `residue` interaction in binding modes (2026-01-19, PR#170)
 - Addition of force field version selection for `GAFF` & `SMINROFF` (2025-12-15, PR #169)
 - Addition of `CHARM2024` forcefield (2025-11-03, PR #163)
 

openmmdl/openmmdl_analysis/analysis/rmsd.py

@@ -121,7 +121,7 @@ def rmsd_dist_frames(self, fig_type, lig, nucleic=False):
 
         return pairwise_rmsd_prot, pairwise_rmsd_lig
 
-    def calculate_distance_matrix(self, selection):
+    def calculate_distance_matrix(self, selection, n_frames=None):
         """
         Calculates the pairwise RMSD-based distance matrix for all trajectory frames
         for the selected atom selection.
@@ -137,16 +137,20 @@ def calculate_distance_matrix(self, selection):
         np.ndarray
             Numpy array containing RMSD values between all pairs of frames.
         """
+        if n_frames is None:
+            n_frames = len(self.universe.trajectory)
+        n_frames = min(int(n_frames), len(self.universe.trajectory))
+
         distances = np.zeros((len(self.universe.trajectory), len(self.universe.trajectory)))
         # calculate distance matrix
         for i in tqdm(
-            range(len(self.universe.trajectory)),
+            range(n_frames),
             desc="\033[1mCalculating distance matrix:\033[0m",
         ):
             self.universe.trajectory[i]
             frame_i = self.universe.select_atoms(selection).positions
             # distances[i] = md.rmsd(traj_aligned, traj_aligned, frame=i)
-            for j in range(i + 1, len(self.universe.trajectory)):
+            for j in range(i + 1, n_frames):
                 self.universe.trajectory[j]
                 frame_j = self.universe.select_atoms(selection).positions
                 rmsd = self._calc_rmsd_2frames(frame_i, frame_j)