format of file_table.csv

[lindafei01]

Hello, I'm not sure how to use the command line 'bust -t file_table.csv' correctly.

What should the format of file_table.csv be like if I want to check numerous re-docked ligands?

Thank you in advance for your assistance!

[maabuu]

This could indeed be documented better.

For re-docking, three columns are needed:

• mol_pred: predicted (re-docked) ligand(s) file to test
• mol_true: ground truth (crystal) ligand(s) file
• mol_cond: (crystal) receptor file

For example:

mol_cond,mol_true,mol_pred
1ia1_tq3/receptor.pdb,1ia1_tq3/crystal_ligands.sdf,1ia1_tq3/redocked_ligands.sdf
1of6_dty/receptor.pdb,1of6_dty/crystal_ligands.sdf,1of6_dty/redocked_ligands.sdf
1s3v_tqd/receptor.pdb,1s3v_tqd/crystal_ligands.sdf,1s3v_tqd/redocked_ligands.sdf
1uou_cmu/receptor.pdb,1uou_cmu/crystal_ligands.sdf,1uou_cmu/redocked_ligands.sdf

The bust command with the -t option will run the bust command on the file triplet in each row and combine the output.

>>> bust -t redock_table.csv --outfmt csv
file,molecule,mol_pred_loaded,mol_true_loaded,mol_cond_loaded,sanitization,all_atoms_connected,molecular_formula,molecular_bonds,double_bond_stereochemistry,tetrahedral_chirality,bond_lengths,bond_angles,internal_steric_clash,aromatic_ring_flatness,double_bond_flatness,internal_energy,protein-ligand_maximum_distance,minimum_distance_to_protein,minimum_distance_to_organic_cofactors,minimum_distance_to_inorganic_cofactors,minimum_distance_to_waters,volume_overlap_with_protein,volume_overlap_with_organic_cofactors,volume_overlap_with_inorganic_cofactors,volume_overlap_with_waters,rmsd_≤_2å
1ia1_tq3/redocked_ligands.sdf,dock35,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True
1ia1_tq3/redocked_ligands.sdf,dock36,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True
...

To save the output, a redirect can be used:

bust -t redock_table.csv --outfmt csv >> test_results.csv

[lindafei01]

This helps a lot! Thank you very much!