Blastermaster2.0: Difference between revisions

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[deprecated]


= Installation =
See [[blastermaster (pydock3 script)]]
 
== System dependencies ==
 
You will need CSH to run .csh files.
 
E.g., on Ubuntu 20:
sudo apt-get install csh
 
At least some of the blaster programs that BM2 depends on are 32-bit, so '''if you are installing on a 64-bit architecture then you will need to enable 32-bit architecture and install the relevant libraries'''
 
E.g., on Ubuntu 20:
sudo dpkg --add-architecture i386
sudo apt-get update -y
sudo apt-get install libc6:i386 libncurses5:i386 libstdc++6:i386
 
E.g., on CentOS 7:
yum install glibc.i686 libstdc++.i686
 
== Installing using Pip ==
 
Assuming you have a valid [https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token GitHub personal access token (PAT)] attached to a GitHub account that has read-access to [https://github.com/docking-org/blastermaster-2.0 Blastermaster 2.0 repository within the Docking.org GitHub organization], you can install BM2 to a given Python environment using Pip:
 
pip install https://<GIT_ACCESS_TOKEN>@raw.githubusercontent.com/docking-org/blastermaster-2.0/main/dist/bm2-<SEMANTIC_VERSION>-py3-none-any.whl
 
where <GIT_ACCESS_TOKEN> and <SEMANTIC_VERSION> are replaced by their corresponding / desired values. E.g. semantic version: 0.1.0
 
= Using Blastermaster 2.0 =
 
== UCSF Shoichet Lab members ==
 
If you are a member of the UCSF Shoichet Lab, you can use BM2 on one of the UCSF computers where it is already set-up. See here: [[How_to_use_Blastermaster_2.0_on_UCSF_computers|https://wiki.docking.org/index.php/How_to_use_Blastermaster_2.0_on_UCSF_computers]]
 
== All others ==
 
=== 0. Copy the relevant files to your directory ===
Copy your rec.pdb and xtal-lig.pdb files to your directory. If you want to provide your own rec.crg.pdb, copy that in too. Blastermaster 2.0 will look for these in the directory in which you run it (or at whichever file paths you set for their corresponding parameters in the config file).
 
=== 1. Generate a blaster config file to your directory ===
The following will generate a file called "blasterconfig.yaml"
blasterconfig
The following will generate a file called whatever you put for <BLASTER_CONFIG_FILE_NAME>
blasterconfig <BLASTER_CONFIG_FILE_NAME>
 
=== 2. Edit the blaster config file to your specifications ===
 
The parameters in the config file govern the behavior of blastermaster.
 
Note: if you are using your own files other than rec.pdb and xtal-lig.pdb (e.g., rec.crg.pdb), you need to point to them in the "existing_files_to_use_section". E.g., receptor_charged_file should be set to "rec.crg.pdb" if you have copied it into the directory you are working in.
 
=== 3. Crucially, set an environmental variable called `DOCKBASE` to the path of your DOCK software directory. ===
export DOCKBASE=<ABSOLUTE_PATH_TO_DOCK_REPOSITORY>
 
=== 3. Run ===
blastermaster --blaster_config_file_path=<BLASTER_CONFIG_FILE_PATH>
 
= Tips for users =
 
You can create and save multiple blaster config files with different settings so long as they have different names (e.g. blasterconfig_default.yaml, blasterconfig_elec_only_thinspheres.yaml). Then it is easy to reuse the same configuration settings at a later time.
 
 
[[Category:blastermaster2.0]]
[[Category:active_development]]

Latest revision as of 08:16, 2 September 2022

[deprecated]

See blastermaster (pydock3 script)

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