diff --git a/Documentation.docx b/Documentation.docx deleted file mode 100644 index 845e96b..0000000 Binary files a/Documentation.docx and /dev/null differ diff --git a/Install_dependencies.txt b/Install_dependencies.txt deleted file mode 100644 index c0385cd..0000000 --- a/Install_dependencies.txt +++ /dev/null @@ -1,211 +0,0 @@ -# ----------------------------------------------------- # -# ------- INSTALL VSpipe ON UBUNTU --------- # -# ----------------------------------------------------- # - -#\\----------------------- # -#\\ INSTALLING MGLTools # -#\\----------------------- # -# Follow the next instructions to install MGLTools on Linux - -# 1. Download the binary for your distribution at -# http://mgltools.scripps.edu/downloads/latest -# If you do not have the 64 bits linux, follow -# the instructions but change the name of the -# package accordingly. -# This installation assumes that you have already -# cloned this repository and it is saved in the -# directory “~/Applications/VSpipe”, -# where MGLTools is going to be installed and where -# the downloaded binary is going to be saved. -# If you have not cloned this repository, please followed -# the instructions detailed in the "VSpipe/Tutorial_VSpipe.md". -# -# If you are not, just remember to change the following -# commands according to your environment. - - cd ~/Applications/VSpipe - tar -xzvf mgltools_x86_64Linux2_latest.tar.gz - chmod +x mgltools_x86_64Linux2_latest - cd mgltools_x86_64Linux2_latest/ - tar -xzvf MGLToolsPckgs.tar.gz - -# 2. Export the path to your .bashrc - - echo "export PATH=$PATH:~/Applications/VSpipe/mgltools_x86_64Linux2_latest" >> ~/.bashrc - -# 3. Run the following still being inside the directory -# ~/Applications/VSpipe/mgltools_x86_64Linux2_latest/ - - install.sh - -# 4. Add these aliases in the .bashrc file: - - alias pmv='~/Applications/VSpipe/mgltools_x86_64Linux2_latest/bin/pmv' - alias adt='~/Applications/VSpipe/mgltools_x86_64Linux2_latest/bin/adt' - alias vision='~/Applications/VSpipe/mgltools_x86_64Linux2_latest/bin/vision' - alias pythonsh='~/Applications/VSpipe/mgltools_x86_64Linux2_latest/bin/pythonsh' - -# 5. Run this command from the directory you are - source ./initMGLtools.sh - -# 6. Install AD4 if you do not have it yet - sudo apt-get install autodock - -# 7. Install Vina. -# Download the corresponding binary files of Vina for LINUX -# autodock_vina_1_1_2_linux_x86.tar.gz: -# http://vina.scripps.edu/download.html -# -# After that, copy both executables "vina" and "vina_split" in the "Tools" -# directory. Remember this directory is inside the cloned Git repository, -# being its path "~/Applications/VSpipe/Tools". Assuming you saved the vina -# zipped file in /Applications/VSpipe: - - tar -xzvf autodock_vina_1_1_2_linux_x86.tar.gz - cp ~/Applications/VSpipe/autodock_vina_1_1_2_linux_x86/bin/vina ~/Applications/VSpipe/Tools - cp ~/Applications/VSpipe/autodock_vina_1_1_2_linux_x86/bin/vina_split ~/Applications/VSpipe/Tools - -# 8. Download the corresponding binary files of AD4 for LINUX. -# First one has to register and, afterwards, tools can be downloaded -# from -# http://autodock.scripps.edu/downloads/autodock-registration/fg_base_view -# Once it is downloaded, copy both "autogrid" and "autodock4" in the "Tools" -# directory: - - tar -xzvf autodocksuite-4.2.6-x86_64Linux2.tar - cp ~/Applications/VSpipe/x86_64Linux2/autodock4 ~/Applications/VSpipe/Tools - cp ~/Applications/VSpipe/x86_64Linux2/autogrid4 ~/Applications/VSpipe/Tools - -# 9. Now copy the files prepare_dpf4.py, prepare_gpf4.py, prepare_ligand4.py, -# prepare_receptor4.py, and summarize_results4.py to -# "mgltools_x86_64Linux2_latest/MGLToolsPckgs". -# They are located in -# "mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/" - - cp ~/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py ~/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs - - cp ~/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py ~/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs - - cp ~/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py ~/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs - - cp ~/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py ~/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs - - cp ~/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/summarize_results4.py ~/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs - -# 10. Do not forget to give permissions to all the scripts in the "Tools" directory! - chmod 775 ~/Applications/VSpipe/Tools - -# \\ ----------------------- // # -# \\ ----------------------- // # - - - -#\\ ---------------------- # -#\\ INSTALLING OpenBabel # -#\\----------------------- # -# Follow the next instructions to install MGLTools on Linux - -# 1. Install the current version: http://openbabel.org/wiki/Category:Installation - -# 2. Install cairo library and libpython-dev - - sudo apt-get install libpython-dev - sudo apt-get install libcairo2-dev - -# 3. There are some requirements specified in the INSTALL file in OpenBabel -# Even though there are some that are optional, here we are going to explain -# how to install them all: - -# 3.1. CMake 2.4.8 or later - - sudo apt-get install cmake - -# 3.2. Eigen 3.0 or later (optional) - - sudo apt-get install libeigen3-dev - -# 3.3. libxml2 (optional) - - sudo apt-get install libxml2-dev - -# 3.4. zlib (optional) - - sudo apt-get install zlib1g-dev - -# 3.5. wxWidgets 2.8 (optional, needed to build GUI) - - sudo apt-get install libwxgtk3.0-dev - -# 4. Follow OpenBabel installation. Here we only add the basic installation. -# If you want an advanced installation, check their INSTALL file -# -# The following instructions assume that the Open Babel source distribution is in -# the directory ~/Applications/openbabel-2.4.1. - -# 4.1. Create a 'build' directory: - cd ~/Applications/openbabel-2.4.1 - mkdir build - cd build - -# 4.2. Configure the build system. You can specify additional build -# options at this time (see below): - - cmake .. - -# 4.3. Compile: - - make -j2 - -# 4.4. Test (optional): - - make test - -# 4.5. Install: - - sudo make install - -# \\ --------------------- // # -# \\ --------------------- // # - - - -#\\----------------------- # -#\\ INSTALLING Anaconda # -#\\----------------------- # - -# If you do not have Anaconda, we recommend you to install it. -# 1. Download Anaconda for linux from https://www.anaconda.com/download/#download - -# 2. Follow the instructions in https://conda.io/docs/user-guide/install/linux.html -# so then run the bash script you have downloaded to install Anaconda - - bash Anaconda-latest-Linux-x86_64.sh - -# 3. Follow the instructions of the installer. -# Theoretically, you can customize your installation, -# but when we tried it, we could only install it -# in the directory ~/anaconda2 - -# 4. Apparently, there is a problem with the new version of Numpy (numpy>1.9) -# which does not support numpy.oldnumeric (used by some AutoDock python scripts -# during the VS). In Bitbucket, -# (see https://bitbucket.org/khinsen/scientificpython/issues/13) -# they make some suggestions, although we decided to install a lower -# version of numpy by doing the following and the AutoDock scripts that -# VSpipe uses could then work: - - pip install "numpy<1.9" - -# 5. If you saw any warnings regarding mgltools python packages, -# for instance mgltools-molkit, you can install them -# by typing the following command - - sudo apt-get install mgltools-[name] - -# They are listed here https://www.howtoinstall.co/en/ubuntu/trusty/?condition=starts-with&search=mg -# or you can type "sudo apt-get install mgltools-", press the tab, -# and you will see which packages are available - -# \\ --------------------- // # -# \\ --------------------- // # - diff --git a/Installation/Install_dependencies_MacOSX.md b/Installation/Install_dependencies_MacOSX.md new file mode 100644 index 0000000..7879574 --- /dev/null +++ b/Installation/Install_dependencies_MacOSX.md @@ -0,0 +1,221 @@ +# Install VSpipe on Mac OS X + +## Installing MGLTools + +First, go to [their website](http://mgltools.scripps.edu/downloads) and download the [Mac OS X release](http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_i86Darwin9_1.5.6.tar.gz) +This installation procedure assumes that: + 1. You have already cloned this repository (e.g., you might see `VSpipe-master`). + 2. You have downloaded the `VSpipe.zip` file from [releases](https://github.com/sabifo4/VSpipe/releases), unzipped it, and you have + saved it in this cloned directory (e.g., `VSpipe-master/VSpipe`). + 3. You have saved the downloaded tar file from `MGLTools`, untarred it, and saved it inside the previously unzipped directory + `VSpipe`, i.e., `VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6.tar.gz`) + +Let's consider that you have decided to clone this repository (e.g., `VSpipe-master`) inside `~/Applications`. +Therefore, before starting with the MGLTools installation, you should make sure your directory architecture looks like +something such as: + +``` +Applications + |- VSpipe-master + |- .git + |- Installation + | |- Install_dependencies_MacOSX.md + | |- Install_dependencies_Linux.md + | |- Install_dependencies_WLS.md + | |- VSpipe_details.docx + | + |- Tutorial + | |- Tutorial_VSpipe.md + | + |- VSpipe + | |- Tools + | |- mgltools_x86_64Linux2_latest.tar.gz + | + |- README.md + +``` + +*Note: Depending on how you have cloned this repository, you might see `VSpipe` instead of `VSpipe-master`* + +Once you make sure that everything is ready, then follow the next commands. +Make sure that you do not just copy and paste, as here we assume the file architecture described +above (i.e., `~/Applications/VSpipe-master/VSpipe`). **Change the paths according to your path system**. + +``` +cd ~/Applications/VSpipe-master/VSpipe +tar -xzvf mgltools_i86Darwin9_1.5.6.tar.gz +chmod +x mgltools_i86Darwin9_1.5.6 +cd mgltools_i86Darwin9_1.5.6/ +tar -xzvf MGLToolsPckgs.tar.gz +``` + +After that, please export the path to your `~/.bashrc` or `~/.bash_profile`. You can either open one of these files with your +preferred text editor (e.g., `vim`, `nano`, `atom`, etc.) and add the path or you can just type one of the following +commands in the terminal (depending on the file where you want to export the path): + +``` +# Run this if you want to export the path to your ~/.bashrc +echo "export PATH=$PATH:~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6" >> ~/.bashrc + +# Run this if you want to export the path to your ~/.bash_profile +echo "export PATH=$PATH:~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6" >> ~/.bash_profile +``` + +Now, make sure you are still at `~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6` +and then, from the terminal, execute the `install.sh` script: + +``` +# Our current directory is: ~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6 +./install.sh +``` + +You will see how several messages are printed out in your terminal as `MGLTools` is being installed. At the end +of the installation, you will see some instructions about adding the following aliases to your `~/.bashrc`. +If you have downloaded the `mgltools_i86Darwin9_1.5.6` version, you should see something like this: + +``` +alias pmv='~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6/bin/pmv' +alias adt='~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6/bin/adt' +alias vision='~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6/bin/vision' +alias pythonsh='~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6/bin/pythonsh' +``` + +Again, open either your `~/.bashrc` or your `~/.bash_profile` and add the aliases you have been asked +to append to these files at the end of the `MGLTools` installation. + +Subsequently, without changing directory, type the following on the terminal: + +``` +# Our current directory is: ~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6 +source ./initMGLtools.sh +``` + +Then, append to either the `~/.bash_profile` or the `~/.bashrc` the following path - make sure you +use the correct path according to where you have installed `VSpipe`: + +``` +export PYTHONPATH="~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6/MGLToolsPckgs" +``` + +## Installing AutoDock tools + +### AD4 + +Download AD4 tools `autogrid4` and `autodock4` for Mac OS X: + +``` +cd ~/Applications/VSpipe-master/VSpipe/ +wget http://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/autodocksuite-4.2.6-MacOSX.tar +tar -xvf autodocksuite-4.2.6-MacOSX.tar +``` + +Once it is downloaded, copy both `autogrid` and `autodock4` in the `~/Applications/VSpipe-master/VSpipe/Tools` directory: +If you want, you can then clean this directory by removing the tar and untarred files with the +`AD4` tools (last two comments in the next snippet): + +``` +# Our current directory is "~/Applications/VSpipe-master/VSpipe/" +cp ~/Applications/VSpipe-master/VSpipe/MacOSX/autodock4 ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/MacOSX/autogrid4 ~/Applications/VSpipe-master/VSpipe/Tools + +# Clean directory - remove unnecessary files and/or directories +rm -r ~/Applications/VSpipe-master/VSpipe/MacOSX +rm autodocksuite-4.2.6-MacOSX.tar +``` + +### Vina +Go to the [Vina website](http://vina.scripps.edu/download.html) and download the corresponding Vina files +for Mac OS X (you can also download this by clicking [here](http://vina.scripps.edu/download/autodock_vina_1_1_2_mac.tgz)). After that, copy both executables `vina` and `vina_split` in the `~/Applications/VSpipe-master/VSpipe/Tools` +directory: + +``` +# Our current directory is "~/Applications/VSpipe-master/VSpipe/" +tar -xzvf autodock_vina_1_1_2_mac.tgz +cp ~/Applications/VSpipe-master/VSpipe/autodock_vina_1_1_2_mac/bin/vina ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/autodock_vina_1_1_2_mac/bin/vina_split ~/Applications/VSpipe-master/VSpipe/Tools + +# Clean directory - remove unnecessary files and/or directories +rm -r autodock_vina_1_1_2_mac +rm autodock_vina_1_1_2_mac.tgz +``` + +### AutoDock python scripts +Now, copy the files `prepare_dpf4.py`, `prepare_gpf4.py`, `prepare_ligand4.py`, `prepare_receptor4.py`, +and `summarize_results4.py` to `~/Applications/VSpipe-master/VSpipe/Tools`. +They are located in `~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/" + +``` +cp ~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_i86Darwin9_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/summarize_results4.py ~/Applications/VSpipe-master/VSpipe/Tools +``` + +### Give permissions to execute ! +Do not forget to give permissions to all the scripts in the `Tools` directory! + +``` +chmod 775 ~/Applications/VSpipe-master/VSpipe/Tools +``` + + +## Installing OpenBabel + +If you want to install OpenBabel, you can follow the instructions [here](http://openbabel.org/wiki/Category:Installation). +We recommend you install it with `HomeBrew`: + +``` +brew install open-babel +``` + +If you had problems to install OpenBabel with `HomeBrew`, you can always compile it from source as described in their +installation website. If you choose this alternative installation, once you have the tar file with the source code +you can use the following commands (please see their website for more advanced options during compilation): + +``` +# Location of your OpenBabel is ~/Applications/VSpipe-master/VSpipe/ +# If you had v2.4.1 and you had directory called `openbabel-2.4.1` ... +cd openbabel-2.4.1 +mkdir -p build && cd build +cmake -DCMAKE_INSTALL_PREFIX=~/Applications/VSpipe-master/VSpipe/openbabel_v2.4.1 .. +make && make install + +# Clean directories +rm -rf ~/Applications/VSpipe-master/VSpipe/openbabel-2.4.1 +``` + +_**(OPTIONAL) Installing Anaconda**_ +If you have Python installed on your PC, Anaconda is not needed by `VSpipe`. +Nevertheless, if you do not have Anaconda but you would like to have it, you can download the Mac OS X release [here](https://www.anaconda.com/download/#download) +Just follow the instructions of the installer - it should be an easy procedure! + +## Problems with Numpy + +Apparently, there is a problem with the new version of Numpy (numpy>1.9) when you run some of the +AutoDock python scripts because it does not support `numpy.oldnumeric`. In Bitbucket, +see the discussion [here](https://bitbucket.org/khinsen/scientificpython/issues/13), +they make some suggestions about how to deal with this particular issue. We decided to install a lower version of numpy +so the AutoDock scripts could work: + +``` +pip install "numpy<1.9" +``` + +## Adding VSpipe to your path +You might be keen on adding an alias to run `VSpipe` from any directory by just typing +`VSpipe` on the terminal. If that is your case, open either your `~/.bash_profile` or your `~/.bashrc` with +your preferred text editor and type the following (note that the path is the one used in the examples above, +just modify it according to yours): + +``` +alias VSpipe='~/Applications/VSpipe-master/VSpipe/Tools/VSpipe' +``` + +--- + +If you have managed to install these third-party tools, now you should be able to open a terminal on +your working directory, type `VSpipe`, and get the pipeline started. + +Happy docking! :) + diff --git a/Installation/Install_dependencies_Ubuntu.md b/Installation/Install_dependencies_Ubuntu.md new file mode 100644 index 0000000..4515627 --- /dev/null +++ b/Installation/Install_dependencies_Ubuntu.md @@ -0,0 +1,272 @@ +# Install VSpipe on Linux distributions - tested on Ubuntu only! + +## Installing MGLTools + +First, go to [their website](http://mgltools.scripps.edu/downloads/latest) and download the [Linux release](http://mgltools.scripps.edu/downloads/tars/releases/nightly/latest/REL/mgltools_x86_64Linux2_latest.tar.gz) +This installation procedure assumes that: + 1. You have already cloned this repository (e.g., you might see `VSpipe-master`). + 2. You have downloaded the `VSpipe.zip` file from [releases](https://github.com/sabifo4/VSpipe/releases), unzipped it, and you have + saved it in this cloned directory (e.g., `VSpipe-master/VSpipe`). + 3. You have saved the downloaded tar file from `MGLTools`, untarred it, and saved it inside the previously unzipped directory + `VSpipe`, i.e., `VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest`) + +Let's consider that you have decided to clone this repository (e.g., `VSpipe-master`) inside `~/Applications`. +Therefore, before starting with the MGLTools installation, you should make sure your directory architecture looks like +something such as: + +``` +Applications + |- VSpipe-master + |- .git + |- Installation + | |- Install_dependencies_MacOSX.md + | |- Install_dependencies_Linux.md + | |- Install_dependencies_WLS.md + | |- VSpipe_details.docx + | + |- Tutorial + | |- Tutorial_VSpipe.md + | + |- VSpipe + | |- Tools + | |- mgltools_x86_64Linux2_latest.tar.gz + | + |- README.md + +``` + +*Note: Depending on how you have cloned this repository, you might see `VSpipe` instead of `VSpipe-master`* + +Once you make sure that everything is ready, then follow the next commands. +Make sure that you do not just copy and paste, as here we assume the file architecture described +above (i.e., `~/Applications/VSpipe-master/VSpipe`). **Change the paths according to your path system**. + +``` +cd ~/Applications/VSpipe-master/VSpipe +tar -xzvf mgltools_x86_64Linux2_latest.tar.gz +chmod +x mgltools_x86_64Linux2_latest +cd mgltools_x86_64Linux2_latest/ +tar -xzvf MGLToolsPckgs.tar.gz +``` + +After that, please export the path to your `~/.bashrc`. You can open this file with your +preferred text editor (e.g., `vim`, `nano`, `atom`, etc.) and add the path or you can just type the following +command in the terminal : + +``` +# Run this to export the path to your ~/.bashrc +echo "export PATH=$PATH:~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest" >> ~/.bashrc +``` + +Now, make sure you are still at `~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest` +and then, from the terminal, execute the `install.sh` script: + +``` +# Our current directory is: ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest +./install.sh +``` + +--- +*NOTE: If you get an error message about line 78, you should use the next command. It will comment this line and +add a new command that makes the installation procedure work: +``` +sed -i 's/export\ PATH\=\"\$MGL\_ROOT\/bin\:\"\$PATH/\#export\ PATH\=\"\$MGL\_ROOT\/bin\:\"\$PATH\ \#\ SAC\:\ original\ line\ commented\ + \necho\ \"export\ PATH\=\$PATH\:\$MGL\_ROOT\/bin\"\ \>\>\ \~\/\.bashrc\ \#\ SAC\: new\ line\ added/' install.sh +``` + +After that, you could just rerun the script, `./install.sh`, and it should install without errors `MGLTools`. +--- + +You will see how several messages are printed out in your terminal as `MGLTools` is being installed. At the end +of the installation, you will see some instructions about adding the following aliases to your `~/.bashrc`. +If you have downloaded the `mgltools_x86_64Linux2_latest` version, you should see something like this: + +``` +alias pmv='~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/bin/pmv' +alias adt='~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/bin/adt' +alias vision='~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/bin/vision' +alias pythonsh='~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/bin/pythonsh' +``` + +Again, open your `~/.bashrc` and add the aliases you have been asked +to append to this file at the end of the `MGLTools` installation. + +Subsequently, without changing directory, type the following on the terminal: + +``` +# Our current directory is: ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest +source ./initMGLtools.sh +``` + +Then, append to the `~/.bashrc` the following path - make sure you +use the correct path according to where you have installed `VSpipe`: + +``` +export PYTHONPATH="~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs" +``` + +## Installing AutoDock tools + +### AD4 + +Download AD4 tools `autogrid4` and `autodock4` for Linux: + +``` +cd ~/Applications/VSpipe-master/VSpipe/ +wget http://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/autodocksuite-4.2.6-x86_64Linux2.tar +tar -xvf autodocksuite-4.2.6-x86_64Linux2.tar +``` + +Once it is downloaded, copy both `autogrid` and `autodock4` in the `~/Applications/VSpipe-master/VSpipe/Tools` directory: +If you want, you can then clean this directory by removing the tar and untarred files with the +`AD4` tools (last two comments in the next snippet): + +``` +# Our current directory is "~/Applications/VSpipe-master/VSpipe/" +cp ~/Applications/VSpipe-master/VSpipe/x86_64Linux2/autodock4 ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/x86_64Linux2/autogrid4 ~/Applications/VSpipe-master/VSpipe/Tools + +# Clean directory - remove unnecessary files and/or directories +rm -r ~/Applications/VSpipe-master/VSpipe/x86_64Linux2 +rm autodocksuite-4.2.6-x86_64Linux2.tar +``` + +### Vina +Go to the [Vina website](http://vina.scripps.edu/download.html) and download the corresponding Vina files +for Linux (you can also download this by clicking [here](http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz)). After that, copy both executables `vina` and `vina_split` in the `~/Applications/VSpipe-master/VSpipe/Tools` +directory: + +``` +# Our current directory is "~/Applications/VSpipe-master/VSpipe/" +tar -xzvf autodock_vina_1_1_2_linux_x86.tgz +cp ~/Applications/VSpipe-master/VSpipe/autodock_vina_1_1_2_linux_x86/bin/vina ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/autodock_vina_1_1_2_linux_x86/bin/vina_split ~/Applications/VSpipe-master/VSpipe/Tools + +# Clean directory - remove unnecessary files and/or directories +rm -r autodock_vina_1_1_2_linux_x86 +rm autodock_vina_1_1_2_linux_x86.tgz +``` + +### AutoDock python scripts +Now, copy the files `prepare_dpf4.py`, `prepare_gpf4.py`, `prepare_ligand4.py`, `prepare_receptor4.py`, +and `summarize_results4.py` to `mgltools_x86_64Linux2_latest/MGLToolsPckgs`. +They are located in `mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/" + +``` +cp ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/summarize_results4.py ~/Applications/VSpipe-master/VSpipe/Tools +``` + +### Give permissions to execute ! +Do not forget to give permissions to all the scripts in the `Tools` directory! + +``` +chmod 775 ~/Applications/VSpipe-master/VSpipe/Tools +``` + + +## Installing OpenBabel + +# 1. Install the current version: + +Before going through the OpenBabel installation, there are some additional packages that you might want to install if +you want to have OpenBabel with all the features it can offer: + +``` +# Install CMake 2.4.8 or later +sudo apt-get install cmake + +# Install cairo library and libpython-dev +sudo apt-get install libpython-dev +sudo apt-get install libcairo2-dev + +# Install Eigen 3.0 or later +sudo apt-get install libeigen3-dev + +# Install libxml2 +sudo apt-get install libxml2-dev + +# Install zlib +sudo apt-get install zlib1g-dev + +# Install wxWidgets 2.8 +sudo apt-get install libwxgtk3.0-dev +``` + +After that, you can go to the [OpenBabel website](http://openbabel.org/wiki/Category:Installation), download +OpenBabel (you can also find all the previous versions of OpenBabel [here](https://sourceforge.net/projects/openbabel/files/openbabel/)) +and follow the instructions to compile OpenBabel [here](https://open-babel.readthedocs.io/en/latest/Installation/install.html#compiling-open-babel). + +Here, you have a summary of the basic OpenBabel installation. If you want an advanced installation, check their +INSTALL file or the link provided above. + +*NOTE: The following instructions assume that the OpenBabel source distribution is in +the directory ~/Applications/VSpipe-master/VSpipe/openbabel-2.4.1. + +``` +# 1. Create a 'build' directory: +cd ~/Applications/openbabel-2.4.1 +mkdir build +cd build + +# 2. Configure the build system. You can specify additional build +# options at this time (see below): +cmake .. + +# 3. Compile: +make -j2 + +# 4. Test (optional): +make test + +# 5. Install: +sudo make install +``` + +--- + +_**(OPTIONAL) Installing Anaconda**_ +If you have already installed Python 2.7, `VSpipe` and the AutoDock scripts it relies on should work without any issue. +Nevertheless, if you would like to have Anaconda installed, you can download the Linux release [here](https://www.anaconda.com/download/#download) +Just follow the instructions of the installer [here](https://conda.io/docs/user-guide/install/linux.html) +and then run the bash script you would have previously downloaded + +``` +bash Anaconda-latest-Linux-x86_64.sh +``` + +--- + +## Problems with Numpy + +Apparently, there is a problem with the new version of Numpy (numpy>1.9) when you run some of the +AutoDock python scripts because it does not support `numpy.oldnumeric`. In Bitbucket, +see the discussion [here](https://bitbucket.org/khinsen/scientificpython/issues/13), +they make some suggestions about how to deal with this particular issue. We decided to install a lower version of numpy +so the AutoDock scripts could work: + +``` +pip install "numpy<1.9" +``` + +## Adding VSpipe to your path +You might be keen on adding an alias to run `VSpipe` from any directory by just typing +`VSpipe` on the terminal. If that is your case, open your `~/.bashrc` with +your preferred text editor and type the following (note that the path is the one used in the examples above, +just modify it according to yours): + +``` +alias VSpipe='~/Applications/VSpipe-master/VSpipe/Tools/VSpipe' +``` + +--- + +If you have managed to install these third-party tools, now you should be able to open a terminal on +your working directory, type `VSpipe`, and get the pipeline started. + +Happy docking! :) + + diff --git a/Installation/Install_dependencies_WLS.md b/Installation/Install_dependencies_WLS.md new file mode 100644 index 0000000..e4a2a88 --- /dev/null +++ b/Installation/Install_dependencies_WLS.md @@ -0,0 +1,267 @@ +# Install VSpipe on the Windows Linux Subsystem (WLS) + +## Installing MGLTools + +First, go to [their website](http://mgltools.scripps.edu/downloads/latest) and download the [Linux release](http://mgltools.scripps.edu/downloads/tars/releases/nightly/latest/REL/mgltools_x86_64Linux2_latest.tar.gz) +This installation procedure assumes that: + 1. You have already cloned this repository (e.g., you might see `VSpipe-master`). + 2. You have downloaded the `VSpipe.zip` file from [releases](https://github.com/sabifo4/VSpipe/releases), unzipped it, and you have + saved it in this cloned directory (e.g., `VSpipe-master/VSpipe`). + 3. You have saved the downloaded tar file from `MGLTools`, untarred it, and saved it inside the previously unzipped directory + `VSpipe`, i.e., `VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest`) + +Let's consider that you have decided to clone this repository (e.g., `VSpipe-master`) inside `~/Applications`. +Therefore, before starting with the MGLTools installation, you should make sure your directory architecture looks like +something such as: + +``` +Applications + |- VSpipe-master + |- .git + |- Installation + | |- Install_dependencies_MacOSX.md + | |- Install_dependencies_Linux.md + | |- Install_dependencies_WLS.md + | |- VSpipe_details.docx + | + |- Tutorial + | |- Tutorial_VSpipe.md + | + |- VSpipe + | |- Tools + | |- mgltools_x86_64Linux2_latest.tar.gz + | + |- README.md + +``` + +*Note: Depending on how you have cloned this repository, you might see `VSpipe` instead of `VSpipe-master`* + +Once you make sure that everything is ready, then follow the next commands. +Make sure that you do not just copy and paste, as here we assume the file architecture described +above (i.e., `~/Applications/VSpipe-master/VSpipe`). **Change the paths according to your path system**. + +``` +cd ~/Applications/VSpipe-master/VSpipe +tar -xzvf mgltools_x86_64Linux2_latest.tar.gz +chmod +x mgltools_x86_64Linux2_latest +cd mgltools_x86_64Linux2_latest/ +tar -xzvf MGLToolsPckgs.tar.gz +``` + +After that, please export the path to your `~/.bashrc`. You can open this file with your +preferred text editor (e.g., `vim`, `nano`, `atom`, etc.) and add the path or you can just type the following +command in the terminal : + +``` +# Run this to export the path to your ~/.bashrc +echo "export PATH=$PATH:~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest" >> ~/.bashrc +``` + +Now, make sure you are still at `~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest` +and then, from the terminal, execute the `install.sh` script: + +``` +# Our current directory is: ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest +./install.sh +``` + +--- +*NOTE: You might get an error message about line 78. If that is the case, please use the next command to sort this out. +This command will comment line 78 and add a new command that makes the installation procedure work: +``` +sed -i 's/export\ PATH\=\"\$MGL\_ROOT\/bin\:\"\$PATH/\#export\ PATH\=\"\$MGL\_ROOT\/bin\:\"\$PATH\ \#\ SAC\:\ original\ line\ commented\ + \necho\ \"export\ PATH\=\$PATH\:\$MGL\_ROOT\/bin\"\ \>\>\ \~\/\.bashrc\ \#\ SAC\: new\ line\ added/' install.sh +``` + +After that, just rerun the script, `./install.sh`, and it should install without errors `MGLTools`. +--- + +You will see how several messages are printed out in your terminal as `MGLTools` is being installed. At the end +of the installation, you will see some instructions about adding the following aliases to your `~/.bashrc`. +If you have downloaded the `mgltools_x86_64Linux2_latest` version, you should see something like this: + +``` +alias pmv='~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/bin/pmv' +alias adt='~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/bin/adt' +alias vision='~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/bin/vision' +alias pythonsh='~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/bin/pythonsh' +``` + +Again, open your `~/.bashrc` and add the aliases you have been asked +to append to this file at the end of the `MGLTools` installation. + +Subsequently, without changing directory, type the following on the terminal: + +``` +# Our current directory is: ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest +source ./initMGLtools.sh +``` + +Then, append to the `~/.bashrc` the following path - make sure you +use the correct path according to where you have installed `VSpipe`: + +``` +export PYTHONPATH="~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs" +``` + +## Installing AutoDock tools + +### AD4 + +Download AD4 tools `autogrid4` and `autodock4` for Linux: + +``` +cd ~/Applications/VSpipe-master/VSpipe/ +wget http://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/autodocksuite-4.2.6-x86_64Linux2.tar +tar -xvf autodocksuite-4.2.6-x86_64Linux2.tar +``` + +Once it is downloaded, copy both `autogrid` and `autodock4` in the `~/Applications/VSpipe-master/VSpipe/Tools` directory: +If you want, you can then clean this directory by removing the tar and untarred files with the +`AD4` tools (last two comments in the next snippet): + +``` +# Our current directory is "~/Applications/VSpipe-master/VSpipe/" +cp ~/Applications/VSpipe-master/VSpipe/x86_64Linux2/autodock4 ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/x86_64Linux2/autogrid4 ~/Applications/VSpipe-master/VSpipe/Tools + +# Clean directory - remove unnecessary files and/or directories +rm -r ~/Applications/VSpipe-master/VSpipe/x86_64Linux2 +rm autodocksuite-4.2.6-x86_64Linux2.tar +``` + +### Vina +Go to the [Vina website](http://vina.scripps.edu/download.html) and download the corresponding Vina files +for Windows (you can also download this by clicking [here](http://vina.scripps.edu/download/autodock_vina_1_1_2_win32.msi)). After that, copy both executable files `vina.exe` and `vina_split.exe` in the `~/Applications/VSpipe-master/VSpipe/Tools` +Just follow the installation steps when you execute autodock_vina_1_1_2_win32.msi and then copy the executables by typing the following: + +``` +# Our current directory is "~/Applications/VSpipe-master/VSpipe/" +cp ~/Applications/VSpipe-master/VSpipe/Vina/vina.exe ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/Vina/vina_split.exe ~/Applications/VSpipe-master/VSpipe/Tools +``` + +### AutoDock python scripts +Now, copy the files `prepare_dpf4.py`, `prepare_gpf4.py`, `prepare_ligand4.py`, `prepare_receptor4.py`, +and `summarize_results4.py` to `mgltools_x86_64Linux2_latest/MGLToolsPckgs`. +They are located in `mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/" + +``` +cp ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py ~/Applications/VSpipe-master/VSpipe/Tools +cp ~/Applications/VSpipe-master/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs/AutoDockTools/Utilities24/summarize_results4.py ~/Applications/VSpipe-master/VSpipe/Tools +``` + +### Give permissions to execute ! +Do not forget to give permissions to all the scripts in the `Tools` directory! + +``` +chmod 775 ~/Applications/VSpipe-master/VSpipe/Tools +``` + + +## Installing OpenBabel + +# 1. Install the current version: + +Before going through the OpenBabel installation, there are some additional packages that you might want to install if +you want to have OpenBabel with all the features it can offer: + +``` +# Install CMake 2.4.8 or later +sudo apt-get install cmake + +# Install cairo library and libpython-dev +sudo apt-get install libpython-dev +sudo apt-get install libcairo2-dev + +# Install Eigen 3.0 or later +sudo apt-get install libeigen3-dev + +# Install libxml2 +sudo apt-get install libxml2-dev + +# Install zlib +sudo apt-get install zlib1g-dev + +# Install wxWidgets 2.8 +sudo apt-get install libwxgtk3.0-dev +``` + +After that, you can go to the [OpenBabel website](http://openbabel.org/wiki/Category:Installation), download +OpenBabel (you can also find all the previous versions of OpenBabel [here](https://sourceforge.net/projects/openbabel/files/openbabel/)) +and follow the instructions to compile OpenBabel [here](https://open-babel.readthedocs.io/en/latest/Installation/install.html#compiling-open-babel). + +Here, you have a summary of the basic OpenBabel installation. If you want an advanced installation, check their +INSTALL file or the link provided above. + +*NOTE: The following instructions assume that the OpenBabel source distribution is in +the directory ~/Applications/VSpipe-master/VSpipe/openbabel-2.4.1. + +``` +# 1- Create a 'build' directory +cd ~/Applications/openbabel-2.4.1 +mkdir build +cd build + +# 2- Configure the build system. You can specify additional build +# options at this time (see below) +cmake .. + +# 3- Compile +make -j2 + +# 4- Test (optional) +make test + +# 5- Install +sudo make install +``` + +--- + +_**(OPTIONAL) Installing Anaconda**_ +If you have already installed Python 2.7, `VSpipe` and the AutoDock scripts it relies on should work without any issue. +Nevertheless, if you would like to have Anaconda installed, you can download the Linux release [here](https://www.anaconda.com/download/#download) +Just follow the instructions of the installer [here](https://conda.io/docs/user-guide/install/linux.html) +and then run the bash script you would have previously downloaded + +``` +bash Anaconda-latest-Linux-x86_64.sh +``` + +--- + +## Problems with Numpy + +Apparently, there is a problem with the new version of Numpy (numpy>1.9) when you run some of the +AutoDock python scripts because it does not support `numpy.oldnumeric`. In Bitbucket, +see the discussion [here](https://bitbucket.org/khinsen/scientificpython/issues/13), +they make some suggestions about how to deal with this particular issue. We decided to install a lower version of numpy +so the AutoDock scripts could work: + +``` +pip install "numpy<1.9" +``` + +## Adding VSpipe to your path +You might be keen on adding an alias to run `VSpipe` from any directory by just typing +`VSpipe` on the terminal. If that is your case, open your `~/.bashrc` with +your preferred text editor and type the following (note that the path is the one used in the examples above, +just modify it according to yours): + +``` +alias VSpipe='~/Applications/VSpipe-master/VSpipe/Tools/VSpipe' +``` + +--- + +If you have managed to install these third-party tools, now you should be able to open a terminal on +your working directory, type `VSpipe`, and get the pipeline started. + +Happy docking! :) + + diff --git a/Tutorial/Tutorial_VSpipe.md b/Tutorial/Tutorial_VSpipe.md new file mode 100644 index 0000000..75afcf8 --- /dev/null +++ b/Tutorial/Tutorial_VSpipe.md @@ -0,0 +1,218 @@ +## __Download VSpipe local__ + +First of all, you should clone this repository in your local PC. You can download it +as a zip file by clicking either the `Clone or download` button in the Git repository or [here](https://github.com/sabifo4/VSpipe/archive/master.zip). +If you have `git` installed, you can also create a directory in your local PC to where you +want to save it, and type the following in a terminal: + +```bash +git clone https://github.com/sabifo4/VSpipe +``` + +This repository consists of the following: + +``` +Applications + |- VSpipe-master + |- .git + |- Installation + | |- Install_dependencies_MacOSX.md + | |- Install_dependencies_Linux.md + | |- Install_dependencies_WLS.md + | |- VSpipe_details.docx + | + |- Tutorial + | |- Tutorial_VSpipe.md + | + |- README.md + |- Tutorial_VSpipe.md +``` + +Once you have cloned this repository, you can find the source code for each operating system under the `release` ([Mac OS X](), [Linux](), [WLS]()). +Once you have downloaded the corresponding `zip` file, please unzip it and save it inside this GitHub repository. If you saved the GitHub repository +under the `~/Applications` directory, you should have something like this once you have untarred the `zip` file: + +``` +Applications + |- VSpipe-master + |- .git + |- Installation + | |- Install_dependencies_MacOSX.md + | |- Install_dependencies_Linux.md + | |- Install_dependencies_WLS.md + | |- VSpipe_details.docx + | + |- Tutorial + | |- Tutorial_VSpipe.md + | + |- VSpipe + | |- Tools + | + |- README.md +``` + +After that, please follow the installation instructions for your operating system to install the third-party +tools `VSpipe` relies on: + + 1. Installation for Linux *- only tested on Ubuntu but should work for any Linux distribution*: click [here](). + 2. Installation for WLS: click [here]() + 3. Installation for Mac OS X: click [here]() + +If you have followed the steps described in the installation file, you might have an alias to run +`VSpipe` on the terminal just by typing `VSpipe` on the terminal. If you have already typed `VSpipe` on +your terminal and you see this message: + +``` +|-------------------------------------------------------------------| +| VSpipe v1.0 | +|-------------------------------------------------------------------| +| Pipeline designed and developed by: | +| Sandra Alvarez-Carretero, Niki Pavlopoulou, | +| Jane Gilsenan, and Lydia Tabernero | +| | +| Pipeline currently maintained by: | +| Sandra Alvarez-Carretero | +| | +| If you use VSpipe to carry out yor VSs, please cite: | +| Alvarez-Carretero, et al. (2018) Molecules, 23(2), 353 | +| https://doi.org/10.3390/molecules23020353 | +| | +| You can find a tutorial and the manual for VSpipe here: | +| https://github.com/sabifo4/VSpipe | +| | +| If you have further questions or need to report a bug, please | +| send a message to: | +| vspipe.local@gmail.com | +| | +| Happy Docking! :) | +|-------------------------------------------------------------------| + + +#------------------------# +# RECEPTOR PREARATION # +#------------------------# + +If you have already prepared your receptor, +which means that you must have a directory, for instance called +"receptor", with the following content + + receptor + |- XXX.pdb + |- XXX_clean.pdb + |- XXX.pdbqt + |- sample.gpf + +then you can also reuse your prepared receptor. +Please type "yes" if you want to reuse your receptor. Otherwise, +please type "no" and then press [ENTER]: + +``` + +Then you can follow the tutorial in the next section! Otherwise, you might have missed an important step +during the installation of the third-party tools. + + +## __Run VSpipe local__ + +### 1. Set the working directory + +First of all, set your working directory. Open a terminal in your preferred location and +create your working directory. In this tutorial, the working directory is going to be called `test_VSpipe`, +although you can change its name. Note that this will not change the next steps in the tutorial. +The path to `test_VSpipe` for this example is `/home/user/my_dockings/test_VSpipe`, hence: + +```bash +$ pwd +/home/user/my_dockings +$ mkdir test_VSpipe +$ cd test_VSpipe +$ pwd +/home/user/my_dockings/test_VSpipe +``` + +### 2. Run a virtual screening with VSpipe +Once you are inside your working directory, you are ready to run `VSpipe`. If you have followed the installation +procedure, you might jus be able to run `VSpipe` by typing `VSpipe` on the terminal. Otherwise, you will need +to type the whole path to the bash script: + +1. Make sure you are in your working directory + +```bash +$ pwd +/home/user/my_dockings/test_VSpipe +``` + +2. Run VSpipe for the first time + +```bash +$ VSpipe +``` +``` +|-------------------------------------------------------------------| +| VSpipe v1.0 | +|-------------------------------------------------------------------| +| Pipeline designed and developed by: | +| Sandra Alvarez-Carretero, Niki Pavlopoulou, | +| Jane Gilsenan, and Lydia Tabernero | +| | +| Pipeline currently maintained by: | +| Sandra Alvarez-Carretero | +| | +| If you use VSpipe to carry out yor VSs, please cite: | +| Alvarez-Carretero, et al. (2018) Molecules, 23(2), 353 | +| https://doi.org/10.3390/molecules23020353 | +| | +| You can find a tutorial and the manual for VSpipe here: | +| https://github.com/sabifo4/VSpipe | +| | +| If you have further questions or need to report a bug, please | +| send a message to: | +| vspipe.local@gmail.com | +| | +| Happy Docking! :) | +|-------------------------------------------------------------------| + + +#------------------------# +# RECEPTOR PREARATION # +#------------------------# + +If you have already prepared your receptor, +which means that you must have a directory, for instance called +"receptor", with the following content + + receptor + |- XXX.pdb + |- XXX_clean.pdb + |- XXX.pdbqt + |- sample.gpf + +then you can also reuse your prepared receptor. +Please type "yes" if you want to reuse your receptor. Otherwise, +please type "no" and then press [ENTER]: +``` + +This step asks you if you want to reuse your receptor. If you have not run +VSpipe before, please type `no` as you need to clean the PDB file with your +target protein. After typing `no` and pressing `ENTER` (RETURN key), you are asked the following +questions: + +``` +Please type a name for the directory where all the files concerning +the receptor will be. After that, please press [ENTER]: +receptor + +Please type the name of the PDB file for the receptor and upload +it in the directory receptor. After that, please press +[ENTER]: +3X4P.pdb + +Please use ADT to manually create your "gpf" file, in which you +will define the grid box. Then, please manually save the file as +"sample.gpf" under the directory receptor. +Once this is done, please press [ENTER]: + +``` + +In this snippet, we assume that you call the directory to prepare the receptor **`receptor`** and that the file +with your target protein is **`3X4P.pdb`**. In order \ No newline at end of file diff --git a/Tutorial_VSpipe.md b/Tutorial_VSpipe.md deleted file mode 100644 index 7199d11..0000000 --- a/Tutorial_VSpipe.md +++ /dev/null @@ -1,141 +0,0 @@ -## __Download VSpipe local__ - -First of all, you should clone this repository in your local PC. You can download it -as a zip file by clicking either the `Clone or download` button in the Git repository or [here](https://github.com/sabifo4/VSpipe/archive/master.zip). -If you have `git` installed, you can also create a directory in your local PC to where you -want to save it, and type the following in a terminal: - -`git clone https://github.com/sabifo4/VSpipe` - -This repository consists of the following: - -``` -VSpipe - |- Documentation.docx - |- Install_dependencies.txt - |- README.md - |- Tutorial_VSpipe.md - |- [tag] release - |- VSpipe.zip <-- SOURCE CODE TO DOWNLOAD! -``` - -Once you have cloned this repository, you can find the source code in the [**`VSpipe.zip`**](https://github.com/sabifo4/VSpipe/releases/download/v0.1.0/VSpipe.zip) file available under the tag `release`. Click [here](https://github.com/sabifo4/VSpipe/releases) to access the `release` site or click the previous link within the zip filename to download it. -Once you have downloaded `VSpipe.zip`, please unzip it and save it in your preferred location. For this tutorial, we will let the path to the unzipped `VSpipe` be `/home/Applications/VSpipe`. If you are saving `VSpipe` in another location, please remember to use your chosen path instead when following this tutorial. -The contents inside `VSpipe` are the following: - -``` -VSpipe - |- Tools - | |- database_libraries - | |- *different scripts VSpipe uses* - | - |- Documentation.txt - |- Install_dependencies.txt -``` - -All the source code can be found inside **Tools**, where the different ligand databases `VSpipe` are available together with the scripts `VSpipe` runs. In case these scripts do not have full permissions, please give them as it follows. As previously mentioned, the path used in this tutorial and in the following command is `/home/Applications/VSpipe`, but please change this according to the path where you have saved `VSpipe`. Once taken that into account, please open a terminal and type the following: - -```bash -$ cd /home/Applications/VSpipe -$ chmod 775 Tools -``` - -## __Install VSpipe dependencies__ - -Follow the instructions detailed in the [__Install_dependencies.txt__](https://github.com/sabifo4/VSpipe/blob/master/Install_dependencies.txt) -file. Once you have cloned this repository and MGLTools, OpenBabel, and Anaconda are installed, you can proceed to run VSpipe. - -**NOTE**: When installing Anaconda, it is very important that you check the Numpy version you install, as detailed from line 179 -onwards in the [__Install_dependencies.txt__](https://github.com/sabifo4/VSpipe/blob/master/Install_dependencies.txt) -file. The AutoDock scripts use the `numpy.oldnumeric` module and only work when the Numpy version installed is lower than v1.9. -We explain this as well in the file mentioned above, but you can check [this site](https://bitbucket.org/khinsen/scientificpython/issues/13)) -for more information on the issue. - - -## __Run VSpipe local__ - -#### 1. Set the working directory - -Once the permissions to this directory have been given, you should be able to run `VSpipe`. -First of all, set your working directory. Open a terminal in your preferred location and -create your working directory. In this tutorial, the working directory is going to be called **test_VSpipe**, -although you can change its name. Note that this will not change the next steps in the tutorial. For example, if -**test_VSpipe** was to be created in */home/user/wd*, then we can create our working directory and move into -it as it follows: - -```bash -$ pwd -/home/user/wd -$ mkdir test_VSpipe -$ cd test_VSpipe -$ pwd -/home/user/wd/test_VSpipe -``` - -#### 2. Run a virtual screening with VSpipe -Once you are inside your working directory, you are ready to run `VSpipe`. You should type the whole path to the bash -script `VSpipe` (for targeted docking) or to the bash script `VSpipe_blind` (for blind docking) -which are stored in `VSpipe/Tools`. If it is properly working, the following message will appear -in both cases: - -```bash -# Case 1: Run targeted docking from your working directory -$ pwd -/home/user/wd/test_VSpipe -$ /home/Applications/VSpipe/Tools/VSpipe - -"Please type the full path where the prepare_dpf4.py, prepare_gpf4.py, -prepare_ligand4.py, and prepare_receptor4.py are. After that, please -press [ENTER]:" - - -# Case 2: Run blind docking from your working directory -$ pwd -/home/user/wd/test_VSpipe -$ /home/Applications/VSpipe/Tools/VSpipe_blind - -Please type the full path where the prepare_dpf4.py, prepare_gpf4.py, -prepare_ligand4.py, and prepare_receptor4.py are. After that, please -press [ENTER]: - -``` - -If you do not want to type the absolute path everytime you want to run -`VSpipe`, you can always create an alias in your `.bashrc`. You can open -this file with your favourite text editor and add the following lines: - -```bash -alias VSpipe_t="/home/Applications/VSpipe/Tools/VSpipe_targeted" -alias VSpipe_b="/home/Applications/VSpipe/Tools/VSpipe_blind" -``` - -We have chosen to use the alias `VSpipe_t` to call the script that runs targeted docking and -`VSpipe_b` the one who runs blind docking. Nevertheless, note that you can choose the name you -prefer to use to run both dockings. - -#### 3. Set the path to the AutoDock scripts - -If you have properly installed the dependencies VSpipe needs as it is -detailed in the [__Install_dependencies.txt__](https://github.com/sabifo4/VSpipe/blob/master/Installation_Ubuntu.txt) -file, then the `prepare_dpf4.py`, `prepare_gpf4.py`, `prepare_ligand4.py`, and `prepare_receptor4.py` -should be in `/home/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs`. If you changed the path -to where MGLTools were to be installed, then just change the absolute path accordingly. -For this tutorial, we will keep the path as detailed in the [__Install_dependencies.txt__](https://github.com/sabifo4/VSpipe/blob/master/Installation_Ubuntu.txt) -file. Therefore, once VSpipe starts, you should type this absolute path as it follows: - -```bash -# Example: Run targeted docking from your working directory -$ pwd -/home/user/wd/test_VSpipe -$ /home/Applications/VSpipe/pidock/VSpipe - -Please type the full path where the prepare_dpf4.py, prepare_gpf4.py, -prepare_ligand4.py, and prepare_receptor4.py are. After that, please -press [ENTER]: -/home/Applications/VSpipe/mgltools_x86_64Linux2_latest/MGLToolsPckgs - -``` - -After that, just follow the instructions `VSpipe` will be printing on the screen in -order to proceed with the virtual screening! -