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Blaster18 is the new interface to molecular docking on the webThere are a number of functions under development. Here we list the functions you can currently use, with usage notes.  
TLDR (tldr.docking.org) is a web-based interface to molecular docking and related tools.
The system currently consists of a dozen appsWe plan to support dozens, perhaps a hundred all told.
Here we list the apps you can currently use, with usage notes.  


== Analog ==  
This is also called "Add TLDR Module"
Not working yet.
 
{{TOCright}}
 
== Current available modules ==
=== [[TLDR:Arthorbatch|Arthorbatch]] ===
 
=== [[TLDR:Bioisostere|Bioisostere]] ===
 
=== [[TLDR:Bootstrap1|Bootstrap1]] ===
 
=== [[TLDR:Bootstrap2|Bootstrap2]] ===
 
=== [[TLDR:DUDE-Z|DUDE-Z]] ===
 
=== [[TLDR:Extrema|Extrema]] ===
 
=== [[TLDR:Newbuild3d|Newbuild3d]] ===
 
=== [[TLDR:Strain|Strain]] ===
 
=== [[TLDR:Swbatch|Swbatch]] ===
 
== In Development ==
=== Blaster ===
The purpose of the blaster app is to prepare a receptor for docking, including some basic analysis.
 
This app requires:
* A structure for your receptor protein provided as a pdb file
* A binding site provided in one of the following ways:
  1) Supply ligand in binding site
  2) Provide binding site residues
  3) Use a program to identify all potential binding sites.  Choose which of the binding sites to test or test them all.
 
The app returns:
* dockfiles, which may be used for large library docking
* workfiles, which may be used for grid and sphere optimization.
 
The output of this app can be used by:
* asdf
* sef
* sdfafd
 
Status: works. (equivalent of blastermaster.py)
 
 
 
=== Covalent ===
Purpose:
 
This app requires:
* asdf
 
This app returns:
* asdf
 
The output of this app can be used by:
* adsfasdf
 
Status: Works with special cases only. Nearly ready to use.  If interested, ask jji for assistance.
 
=== Cluster ===
Purpose:
 
This app requires:
* asdf
 
This app returns:
* asdf
 
The output of this app can be used by:
* adsfasdf
 
Status:  Works.  


== Blaster ==
works. (equivalent of blastermaster.py)


== Build3D ==
Works


{{TOCright}}
=== Libanalysis ===
Purpose:
 
This app requires:
* asdf
 
This app returns:
* asdf
 
The output of this app can be used by:
* adsfasdf
 
Status:  Not working yet
 
=== Reaction ===


== Covalent ==
Purpose:
Works with special cases only.
Nearly ready to use.
If interested, ask jji for assistance.


== Cluster ==
This app requires:
Works.
* asdf


== Dude ==
This app returns:
Nearly ready to use.
* asdf
Awaiting advice from Reed


== Libanalysis ==
The output of this app can be used by:
Not working yet
* adsfasdf


== Reaction ==
Status:  Works at a basic level, with minor caveats.
Works at a basic level, with minor caveats.
* need to handle mwt and logP cutoff parametrically.
* need to handle mwt and logP cutoff parametrically.
* needs work to handle millions of molecules
* needs work to handle millions of molecules
* needs work to connect to reagents, reactions and schemes
* needs work to connect to reagents, reactions and schemes


== Report2d ==
=== Report2d ===
Not working yet
Purpose:
 
This app requires:
* asdf
 
This app returns:
* asdf


== ZINCbatch ==
The output of this app can be used by:
Not working yet
* adsfasdf
 
Status:  Not working yet
 
=== Shape ===
Purpose:
 
Search for similar shape molecules for ligands
 
This app requires:
* asdf
 
This app returns:
* asdf
 
The output of this app can be used by:
* adsfasdf
 
Status:  Not working yet
 
=== ZINCbatch ===
Purpose:
 
This app requires:
* asdf
 
This app returns:
* asdf
 
The output of this app can be used by:
* adsfasdf
 
Status: Not working yet
 
= Technical info =


== starting the server in single-threaded mode ==  
== starting the server in single-threaded mode ==  
Line 43: Line 162:
  python code/DOCKBlaster/autoapp.py
  python code/DOCKBlaster/autoapp.py


== How to add new module ==
See [[Add Tools18 module]]
== Supported field types ==  
== Supported field types ==  
  For now, the model accepts "text_box", "check_box", "drop_down" , "radio_button",  and so on
  For now, the model accepts "text_box", "check_box", "drop_down" , "radio_button",  and so on
Line 51: Line 172:


7. Every job type has a "job_output" field, which currently stores an empty results.txt file which can be modified to do another action later. For now, the inputs uploaded, and the output file name specified by the user gets stored in the file system under the path that I mentioned in point 6.
7. Every job type has a "job_output" field, which currently stores an empty results.txt file which can be modified to do another action later. For now, the inputs uploaded, and the output file name specified by the user gets stored in the file system under the path that I mentioned in point 6.
[[Category: TLDR]]
[[Category: Tools18]]

Revision as of 06:14, 8 August 2022

TLDR (tldr.docking.org) is a web-based interface to molecular docking and related tools. The system currently consists of a dozen apps. We plan to support dozens, perhaps a hundred all told. Here we list the apps you can currently use, with usage notes.

This is also called "Add TLDR Module"

Current available modules

Arthorbatch

Bioisostere

Bootstrap1

Bootstrap2

DUDE-Z

Extrema

Newbuild3d

Strain

Swbatch

In Development

Blaster

The purpose of the blaster app is to prepare a receptor for docking, including some basic analysis.

This app requires:

  • A structure for your receptor protein provided as a pdb file
  • A binding site provided in one of the following ways:
 1) Supply ligand in binding site
 2) Provide binding site residues
 3) Use a program to identify all potential binding sites.  Choose which of the binding sites to test or test them all.

The app returns:

  • dockfiles, which may be used for large library docking
  • workfiles, which may be used for grid and sphere optimization.

The output of this app can be used by:

  • asdf
  • sef
  • sdfafd

Status: works. (equivalent of blastermaster.py)


Covalent

Purpose:

This app requires:

  • asdf

This app returns:

  • asdf

The output of this app can be used by:

  • adsfasdf

Status: Works with special cases only. Nearly ready to use. If interested, ask jji for assistance.

Cluster

Purpose:

This app requires:

  • asdf

This app returns:

  • asdf

The output of this app can be used by:

  • adsfasdf

Status: Works.


Libanalysis

Purpose:

This app requires:

  • asdf

This app returns:

  • asdf

The output of this app can be used by:

  • adsfasdf

Status: Not working yet

Reaction

Purpose:

This app requires:

  • asdf

This app returns:

  • asdf

The output of this app can be used by:

  • adsfasdf

Status: Works at a basic level, with minor caveats.

  • need to handle mwt and logP cutoff parametrically.
  • needs work to handle millions of molecules
  • needs work to connect to reagents, reactions and schemes

Report2d

Purpose:

This app requires:

  • asdf

This app returns:

  • asdf

The output of this app can be used by:

  • adsfasdf

Status: Not working yet

Shape

Purpose:

Search for similar shape molecules for ligands

This app requires:

  • asdf

This app returns:

  • asdf

The output of this app can be used by:

  • adsfasdf

Status: Not working yet

ZINCbatch

Purpose:

This app requires:

  • asdf

This app returns:

  • asdf

The output of this app can be used by:

  • adsfasdf

Status: Not working yet

Technical info

starting the server in single-threaded mode

source /mnt/nfs/work/chinzo/Projects/BlasterX_supritha/venv/bin/activate
python code/DOCKBlaster/autoapp.py

How to add new module

See Add Tools18 module

Supported field types

For now, the model accepts "text_box", "check_box", "drop_down" , "radio_button",  and so on

If "type" is "text_box", it can contain a text or number with a min and a max range. If there is a min and a max range, then they have to be mentioned as "value_type": "number", "value_range": {"min_value": 0.1,"max_value": 0.99} as in parameters.json for cluster. If "type" is "text_box" and "value_type" is "text", then it is a normal text box with no range or validations. 6. Every input mentioned under the key "inputs" has a field called "file_name", which the name by which the input file uploaded/filled by the user gets stored in the file system at /nfs/ex7/blaster/jobs/JobID%10/Jobname_jobID folder.

7. Every job type has a "job_output" field, which currently stores an empty results.txt file which can be modified to do another action later. For now, the inputs uploaded, and the output file name specified by the user gets stored in the file system under the path that I mentioned in point 6.