MCPcopy Create free account

hub / github.com/DeepGraphLearning/DiffPack / functions

Functions76 in github.com/DeepGraphLearning/DiffPack

⨍ Functions 76◇ Types & classes 9
↓ 4 callersMethodt_to_sigma
Transfer timesteps to standard deviation. Args: t (Tensor): timesteps ranging from 0 to 1 Returns: Tensor: s
diffpack/schedule.py:171
↓ 3 callersFunctionrow_mul
(i)
diffpack/util.py:97
↓ 2 callersMethod__init__
(self, input_dim, hidden_dims, sigma_dim, embed_type="sinusoidal", operation="post_add")
diffpack/layer.py:15
↓ 2 callersFunction_rmsd_per_residue
(pred_pos_per_residue, true_pos_per_residue, mask)
diffpack/rotamer.py:968
↓ 2 callersFunctionget_atom14_position
Get the position of 14 atoms for each residue Args: protein: Protein object node_position: (num_atom, 3) Returns:
diffpack/rotamer.py:793
↓ 2 callersFunctionget_chi_atom_position
Get atom position for each chi torsion angles of each residue. Args: protein: Protein object. node_position: (num_atom, 3) t
diffpack/rotamer.py:683
↓ 2 callersFunctionget_chi_mask
(protein, chi_id=None)
diffpack/rotamer.py:659
↓ 2 callersMethodload_pdbs
Load the dataset from pdb files. Parameters: pdb_files (list of str): pdb file names transform (Callable, op
diffpack/dataset.py:57
↓ 2 callersMethodpredict
(self, batch, all_loss=None, metric=None)
diffpack/task.py:116
↓ 2 callersFunctionrot_matmul
Performs matrix multiplication of two rotation matrix tensors. Written out by hand to avoid AMP downcasting. Args:
diffpack/util.py:83
↓ 2 callersFunctionrot_vec_mul
Applies a rotation to a vector. Written out by hand to avoid transfer to avoid AMP downcasting. Args: r: [*, 3,
diffpack/util.py:123
↓ 2 callersFunctionrotate_side_chain
(protein, rotate_angles)
diffpack/rotamer.py:734
↓ 2 callersMethodscore
(self, x, sigma)
diffpack/schedule.py:68
↓ 2 callersMethodscore_norm
(self, sigma)
diffpack/schedule.py:90
↓ 2 callersMethodstep
Update the input tensor (torsion angles). Args: x (Tensor): input tensor x_score (Tensor): input tensor's score
diffpack/schedule.py:119
↓ 1 callersMethod__init__
(self, sigma_embedding: nn.Module, model: nn.Module, torsion_mlp_hidden_dims
diffpack/task.py:41
↓ 1 callersMethod__init__
(self, PI, cache_folder)
diffpack/schedule.py:38
↓ 1 callersFunction_get_symm_atoms
(pos_per_residue, residue_type)
diffpack/rotamer.py:975
↓ 1 callersMethodadd_noise
Add noise to protein and update protein Args: batch (dict): batch t (torch.Tensor): [num_graph] random number in [0,
diffpack/task.py:82
↓ 1 callersFunctionbuild_solver
(cfg, logger)
script/inference.py:52
↓ 1 callersFunctiondetect_variables
(cfg_file)
util.py:61
↓ 1 callersMethodevaluate
(self, pred, target)
diffpack/task.py:148
↓ 1 callersMethodgenerate
(self, batch, randomize=True)
diffpack/task.py:159
↓ 1 callersMethodgenerate
(self, test_set, path)
diffpack/engine.py:14
↓ 1 callersFunctionget_atom37_position
Get the position of 37 atoms for each residue Args: protein: Protein object node_position: (num_atom, 3) return_nan:
diffpack/rotamer.py:815
↓ 1 callersFunctionget_chis
(protein, node_position=None)
diffpack/rotamer.py:674
↓ 1 callersFunctionget_dihedral
Given p0-p3, compute dihedral b/t planes p0p1p2 and p1p2p3.
diffpack/rotamer.py:634
↓ 1 callersMethodget_metric
(self, pred_protein, true_protein, metric)
diffpack/task.py:186
↓ 1 callersFunctionget_rigid_transform
Returns a transformation object from reference coordinates. Note that this method does not take care of symmetries. If you provide the a
diffpack/rotamer.py:860
↓ 1 callersFunctionget_timestep_embedding
(embedding_type, embedding_dim, embedding_scale=10000)
diffpack/layer.py:78
↓ 1 callersFunctiongrad
(x, sigma, N=10, PI=np.pi)
diffpack/schedule.py:21
↓ 1 callersFunctionp
(x, sigma, N=10, PI=np.pi)
diffpack/schedule.py:14
↓ 1 callersFunctionparse_args
()
script/inference.py:24
↓ 1 callersMethodpredict_rmsd
(self, batch, all_loss=None, metric=None)
diffpack/task.py:252
↓ 1 callersFunctionsample
(sigma, PI=np.pi)
diffpack/schedule.py:28
↓ 1 callersMethodsample_train_t
Sample timesteps for training. Args: shape (tuple): shape of the output tensor Returns: Tensor: sampled time
diffpack/schedule.py:135
↓ 1 callersFunctionset_atom14_position
Set the position of 14 atoms for each residue Args: protein: Protein object node_position14: (num_residue, 14, 3) Retur
diffpack/rotamer.py:840
↓ 1 callersFunctionset_seed
(seed)
script/inference.py:38
↓ 1 callersMethodtarget
(self, batch)
diffpack/task.py:142
Method__init__
(self, sigma_embedding: nn.Module, model: nn.Module, confidence_model: nn.Mo
diffpack/task.py:228
Method__init__
Args: sigma_min (float): minimum standard deviation sigma_max (float): maximum standard deviation
diffpack/schedule.py:156
Method__init__
(self, path=None, pdb_files=None, verbose=1, **kwargs)
diffpack/dataset.py:25
Method__init__
(self, embedding_dim, max_positions=10000, scale=1.0)
diffpack/layer.py:44
Method__init__
(self, embedding_size=256, scale=1.0)
diffpack/layer.py:68
Method__repr__
(self)
diffpack/dataset.py:140
Methodadd_noise
Add noise to the input tensor (torsion angles). Args: x (Tensor): input tensor t (Tensor): timesteps tensor
diffpack/schedule.py:105
Methodadd_noise
Add noise to the input tensor (torsion angles). Args: x (Tensor): Torsion angles of shape :math:`(num_res, 4)` x_mask
diffpack/schedule.py:183
Functionbuild_downstream_solver
(cfg, dataset)
util.py:97
Functionbuild_pretrain_solver
(cfg, dataset)
util.py:131
Functionconvert_model_ckpt
(state_dict)
diffpack/util.py:148
Functioncreate_working_directory
(cfg)
util.py:34
Functioncreate_working_directory
(cfg)
diffpack/util.py:57
Methodforward
(self, batch)
diffpack/task.py:61
Methodforward
(self, input, sigma)
diffpack/layer.py:30
Methodforward
(self, timesteps)
diffpack/layer.py:50
Methodforward
(self, x)
diffpack/layer.py:72
Methodfrom_pdb_files
(pdb_files, verbose=1, **kwargs)
diffpack/dataset.py:137
Methodgenerate
(self, batch, randomize=True)
diffpack/task.py:263
Functionget_chi_periodic_mask
(protein, chi_id=None)
diffpack/rotamer.py:709
Methodget_item
(self, index)
diffpack/dataset.py:99
Functionget_root_logger
(file=True)
util.py:21
Functionget_root_logger
(file=True)
diffpack/util.py:44
Functioninit_sidechain
Initialize the side chain of the protein from restype_atom14_rigid_group_positions (shape: 21, 14, 3) Args: protein: Protein object
diffpack/rotamer.py:933
Functionload_config
(cfg_file, context=None)
util.py:70
Functionload_config
(cfg_file)
diffpack/util.py:35
Functionmeshgrid
(dict)
diffpack/util.py:17
Methodp
(self, x, sigma)
diffpack/schedule.py:80
Functionparse_args
()
util.py:80
Functionrandomize
(protein)
diffpack/rotamer.py:962
Functionremove_by_chi
(protein, chi_id)
diffpack/rotamer.py:774
Methodreverse_t_schedule
Reverse timesteps schedule.
diffpack/schedule.py:148
Methodreverse_t_schedule
(self)
diffpack/schedule.py:293
Methodsample_train_t
Sample timesteps from uniform distribution. Args: shape (tuple): shape of the timesteps Returns: Tensor: tim
diffpack/schedule.py:281
Functionset_chis
(protein, chis)
diffpack/rotamer.py:723
Methodstep
Denoise step for the input tensor (torsion angles). Args: x (Tensor): Torsion angles of shape :math:`(num_res, 4)` x_
diffpack/schedule.py:205
Methodstep_correct
Correct step for the input tensor (torsion angles). Args: x (Tensor): Torsion angles of shape :math:`(num_res, 4)` x_
diffpack/schedule.py:244