Merge pull request #72 from CCPBioSim/63-conformational-entropy

Issue 63- Conformational Entropy Calculation. This merge closes #63 and resolves differences between the two versions of the code for aliphatic residues.

Author: ioanaapapa

CodeEntropy/LevelFunctions.py

@@ -175,9 +175,7 @@ def get_dihedrals(data_container, level):
 
     # if united atom level, read dihedrals from MDAnalysis universe
     if level == "united_atom":
-        # only use dihedrals made of heavy atoms
-        heavy_atom_group = data_container.select_atoms("not name H*")
-        dihedrals = heavy_atom_group.dihedrals
+        dihedrals = data_container.dihedrals
 
     # if residue level, looking for dihedrals involving residues
     if level == "residue":

CodeEntropy/main_mcc.py

@@ -258,6 +258,7 @@ def main():
                 S_trans = 0
                 S_rot = 0
                 S_conf = 0
+
                 for residue in range(num_residues):
                     # molecule data container of MDAnalysis Universe type for internal
                     # degrees of freedom getting indices of first and last atoms in the
@@ -269,10 +270,14 @@ def main():
                     residue_container = MDAHelper.new_U_select_atom(
                         molecule_container, selection_string
                     )
+                    residue_heavy_atoms_container = MDAHelper.new_U_select_atom(
+                        residue_container, "not name H*"
+                    )  # only heavy atom dihedrals are relevant
 
                     # Vibrational entropy at every level
                     # Get the force and torque matrices for the beads at the relevant
                     # level
+
                     force_matrix, torque_matrix = LF.get_matrices(
                         residue_container,
                         level,
@@ -342,11 +347,11 @@ def main():
                     # Gives entropy of conformations within each residue
 
                     # Get dihedral angle distribution
-                    dihedrals = LF.get_dihedrals(residue_container, level)
+                    dihedrals = LF.get_dihedrals(residue_heavy_atoms_container, level)
 
                     # Calculate conformational entropy
                     S_conf_residue = EF.conformational_entropy(
-                        residue_container,
+                        residue_heavy_atoms_container,
                         dihedrals,
                         bin_width,
                         start,