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Resolve issue #80 fixing indexing issue for start parameter affecting timesteps #82

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Merged
skfegan merged 1 commit into from
Apr 8, 2025
Merged

Resolve issue #80 fixing indexing issue for start parameter affecting timesteps #82

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3 changes: 2 additions & 1 deletion CodeEntropy/calculations/ConformationFunctions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,13 +38,14 @@ def assign_conformation(
# get the values of the angle for the dihedral
# dihedral angle values have a range from -180 to 180
for timestep in data_container.trajectory[start:end:step]:
timestep_index = timestep.frame - start
value = dihedral.value()
# we want postive values in range 0 to 360 to make the peak assignment work
# using the fact that dihedrals have circular symetry
# (i.e. -15 degrees = +345 degrees)
if value < 0:
value += 360
phi[timestep.frame] = value
phi[timestep_index] = value

# create a histogram using numpy
number_bins = int(360 / bin_width)
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5 changes: 3 additions & 2 deletions CodeEntropy/calculations/LevelFunctions.py
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Expand Up @@ -94,10 +94,11 @@ def get_matrices(
trans_axes, rot_axes = GF.get_axes(data_container, level, bead_index)

# Sort out coordinates, forces, and torques for each atom in the bead
weighted_forces[bead_index][timestep.frame] = GF.get_weighted_forces(
timestep_index = timestep.frame - start
weighted_forces[bead_index][timestep_index] = GF.get_weighted_forces(
data_container, list_of_beads[bead_index], trans_axes, highest_level
)
weighted_torques[bead_index][timestep.frame] = GF.get_weighted_torques(
weighted_torques[bead_index][timestep_index] = GF.get_weighted_torques(
data_container, list_of_beads[bead_index], rot_axes
)

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