fix: some package names + move blosum to optional

.conda/arm64/meta.yaml

@@ -30,7 +30,7 @@ requirements:
     - Biopython==1.79 
     - click>=8.1.3
     - biopandas>=0.4.1
-    - boto3==1.24.59
+    - boto3
     - p-tqdm
     - networkx==2.8.8
     - einops
@@ -41,8 +41,12 @@ requirements:
     - awscli==1.25.60
     - bs4
     - rcsbsearch
-    - tmtools
-    - fair-esm
+    - pyyaml
+    - rdkit
+    - pypdb
+    - prody
+
+
 
 about:
   home: https://github.com/adaptyvbio/ProteinFlow

proteinflow/data/__init__.py

@@ -1993,7 +1993,7 @@ def align_structure(self, reference_pdb_path, save_pdb_path, chain_ids=None):
         io.save(save_pdb_path)
 
     @staticmethod
-    @requires_extra("mda", install_name="MDAnalysis")
+    @requires_extra("MDAnalysis")
     def combine_multiple_frames(files, output_path="combined.pdb"):
         """Combine multiple PDB files into a single multiframe PDB file.
 

proteinflow/metrics/__init__.py

@@ -3,14 +3,17 @@
 import os
 
 import biotite.structure.io as bsio
-import blosum as bl
 import numpy as np
 import torch
 from torch.nn import functional as F
 from tqdm import tqdm
 
 from proteinflow.extra import requires_extra
 
+try:
+    import blosum as bl
+except ImportError:
+    pass
 try:
     import esm
 except ImportError:
@@ -33,6 +36,7 @@
     pass
 
 
+@requires_extra("blosum")
 def blosum62_score(seq_before, seq_after):
     """Calculate the BLOSUM62 score between two sequences.
 
@@ -264,9 +268,7 @@ def tm_score(coordinates1, coordinates2, sequence1, sequence2):
     return (res.tm_norm_chain1 + res.tm_norm_chain2) / 2
 
 
-requires_extra("esm", install_name="fair-esm[esmfold]")
-
-
+@requires_extra("esm", install_name="fair-esm[esmfold]")
 def esmfold_generate(sequences, filepaths=None):
     """Generate PDB structures using ESMFold.
 

pyproject.toml

@@ -30,11 +30,9 @@ dependencies = [
     "bs4>=0.0.1",
     "pyyaml>=6",
     "rcsbsearch",
-    "blosum>=2.0",
     "pre-commit",
     "rdkit",
     "pypdb",
-    "prody",
     "joblib",
 ]
 keywords = ["bioinformatics", "dataset", "protein", "PDB", "deep learning", "antibody"]
@@ -52,6 +50,7 @@ processing = [
     "ablang",
     "igfold",
     "immunebuilder",
+    "blosum>=2.0",
 ]
 
 [tool.setuptools.packages]