added alignH5.py

example/alignH5.py

@@ -0,0 +1,72 @@
+# This script is used to align complexes in hdf5.
+# INPUT:
+#   1. a hdf5 file that contains pdb of all complexes (it is the output of generate_dataset_noalign.py).
+#   2. pssm files if the pssm feature is needed for the training later
+
+
+from deeprank.generate import *
+from mpi4py import MPI
+
+comm = MPI.COMM_WORLD
+
+# name of the hdf5 to generate
+h5file = './hdf5/1ak4.hdf5'
+
+# for each hdf5 file where to find the pdbs
+# pdb_source = '../test/1AK4/decoys/'
+#
+# # where to find the native conformations
+# # pdb_native is only used to calculate i-RMSD, dockQ and so on.
+# # The native pdb files will not be saved in the hdf5 file
+# pdb_native = '../test/1AK4/native/'
+
+# where to find the pssm
+pssm_source = '../test/1AK4/pssm_new/'
+
+# initialize the database
+# database = DataGenerator(
+#     pdb_source=pdb_source,
+#     pdb_native=pdb_native,
+#     pssm_source=pssm_source,
+#     data_augmentation=2,
+#     compute_targets=[
+#         'deeprank.targets.dockQ',
+#         'deeprank.targets.binary_class'],
+#     compute_features=[
+#         'deeprank.features.AtomicFeature',
+#         'deeprank.features.FullPSSM',
+#         'deeprank.features.PSSM_IC',
+#         'deeprank.features.BSA',
+#         'deeprank.features.ResidueDensity'],
+#     hdf5=h5file,
+#     mpi_comm=comm)
+#
+
+# compute features/targets for all complexes and write to a hdf5 file
+# print('{:25s}'.format('Create new database') + database.hdf5)
+# database.create_database(prog_bar=True)
+
+# align the principle component 1 of complexes to axis z
+newdb = DataGenerator(hdf5=h5file)
+newdb.realign_complexes(align={'axis':'z'})
+
+
+# define the 3D grid
+# grid_info = {
+#   'number_of_points' : [30,30,30],
+#   'resolution' : [1.,1.,1.],
+#   'atomic_densities': {'C': 1.7, 'N': 1.55, 'O': 1.52, 'S': 1.8},
+# }
+
+# generate the grid
+#print('{:25s}'.format('Generate the grid') + database.hdf5)
+#database.precompute_grid(grid_info,try_sparse=True, time=False, prog_bar=True)
+
+
+# print('{:25s}'.format('Map features in database') + database.hdf5)
+# database.map_features(grid_info,try_sparse=True, time=False, prog_bar=True)
+
+# # get the normalization of the features
+# print('{:25s}'.format('Normalization') + database.hdf5)
+# norm = NormalizeData(database.hdf5)
+# norm.get()