PDB format is not based on space separators like PQR. Regex might fail when looking for ligands..

hello, the lfetch.py script in the windows system would generate illegal Ligand file name (could occur colon in the file name) and therefore cannot extrat the ligand corretly. But it runs perfectly in linux, see below:

windows 10, 64

(gpu02_py) G:\05Coding\GNN_DTI-master\dpi_v4\pretrain\MOAD_ligandFinder-1.1>python lfetch.py
Insert pdb name
1FWE
Valid ligands found: 1
Excluded: 0
Ligands: ['HAE_C:989']
Insert pdb name

linux

(/home/dejun/work_spaces/py/conda_env/py365) [dejun@mu01 MOAD_ligandFinder-main]$ python lfetch.py
Insert pdb name
1FWE
Valid ligands found: 1
Excluded: 0
Ligands: ['HAE_C989']
Insert pdb name

The naming scheme of binding moad is to associate any residue name appearing on a line to a increasing res number, for each chain (for instance 1cqf--> BGC GAL GLA F:1 G:1 I:1 ..) will look for ligand1=(BGC F 1, GAL F 2, GLA F 3), ligand2 =(BGC G 1, GAL G 2, GLA G 3), ligand2 =(BGC I 1, GAL I 2, GLA I 3) ecc..

So far, the strategy used to overcome mismatches is to skip progressively in order (from the MOAD naming scheme) the name-chainID-ResNumber. This works most of times but not always. An example is 4z0u.pdb where the pdb skips the first 4 names and start from the 5th but keeping to index of the number at the beginning (usually everything is shifted accordingly).

In general, one could device more flexible strategies to overcome mismatches