only retain first ligand if there are multiple copies

README.md

@@ -9,7 +9,7 @@ tags:
 
 ## How to use the data sets
 
-This dataset contains more about 60,000 unique pairs of protein sequences and ligand SMILES, and the coordinates
+This dataset contains more about 36,000 unique pairs of protein sequences and ligand SMILES, and the coordinates
 of their complexes from the PDB.
 
 SMILES are assumed to be tokenized by the regex from P. Schwaller.
@@ -22,11 +22,11 @@ The dataset can be used to fine-tune a language model.
 
 ## Ligand selection criteria
 
-Only ligands with
+Only ligands
 
-- at least 3 atoms,
+- that have at least 3 atoms,
 - a molecular weight >= 100 Da,
-- that don't occur more than 75 times in different PDB complexes (this includes common additives like PEG, ADP, ..)
+- and which are not among the 280 most common ligands in the PDB (this includes common additives like PEG, ADP, ..)
 
 are considered.
 

data/pdb.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:bbe6a448b46a5e6c2dd1b32ca878b5a658505f06334c173aa7565a3a6a848413
-size 988455052
+oid sha256:2f6ef36582e7e9e8a29ac07976da378194216ad2144d33daa8a639e93300fcb9
+size 396814137

parse_complexes.py

@@ -183,8 +183,8 @@ def process_entry(df_dict, pdb_fn):
                 natoms = template.GetNumAtoms()
 
                 if mol_wt >= mol_wt_cutoff and natoms >= min_atoms and res not in ubiquitous_ligands:
-                    if len(mols) > 1:
-                        print('Found {} copies of {} ligand {}'.format(len(mols),pdb_name,res))
+                    # only use first copy of ligand
+                    mols = mols[:1]
                     ligand_mols += mols
                     ligand_names += [res]*len(mols)
 
@@ -215,7 +215,7 @@ if __name__ == '__main__':
             # read ligand table
             df_dict = read_ligand_expo()
 
-            result = executor.map(partial(process_entry, df_dict), filenames, chunksize=2048)
+            result = executor.map(partial(process_entry, df_dict), filenames, chunksize=512)
             result = list(result)
 
             # expand sequences and ligands