diff --git a/Packages/PyLOOS/cluster-structures.py b/Packages/PyLOOS/cluster-structures.py index 940aa338d..ae6eac5e9 100755 --- a/Packages/PyLOOS/cluster-structures.py +++ b/Packages/PyLOOS/cluster-structures.py @@ -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)): diff --git a/Packages/PyLOOS/contact_distance.py b/Packages/PyLOOS/contact_distance.py index 1cad0cb7b..42794fd5a 100755 --- a/Packages/PyLOOS/contact_distance.py +++ b/Packages/PyLOOS/contact_distance.py @@ -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 diff --git a/Packages/PyLOOS/packing_score_per_res.py b/Packages/PyLOOS/packing_score_per_res.py index a4036adc7..8ea04b08d 100755 --- a/Packages/PyLOOS/packing_score_per_res.py +++ b/Packages/PyLOOS/packing_score_per_res.py @@ -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: diff --git a/Packages/PyLOOS/rare-event-detection.py b/Packages/PyLOOS/rare-event-detection.py index 5fe72277a..d2422f7ff 100755 --- a/Packages/PyLOOS/rare-event-detection.py +++ b/Packages/PyLOOS/rare-event-detection.py @@ -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))): diff --git a/Tools/potential_profile.py b/Tools/potential_profile.py index 14d096179..edc91d84e 100755 --- a/Tools/potential_profile.py +++ b/Tools/potential_profile.py @@ -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)): diff --git a/loos/src/loos/Voronoi/area_per_molecule.py b/loos/src/loos/Voronoi/area_per_molecule.py index 50a2d9ca2..e1a16b34f 100755 --- a/loos/src/loos/Voronoi/area_per_molecule.py +++ b/loos/src/loos/Voronoi/area_per_molecule.py @@ -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)) diff --git a/loos/src/loos/Voronoi/lipid_lifetime.py b/loos/src/loos/Voronoi/lipid_lifetime.py index 761482839..abada0d9e 100755 --- a/loos/src/loos/Voronoi/lipid_lifetime.py +++ b/loos/src/loos/Voronoi/lipid_lifetime.py @@ -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