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jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
GNU Lesser General Public License v2.1
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Error in construction of a network of hydrogen bonds #128

Closed boristim66 closed 3 years ago

boristim66 commented 3 years ago

The construction of a network of hydrogen bonds does not work for atoms of the same residues with the same numbers, but belonging to different chains due sort error : 3hto_chainsOB.zip $ pdb2pqr30 --ff AMBER --with-ph 4.5 --drop-water --keep-chain "3hto_chainsOB.pdb" "3hto_chainsOB.pqr" ............ DEBUG: Optimizeable to optimizeable DEBUG: Water to Water DEBUG:Starting network ASN B 595 (Flip), ASN D 595 (Flip), ASN F 595 (Flip) DEBUG: Optimizeable to backbone Traceback (most recent call last): File "/usr/local/bin/pdb2pqr30", line 8, in sys.exit(main()) File "/usr/local/lib/python3.7/dist-packages/pdb2pqr/main.py", line 796, in main main_driver(args) File "/usr/local/lib/python3.7/dist-packages/pdb2pqr/main.py", line 765, in main_driver is_cif=is_cif, File "/usr/local/lib/python3.7/dist-packages/pdb2pqr/main.py", line 641, in non_trivial hydrogen_routines.optimize_hydrogens() File "/usr/local/lib/python3.7/dist-packages/pdb2pqr/hydrogens/init.py", line 485, in optimize_hydrogens hbondlist = util.sort_dict_by_value(hbondmap) File "/usr/local/lib/python3.7/dist-packages/pdb2pqr/utilities.py", line 33, in sort_dict_by_value items.sort() TypeError: '<' not supported between instances of 'PotentialBond' and 'PotentialBond'

boristim66 commented 3 years ago

This is a bug of pdb2pqr, sorry