Update analysis_output.rst

docs/analysis_output.rst

@@ -40,7 +40,7 @@ Barcodes
 Binding_Modes_Markov_States
 ------------------------------
 
-**Binding_Modes_Markov_States**: A folder that contains the figures of the Markov state figures and 2D depiction figure of the  top 10 occuring binding modes.
+**Binding_Modes_Markov_States**: A folder that contains the figures of the markov state figures and 2D depiction figure of the top 10 occuring binding modes in addition to PDB and PML files of the representative frames of the binding modes.
 
 
 .. list-table::
@@ -49,65 +49,41 @@ Binding_Modes_Markov_States
 
    * - Name
      - Description
-   * - checkpoint.chk
-     - Checkpoint saved every 10000 steps.
-   * - 10x_checkpoint.chk
-     - Checkpoint saved every 100000 steps.
-   * - 100x_checkpoint.chk*
-     - Checkpoint saved every 1000000 steps.
-
-MD Files
+   * - 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
 ------------------------------
-**MD Files**: A folder that contains the files that were generated during the MD Simulation. This folder contains 3 subfolders.
-
-*Pre MD*: Folder that contains the files that were prepared by the script before the MD Simulation.
-
-.. list-table::
-   :header-rows: 1
-   :widths: 25 75
-
-   * - Name
-     - Description
-   * - prepared_no_solvent_protein_name.pdb
-     - Prepared PDB File without solvent or membrane.
-   * - solvent_padding_protein_name.pdb*
-     - Prepared PDB File with padding solvent.
-   * - solvent_absoulte_protein_name.pdb*
-     - Prepared PDB File with absolute solvent.
-   * - membrane_protein_name.pdb*
-     - Prepared PDB File with membrane.
-
-*Minimization Equilibration*: Folder that contains topology files after the minimization and equilibration with **OpenMM**.
-
-.. list-table::
-   :header-rows: 1
-   :widths: 25 75
-
-   * - Name
-     - Description
-   * - Energyminimization_protein_name.pdb
-     - Prepared PDB File after OpenMM energy minimization.
-   * - Equilibration_protein_name.pdb
-     - Prepared PDB File after OpenMM energy minimization and equilibration.
-
-*MD Output*: Folder that contains the Output trajectory files generated during the MD Simulation.
-
+**RMSD**: A folder that contains the files for the RMSD calculation during the simulation. The RMSD over time is default, while the RMSD between the frames is optional
 
 .. list-table::
    :header-rows: 1
    :widths: 25 75
 
    * - Name
      - Description
-   * - output_protein_name.pdb
-     - PDB Topology File of the first frame of the simulation.
-   * - trajectory.dcd
-     - Trajectory of the OpenMM Simulation.
-
-
-MD Postprocessing
+   * - 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.
+
+Binding Modes Markov States
 ------------------------------
-**MD Postprocessing**: A folder that contains the postprocessing files after the MD Simulation.
+**Binding Modes Markov States**: A folder that contains the Figures for the binding modes, the pdb files and pml files of the representative frames of the binding modes and the markov chain figure with the transitions between the binding modes.
 
 .. list-table::
    :header-rows: 1