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Issue 63- Conformational Entropy Calculation #72

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Merged
ioanaapapa merged 2 commits into from
Mar 21, 2025
Merged

Issue 63- Conformational Entropy Calculation #72

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a heavy atoms universe is created for each residue and called by the …
ioanaapapa Mar 15, 2025
46c6f9d
get_dihedrals function calls a heavy atom-only universe so selecting …
ioanaapapa Mar 19, 2025
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4 changes: 1 addition & 3 deletions CodeEntropy/LevelFunctions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -181,9 +181,7 @@ 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":
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9 changes: 7 additions & 2 deletions CodeEntropy/main_mcc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -308,6 +308,7 @@ 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
Expand All @@ -319,10 +320,14 @@ 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,
Expand Down Expand Up @@ -392,11 +397,11 @@ 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,
Expand Down