**OpenMMDL Analysis Output Files**
=================================

The **OpenMMDL Analysis** script creates output folders and files during and after the analysis.

The following list contains a detailed overview of the folders and files:
The Optional files are highlighted with an *asterisk**


The following Files are generated and stored directly in the working folder where you start the **OpenMMDL Analysis**:

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   * - Name
     - Description
   * - complex.pdb
     - PDB file of the protein, ligand, waters 10Å around the ligand and special ligand if selected).
   * - df_all.csv
     - CSV file of the calculated interaction together with the generated fingerprints.
   * - interactions_gathered.csv
     - CSV File of the calculated interaction together without the generated fingerprints.
   * - lig.pdb
     - PDB file of the ligand with hydrogens.
   * - lig.smi
     - Smiles file of the ligand.
   * - ligand_numbering.png*
     - File that displays the ligand in 2D depiction with the correct assignment of atom numbers, which makes it easier to understand the interacting atoms.
   * - ligand_special.pdb*
     - PDB file of the ligand with the special ligand.
   * - lig_no_h.pdb
     - PDB file of the ligand without hydrogens.
   * - missing_frames_filled.csv
     - CSV file of the calculated interactions with added frames for frames without interactions
   * - top_10_binding_modes.csv
     - CSV file of the top 10 most occurring binding modes.


Barcodes
------------------------------
**Barcodes**: A folder that contains the figures of the barcodes for the interactions.



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   * - Name
     - Description
   * - acceptor_interactions.png*
     - File displaying the barcodes for all hydrogen bond acceptor interactions.
   * - donor_interactions.png*
     - File displaying the barcodes for all hydrogen bond donor interactions.
   * - halogen_interactions.png*
     - File displaying the barcodes for all halogen interactions.
   * - hydrophobic_interactions.png*
     - File displaying the barcodes for all hydrophobic interactions.
   * - metal_interactions.png*
     - File displaying the barcodes for all metal interactions.
   * - saltbridge_interactions.png*
     - File displaying the barcodes for all saltbridge interactions.
   * - pication_interactions.png*
     - File displaying the barcodes for all pication interactions.
   * - pistacking_interactions.png*
     - File displaying the barcodes for all pistacking interactions.
   * - waterbridge_interactions.png*
     - File displaying the barcodes for all waterbridge interactions.

Binding_Modes_Markov_States
------------------------------

**Binding_Modes_Markov_States**: A folder that contains the figures of the Markov state figures and a 2D depiction figure of the top 10 occurring binding modes in addition to PDB and PML files of the representative frames of the binding modes.


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   * - Name
     - Description
   * - all_binding_modes_arranged.png
     - Figure of the 2D depictions of the top 10 binding modes with the interacting protein partners.
   * - Binding_mode_x.pdb
     - PDB File of the representative frame of the binding mode.
   * - Binding_mode_x.pml*
     - PML File of the representative frame of the binding mode.
   * - markov_chain_plot_1.png
     - Markov chain Figure displaying binding modes with a minimum transition of 1% of the frames between the binding modes.
   * - markov_chain_plot_2.png
     - Markov chain Figure displaying binding modes with a minimum transition of 2% of the frames between the binding modes.
   * - markov_chain_plot_5.png
     - Markov chain Figure displaying binding modes with a minimum transition of 5% of the frames between the binding modes.
   * - markov_chain_plot_10.png
     - Markov chain Figure displaying binding modes with a minimum transition of 10% of the frames between the binding modes.

RMSD
------------------------------
**RMSD**: A folder that contains the files for the RMSD calculation during the simulation. The RMSD over time is always calculated, while the RMSD between the frames is optional.

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   * - Name
     - Description
   * - RMSD_over_time.csv
     - CSV file with the values of the RMSD  of the protein/backbone/ligand during the simulation time.
   * - RMSD_over_time.png
     - Figure of the RMSD of the protein/backbone/ligand during the simulation time.
   * - RMSD_between_the_frames.png*
     - Matrix figure displaying the RMSD between each consecutive frame.

Visualization
------------------------------
**Visualization**: A folder the files that are necessary for the NGLView visualization of the interactions.

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   * - Name
     - Description
   * - clouds.json
     - JSON file that contains the information for the point clouds.
   * - interacting_waters.dcd
     - Trajectory file for the point clouds visualization.
   * - interacting_waters.pdb
     - Topology file for the point clouds visualization.
   * - interacting_waters.pkl
     - pickle file of the interacting water ids for the point clouds visualization.