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writeScipion option norm to normalise #1936

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writeScipion option norm to normalise #1936

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0c4f656
norm option in writeScipionModes for defvec fix
jamesmkrieger Mar 10, 2022
d24183c
Merge branch 'scipion' of https://github.com/jamesmkrieger/ProDy into…
jamesmkrieger Mar 30, 2022
539d84b
Merge branch 'master' of github.com:prody/ProDy into writeScipion_norm
jamesmkrieger Apr 9, 2024
12156aa
Merge branch 'main' of github.com:prody/ProDy into writeScipion_norm
jamesmkrieger Aug 14, 2024
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16 changes: 15 additions & 1 deletion prody/dynamics/functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -512,7 +512,7 @@ def parseScipionModes(metadata_file, title=None, pdb=None, parseIndices=False):


def writeScipionModes(output_path, modes, write_star=False, scores=None,
only_sqlite=False, collectivityThreshold=0.):
only_sqlite=False, collectivityThreshold=0., norm=True):
"""Writes *modes* to a set of files that can be recognised by Scipion.
A directory called **"modes"** will be created if it doesn't already exist.
Filenames inside will start with **"vec"** and have the mode number as the extension.
Expand All @@ -538,6 +538,10 @@ def writeScipionModes(output_path, modes, write_star=False, scores=None,
:arg collectivityThreshold: collectivity threshold below which modes are not enabled
Default is 0.
:type collectivityThreshold: float

:arg norm: whether to normalize mode vectors before calculating collectivities
Default is **True**
:type norm: bool
"""
if not isinstance(output_path, str):
raise TypeError('output_path should be a string, not {0}'
Expand Down Expand Up @@ -567,6 +571,10 @@ def writeScipionModes(output_path, modes, write_star=False, scores=None,
raise TypeError('collectivityThreshold should be float, not {0}'
.format(type(collectivityThreshold)))

if not isinstance(norm, bool):
raise TypeError('norm should be boolean, not {0}'
.format(type(norm)))

if modes.numModes() == 1 and not isinstance(modes, (NMA, ModeSet)):
old_modes = modes
modes = NMA(old_modes)
Expand All @@ -586,6 +594,12 @@ def writeScipionModes(output_path, modes, write_star=False, scores=None,
modefiles.append(writeArray(modes_dir + 'vec.{0}'.format(mode_num),
mode.getArray(), '%12.4e', ''))

if norm:
eigvecs = modes.getEigvecs()
eigvecs /= np.array([((evecs[:, i]) ** 2).sum() ** 0.5
for i in range(evecs.shape[1])])
modes.setEigens(eigvecs, eigvals)

if modes.numModes() > 1:
order = modes.getIndices()
collectivities = list(calcCollectivity(modes))
Expand Down
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