jglaser commited on
Commit
bc9f870
1 Parent(s): d13e5f1

only retain first ligand if there are multiple copies

Browse files
Files changed (3) hide show
  1. README.md +4 -4
  2. data/pdb.parquet +2 -2
  3. parse_complexes.py +3 -3
README.md CHANGED
@@ -9,7 +9,7 @@ tags:
9
 
10
  ## How to use the data sets
11
 
12
- This dataset contains more about 60,000 unique pairs of protein sequences and ligand SMILES, and the coordinates
13
  of their complexes from the PDB.
14
 
15
  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.
22
 
23
  ## Ligand selection criteria
24
 
25
- Only ligands with
26
 
27
- - at least 3 atoms,
28
  - a molecular weight >= 100 Da,
29
- - that don't occur more than 75 times in different PDB complexes (this includes common additives like PEG, ADP, ..)
30
 
31
  are considered.
32
 
 
9
 
10
  ## How to use the data sets
11
 
12
+ This dataset contains more about 36,000 unique pairs of protein sequences and ligand SMILES, and the coordinates
13
  of their complexes from the PDB.
14
 
15
  SMILES are assumed to be tokenized by the regex from P. Schwaller.
 
22
 
23
  ## Ligand selection criteria
24
 
25
+ Only ligands
26
 
27
+ - that have at least 3 atoms,
28
  - a molecular weight >= 100 Da,
29
+ - and which are not among the 280 most common ligands in the PDB (this includes common additives like PEG, ADP, ..)
30
 
31
  are considered.
32
 
data/pdb.parquet CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:bbe6a448b46a5e6c2dd1b32ca878b5a658505f06334c173aa7565a3a6a848413
3
- size 988455052
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:2f6ef36582e7e9e8a29ac07976da378194216ad2144d33daa8a639e93300fcb9
3
+ size 396814137
parse_complexes.py CHANGED
@@ -183,8 +183,8 @@ def process_entry(df_dict, pdb_fn):
183
  natoms = template.GetNumAtoms()
184
 
185
  if mol_wt >= mol_wt_cutoff and natoms >= min_atoms and res not in ubiquitous_ligands:
186
- if len(mols) > 1:
187
- print('Found {} copies of {} ligand {}'.format(len(mols),pdb_name,res))
188
  ligand_mols += mols
189
  ligand_names += [res]*len(mols)
190
 
@@ -215,7 +215,7 @@ if __name__ == '__main__':
215
  # read ligand table
216
  df_dict = read_ligand_expo()
217
 
218
- result = executor.map(partial(process_entry, df_dict), filenames, chunksize=2048)
219
  result = list(result)
220
 
221
  # expand sequences and ligands
 
183
  natoms = template.GetNumAtoms()
184
 
185
  if mol_wt >= mol_wt_cutoff and natoms >= min_atoms and res not in ubiquitous_ligands:
186
+ # only use first copy of ligand
187
+ mols = mols[:1]
188
  ligand_mols += mols
189
  ligand_names += [res]*len(mols)
190
 
 
215
  # read ligand table
216
  df_dict = read_ligand_expo()
217
 
218
+ result = executor.map(partial(process_entry, df_dict), filenames, chunksize=512)
219
  result = list(result)
220
 
221
  # expand sequences and ligands