Data Layout

Input file layout

Directorys containing input files are placed at the same level as run_ligx.py.

work_dir/
├── run_ligx.py
├── ligand_xyz/
│   └── ligand_name/
│       ├── ligand_name.xyz
│       └── charge.txt
├── protein_xyz/
│   └── protein_name.xyz
├── fragment/ (optional)
│   ├── ***
│   ├── .
│   └── .    
└── rollout_fragment/ (optional)
    ├── ***
    ├── .
    └── .

The directory names ligand_xyz/ and protein_xyz/ are specified as LigX default values. ligand_name.xyz is a xyz file of initiator prepared according to the instructions on Initiator Preparation. The results will be output to work_dir. These name can be specified by Attributes of LigXRun.

Note: The fragment and rollout_fragment in the above example illustrate the layout when using external fragments. These two are optional because LigX contains default fragment sets required for the execution. For details, refer to Using User-Specified Fragments].

Output file layout

Output files in LigX are stored in result/. Log files are stored in current directory. result_all_total_conf_(number).xyz is suitable for the docking simulations. This file can be visualized using programs such as PyMOL. result_score.csv contains SMILES and interaction energies roughlly estimated by LigX. (Using this value for evaluation of compounds is not recommended. Please use other reliable docking tools for affinity evaluation.)

After the termination, result_conf_(number)/ will be created that strores all xyz files and charge parameters.

work_dir/
├── run_ligx.py
├── .
├── .
├── .
├── logfile.log
├── paramfile.log
└── result/
    ├── image_ligx/
    │   ├── chemical_structure1.png
    │   └── .
    ├── result_all_total_conf_(number).xyz  #suitable for the following docking simulations.
    ├── result_conf_(number)/
    │   ├── sorted_structures1/
    │   ├── .
    │   ├── .
    │   ├── sorted_structures.xyz
    │   ├── .
    │   └── .
    └── result_score.csv  #contains interaction energy and SMILES