initial commit without docking excecutables

.gitignore

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+/data/*
+!/data/config*
+!data/receptor/*.py
+!data/ligands/*.py
+.spyproject
+.vscode
+
+

LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2021 Eduardo Mayo
-
-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.
+MIT License
+
+Copyright (c) 2021 Eduardo Mayo
+
+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.

README.txt

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+Mscreen try to be a common user interface for different ligand-protein docking programs.
+
+It's quite simple to use: prepare a ligand and receptor for screening
+
+python mscreen.py prepare -bk [backend] -l [ligand_folder] -r [receptor_folder] -o [otput_folder]
+
+python mscreen.py screen -bk plants -l [ligand_folder] -r [receptor_folder] -o [otput_folder] -c [conf_file] -log [log_file]
+
+python mscreen.py analysis pending
+
+# Ependencies
+Make sure you have the following dependencies:
+rdkit 
+numpy
+

data/config_ledock_sample.txt

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+Receptor
+pro.pdb
+
+RMSD
+1.0
+
+Binding pocket
+45.3 62.6
+-25.9 -12.9
+29.7 47.1
+
+Number of binding poses
+20
+
+Ligands list
+ligand.list
+
+END

data/config_plants_speed1.txt

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+
+##########################################################################################
+# All parameters are set to default
+##########################################################################################
+
+# SEARCH ALGORITHM
+search_speed speed1              # speed1 (highes realibility) speed2 speed4 (higer speed, low realibility)
+
+# aco_ants  20                  # number of ants (standard: 20)
+# aco_evap  0.5                 # evaporation factor [0; 1]
+# aco_sigma  2.3                # iteration scaling factor
+
+# flip_amide_bonds 0              # activate (1) or deactivate ipping of amide bonds (standard:0)
+# flip_planar_n 1                 # activate (1) or deactivate flipping of bonds next to planar nitrogens (standard: 1)
+# force_flipped_bonds_planarity 0 # activate (1) or deactivate (0) automatic planarity correction for  flippable bonds (standard: 0)
+# force_planar_bond_rotation 1    # activate (1) or deactivate (0) free rotation of planar bonds (standard: 1) rescore mode value: perform simplex optimization during rescoring (value=simplex) or only direct input conformation scoring (value=no simplex) (standard: simplex)
+# flip_ring_corners 0             # activate (1) or deactivate flipping of free ring corners (standard: 0)
+
+# BINDING SITE 
+bindingsite_center 53.96 -19.44 38.39 
+bindingsite_radius 13.91
+
+# CLUSTER ALGORITHM
+cluster_rmsd 2.0                 # RMSD similarity threshold for cluster algorithm (standard:2.0)
+cluster_structures 10            # number of structures generated by the cluster algorithm (standard: 10)
+
+# SCORING FUNCTION
+ # Intermolecular
+# scoring_function chemplp            # plp, plp95 or chemplp (standard: chemplp)
+# outside_binding_site_penalty 50.0   # scoring functions using precalculated grids use value to fill grid points outside the binding site definition (standard: 50.0)
+# enable_sulphur_acceptors 0          # activate (1) or deactivate (0) scoring of sulphur acceptors (standard: 0)
+ # Intramolecular
+# ligand_intra_score clash2                 # [clash, clash2] (simple heavy-atom clash terms) or lj (all-atom Lennard-Jones term) (standard: clash2)
+# chemplp_clash_include_14 1                # activate (1) or deactivate (0) scoring of 1-4 interactions (standard: 1)
+# chemplp_clash_include_HH 0                # activate (1) or deactivate (0) scoring of hydrogenhydrogen interactions (standard: 0)
+
+# missing Keywords affecting scoring function plp, plp95 and chemplp
+
+# INPUT OPTIONS (no gold input allowed)
+# protein_file rec_2.pdbqt                 # protein filename
+# ligand_file lig.pdbqt                    # ligand filename
+# ligand_list ligands.txt                  # text file containing ligand filenames
+
+# OUTPUT OPTIONS 
+output_dir /folder/out                 # name of output directory; PLANTS automatically tries to create a subdirectory with the specified name and exits if the directory already exists to prevent overwriting existing data
+
+# FLEXIBLE SIDE-CHAINS (reccomended flexible_protein_side_chain)
+
+# flexible_protein_side_chain VAL123,VAL123  # string: residue label of flexible side-chain (e.g. VAL123)
+# flexible_protein_side_chain 100            # value: residue number of flexible side-chain (e.g. 100 )
+# intra_protein_score_weight 0.6             # weighting factor for the intramolecular protein score (standard: 0.6)
+# fix_protein_bond value                     # keep protein bond with bond-number value fixed.

data/config_plants_speed2.txt

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+
+##########################################################################################
+# All parameters are set to default
+##########################################################################################
+
+# SEARCH ALGORITHM
+search_speed speed2              # speed1 (highes realibility) speed2 speed4 (higer speed, low realibility)
+
+# aco_ants  20                  # number of ants (standard: 20)
+# aco_evap  0.5                 # evaporation factor [0; 1]
+# aco_sigma  2.3                # iteration scaling factor
+
+# flip_amide_bonds 0              # activate (1) or deactivate ipping of amide bonds (standard:0)
+# flip_planar_n 1                 # activate (1) or deactivate flipping of bonds next to planar nitrogens (standard: 1)
+# force_flipped_bonds_planarity 0 # activate (1) or deactivate (0) automatic planarity correction for  flippable bonds (standard: 0)
+# force_planar_bond_rotation 1    # activate (1) or deactivate (0) free rotation of planar bonds (standard: 1) rescore mode value: perform simplex optimization during rescoring (value=simplex) or only direct input conformation scoring (value=no simplex) (standard: simplex)
+# flip_ring_corners 0             # activate (1) or deactivate flipping of free ring corners (standard: 0)
+
+# BINDING SITE 
+bindingsite_center 53.96 -19.44 38.39 
+bindingsite_radius 13.91
+
+# CLUSTER ALGORITHM
+cluster_rmsd 2.0                 # RMSD similarity threshold for cluster algorithm (standard:2.0)
+cluster_structures 10            # number of structures generated by the cluster algorithm (standard: 10)
+
+# SCORING FUNCTION
+ # Intermolecular
+# scoring_function chemplp            # plp, plp95 or chemplp (standard: chemplp)
+# outside_binding_site_penalty 50.0   # scoring functions using precalculated grids use value to fill grid points outside the binding site definition (standard: 50.0)
+# enable_sulphur_acceptors 0          # activate (1) or deactivate (0) scoring of sulphur acceptors (standard: 0)
+ # Intramolecular
+# ligand_intra_score clash2                 # [clash, clash2] (simple heavy-atom clash terms) or lj (all-atom Lennard-Jones term) (standard: clash2)
+# chemplp_clash_include_14 1                # activate (1) or deactivate (0) scoring of 1-4 interactions (standard: 1)
+# chemplp_clash_include_HH 0                # activate (1) or deactivate (0) scoring of hydrogenhydrogen interactions (standard: 0)
+
+# missing Keywords affecting scoring function plp, plp95 and chemplp
+
+# INPUT OPTIONS (no gold input allowed)
+# protein_file prepared_receptors_plants/receptor_3b2x.mol2                 # protein filename
+# ligand_file lig.pdbqt                                                      # ligand filename
+# ligand_list ligands.list                                                 # text file containing ligand filenames
+
+# OUTPUT OPTIONS 
+output_dir out-plants4                 # name of output directory; PLANTS automatically tries to create a subdirectory with the specified name and exits if the directory already exists to prevent overwriting existing data
+
+# FLEXIBLE SIDE-CHAINS (reccomended flexible_protein_side_chain)
+
+# flexible_protein_side_chain VAL123,VAL123  # string: residue label of flexible side-chain (e.g. VAL123)
+# flexible_protein_side_chain 100            # value: residue number of flexible side-chain (e.g. 100 )
+# intra_protein_score_weight 0.6             # weighting factor for the intramolecular protein score (standard: 0.6)
+# fix_protein_bond value                     # keep protein bond with bond-number value fixed.

data/config_plants_speed4.txt

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+
+##########################################################################################
+# All parameters are set to default
+##########################################################################################
+
+# SEARCH ALGORITHM
+search_speed speed4              # speed1 (highes realibility) speed2 speed4 (higer speed, low realibility)
+
+# aco_ants  20                  # number of ants (standard: 20)
+# aco_evap  0.5                 # evaporation factor [0; 1]
+# aco_sigma  2.3                # iteration scaling factor
+
+# flip_amide_bonds 0              # activate (1) or deactivate ipping of amide bonds (standard:0)
+# flip_planar_n 1                 # activate (1) or deactivate flipping of bonds next to planar nitrogens (standard: 1)
+# force_flipped_bonds_planarity 0 # activate (1) or deactivate (0) automatic planarity correction for  flippable bonds (standard: 0)
+# force_planar_bond_rotation 1    # activate (1) or deactivate (0) free rotation of planar bonds (standard: 1) rescore mode value: perform simplex optimization during rescoring (value=simplex) or only direct input conformation scoring (value=no simplex) (standard: simplex)
+# flip_ring_corners 0             # activate (1) or deactivate flipping of free ring corners (standard: 0)
+
+# BINDING SITE 
+bindingsite_center 53.96 -19.44 38.39 
+bindingsite_radius 13.91
+
+# CLUSTER ALGORITHM
+cluster_rmsd 2.0                 # RMSD similarity threshold for cluster algorithm (standard:2.0)
+cluster_structures 10            # number of structures generated by the cluster algorithm (standard: 10)
+
+# SCORING FUNCTION
+ # Intermolecular
+# scoring_function chemplp            # plp, plp95 or chemplp (standard: chemplp)
+# outside_binding_site_penalty 50.0   # scoring functions using precalculated grids use value to fill grid points outside the binding site definition (standard: 50.0)
+# enable_sulphur_acceptors 0          # activate (1) or deactivate (0) scoring of sulphur acceptors (standard: 0)
+ # Intramolecular
+# ligand_intra_score clash2                 # [clash, clash2] (simple heavy-atom clash terms) or lj (all-atom Lennard-Jones term) (standard: clash2)
+# chemplp_clash_include_14 1                # activate (1) or deactivate (0) scoring of 1-4 interactions (standard: 1)
+# chemplp_clash_include_HH 0                # activate (1) or deactivate (0) scoring of hydrogenhydrogen interactions (standard: 0)
+
+# missing Keywords affecting scoring function plp, plp95 and chemplp
+
+# INPUT OPTIONS (no gold input allowed)
+# protein_file prepared_receptors_plants/receptor_3b2x.mol2                 # protein filename
+# ligand_file lig.pdbqt                                                      # ligand filename
+# ligand_list ligands.list                                                 # text file containing ligand filenames
+
+# OUTPUT OPTIONS 
+output_dir out-plants4                 # name of output directory; PLANTS automatically tries to create a subdirectory with the specified name and exits if the directory already exists to prevent overwriting existing data
+
+# FLEXIBLE SIDE-CHAINS (reccomended flexible_protein_side_chain)
+
+# flexible_protein_side_chain VAL123,VAL123  # string: residue label of flexible side-chain (e.g. VAL123)
+# flexible_protein_side_chain 100            # value: residue number of flexible side-chain (e.g. 100 )
+# intra_protein_score_weight 0.6             # weighting factor for the intramolecular protein score (standard: 0.6)
+# fix_protein_bond value                     # keep protein bond with bond-number value fixed.

data/config_vina_ex1.txt

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+center_x = 54.0 
+center_y = -19.4 
+center_z = 38.4 
+size_x = 17.3 
+size_y = 13.0 
+size_z = 17.4
+exhaustiveness = 1
+num_modes = 10
+
+
+

data/config_vina_ex16.txt

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+center_x = 54.0 
+center_y = -19.4 
+center_z = 38.4 
+size_x = 17.3 
+size_y = 13.0 
+size_z = 17.4
+exhaustiveness = 16
+num_modes = 10
+
+
+

data/config_vina_ex8.txt

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+center_x = 54.0 
+center_y = -19.4 
+center_z = 38.4 
+size_x = 17.3 
+size_y = 13.0 
+size_z = 17.4
+exhaustiveness = 8
+num_modes = 10
+
+
+

docs/docs.md

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+#Mscree documentation
+Hello finally mscreen is out:
+mscreen is an open source program for running virtual screening. It help you running virtual screening using different open source programs. We choose the huge family of autodock vina. 
+Docking programs avalaibles:
+    vina 
+    gwovina:
+    Wong, K. M., Tai, H. K., & Siu, S. W. (2021). GWOVina: A grey wolf optimization approach to rigid and flexible receptor docking. Chemical Biology & Drug Design, 97(1), 97-110.
+    psovina2.0: 
+    Hio Kuan Tai, Siti Azma Jusoh, and Shirley W. I. Siu*. Chaos-embedded particle swarm optimization approach for protein-ligand docking and virtual screening. Journal of Cheminformatics  10:62, 2018.    
+    fwavina:
+    Jin Li, Yongping Song, Fajin Li, Henggui Zhang, Weichao Liu, FWAVina: A novel optimization algorithm for protein-ligand docking based on the fireworks algorithm, Computational Biology and Chemistry,  88,2020
+    qvina-2.1:
+    Alhossary, A., Handoko, S. D., Mu, Y., & Kwoh, C. K. (2015). Fast, accurate, and reliable molecular docking with QuickVina 2. Bioinformatics, 31(13), 2214-2216.
+    qvina-w:
+    Hassan, N. M., Alhossary, A. A., Mu, Y., & Kwoh, C. K. (2017). Protein-ligand blind docking using QuickVina-W with inter-process spatio-temporal integration. Scientific reports, 7(1), 1-13.
+    SMINA:
+    Koes, D. R., Baumgartner, M. P., & Camacho, C. J. (2013). Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise. Journal of chemical information and modeling, 53(8), 1893-1904.
+
+#What's our goal?
+Make open source virtual screening as easy as possible.
+
+How does mscreen work?
+If you want run a virtual screening run the follow comand.
+python mscreen.py screen -l path_to_ligand_folder
+                        -r path_to_receptor_folder
+                        -o path_to_the_output_folder
+                        -c path_to_the_configuration_fila
+
+#Tutorial
+Setting mscreen up.
+Download mscreen link
+Install dependecies.
+Add mscreen.py to your path.
+
+#Running a virtual screening.
+
+##setting up the screening workplace
+Create the following directory tree.
+
+virtual_screening-|- ligands
+                  |- receptors
+                  |- conf.txt
+
+Minimal configuration file must contain the following parameters.
+center_x =  14.2
+center_y = 43.6
+center_z = 36.9
+size_x = 31.3
+size_y = 20.4
+size_z = 21.5
+exhaustiveness = 8
+num_modes = 10
+
+##screening a library of ligand against one or more receptor
+Run the following command and voila!
+mscreen screen -l ligand_folder [The path to ligands Default: ligands]
+                -r receptor_folder [The path to receptors Default: receptors]
+                -o output_folder [The path to the output folder Default: out]
+                -c configuration_fila [The name of the configuration file for docking']
+                -bk vina [The docking software to use, choose one of the next 'fwavina', 'gwovina',     'ledock', 'psovina2', 'qvina2.1', 'qvina-w', 'smina', 'vina' default: qvina-w]
+
+After running it you will find into output folder the following files and folder.
+One folder for each receptor used and the configuration file used.
+Inside the receptor folder you will find one folder for each ligand docked.
+If you want use a deferent docking program add the -bk flag and the name of the program. Available programs 'fwavina', 'gwovina', 'ledock', 'psovina', 'qvina2', 'qvina-w', 'smina', 'vina'. Unfortunatelly for windows only vina is available. 
+
+##analysis of the virtual screening result.
+mscreen analysis -a full/short [The type of analysis default: short]
+                 -o output_folder [The name of the output folder. Default: out]
+                 -rn [Report file name default:results.txt]
+
+###short analysis
+output a single file inside each receptor folder with the ligands names and score sorted from low to high
+
+###full analysis
+run a short analysis but also output a single file sdf file containing all structures docked with the following information:
+ligand name, ligand score, ligand cluster, is representative
+
+