diff --git a/deeprank/generate/DataGenerator.py b/deeprank/generate/DataGenerator.py index ac152c25..e6fd8c31 100644 --- a/deeprank/generate/DataGenerator.py +++ b/deeprank/generate/DataGenerator.py @@ -1022,7 +1022,6 @@ def precompute_grid(self, # # ==================================================================================== - def map_features(self, grid_info={}, cuda=False, gpu_block=None, cuda_kernel='/kernel_map.c', @@ -1102,7 +1101,8 @@ def map_features(self, grid_info={}, # by default we do not map atomic densities if 'atomic_densities' not in grid_info: - grid_info['atomic_densities'] = None + grid_info['atomic_densities'] = { + 'C': 1.7, 'N': 1.55, 'O': 1.52, 'S': 1.8} # fills in the features mode if somes are missing : default = IND modes = ['atomic_densities_mode', 'feature_mode'] @@ -1267,7 +1267,6 @@ def remove(self, feature=True, pdb=True, points=True, grid=False): # # ==================================================================================== - def _tune_cuda_kernel(self, grid_info, cuda_kernel='kernel_map.c', func='gaussian'): # pragma: no cover """Tune the CUDA kernel using the kernel tuner http://benvanwerkhoven.github.io/kernel_tuner/ @@ -1343,7 +1342,6 @@ def _tune_cuda_kernel(self, grid_info, cuda_kernel='kernel_map.c', func='gaussia # # ==================================================================================== - def _test_cuda(self, grid_info, gpu_block=8, cuda_kernel='kernel_map.c', func='gaussian'): # pragma: no cover """Test the CUDA kernel. @@ -1478,7 +1476,6 @@ def _tunable_kernel(kernel): # pragma: no cover # # =================================================================================== - def _filter_cplx(self): """Filter the name of the complexes.""" @@ -1561,7 +1558,6 @@ def _compute_targets(targ_list, pdb_data, targrp): # # ==================================================================================== - def _add_pdb(self, molgrp, pdbfile, name): """Add a pdb to a molgrp.