While AFITT does not require the use of the command line, it does support limited functionality such as loading files and starting a basic fitting run.
A description of the command line interface can be obtained by executing AFITT with the --help option.
prompt> afitt --help
will generate the following output:
Help functions:
afitt --help simple : Get a list of simple parameters
afitt --help all : Get a complete list of parameters
afitt --help <parameter> : Get detailed help on a parameter
afitt --help html : Create an html help file for this program
Load a file into AFITT. Typical files includes, ligands proteins and density that can be automatically loaded.
File containing a molecule to be fit to density.
| File type | Extension |
|---|---|
| SMILES | .smi .ism .smi.gz .ism.gz |
| OEBinary | .oeb .oeb.gz |
| SDF | .sdf .mol .sdf.gz .mol.gz |
| MOL2 | .mol2 .mol2.gz |
| PDB | .pdb .ent .pdb.gz .ent.gz |
| MacroModel | .mmod .mmod.gz |
Input density grid used to fit ligand.
| Grid File type | Extension |
|---|---|
| MTZ | .mtz |
| OpenEye | .grd |
| Grasp | .phi |
| CCP4 | .map .ccp4 |
| XPLOR | .xplor xplmap |
| ASCII Grid | .agd |
Run a basic fit on the loaded molecules. This is the same as hitting the fit button.
Run a basic fit on the loaded molecules. This is the same as hitting the fit button. Automatically save the output and optionally load it into the viewer selected in the current workflow.