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conversion.py

@@ -14,7 +14,10 @@ import networkx as nx
 import numpy as np
 import torch
 
-from graphein.utils.dependencies import import_message
+try:
+    from graphein.utils.dependencies import import_message
+except ImportError:
+    raise Exception('You need to install graphein from source in addition to DSSP to use this model please refer to https://github.com/a-r-j/graphein and https://ssbio.readthedocs.io/en/latest/instructions/dssp.html')
 
 try:
     import torch_geometric

graphs.py

@@ -15,37 +15,44 @@ from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 import networkx as nx
 import numpy as np
 import pandas as pd
-# from Bio.PDB.Polypeptide import three_to_one
-from biopandas.pdb import PandasPdb
-from biopandas.mmcif import PandasMmcif
+
+try:
+    from biopandas.pdb import PandasPdb
+    from biopandas.mmcif import PandasMmcif
+except ImportError:  
+    raise Exception('You need to install BioPandas and its dependecies to use this model.')
+
 from rich.progress import Progress
 from tqdm.contrib.concurrent import process_map
 
-from graphein.protein.config import (
-    DSSPConfig,
-    GetContactsConfig,
-    ProteinGraphConfig,
-)
-from graphein.protein.edges.distance import (
-    add_distance_to_edges,
-    compute_distmat,
-)
-from graphein.protein.resi_atoms import BACKBONE_ATOMS, RESI_THREE_TO_1
-from graphein.protein.subgraphs import extract_subgraph_from_chains
-from graphein.protein.utils import (
-    ProteinGraphConfigurationError,
-    compute_rgroup_dataframe,
-    filter_dataframe,
-    get_protein_name_from_filename,
-    three_to_one_with_mods,
-)
-from graphein.rna.constants import RNA_ATOMS
-from graphein.utils.utils import (
-    annotate_edge_metadata,
-    annotate_graph_metadata,
-    annotate_node_metadata,
-    compute_edges,
-)
+try:
+    from graphein.protein.config import (
+        DSSPConfig,
+        GetContactsConfig,
+        ProteinGraphConfig,
+    )
+    from graphein.protein.edges.distance import (
+        add_distance_to_edges,
+        compute_distmat,
+    )
+    from graphein.protein.resi_atoms import BACKBONE_ATOMS, RESI_THREE_TO_1
+    from graphein.protein.subgraphs import extract_subgraph_from_chains
+    from graphein.protein.utils import (
+        ProteinGraphConfigurationError,
+        compute_rgroup_dataframe,
+        filter_dataframe,
+        get_protein_name_from_filename,
+        three_to_one_with_mods,
+    )
+    from graphein.rna.constants import RNA_ATOMS
+    from graphein.utils.utils import (
+        annotate_edge_metadata,
+        annotate_graph_metadata,
+        annotate_node_metadata,
+        compute_edges,
+    )
+except ImportError:
+    raise Exception('You need to install graphein from source in addition to DSSP to use this model please refer to https://github.com/a-r-j/graphein and https://ssbio.readthedocs.io/en/latest/instructions/dssp.html')
 
 from .utils_convert import biopandas_mmcif2pdb
 

modeling_prot2text.py

@@ -17,15 +17,21 @@ from .pdb2graph import PDB2Graph, download_alphafold_structure
 from .graphs import *
 from .utils_dataset import *
 
-from graphein.protein.config import ProteinGraphConfig, DSSPConfig
-from graphein.protein.features.nodes.amino_acid import amino_acid_one_hot, meiler_embedding, expasy_protein_scale, hydrogen_bond_acceptor, hydrogen_bond_donor
-from graphein.protein.features.nodes.dssp import  phi, psi, asa, rsa, secondary_structure
-from graphein.protein.edges.distance import (add_peptide_bonds,
-                                             add_hydrogen_bond_interactions,
-                                             add_distance_threshold,
-                                            )
+try:
+    from graphein.protein.config import ProteinGraphConfig, DSSPConfig
+    from graphein.protein.features.nodes.amino_acid import amino_acid_one_hot, meiler_embedding, expasy_protein_scale, hydrogen_bond_acceptor, hydrogen_bond_donor
+    from graphein.protein.features.nodes.dssp import  phi, psi, asa, rsa, secondary_structure
+    from graphein.protein.edges.distance import (add_peptide_bonds,
+                                                add_hydrogen_bond_interactions,
+                                                add_distance_threshold,
+                                                )
+except ImportError:
+    raise Exception('You need to install graphein from source in addition to DSSP to use this model please refer to https://github.com/a-r-j/graphein and https://ssbio.readthedocs.io/en/latest/instructions/dssp.html')
 
-from torch_geometric.nn import RGCNConv, global_mean_pool
+try:
+    from torch_geometric.nn import RGCNConv, global_mean_pool
+except ImportError:  
+    raise Exception('You need to install torch geometric and its dependecies to use this model please refer to https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html')
 
 
 

pdb2graph.py

@@ -3,23 +3,30 @@ import os
 from tqdm import tqdm
 from sklearn.preprocessing import MultiLabelBinarizer
 
-from torch_geometric.data import Data
+try:
+    from torch_geometric.data import Data
+except ImportError:  
+    raise Exception('You need to install torch geometric and its dependecies to use this model please refer to https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html')
 import torch
 
 import numpy as np
 
 from .conversion import convert_nx_to_pyg_data
-from graphein.protein.config import ProteinGraphConfig, DSSPConfig
-from graphein.protein.features.nodes.amino_acid import amino_acid_one_hot, meiler_embedding, expasy_protein_scale, hydrogen_bond_acceptor, hydrogen_bond_donor
-from graphein.protein.features.nodes.dssp import  phi, psi, asa, rsa, secondary_structure
-from graphein.protein.edges.distance import (add_peptide_bonds,
-                                             add_hydrogen_bond_interactions,
-                                             add_disulfide_interactions,
-                                             add_ionic_interactions,
-                                             add_delaunay_triangulation,
-                                             add_distance_threshold,
-                                             add_sequence_distance_edges,
-                                             add_k_nn_edges)
+
+try:
+    from graphein.protein.config import ProteinGraphConfig, DSSPConfig
+    from graphein.protein.features.nodes.amino_acid import amino_acid_one_hot, meiler_embedding, expasy_protein_scale, hydrogen_bond_acceptor, hydrogen_bond_donor
+    from graphein.protein.features.nodes.dssp import  phi, psi, asa, rsa, secondary_structure
+    from graphein.protein.edges.distance import (add_peptide_bonds,
+                                                add_hydrogen_bond_interactions,
+                                                add_disulfide_interactions,
+                                                add_ionic_interactions,
+                                                add_delaunay_triangulation,
+                                                add_distance_threshold,
+                                                add_sequence_distance_edges,
+                                                add_k_nn_edges)
+except ImportError:
+    raise Exception('You need to install graphein from source in addition to DSSP to use this model please refer to https://github.com/a-r-j/graphein and https://ssbio.readthedocs.io/en/latest/instructions/dssp.html')
 
 from functools import partial
 from .graphs import *

utils.py

@@ -10,8 +10,11 @@ from transformers.generation.stopping_criteria import StoppingCriteriaList
 from transformers.generation.utils import GreedySearchOutput, GreedySearchEncoderDecoderOutput, BeamSearchOutput, BeamSearchEncoderDecoderOutput
 from transformers.generation.beam_search import BeamScorer
 
-from torch_geometric.loader import DataLoader
-from torch_geometric.data import Dataset
+try:
+    from torch_geometric.loader import DataLoader
+    from torch_geometric.data import Dataset
+except ImportError:  
+    raise Exception('You need to install torch geometric and its dependecies to use this model please refer to https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html')
 
 class _GPT2LMHeadModel(GPT2LMHeadModel):
     def _init_(self, config):