def df_to_feature(struct_df, grid_config, random_seed=None):
pos = struct_df[['x', 'y', 'z']].astype(np.float32)
center = util.get_center(pos)
rot_mat = subgrid_gen.gen_rot_matrix(grid_config, random_seed=random_seed)
grid = subgrid_gen.get_grid(
struct_df, center, config=grid_config, rot_mat=rot_mat)
return grid
def __feature(struct, center):
rot_mat = subgrid_gen.gen_rot_matrix(grid_config,
random_seed=random_seed)
grid = subgrid_gen.get_grid(struct,
center,
config=grid_config,
rot_mat=rot_mat)
return grid
def df_to_feature(struct_df, label_info, grid_config, center_at_mut=True,
random_seed=None):
mutation_center = __get_mutation_center(struct_df, label_info, center_at_mut)
rot_mat = subgrid_gen.gen_rot_matrix(grid_config, random_seed=random_seed)
grid = subgrid_gen.get_grid(
struct_df, mutation_center, config=grid_config, rot_mat=rot_mat)
return grid
def df_to_feature(struct_df, grid_config, random_seed=None):
# Use center of ligand for subgrid center
ligand_pos = struct_df[struct_df.chain == 'LIG'][['x', 'y',
'z']].astype(np.float32)
ligand_center = util.get_center(ligand_pos)
rot_mat = subgrid_gen.gen_rot_matrix(grid_config, random_seed=random_seed)
grid = subgrid_gen.get_grid(struct_df,
ligand_center,
config=grid_config,
rot_mat=rot_mat)
return grid
def df_to_feature(struct_df, grid_config, center_around_Cs, random_seed=None):
# Consider only atoms that have mapping for computing center.
# If <center_around_Cs> is set, consider only carbon atoms.
if center_around_Cs:
pruned_struct_df = struct_df[struct_df.element == 'C']
else:
pruned_struct_df = struct_df[struct_df.element.isin(
grid_config.element_mapping.keys())]
pos = pruned_struct_df[['x', 'y', 'z']].astype(np.float32)
# Use center of ligand for subgrid center
ligand_pos = pruned_struct_df[pruned_struct_df.chain == 'L'][[
'x', 'y', 'z'
]].astype(np.float32)
ligand_center = util.get_center(ligand_pos)
rot_mat = subgrid_gen.gen_rot_matrix(grid_config, random_seed=random_seed)
grid = subgrid_gen.get_grid(struct_df,
ligand_center,
config=grid_config,
rot_mat=rot_mat)
return grid