Blastermaster2.0 - Revision history

Ianscottknight at 08:16, 2 September 2022

2022-09-02T08:16:35Z

← Older revision		Revision as of 08:16, 2 September 2022
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	[deprecated]		[deprecated]

	See [[~~ucsfdock~~]]		See [[blastermaster (pydock3 script)]]

Ianscottknight at 23:46, 10 August 2022

2022-08-10T23:46:33Z

← Older revision	Revision as of 23:46, 10 August 2022
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		[deprecated]

		See [[ucsfdock]]

Ianscottknight: deletes deprecated page

2022-08-10T23:45:49Z

deletes deprecated page

← Older revision		Revision as of 23:45, 10 August 2022
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	~~= Installation =~~

	~~== 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.~~

	~~=== 3. Run ===~~

	~~If you used the default blaster config file name, then you can simply run:~~

	~~blastermaster~~

	~~Otherwise:~~

	~~blastermaster --blaster_config_file_path=<BLASTER_CONFIG_FILE_PATH>~~

	~~If you want to supply your own charged receptor file (usually called rec.crg.pdb), you can do so as follows:~~

	~~blastermaster --charged_receptor_file_path=<PATH_TO_FILE>~~

	~~= 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]]~~

Ianscottknight: /* 3. Run */

2022-06-07T19:37:10Z

3. Run

← Older revision		Revision as of 19:37, 7 June 2022
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	=== 3. Run ===		=== 3. Run ===

			If you used the default blaster config file name, then you can simply run:

			blastermaster

	Otherwise:		Otherwise:

	blastermaster --blaster_config_file_path=<BLASTER_CONFIG_FILE_PATH>		blastermaster --blaster_config_file_path=<BLASTER_CONFIG_FILE_PATH>

	If you want to supply your own charged receptor file (usually called rec.crg.pdb), you can do so as follows:		If you want to supply your own charged receptor file (usually called rec.crg.pdb), you can do so as follows:

	blastermaster --charged_receptor_file_path=<PATH_TO_FILE>		blastermaster --charged_receptor_file_path=<PATH_TO_FILE>

	= Tips for users =		= Tips for users =

Ianscottknight: /* 3. Run */

2022-06-07T19:36:38Z

3. Run

← Older revision		Revision as of 19:36, 7 June 2022
Line 49:		Line 49:

	=== 3. Run ===		=== 3. Run ===

			Otherwise:
	blastermaster --blaster_config_file_path=<BLASTER_CONFIG_FILE_PATH>		blastermaster --blaster_config_file_path=<BLASTER_CONFIG_FILE_PATH>

			If you want to supply your own charged receptor file (usually called rec.crg.pdb), you can do so as follows:

			blastermaster --charged_receptor_file_path=<PATH_TO_FILE>

	= Tips for users =		= Tips for users =

Ianscottknight: /* 2. Edit the blaster config file to your specifications */

2022-06-07T19:36:05Z

2. Edit the blaster config file to your specifications

← Older revision		Revision as of 19:36, 7 June 2022
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	The parameters in the config file govern the behavior of blastermaster.		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. Run ===		=== 3. Run ===

Ianscottknight: /* 3. Crucially, set an environmental variable called `DOCKBASE` to the path of your DOCK software directory. */

2022-06-07T19:35:35Z

3. Crucially, set an environmental variable called `DOCKBASE` to the path of your DOCK software directory.

← Older revision		Revision as of 19:35, 7 June 2022
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	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.		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 ===		=== 3. Run ===

Ianscottknight at 20:53, 28 April 2022

2022-04-28T20:53:56Z

← Older revision		Revision as of 20:53, 28 April 2022
Line 58:		Line 58:
	= Tips for users =		= 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_use_existing_charged_receptor~~.yaml). Then it is easy to reuse the same configuration settings at a later time.		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:blastermaster2.0]]
	[[Category:active_development]]		[[Category:active_development]]

Ianscottknight at 20:53, 28 April 2022

2022-04-28T20:53:07Z

← Older revision		Revision as of 20:53, 28 April 2022
Line 54:		Line 54:

	=== 3. Run ===		=== 3. Run ===
	blastermaster <~~BLASTER_CONFIG_FILE_NAME~~>		blastermaster --blaster_config_file_path=<BLASTER_CONFIG_FILE_PATH>

	= Tips for users =		= Tips for users =

Ianscottknight: /* 2. Edit the blaster config file to your specifications */

2022-04-08T18:33:42Z

2. Edit the blaster config file to your specifications

← Older revision		Revision as of 18:33, 8 April 2022
Line 45:		Line 45:

	=== 2. Edit the blaster config file to your specifications ===		=== 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. ===		=== 3. Crucially, set an environmental variable called `DOCKBASE` to the path of your DOCK software directory. ===