Discngine / fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).
MIT License
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No atom found when processing cif file 2po6 #151

Open xvlaurent opened 2 weeks ago

xvlaurent commented 2 weeks ago

Describe the bug Fpocket fail to parse atom_site section of 2po6 rcsb cif file.

To Reproduce Steps to reproduce the behavior:

  1. Go dowload cif file of '2PO6' RCSB entry
  2. run fpocket with command fpocket -f 2po6.cif -d -w cif -l 1

Expected behavior Pocket detection should run smoothly.

Screenshots image

pschmidtke commented 2 weeks ago

Issue with revisions in the cif file:

10 6 'Structure model' '_atom_site.B_iso_or_equiv'                   
11 6 'Structure model' '_atom_site.Cartn_x'                          
12 6 'Structure model' '_atom_site.Cartn_y'                          
13 6 'Structure model' '_atom_site.Cartn_z'                          
14 6 'Structure model' '_atom_site.auth_asym_id'                     
15 6 'Structure model' '_atom_site.auth_atom_id'                     
16 6 'Structure model' '_atom_site.auth_comp_id'                     
17 6 'Structure model' '_atom_site.auth_seq_id'                      
18 6 'Structure model' '_atom_site.label_asym_id'                    
19 6 'Structure model' '_atom_site.label_atom_id'                    
20 6 'Structure model' '_atom_site.label_comp_id'                    
21 6 'Structure model' '_atom_site.label_entity_id'                  
22 6 'Structure model' '_atom_site.type_symbol'  

double check how the molfile parser is parsing this (false positive hits here)

pschmidtke commented 6 days ago

likely the issue is here: image

only paring if _atom_site. is present, not where it is on the line