streamd 0.2.4__tar.gz

streamd-0.2.4/LICENSE.txt

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+MIT License
+
+Copyright (c) 2024 Aleksandra Ivanova, Olena Mokshyna, Pavel Polishchuk
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

streamd-0.2.4/MANIFEST.in

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+graft streamd/scripts
+graft streamd/example

streamd-0.2.4/PKG-INFO

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+Metadata-Version: 2.1
+Name: streamd
+Version: 0.2.4
+Summary: Streamd Python module to facilitate molecular dynamics
+Home-page: https://github.com/ci-lab-cz/streamd
+Author: Aleksandra Ivanova, Olena Mokshyna, Pavel Polishchuk
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: POSIX :: Linux 
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Provides-Extra: rdkit
+Requires-Dist: rdkit>=2017.09; extra == "rdkit"
+
+# StreaMD: a tool to perform high-throughput automated molecular dynamics simulations
+
+## installation
+*Source: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/installation/*
+
+[env.yml](https://github.com/ci-lab-cz/streamd/blob/master/env.yml)
+```
+conda env create -n md --file env.yml
+
+```
+
+## **Description**
+#### **Fully automatic pipeline for molecular dynamics**
+
+#### Features:  
+- supports run of multiple simultaneous molecular dynamics simulations
+- supports simulation for different systems:  
+    - Protein in Water;  
+    - Protein - Ligand;  
+    - Protein - Cofactor (multiple);  
+    - Protein - Ligand - Cofactor (multiple);  
+  
+- supports of simulations of boron-containing molecules using Gaussian Software
+- supports of simulations of ligand binding metalloproteins with MCPB.py
+- supports distributed computing using dask library
+- supports of running of parallel simulations on multiple servers
+- supports to extend time of MD simulations 
+- supports to continue of interrupted MD simulation
+- interrupted MD preparation can be restarted by invoking the same command
+- implemented tools for end-state free energy calculations (gmx_MMPBSA) and Protein-Ligand Interaction analysis (ProLIF)
+
+### **USAGE**
+```
+run_md -h
+usage: run_md [-h] [-p FILENAME] [-d WDIR] [-l FILENAME] [--cofactor FILENAME] [--clean_previous_md] [--hostfile FILENAME] [-c INTEGER] [--topol topol.top]
+              [--topol_itp topol_chainA.itp topol_chainB.itp [topol_chainA.itp topol_chainB.itp ...]] [--posre posre.itp [posre.itp ...]]
+              [--protein_forcefield amber99sb-ildn] [--md_time ns] [--npt_time ps] [--nvt_time ps] [--seed int] [--not_clean_log_files] [--steps [STEPS ...]]
+              [--wdir_to_continue DIRNAME [DIRNAME ...]] [--deffnm preffix for md files] [--tpr FILENAME] [--cpt FILENAME] [--xtc FILENAME]
+              [--ligand_list_file all_ligand_resid.txt] [--ligand_id UNL] [--activate_gaussian module load Gaussian/09-d01]
+              [--gaussian_exe g09 or /apps/all/Gaussian/09-d01/g09/g09] [--gaussian_basis B3LYP/6-31G*] [--gaussian_memory 120GB] [--metal_resnames [MN ...]]
+              [--metal_cutoff 2.8] [--metal_charges {MN:2, ZN:2, CA:2}]
+
+Run or continue MD simulation. Allowed systems: Protein, Protein-Ligand, Protein-Cofactors(multiple), Protein-Ligand-Cofactors(multiple)
+
+options:
+  -h, --help            show this help message and exit
+
+Standard Molecular Dynamics Simulation Run:
+  -p FILENAME, --protein FILENAME
+                        input file of protein. Supported formats: *.pdb or gro
+  -d WDIR, --wdir WDIR  Working directory. If not set the current directory will be used.
+  -l FILENAME, --ligand FILENAME
+                        input file with compound(s). Supported formats: *.mol or sdf
+  --cofactor FILENAME   input file with compound(s). Supported formats: *.mol or sdf
+  --clean_previous_md   remove a production MD simulation directory if it exists to re-initialize production MD setup
+  --hostfile FILENAME   text file with addresses of nodes of dask SSH cluster. The most typical, it can be passed as $PBS_NODEFILE variable from inside a PBS script.
+                        The first line in this file will be the address of the scheduler running on the standard port 8786. If omitted, calculations will run on a
+                        single machine as usual.
+  -c INTEGER, --ncpu INTEGER
+                        number of CPU per server. Use all cpus by default.
+  --topol topol.top     topology file (required if a gro-file is provided for the protein).All output files obtained from gmx2pdb should preserve the original names
+  --topol_itp topol_chainA.itp topol_chainB.itp [topol_chainA.itp topol_chainB.itp ...]
+                        Itp files for individual protein chains (required if a gro-file is provided for the protein).All output files obtained from gmx2pdb should
+                        preserve the original names
+  --posre posre.itp [posre.itp ...]
+                        posre file(s) (required if a gro-file is provided for the protein).All output files obtained from gmx2pdb should preserve the original names
+  --protein_forcefield amber99sb-ildn
+                        Force Field for protein preparation
+  --md_time ns          time of MD simulation in ns
+  --npt_time ps         time of NPT equilibration in ps
+  --nvt_time ps         time of NVT equilibration in ps
+  --seed int            seed
+  --not_clean_log_files
+                        Not to remove all backups of md files
+  --steps [STEPS ...]   Run a particular step(s) of the StreaMD run. Options:
+                        1 - run preparation step (protein, ligand, cofactor preparation)
+                        2 - run MD equilibration step (minimization, NVT, NPT)
+                        3 - run MD simulation
+                        4 - run MD analysis
+                        Ex: 3 4. 
+                        If 2 or 3 or 4 step(s) are used --wdir_to_continue argument should be
+                        used to provide directories with files obtained during the previous steps
+  --wdir_to_continue DIRNAME [DIRNAME ...]
+                        single or multiple directories contain simulations created by the tool. 
+                        Use with steps 2,3,4 to continue the run. Should consist of: tpr, cpt,
+                        xtc and all_ligand_resid.txt files. File all_ligand_resid.txt is optional and used to run md analysis for the ligands. If you want to continue
+                        your own simulation not created by the tool use --tpr, --cpt, --xtc and --wdir or arguments (--ligand_list_file is optional and required to
+                        run md analysis after simulation )
+
+Continue or Extend Molecular Dynamics Simulation:
+  --deffnm preffix for md files
+                        Used to run, extend or continue the simulation.
+                        If --wdir_to_continue is used files as deffnm.tpr, deffnm.cpt, deffnm.xtc will be searched from --wdir_to_continue directories
+  --tpr FILENAME        use explicit tpr to continue a non-StreaMD simulation
+  --cpt FILENAME        use explicit cpt to continue a non-StreaMD simulation
+  --xtc FILENAME        use explicit xtc to continue a non-StreaMD simulation
+  --ligand_list_file all_ligand_resid.txt
+                        If you want automatic md analysis for ligands was run after continue of non-StreaMD simulation you should set ligand_list file. Format of the file (no
+                        headers): user_ligand_id gromacs_ligand_id. Example: my_ligand UNL. Can be set up or placed into --wdir_to_continue directory(ies)
+  --ligand_id UNL       If you want to run an automatic md analysis for a ligand after continue of simulation you can set ligand_id if it is not UNL as a default value
+
+Boron-containing molecules or MCPBPY usage (use together with Standard Molecular Dynamics Simulation Run arguments group):
+  --activate_gaussian module load Gaussian/09-d01
+                        string that load gaussian module if necessary
+  --gaussian_exe g09 or /apps/all/Gaussian/09-d01/g09/g09
+                        path to gaussian executable or alias. Requred to run preparation of boron-containing compounds.
+  --gaussian_basis B3LYP/6-31G*
+                        Gaussian Basis
+  --gaussian_memory 120GB
+                        Gaussian Memory Usage
+
+MCPBPY usage (use together with Standard Molecular Dynamics Simulation Run and Boron-containing molecules arguments group):
+  --metal_resnames [MN ...]
+                        Metal residue names to run MCPB.py procedure. Start MCPBPY procedure only if gaussian_exe and activate_gaussian arguments are set up,Otherwise
+                        standard gmx2pdb procedure will be run.
+  --metal_cutoff 2.8    Metal residue cutoff to run MCPB.py procedure
+  --metal_charges {MN:2, ZN:2, CA:2}
+                        Metal residue charges in dictionary formatStart MCPBPY procedure only if metal_resnames and gaussian_exe and activate_gaussian arguments are
+                        set up,Otherwise standard gmx2pdb procedure will be run.
+
+```
+
+### **Examples**
+Before run MD simulation it is important to prepare protein by yourself to make sure you simulate correct system.
+#### Example of preparation steps before MD: 
+#### 1) Target Preparation:  
+*Manual preparation:*
+- **Fill missing residues and loops**  
+
+*Using Chimera:*   
+
+``Tools -> Sequence -> Structure -> Modeller (loops/refinement)``  
+``Tools -> Structure Editing -> Dock Prep ``
+* **Explicit water molecules as well as cofactors from a crystal structure can be removed, or if necessarily retained manually;**
+
+* **Remove co-crystallizated ligands;**
+
+* **Add hydrogens based on protonation states.**
+  * Check states of histidines and put proper aliases HIE, HID or HIP instead of HIS (otherwise protonation can be distorted during MD preparation stage)  
+
+*type into Chimera cmd:*
+```
+setattr r type HID :HIS@HD1,DD1,TD1,HND
+setattr r type HIP :HID@HE2,DE2,TE2
+setattr r type HIE :HIS@HE2
+```
+
+#### 2) Docking procedure
+Required to obtain relevant poses of the ligand if needed
+* **Perform docking procedure**  
+https://github.com/ci-lab-cz/easydock
+
+### Run molecular dynamics simulation
+``` source activate md ```  
+ 
+**Run simulation for different sytems:**
+- Protein in Water
+```
+run_md -p protein_H_HIS.pdb --md_time 0.1 --nvt_time 100 --npt_time 100 --ncpu 128 
+```
+
+- Protein - Ligand
+```
+run_md -p protein_H_HIS.pdb -l ligand.mol --md_time 0.1 --nvt_time 100 --npt_time 100 --ncpu 128 
+```
+
+- Protein - Cofactor
+All molecules should present in simulated system, so any problem with preparation of cofactors will interrupt the program. 
+```
+run_md -p protein_H_HIS.pdb --cofactor cofactors.sdf --md_time 0.1 --nvt_time 100 --npt_time 100 --ncpu 128 
+
+```
+
+**To run simulations with boron-containing compounds**  
+*Gaussian Software* should be available.  
+Gaussian optimization and charge calculation will be run only for molecules with boron atoms, other molecules will be processed by regular procedure by Antechamber.
+If Gaussian cannot be load boron-containing molecules will be skipped.  
+Any --ligand or --cofactor files can consist of boron-containing compounds
+```
+run_md -p protein_H_HIS.pdb -l molecules.sdf --cofactor cofactors.sdf --md_time 0.1 --npt_time 10 --nvt_time 10 --activate_gaussian "module load Gaussian/09-d01" --gaussian_exe g09 --ncpu 128
+
+```
+
+**To run simulations with MCPBPY using parametrization procedure**  
+*Gaussian Software* should be available.
+```
+run_md -p protein_H_HIS.pdb -l molecules.sdf --cofactor cofactors.sdf --md_time 0.1 --npt_time 10 --nvt_time 10 --activate_gaussian "module load Gaussian/09-d01" --gaussian_exe g09 --ncpu 128 --metal_resnames ZN
+
+```
+**To run simulations using multiple servers**
+```
+PBS:
+run_md -p protein_H_HIS.pdb -l molecules.sdf --cofactor cofactors.sdf --md_time 0.1 --npt_time 10 --nvt_time 10 --hostfile $PBS_NODEFILE --ncpu 128
+
+SLURM:
+srun hostname | sort | uniq > hostfile  
+run_md -p protein_H_HIS.pdb -l molecules.sdf --cofactor cofactors.sdf --md_time 0.1 --npt_time 10 --nvt_time 10 --hostfile hostfile --ncpu 128
+
+```
+
+**To extend the simulation**
+you can continue your simulation unlimited times. As the --md_time argument user should set up the overall time of the simulation
+```
+run_md --wdir_to_continue md_files/md_run/protein_H_HIS_ligand_*/ --md_time 0.2
+```
+or use explicit tpr, cpt and xtc arguments to continue a non-StreaMD simulation
+```
+run_md --wdir_to_continue md_files/md_run/protein_H_HIS_ligand_1/  --md_time 0.3 --tpr protein_H_HIS_ligand_1/md_out.tpr --cpt protein_H_HIS_ligand_1/md_out.cpt --xtc protein_H_HIS_ligand_1/md_out.xtc
+```
+in case you don't want to check/run all preparation steps with using non-StreaMD simulations you can use --steps argument 
+```
+run_md --wdir_to_continue md_files/md_run/protein_H_HIS_ligand_1/ --md_time 0.3 --steps 3 4
+```
+  
+**Output**   
+*each run creates in the working directory (or in the current directory if wdir argument was not set up):*
+ 1) a unique streaMD log file which name contains name of the protein, ligand file, cofactor file and time of run.  
+ log_*protein-fname*\_*ligand-fname*\_*cofactor-fname*\_*start-time*.log  
+ Contains important information/warnings/errors about the main program run.
+ 2) a unique bash log file.  
+ streamd_bash_*protein-fname*\_*ligand-fname*\_*cofactor-fname*\_*start-time*.log  
+ Contains stdout from Gromacs and Antechamber.  
+ 
+will be created the next folders:
+```
+md_files/
+- md_preparation/
+ -- protein/
+ -- ligands/
+ -- cofactors/
+- md_run/
+ -- protein-id_ligand-id
+```
+
+```
+md_files/md_preparation/protein/:
+protein.gro  posre.itp  topol.top
+
+OR for multiple chain protein:
+md_files/md_preparation/protein/:
+protein.gro 
+topol.top
+posre_Protein_chain_A.itp    
+posre_Protein_chain_B.itp  
+topol_Protein_chain_A.itp
+topol_Protein_chain_B.itp
+```
+
+```
+md_files/md_preparation/ligands/:
+all_resid.txt
+
+ligand_1/
+ligand_1.frcmod  ligand_1.lib     ligand_1.top        sqm.in
+ligand_1.gro     ligand_1.mol     leap.log            sqm.out
+ligand_1.inpcrd  ligand_1.mol2    posre_ligand_1.itp  sqm.pdb
+ligand_1.itp     ligand_1.prmtop  resid.txt           tleap.in
+
+ligand_2/
+..
+```
+
+```
+md_files/md_preparation/cofactors/:
+all_resid.txt
+
+cofactor_1/
+cofactor_1.frcmod  cofactor_1.lib     cofactor_1.top        sqm.in
+cofactor_1.gro     cofactor_1.mol     leap.log              sqm.out
+cofactor_1.inpcrd  cofactor_1.mol2    posre_cofactor_1.itp  sqm.pdb
+cofactor_1.itp     cofactor_1.prmtop  resid.txt             tleap.in
+
+cofactor_2/
+```
+
+```
+md_files/md_run/
+
+protein_H_HIS_ligand_1/
+ligand_1.itp          density.xvg  em.trr      ions.tpr                md_out.edr         md_out.tpr             npt.cpt  npt.tpr  nvt.log    potential.xvg         rmsd.xvg       temperature.xvg
+cofactor_1.itp        em.edr       frame.pdb   md_centermolsnoPBC.xtc  md_out.gro         md_out.xtc             npt.edr  npt.trr  nvt.mdp    pressure.xvg          rmsf.pdb       topol.top
+all.itp               em.gro       gyrate.xvg  md_fit.xtc              md_out.log         md_short_forcheck.xtc  npt.gro  nvt.cpt  nvt.tpr    rmsd_cofactor_1.xvg   rmsf.xvg
+all_ligand_resid.txt  em.log       index.ndx   md.mdp                  mdout.mdp          minim.mdp              npt.log  nvt.edr  nvt.trr    rmsd_ligand_1.xvg     solv.gro
+complex.gro           em.tpr       ions.mdp    md_out.cpt              md_out_noj_noPBC.xtc  newbox.gro          npt.mdp  nvt.gro  posre.itp  rmsd_xtal.xvg         solv_ions.gro
+
+protein_H_HIS_ligand_2/
+```
+- **MD output files**
+```
+md_fit.xtc - MD trajectory with removed PBC and fitted into Protein or Protein-Ligand group
+md_short_forcheck.xtc - short trajectory to check if simulation was valid
+frame.pdb - a frame for topology
+
+```
+- **Analysis data**  
+```
+potential.png 
+temperature.png
+pressure.png
+density.png
+rmsd.png - rmsd of the protein against minimized structure
+rmsd_xtal.png - rmsd of the protein against crystal structure
+rmsd_cofactor_1.png - rmsd of cofactor against minimized structure
+rmsd_cofactor_1_xtal.png - rmsd of the ligand against crystal structure
+rmsd_ligand_1.png - rmsd of the ligand against minimized structure
+rmsd_ligand_1_xtal.png - rmsd of the ligand against crystal structure
+rmsf.png - root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions in the trajectory
+gyrate.png - radius of gyration
+```
+
+## Supplementary tools
+### MM-PBSA/MM-GBSA energy calculation
+#### The tool is based on [gmx_MMPBSA](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/)
+Calculation arguments can be changed/added by customized [mmpbsa.in](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/input_file/) file 
+#### **USAGE**
+```
+run_gbsa -h
+usage: run_gbsa [-h] [-i DIRNAME [DIRNAME ...]] [--topol topol.top] [--tpr md_out.tpr] [--xtc md_fit.xtc] [--index index.ndx] [-m mmpbsa.in] [-d WDIR]
+                [--out_files OUT_FILES [OUT_FILES ...]] [--hostfile FILENAME] [-c INTEGER] [--ligand_id UNL] [-a [STRING ...]] [--clean_previous]
+
+Run MM-GBSA/MM-PBSA calculation using gmx_MMPBSA tool
+
+options:
+  -h, --help            show this help message and exit
+  -i DIRNAME [DIRNAME ...], --wdir_to_run DIRNAME [DIRNAME ...]
+                        single or multiple directories for simulations. Should consist of: tpr, xtc, ndx files
+  --topol topol.top     topol file from the the MD simulation. Will be ignored if --wdir_to_run is used
+  --tpr md_out.tpr      tpr file from the the MD simulation. Will be ignored if --wdir_to_run is used
+  --xtc md_fit.xtc      xtc file of the simulation. Trajectory should have no PBC and be fitted on the Protein_Ligand group. Will be ignored if --wdir_to_run is used
+  --index index.ndx     Gromacs index file from the simulation. Will be ignored if --wdir_to_run is used
+  -m mmpbsa.in, --mmpbsa mmpbsa.in
+                        MMPBSA input file. If not set up default template will be used.
+  -d WDIR, --wdir WDIR  Working directory for program output. If not set the current directory will be used.
+  --out_files OUT_FILES [OUT_FILES ...]
+                        gmxMMPBSA out files (FINAL*.dat) to parse. If set will be used over other variables.
+  --hostfile FILENAME   text file with addresses of nodes of dask SSH cluster. The most typical, it can be passed as $PBS_NODEFILE variable from inside a PBS script.
+                        The first line in this file will be the address of the scheduler running on the standard port 8786. If omitted, calculations will run on a
+                        single machine as usual.
+  -c INTEGER, --ncpu INTEGER
+                        number of CPU per server. Use all cpus by default.
+  --ligand_id UNL       Ligand residue ID
+  -a [STRING ...], --append_protein_selection [STRING ...]
+                        residue IDs whuch will be included in the protein system (cofactors).Example: ZN MG
+  --clean_previous      Clean previous temporary gmxMMPBSA files
+```
+
+### **Examples**
+```
+run_gbsa  --wdir_to_run md_files/md_run/protein_H_HIS_ligand_1 md_files/md_run/protein_H_HIS_ligand_2  -c 128 -m mmpbsa.in
+```
+**Output**   
+*each run creates in the working directory (or in the current directory if wdir argument was not set up):*
+ 1) a unique streaMD log file  
+ log_mmpbsa_*start-time*.log 
+ Contains important information/warnings/errors about the main run_gbsa program run.
+ 2) a unique bash log file. 
+ log_mmpbsa_bash_*start-time*.log   
+ Contains stdout from gmx_MMPBSA 
+ 3) GBSA_output_*start-time*.csv with summary csv if MMGBSA method was run
+ 4) PBSA_output_*start-time*.csv with summary csv if MMPBSA method was run
+ 
+ each wdir_to_run has FINAL_RESULTS_MMPBSA_*start-time*.csv with GBSA/PBSA output. 
+ 
+### ProLIF Protein-Ligand Interaction Fingerprints
+#### **USAGE**
+```
+run_prolif -h
+usage: run_prolif [-h] [-i DIRNAME [DIRNAME ...]] [--xtc FILENAME] [--tpr FILENAME] [-l STRING] [-s INTEGER] [-a STRING] [-d WDIR] [-v] [--hostfile FILENAME]
+                  [-c INTEGER] [--width FILENAME] [--height FILENAME] [-o FILENAME] [--not_save_pics]
+
+Get protein-ligand interactions from MD trajectories using ProLIF module.
+
+options:
+  -h, --help            show this help message and exit
+  -i DIRNAME [DIRNAME ...], --wdir_to_run DIRNAME [DIRNAME ...]
+                        single or multiple directories for simulations.
+                                                     Should consist of: md_out.tpr and md_fit.xtc files (default: None)
+  --xtc FILENAME        input trajectory file (XTC). Will be ignored if --wdir_to_run is used (default: None)
+  --tpr FILENAME        input topology file (TPR). Will be ignored if --wdir_to_run is used (default: None)
+  -l STRING, --ligand STRING
+                        residue name of a ligand in the input trajectory. (default: UNL)
+  -s INTEGER, --step INTEGER
+                        step to take every n-th frame. ps (default: 1)
+  -a STRING, --append_protein_selection STRING
+                        the string which will be concatenated to the protein selection atoms. Example: "resname ZN or resname MG". (default: None)
+  -d WDIR, --wdir WDIR  Working directory for program output. If not set the current directory will be used. (default: None)
+  -v, --verbose         print progress. (default: False)
+  --hostfile FILENAME   text file with addresses of nodes of dask SSH cluster. The most typical, it can be passed as $PBS_NODEFILE variable from inside a PBS script. The first line in this file will be the address of the scheduler running on the standard port 8786. If omitted, calculations will run on a single machine as usual. (default: None)
+  -c INTEGER, --ncpu INTEGER
+                        number of CPU per server. Use all cpus by default. (default: 32)
+  --width FILENAME      width of the output pictures (default: 15)
+  --height FILENAME     height of the output pictures (default: 10)
+  -o FILENAME, --occupancy FILENAME
+                        occupancy of the unique contacts to show (default: 0.6)
+  --not_save_pics       not create html and png files (by frames) for each unique trajectory. Only overall prolif png file will be created. (default: False)
+
+```
+
+### **Examples**
+```
+run_prolif  --wdir_to_run md_files/md_run/protein_H_HIS_ligand_1 md_files/md_run/protein_H_HIS_ligand_2  -c 128 -v -s 5
+```
+**Output**  
+1) in each directory where xtc file is located  *plifs.csv*, *plifs.png*,*plifs_map.png*, *plifs.html* file for each simulation will be created
+2) *prolif_output_start-time.csv/png* - aggregated csv/png output file for all analyzed simulations
+
+#### Supplementary scripts
+_run_prolif applies all this scripts automatically. Use it if you want more detailed analysis or to change the picture/fonts sizes._  
+**prolif_drawmap**  
+Draw prolif plot for analysis binding mode of multiple ligands
+````
+prolif_drawmap  -h
+usage: prolif_drawmap [-h] -i FILENAME [FILENAME ...] [-o FILENAME] [--width FILENAME] [--height FILENAME] [--base_size FILENAME]
+
+Draw prolif plot for analysis binding mode of multiple ligands
+
+options:
+  -h, --help            show this help message and exit
+  -i FILENAME [FILENAME ...], --input FILENAME [FILENAME ...]
+                        input file with prolif output for the set of molecules. Supported formats: *.csv
+                        Ex: prolif_output.csv
+  --occupancy float
+                        minimum occupancy of the unique contacts to show
+  --width int      width of the output picture
+  --height int     height of the output picture
+  --base_size int  base size of the output picture
+
+````
+
+**prolif_draw_by_frame**
+
+```
+prolif_draw_by_frame -h
+usage: prolif_draw_by_frame [-h] -i [FILENAME ...] [-o FILENAME] [--filt_only_H] [--width FILENAME] [--height FILENAME] [--base_size FILENAME]
+
+options:
+  -h, --help            show this help message and exit
+  -i [FILENAME ...], --input [FILENAME ...]
+                        input file with prolif output for the unique molecule. Supported formats: *.csv
+                        Ex: plifs.csv
+  --occupancy float
+                        minimum occupancy of the unique contacts to show. Show all contacts by default.
+  --filt_only_H         filt residues where only hydrophobic contacts occur
+  --width int      width of the output picture
+  --height int     height of the output picture
+  --base_size int  base size of the output picture
+```
+
+### Logging
+all system info or errors are saved into logging files which would be placed into your main working directory (the current working directory or the path which was passed through --wdir argument):  
+**run_md:**
+```
+log_protein-fname_ligand-fname_cofactor-fname_current-date.log - StreaMD logging user info (status of the )
+streamd_bash_protein-fname_ligand-fname_cofactor-fname_start-time.log - StreaMD bash system logging info
+```
+
+**run_gbsa:**
+```
+log_mmpbsa_start-time.log - StreaMD logging user info
+log_mmpbsa_bash_start-time.log - StreaMD bash system logging info
+```
+
+**run_prolif:**
+```
+log_prolif_start-time.log - StreaMD logging user info
+```
+### Licence
+MIT