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Merge branch 'main' of github.com:GrossfieldLab/loos
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Merging latest changes from main...
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tromo committed Feb 8, 2023
2 parents d08c4e9 + 7ed9636 commit beb58bd
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Showing 7 changed files with 7 additions and 7 deletions.
2 changes: 1 addition & 1 deletion Packages/PyLOOS/cluster-structures.py
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Expand Up @@ -153,7 +153,7 @@

minima = numpy.full_like(numpy.arange(args.num_means),
1.e10,
dtype=numpy.float)
dtype=float)
minima_indices = numpy.zeros([args.num_means], dtype=numpy.int)

for i in range(len(idx)):
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2 changes: 1 addition & 1 deletion Packages/PyLOOS/contact_distance.py
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Expand Up @@ -127,7 +127,7 @@
traj.append(t)

num_pairs = len(residues) * (len(residues)-1) // 2
contacts = numpy.zeros((len(traj), num_pairs), numpy.float)
contacts = numpy.zeros((len(traj), num_pairs), float)

default_box = loos.GCoord(10000., 10000., 10000.)
frame_number = 0
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2 changes: 1 addition & 1 deletion Packages/PyLOOS/packing_score_per_res.py
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Expand Up @@ -167,7 +167,7 @@ def __call__(self, parser, namespace, values, option_string = None):
vtraj.append(traj)

# pre-allocate storage as a numpy array
scores = numpy.zeros([len(residues), len(probes), len(vtraj)], numpy.float)
scores = numpy.zeros([len(residues), len(probes), len(vtraj)], float)

frame_index = 0
for frame in vtraj:
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2 changes: 1 addition & 1 deletion Packages/PyLOOS/rare-event-detection.py
Original file line number Diff line number Diff line change
Expand Up @@ -144,7 +144,7 @@ def LowerTriIndex(row, col, n):
if args.no_backbone:
residues = list([loos.selectAtoms(r, "!backbone") for r in residues])

fc = numpy.zeros([int((len(residues)-1)*len(residues)/2), len(traj)], numpy.float64)
fc = numpy.zeros([int((len(residues)-1)*len(residues)/2), len(traj)], float64)


for (frame, frame_id) in zip(traj, range(len(traj))):
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2 changes: 1 addition & 1 deletion Tools/potential_profile.py
Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@ def read_file(filename):
# dielectric charge density integrated distance
units = 1/eps0 * e_to_C/(ang_to_m**3) * ang_to_m**2

pot = numpy.zeros(data.shape, numpy.float)
pot = numpy.zeros(data.shape, float)
# compute the potential, uncorrected for periodicity
for i in range(len(data)):
for j in range(i+1, len(data)):
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2 changes: 1 addition & 1 deletion loos/src/loos/Voronoi/area_per_molecule.py
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Expand Up @@ -109,7 +109,7 @@ def main():
""")
sys.exit(0)

histograms = numpy.zeros([len(selection_strings[1:]), num_bins], numpy.float)
histograms = numpy.zeros([len(selection_strings[1:]), num_bins], float)

print("# ", " ".join(sys.argv))

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2 changes: 1 addition & 1 deletion loos/src/loos/Voronoi/lipid_lifetime.py
Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,7 @@ def main():
protein_centroid.append(loos.Atom())

# set up space to hold the neigbor time series
neighbor_timeseries = numpy.zeros([len(target_lipids), len(traj)], numpy.float)
neighbor_timeseries = numpy.zeros([len(target_lipids), len(traj)], float)

for frame in traj:
# Use the centroid of the protein slice to represent the protein
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