def __init__(self, lmdb_path, testing, random_seed=None, **kwargs):
self._lmdb_dataset = LMDBDataset(lmdb_path)
self.testing = testing
self.random_seed = random_seed
self.grid_config = dotdict({
# Mapping from elements to position in channel dimension.
'element_mapping': {
'C': 0,
'O': 1,
'N': 2,
'S': 3
},
# Radius of the grids to generate, in angstroms.
'radius': 17.0,
# Resolution of each voxel, in angstroms.
'resolution': 1.0,
# Number of directions to apply for data augmentation.
'num_directions': 20,
# Number of rolls to apply for data augmentation.
'num_rolls': 20,
### PPI specific
# Number of negatives to sample per positive example. -1 means all.
'neg_to_pos_ratio': 1,
'neg_to_pos_ratio_testing': 1,
# Max number of positive regions to take from a structure. -1 means all.
'max_pos_regions_per_ensemble': 5,
'max_pos_regions_per_ensemble_testing': 5,
# Whether to use all negative at test time.
'full_test': False,
})
# Update grid configs as necessary
self.grid_config.update(kwargs)
def __init__(self,
add_flag=False,
center_at_mut=False,
random_seed=None,
**kwargs):
self.add_flag = add_flag
self.center_at_mut = center_at_mut
self.random_seed = random_seed
self.grid_config = dotdict({
# Mapping from elements to position in channel dimension.
'element_mapping': {
'H': 0,
'C': 1,
'O': 2,
'N': 3,
'S': 4,
},
# Radius of the grids to generate, in angstroms.
'radius': 25.0,
# Resolution of each voxel, in angstroms.
'resolution': 1.0,
# Number of directions to apply for data augmentation.
'num_directions': 20,
# Number of rolls to apply for data augmentation.
'num_rolls': 20,
# Number of negatives to sample per positive example. -1 means all.
'neg_to_pos_ratio': 1.0,
# Max number of positive regions to take from a structure. -1 means all.
'max_pos_per_shard': 200,
})
# Update grid configs as necessary
self.grid_config.update(kwargs)
def __init__(self, add_flag=False, random_seed=None, **kwargs):
self.add_flag = add_flag
self.random_seed = random_seed
self.grid_config = dotdict({
# Mapping from elements to position in channel dimension.
'element_mapping': {
'H': 0,
'C': 1,
'O': 2,
'N': 3,
'S': 4,
'CL': 5,
'F': 6,
},
# Radius of the grids to generate, in angstroms.
'radius': 25.0,
# Resolution of each voxel, in angstroms.
'resolution': 1.0,
# Number of directions to apply for data augmentation.
'num_directions': 20,
# Number of rolls to apply for data augmentation.
'num_rolls': 20,
})
# Update grid configs as necessary
self.grid_config.update(kwargs)