Input Files Option¶
Molecular input file name containing 3D coordinates in any format supported by OEChem. In order to comply with the previous SZYBKI releases, an alias
-ican be used instead of
-in. This option might be used as a keyless parameter without the
-ikeys but only when used last or next to last when the last option on the command line is
-out. Warning: File name:
szybki_out.oebis used as the default output file name, so should be avoided as an input file name.
Protein input file with 3D coordinates in any format supported by OEChem. Works in combination with the
-inoption. No removal of pre-existing ligands in file
filenamewill be done as in the case of the
-complexoption. This option can be aliased with
-pfor compatibility with previous SZYBKI releases.
Input file with 3D coordinates of a protein-ligand(s) complex in any format listed in the table above. All ligands contained in the molecule file
filenamewill be optimized one by one in the presence of all others.