Water migration through enzyme tunnels is sensitive to the choice of explicit water model (AldO + CYP2D6)

<p>This repository contains data for the alditol oxidase (AldO) and cytochrome P450 2D6 (CYP2D6). Data underpinning analyses of haloalkane dehalogenase DhaA are available from the related repository:&nbsp;<a href="https://doi.org/10.5281/zenodo.11489893">10.5281/zenodo.11489893</a>.</p> <p><strong>Content:</strong></p> <p><strong>AldO.tar.gz:</strong></p> <p><strong>tt_conda.yml -&gt; conda environment used for the calculations.&nbsp;</strong><br>&nbsp; &nbsp; &nbsp; &nbsp; Usage :<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;conda env create -f tt_conda.yml<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;conda activate tt_conda.yml&nbsp;</p> <p><strong>01_MD_simulations -&gt; the files to run simulation, out and restart files from simulation and simulation analysis results, organized by models and Tunnel Conformational Groups (TCGs).</strong></p> <p>├── 01_MD_simulations<br>│ &nbsp; ├── 01_inputs<br>│ &nbsp; │ &nbsp; ├── opc<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; │ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; │ &nbsp; ├── scripts<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 00_prepare_model.sh<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 01_minimization.sh<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 02_equilibration.sh<br>│ &nbsp; │ &nbsp; │ &nbsp; └── 03_production.sh<br>│ &nbsp; │ &nbsp; ├── tip3p<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; │ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; │ &nbsp; └── tip4pew<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; ├── 02_outputs<br>│ &nbsp; │ &nbsp; ├── opc<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; │ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; │ &nbsp; ├── tip3p<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; │ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; │ &nbsp; └── tip4pew<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; ├── 03_analysis<br>│ &nbsp; │ &nbsp; ├── rmsd_opc.csv<br>│ &nbsp; │ &nbsp; ├── rmsd_tip3p.csv<br>│ &nbsp; │ &nbsp; ├── rmsd_tip4pew.csv<br>│ &nbsp; │ &nbsp; ├── rmsf_opc.csv<br>│ &nbsp; │ &nbsp; ├── rmsf_tip3p.csv<br>│ &nbsp; │ &nbsp; └── rmsf_tip4pew.csv<br>│ &nbsp; └── readme.txt<br><br><strong>02_caver -&gt; results of CAVER calculations, organized by models and TCGs.</strong></p> <p>├── 02_caver<br>│ &nbsp; ├── config_files<br>│ &nbsp; │ &nbsp; ├── calculate_tunnels.txt<br>│ &nbsp; │ &nbsp; └── clustering.txt<br>│ &nbsp; ├── opc<br>│ &nbsp; │ &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; │ &nbsp; └── 5<br>│ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── 5<br>│ &nbsp; ├── readme.txt<br>│ &nbsp; ├── tip3p<br>│ &nbsp; │ &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; │ &nbsp; └── 5<br>│ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── 5<br>│ &nbsp; └── tip4pew<br>│ &nbsp; &nbsp; &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; └── 5<br>│ &nbsp; &nbsp; &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; └── 5</p> <p><strong>03_aquaduct -&gt; results of AQUA-DUCT calculations, organized by models and TCGs. &nbsp; </strong></p> <p>├── 03_aquaduct<br>│ &nbsp; ├── opc<br>│ &nbsp; │ &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; │ &nbsp; └── 5<br>│ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── 5<br>│ &nbsp; ├── readme.txt<br>│ &nbsp; ├── tip3p<br>│ &nbsp; │ &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; │ &nbsp; └── 5<br>│ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── 5<br>│ &nbsp; └── tip4pew<br>│ &nbsp; &nbsp; &nbsp; ├── TCG_d1.0_o1.6<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; └── 5<br>│ &nbsp; &nbsp; &nbsp; └── TCG_d2.0_o1.9<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; └── 5&nbsp;</p> <p><strong>04_transport_tools -&gt; the results of TransportTools and analysis done from TransportTools results.</strong></p> <p>├── 04_transport_tools<br>│ &nbsp; ├── overall_results<br>│ &nbsp; │ &nbsp; ├── config.in<br>│ &nbsp; │ &nbsp; ├── data<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── exact_matching_analysis<br>│ &nbsp; │ &nbsp; │ &nbsp; └── super_clusters<br>│ &nbsp; │ &nbsp; ├── statistics<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1-initial_tunnels_statistics_bottleneck_residues.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1-initial_tunnels_statistics.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2-filtered_tunnels_statistics_bottleneck_residues.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2-filtered_tunnels_statistics.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3-initial_events_statistics_bottleneck_residues.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3-initial_events_statistics.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4-filtered_events_statistics_bottleneck_residues.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4-filtered_events_statistics.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; └── comparative_analysis<br>│ &nbsp; │ &nbsp; ├── transport_tools.log<br>│ &nbsp; │ &nbsp; └── visualization<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 1-visualize_initial_tunnels.py<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 2-visualize_filtered_tunnels.py<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 3-visualize_initial_events.py<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 4-visualize_filtered_events.py<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── comparative_analysis<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── sources<br>│ &nbsp; └── scripts<br>│ &nbsp; &nbsp; &nbsp; ├── bottleneck_residues<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 5_bottleneck_residues.py<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; └── T1.png<br>│ &nbsp; &nbsp; &nbsp; ├── presence_of_tunnels<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 6_tunnels_before_assignment.py<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── before.png<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; └── number_frames.pkl<br>│ &nbsp; &nbsp; &nbsp; └── water_transport_analysis<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 8_main_figure.py<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── figure2.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── output<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── percent_frames_events_AldO.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── transit_time_median.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── tt_events.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; └── water_per_frame_AldO.png</p> <p>&nbsp;</p> <p><strong>CYP2D6.tar.gz:</strong></p> <p><strong>tt_conda.yml -&gt; conda environment used for the calculations.&nbsp;<br>&nbsp; &nbsp; &nbsp; &nbsp; </strong>Usage :<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;conda env create -f tt_conda.yml<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;conda activate tt_conda.yml&nbsp;</p> <p><strong>01_MD_simulations -&gt; the files to run simulation, out and restart files from simulation and simulation analysis results, organized by models and Tunnel Conformational Groups (TCGs).</strong></p> <p>├── 01_MD_simulations<br>│ &nbsp; ├── 01_inputs<br>│ &nbsp; │ &nbsp; ├── opc<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; │ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; │ &nbsp; ├── scripts<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 01_minimization_heating_CPU_ARES_prep.sh<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 02_equilibration_GPU_ARES_prep.sh<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 03_production_ARES.sh<br>│ &nbsp; │ &nbsp; │ &nbsp; └── prepare_model_3tbg.sh<br>│ &nbsp; │ &nbsp; ├── tip3p<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; │ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; │ &nbsp; └── tip4pew<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; ├── 02_outputs<br>│ &nbsp; │ &nbsp; ├── opc<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; │ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; │ &nbsp; ├── tip3p<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; │ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; │ &nbsp; └── tip4pew<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; ├── 03_analysis<br>│ &nbsp; │ &nbsp; ├── rmsd_opc.csv<br>│ &nbsp; │ &nbsp; ├── rmsd_tip3p.csv<br>│ &nbsp; │ &nbsp; ├── rmsd_tip4pew.csv<br>│ &nbsp; │ &nbsp; ├── rmsf_opc.csv<br>│ &nbsp; │ &nbsp; ├── rmsf_tip3p.csv<br>│ &nbsp; │ &nbsp; └── rmsf_tip4pew.csv<br>│ &nbsp; └── readme.txt</p> <p><strong>02_caver -&gt; results of CAVER calculations, organized by models and TCGs.</strong></p> <p>├── 02_caver<br>│ &nbsp; ├── config_files<br>│ &nbsp; ├── opc<br>│ &nbsp; │ &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; │ &nbsp; └── 5<br>│ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── 5<br>│ &nbsp; ├── readme.txt<br>│ &nbsp; ├── tip3p<br>│ &nbsp; │ &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; │ &nbsp; └── 5<br>│ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── 5<br>│ &nbsp; └── tip4pew<br>│ &nbsp; &nbsp; &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; └── 5<br>│ &nbsp; &nbsp; &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; └── 5</p> <p><strong>03_aquaduct -&gt; results of AQUA-DUCT calculations, organized by models and TCGs. &nbsp; </strong></p> <p>├── 03_aquaduct<br>│ &nbsp; ├── opc<br>│ &nbsp; │ &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; │ &nbsp; └── 5<br>│ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── 5<br>│ &nbsp; ├── readme.txt<br>│ &nbsp; ├── tip3p<br>│ &nbsp; │ &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; │ &nbsp; └── 5<br>│ &nbsp; │ &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── 5<br>│ &nbsp; └── tip4pew<br>│ &nbsp; &nbsp; &nbsp; ├── TCG_d1.7_o1.6_TCG_d1.1_o1.4_TCG_d1.1_o.1.1<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 1<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 2<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 3<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 4<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; └── 5<br>│ &nbsp; &nbsp; &nbsp; └── TCG_d2.0_o1.9_TCG_d1.6_o1.6_TCG_d1.6_o1.1<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 1<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 2<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 3<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 4<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; └── 5</p> <p><strong>04_transport_tools -&gt; the results of TransportTools and analysis done from TransportTools results.</strong></p> <p>├── 04_transport_tools<br>│ &nbsp; ├── overall_results<br>│ &nbsp; │ &nbsp; ├── config.in<br>│ &nbsp; │ &nbsp; ├── data<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── exact_matching_analysis<br>│ &nbsp; │ &nbsp; │ &nbsp; └── super_clusters<br>│ &nbsp; │ &nbsp; ├── statistics<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1-initial_tunnels_statistics_bottleneck_residues.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 1-initial_tunnels_statistics.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2-filtered_tunnels_statistics_bottleneck_residues.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 2-filtered_tunnels_statistics.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3-initial_events_statistics_bottleneck_residues.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 3-initial_events_statistics.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4-filtered_events_statistics_bottleneck_residues.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; ├── 4-filtered_events_statistics.txt<br>│ &nbsp; │ &nbsp; │ &nbsp; └── comparative_analysis<br>│ &nbsp; │ &nbsp; ├── transport_tools.log<br>│ &nbsp; │ &nbsp; └── visualization<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 1-visualize_initial_tunnels.py<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 2-visualize_filtered_tunnels.py<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 3-visualize_initial_events.py<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 4.pse<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── 4-visualize_filtered_events.py<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; ├── comparative_analysis<br>│ &nbsp; │ &nbsp; &nbsp; &nbsp; └── sources<br>│ &nbsp; └── scripts<br>│ &nbsp; &nbsp; &nbsp; ├── bottleneck_analyses<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 5_bottleneck_residues.py<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── Ch2B-F.png<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── Ch2C.png<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; └── ChS.png<br>│ &nbsp; &nbsp; &nbsp; ├── presence_of_tunnels<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── 6_tunnels_before_assignment.py<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; ├── before.png<br>│ &nbsp; &nbsp; &nbsp; │ &nbsp; └── number_frames.pkl<br>│ &nbsp; &nbsp; &nbsp; └── water_transport_analysis<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── 8_main_figure.py<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── figure2_Ch2B-Ch2F.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── figure2_Ch2C.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── figure2_Ch2S.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── output<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── percent_frames_events_Ch2B-Ch2F.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── percent_frames_events_Ch2C.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── percent_frames_events_ChS.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── transit_time_median_Ch2B-Ch2F.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── transit_time_median_Ch2C.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── transit_time_median_ChS.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── tt_events_Ch2B-Ch2F.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── tt_events_Ch2C.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── tt_events_Ch2S.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── water_per_frame_Ch2B-Ch2F.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ├── water_per_frame_Ch2C.png<br>│ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; └── water_per_frame_ChS.png</p>