check molecules for errors
This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
The following checks are done for each molecule:
* bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem)
* each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments.
* each atom must have a valid assigned element
* the molecule must be protonated (since this is necessary for docking/(re-)scoring).
* 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
* partial charges may not contain completely senseless values (>5 or <-5).
* each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies.
If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them.