initial commit for adding descriptor of water features

wetmsm/shells.py

@@ -97,6 +97,33 @@ def partial_transform(self, traj):
  shellcounts = analysis.reshape(shellcounts)
  return shellcounts
 
+ def describe_features(self, traj):
+ """Return a Pandas Dataframe describing the Water features."""
+ x = []
+
+ resSeq = [np.array([traj.top.atom(i).residue.resSeq]) for i in self.solute_indices]
+ resid = [np.array([traj.top.atom(i).residue.index]) for i in self.solute_indices]
+ resnames = [[traj.top.atom(i).residue.name] for i in self.solute_indices]
+ aind = [[i] for i in self.solute_indices]
+
+ bigclass = ["water_shells"] * self.n_features
+ otherInfo = ["None"] * self.n_features
+ smallclass = range(self.n_shells)
+
+
+ aind = np.array(aind * self.n_shells)
+ resnames = resnames * self.n_shells
+ resSeq = resSeq * self.n_shells
+ resid = resid * self.n_shells
+ smallclass = [val for val in smallclass for _ in range(self.n_solute)]
+
+ for i in range(len(resnames)):
+ d_i = dict(resname=resnames[i], atomind=aind[i], resSeq=resSeq[i], resid=resid[i],\
+ bigclass=bigclass[i],otherInfo=otherInfo[i], smallclass=smallclass[i])
+ x.append(d_i)
+
+ return x
+
 
 class SolventShellsAssigner(SolventShellsFeaturizer):
  """Assign solvent atoms to shells to compliment SolventShellsFeaturizer.