DISI - User contributions [en]

TLDR

2020-05-27T17:13:51Z

Jyoung:

UCSF Tools 2018 (tools18.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.

{{TOCright}}

== Analog ==
The purpose of the analog app is to find analogs of your active compounds that you can use to explore SAR by catalog around your hits.

This app requires:
* a starting molecule (one at a time for now)
* a tanimoto limit
* mwt and logP limits
* which bioisosteric replacements are acceptable (default all)

This app returns:
* 2D molecules within limits on molecular weight and logP (default 400 and 4.0 respectively) and tanimoto (default 0.5).
* Results are in three separate files.
** a. molecules you can buy according to ZINC
** b. molecules you can make or have made in one, two or three steps from commercially available building blocks
** c. molecules that are intriguingly similar but will require more synthetic effort.

The output of this app can be used by the following other modules in Tools 18
* blaster, for docking.
* build 3d, to build docking libraries
* potentially covalent, depending on warhead
* cluster, to cluster the results
* dude, to generate decoys
* libanalysis, to get a detailed analysis of properties and targets
* report2d, to get a quick summary of physical and chemical properties

status: Not working yet.

== 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)

== Build3D ==
Works

== 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.

== DUDE-Z ==
Purpose: Assemble decoys for docking using the DUDEZ approach. See http://dudez.docking.org for sample data

This app requires:
* Ligands provided in smiles format (actives.smi)
* Current default parameters are shown in the following decoy_generation.in file:

PROTONATE YES
MWT 0 125
LOGP 0 3.6
RB 0 5
HBA 0 4
HBD 0 3
CHARGE 0 0
LIGAND TC RANGE 0.0 0.35
MINIMUM DECOYS PER LIGAND 20
DECOYS PER LIGAND 50
MAXIMUM TC BETWEEN DECOYS 0.8
TANIMOTO YES

See http://wiki.docking.org/index.php/Generating_decoys_(Reed%27s_way) for an explanation of what these parameters mean and how DUDE-Z works.

This app returns:
* List of decoys

Status: Nearly ready to use. Awaiting advice from Reed

== 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.

[[Category: TLDR]]
[[Category: Tools18]]

Add TLDR module

2020-05-27T17:13:20Z

Jyoung: /* Test run! */

Here is quick guide to add your script into [[Tools18]] interface
=== Scripts ===

=== Add job type into psql table ===
*Access the database
$ psql -h mem blaster blasteruser

*Look for the next available index on job_types table
blaster=> select * from job_types order by job_type_id;
You will see table like this
job_type_id | last_updated | short_name
-------------+----------------------------+-------------------
1 | 2018-10-05 00:00:00 | analog
2 | 2018-10-05 00:00:00 | blaster
3 | 2018-10-05 00:00:00 | blasterpdb
4 | 2018-10-05 00:00:00 | build2d
5 | 2018-10-05 00:00:00 | build3d
6 | 2018-10-05 00:00:00 | cluster
7 | 2018-10-05 00:00:00 | covalent
8 | 2018-10-05 00:00:00 | dude
9 | 2018-10-05 00:00:00 | libanalysis
10 | 2018-10-05 00:00:00 | reaction
11 | 2018-10-05 00:00:00 | sea
12 | 2018-10-05 00:00:00 | threec
13 | 2018-10-05 00:00:00 | transform
14 | 2018-10-05 00:00:00 | zincbatch
15 | 2018-12-01 18:47:34 | cluster_molecules

* Insert new job type (Please be extra careful when doing this step)
'''This is important to start command with 'begin;' so that if any syntax mistakes could be undo.'''
blaster=> begin; insert into job_types values(<next_available_id>, now(), '<your_job_name>');
Example:
blaster=> begin; insert into job_types values(16, now(), 'shape');
//To save data
blaster=> commit;
//Or if made mistake, to reserve cmd
blaster=> rollback;

=== Setting up templates ===
* Create directory
$ cd /nfs/ex7/blaster/templates/
$ mkdir <job_name> // job_name must match the shortname in job_types table
$ chmod 777 job_name //for now...
* Get parameters.json
This is recommend that you go though all the currently existing modules on [http://tools18.docking.org/start Tools18] and reuse instead of starting one from scratch.
$ cd job_name
$ cp <whatever parameters.json you pick>
$ vim parameters.json
Change the variables. Check on the website if the module shows up.
* Move your shell scripts in directory

=== Test run! ===

[[Category: Tools18]]
[[Category: TLDR]]

Add TLDR module

2020-05-27T17:13:09Z

Jyoung:

TLDR

2020-05-27T00:54:13Z

Jyoung: /* DUDE-Z */

TLDR

2020-05-27T00:53:50Z

Jyoung: /* DUDE-Z */

UCSF Tools 2018 (tools18.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.

{{TOCright}}

== Analog ==
The purpose of the analog app is to find analogs of your active compounds that you can use to explore SAR by catalog around your hits.

This app requires:
* a starting molecule (one at a time for now)
* a tanimoto limit
* mwt and logP limits
* which bioisosteric replacements are acceptable (default all)

This app returns:
* 2D molecules within limits on molecular weight and logP (default 400 and 4.0 respectively) and tanimoto (default 0.5).
* Results are in three separate files.
** a. molecules you can buy according to ZINC
** b. molecules you can make or have made in one, two or three steps from commercially available building blocks
** c. molecules that are intriguingly similar but will require more synthetic effort.

The output of this app can be used by the following other modules in Tools 18
* blaster, for docking.
* build 3d, to build docking libraries
* potentially covalent, depending on warhead
* cluster, to cluster the results
* dude, to generate decoys
* libanalysis, to get a detailed analysis of properties and targets
* report2d, to get a quick summary of physical and chemical properties

status: Not working yet.

== 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)

== Build3D ==
Works

== 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.

== DUDE-Z ==
Purpose: Assemble decoys for docking using the DUDEZ approach. See http://dudez.docking.org for sample data

This app requires:
* Ligands provided in smiles format (actives.smi)
* Current default parameters are shown in the following decoy_generation.in file:

PROTONATE YES

MWT 0 125

LOGP 0 3.6

RB 0 5

HBA 0 4

HBD 0 3

CHARGE 0 0

LIGAND TC RANGE 0.0 0.35

MINIMUM DECOYS PER LIGAND 20

DECOYS PER LIGAND 50

MAXIMUM TC BETWEEN DECOYS 0.8

TANIMOTO YES

See http://wiki.docking.org/index.php/Generating_decoys_(Reed%27s_way) for an explanation of what these parameters mean and how DUDE-Z works.

This app returns:
* List of decoys

Status: Nearly ready to use. Awaiting advice from Reed

== 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.

TLDR

2020-05-27T00:53:16Z

Jyoung:

UCSF Tools 2018 (tools18.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.

{{TOCright}}

== Analog ==
The purpose of the analog app is to find analogs of your active compounds that you can use to explore SAR by catalog around your hits.

This app requires:
* a starting molecule (one at a time for now)
* a tanimoto limit
* mwt and logP limits
* which bioisosteric replacements are acceptable (default all)

This app returns:
* 2D molecules within limits on molecular weight and logP (default 400 and 4.0 respectively) and tanimoto (default 0.5).
* Results are in three separate files.
** a. molecules you can buy according to ZINC
** b. molecules you can make or have made in one, two or three steps from commercially available building blocks
** c. molecules that are intriguingly similar but will require more synthetic effort.

The output of this app can be used by the following other modules in Tools 18
* blaster, for docking.
* build 3d, to build docking libraries
* potentially covalent, depending on warhead
* cluster, to cluster the results
* dude, to generate decoys
* libanalysis, to get a detailed analysis of properties and targets
* report2d, to get a quick summary of physical and chemical properties

status: Not working yet.

== 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)

== Build3D ==
Works

== 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.

== DUDE-Z ==
Purpose: Assemble decoys for docking using the DUDEZ approach. See http://dudez.docking.org for sample data

This app requires:
* Ligands provided in smiles format (actives.smi)
* Current default parameters are shown in the following decoy_generation.in file:

PROTONATE YES

MWT 0 125

LOGP 0 3.6

RB 0 5

HBA 0 4

HBD 0 3

CHARGE 0 0

LIGAND TC RANGE 0.0 0.35

MINIMUM DECOYS PER LIGAND 20

DECOYS PER LIGAND 50

MAXIMUM TC BETWEEN DECOYS 0.8

TANIMOTO YES

See http://wiki.docking.org/index.php/Generating_decoys_(Reed%27s_way) for an explanation of what these parameters mean and how DUDE-Z works.

This app returns:
* List of decoys

Status: Nearly ready to use. Awaiting advice from Reed

== 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.

ZINC22:Fine Tranching with RDKit using Heavy Atom Count and LogP

2020-04-17T22:29:36Z

Jyoung:

Written by Jennifer Young on April 14, 2020

=Introduction https://github.com/docking-org/ZINC21-Tools=
These scripts perform fine tranching with RDKit to compute the heavy atom count and logP for each molecule and put it in a bucket of the form HxxPyyy for positive valued logp (i.e. 0 < logp) and HxxMyyy for negative valued logp (i.e. logp < 0).

See github repo https://github.com/docking-org/ZINC21-Tools

=How to run=

==(If you are using our cluster) Source conda environment for RDKit==
If you are using our cluster, there is already a conda environment with RDKit available and you just need to source it using the following command. You need to use bash.
bash

source /mnt/nfs/home/devtest/anaconda3/bin/activate my-rdkit-env

==If you need to create a conda environment, follow the instructions at https://rdkit.org/docs/Install.html==
Read the section : How to install RDKit with Conda. Once you do
conda activate my-rdkit-env

conda install -c conda-forge tqdm

You are ready to run the Python script.

==Run Python script with the desired arguments==
The input smiles file should have the following 2 columns
*smiles
*ID

python rdkit_hlogp_batch_mp.py <smiles>

The output file will be a file with the name <smiles_file>_hlogp and will have the following 3 columns
* original smiles
* original ID
* HxxPyyy HxxMyyy

2020-01-22T22:07:35Z

Jyoung: /* Important: Create setenv.sh for environment variables */

2020-01-10T21:51:25Z

Jyoung:

How to Install SmartsEditor on CentOS6

2020-01-10T21:50:56Z

Jyoung:

==Step 1: Register==
See link here https://www.zbh.uni-hamburg.de/forschung/amd/software/smartseditor.html which says

SMARTSeditor is part of the AMD tools software bundle. To download SMARTSeditor, register at https://software.zbh.uni-hamburg.de with your UCSF email

==Step 2: Download RedHat 64 Bit Zip and extract==
They will email you with a link to log in and download Smarts Editor. Download the RedHat 64 Bit Zip from the website. Important! Don't download the linux64 which is for Ubuntu.

tar xvzf SmartsEditor_2.2.0_CentOS-6.10-64bit.tar.gz

==Step 3: Run and enter license key==
Go into the directory after extracting and run SmartsEditor
cd SmartsEditor_2.2.0

./SmartsEditor

In your browser where you downloaded the file, also download the license key. Copy and paste the license key into the box. The SmartsEditor GUI should appear on your desktop after that.

How to Install SmartsEditor on CentOS6

2020-01-10T21:49:24Z

Jyoung:

See link here https://www.zbh.uni-hamburg.de/forschung/amd/software/smartseditor.html which says

SMARTSeditor is part of the AMD tools software bundle. To download SMARTSeditor, register at https://software.zbh.uni-hamburg.de with your UCSF email

They will email you with a link to log in and download Smarts Editor. Download the RedHat 64 Bit Zip from the website.

tar xvzf SmartsEditor_2.2.0_CentOS-6.10-64bit.tar.gz

Go into the directory after extracting and run SmartsEditor
cd SmartsEditor_2.2.0

./SmartsEditor

In your browser where you downloaded the file, also download the license key. Copy and paste the license key into the box. The SmartsEditor GUI should appear on your desktop after that.

How to Install SmartsEditor on CentOS6

2020-01-10T21:47:31Z

Jyoung: Created page with "Register at https://software.zbh.uni-hamburg.de with your UCSF email They will email you with a link to log in and download Smarts Editor. Download the RedHat 64 Bit Zip from..."

Register at https://software.zbh.uni-hamburg.de with your UCSF email

They will email you with a link to log in and download Smarts Editor. Download the RedHat 64 Bit Zip from the website.

tar xvzf SmartsEditor_2.2.0_CentOS-6.10-64bit.tar.gz

Go into the directory after extracting and run SmartsEditor
cd SmartsEditor_2.2.0

./SmartsEditor

In your browser where you downloaded the file, also download the license key. Copy and paste the license key into the box. The SmartsEditor GUI should appear on your desktop after that.

Creating Maps on SmallWorld

2020-01-09T00:11:27Z

Jyoung:

Written by Jennifer Young on April 10, 2019. Last modified on July 12, 2019

==Install: The developer need only do this once. For the user, skip to the Run section==

===Step 1: Create the /sw directory===
SmallWorld requires a /sw directory which contains /anon and /maps
The /sw directory is located on n-9-22 in
/srv/db4

This directory contains:

The /anon directory contains 12 TB of pre-computed subgraphs

The /maps directory contains text files computed by SmallWorld that map your molecules of choice to the corresponding nodes in the anonymous graph index

===Step 2: Find a location for the sw.jar file===

Copy the sw.jar file to a reasonable location such as
/opt/nextmove/sw.jar

==Run==
===Important! Currently, we only run SmallWorld map generation on n-9-22===
Whenever running operations that are rough on the disk, only one one major operation at a time. Also, use nice/renice and ionice to decrease the disruption to other lab members.

You can adjust the priority of a running process using the process ID. Look for the process ID like this
ps aux | grep <something to help you find your process>

Then use renice to change the priority
renice -n +19 -p <PID>
Note that +19 is the lowest priority possible. Consult the man page for more information.

You can also use ionice to limit the io usage
ionice -c 3 -p <PID>
Here the 3 represents idle. Consult the man page for other options such as -c 2 which has different priority levels for best-effort scheduling

==Step 1: Set SWDIR environment variable==
Determine where the /sw directory with the /anon and /maps directory and if using csh, set the SWDIR variable using
setenv SWDIR /srv/db4

If using bash, set the SWDIR variable using
export SWDIR=/srv/db4

==Step 2: Generate the map files for SMILES files LESS THAN 1 Billion==
For files larger than 1 Billion smiles, see the section for Processing Large Smiles Files in SmallWorld

Run sw.jar to convert your smiles file into a map file.

(Optional: use the time command to see how long this takes)

(Optional: tee your results into a log file to check progress)

Here is an example where wait-ok.smi is your .smi file to map:
(time java -jar /opt/nextmove/sw.jar map /mnt/nfs/ex9/work/smallworld/wait-ok.smi
-T /mnt/nfs/ex9/work/smallworld/scratch_sw
-o /mnt/nfs/ex9/work/smallworld/wait-ok.anon.map
-u /mnt/nfs/ex9/work/smallworld/wait-ok.anon.unmapped)
|& tee /mnt/nfs/ex9/work/smallworld/wait-ok_log

This is a long command, so we can break down the different parts.

map The SMILES file you want to map follows the word "map"

-T This is the temp directory you want to write temp files to, rather than writing to /tmp

-o The final name of your output map file

-u Argument to keep track of the unmapped compounds.

Important: The unmapped compounds file may be used to generate extensions and is the same as the .anon.ext.map file mentioned in the SmallWorld documentation

For now, generate the map files in the
/mnt/nfs/ex9/work/smallworld

directory so they can be easily moved to the maps directory when the server is restarted

The sorting is done automatically when you generate the SmallWorld maps in a single step like this.

==Step 2: Processing large SMILES files in SmallWorld GREATER THAN 1 Billion==
If your SMILES file contains more than 1 billion molecules, I think it is better to split the input in to chunks of 1 billion to avoid waiting too long to get intermediate results in case the job fails for some reason.

===Step 1: Split the input file into chunks of 1 billion smiles===
split -l 1000000000 <your-smiles-file>

===Step 2: Process the chunks in SmallWorld using the command above ===
Write a helper script to process these using a loop, usually one or two at a time to be mindful of disk overload. An example is shown below. Just modify the path and pattern to match your files.
#!/bin/csh
foreach j(/mnt/nfs/ex9/work/smallworld/REAL_SPACE_400_to_500/x??)
echo $j
echo '(time java -jar /opt/nextmove/sw.jar map' $j '-T /mnt/nfs/ex9/work/smallworld/scratch_sw -o '${j}'.anon.map -u '${j}'.anon.unmapped) |& tee '${j}'_log'
(time java -jar /opt/nextmove/sw.jar map $j -T /mnt/nfs/ex9/work/smallworld/scratch_sw -o ${j}.anon.map -u ${j}.anon.unmapped) |& tee ${j}_log
end

Important: Make sure that the file you want to process only contains two columns. The first column contains the SMILES and the second column contains the ID.
If this is not the case, you need to use
awk '{print $1"\t"$2}' <your file> > <your_file_smi_ID>
to get only these columns before processing with SmallWorld.

===Step 3-4 Combined: Rather than concatenating and sorting, merge the map file chunks (assuming they are already sorted)===
Use the -T option on sort to set the temp directory of your choice. If your file is large enough, the sort command needs scratch space to write temporary files to later merge.

Adjust the matching in the loop rather than just using *.anon.map if you want to be more specific about the files you are combining

#!/bin/bash
for j in *anon.map
do
ls $j
LC_ALL=C sort -T /nfs/db5/jyoung -m -u $j <combined_map_name> -o <combined_map_name>
done

As suggested in the SmallWorld documentation, you can check if the resulting file is sorted using the sort -c option
#!/bin/bash
for j in <combined_map_name>
do
ls $j
LC_ALL=C sort -T /nfs/db5/jyoung -c -u $j
done

===Step 3: Copy to SSD and Concatenate===
It is much faster and avoids overloading the disk if you concatenate the results on an SSD rather than a regular hard drive. I have been using /nfs/db5/jyoung as a place to concatenate the files. You can use another helper script to perform that concatenation one file at a time.

#!/bin/csh
foreach j(*.anon.map)
ls $j
cat $j >> enamine_private_400_to_500_all
end

===Step 4: Sort the resulting map file using bash with locale LC_ALL=C ===
It is very important to sort using bash using the locale LC_ALL=C!

#!/bin/bash
for j in enamine_private_400_to_500_all.anon.map
do
ls $j
(time LC_ALL=C sort -T /nfs/db5/jyoung $j -o sorted_${j}) |& tee sort_time_${j}
done

===Step 5: Copy the completed file back to /ex9 ===
cp <your map file> /nfs/ex9/work/smallworld

===Step 6: Move the file to the final location===
Move the map file into either the maps/ directory or the private_small_world_maps directory depending on whether file should be public or private
mv <your map file> maps/
mv <your map file> private_smallworld_maps/

==Step 2.5 Incremental Updates==

There are several ways to perform incremental updates for SmallWorld maps which are equivalent.

If you just have a new SMILES file input.smi you wish to add to an already existing map named <already_existing>.anon.map, then you can use the sw map command with the --append option provided in the SmallWorld Java Command Line Interface (CLI)

First, if you have not already done so, set an alias "sw" to the SmallWorld Java file as shown below:
Make sure the SWDIR environment variable is also set

setenv SWDIR /srv/db4

alias sw 'java -jar /opt/nextmove/sw.jar'

Now you can run the sw map command using --append

sw map input.smi --append --o <already_existing>.anon.map

Another method for performing incremental updates is discussed below.
A worked example is located in the SmallWorld version 4 documentation on pages 17-18 in the Incremental Updates Section

===What if you already created a .anon.map file from your new smiles, and simply want to combine the two separate .anon.map files into a single .anon.map file?===

Make a copy and modify the bash script below with the name of your new map file

/nfs/ex9/work/smallworld/bash_merge_maps
This script simply combines two map files that have already been created

Replace the OLD_MAPFILE environment variable with the old map

Replace the ADD_MAPFILE environment variable with the map you wish to incrementally add

Replace the NEW_MAPFILE environment variable with the name you want for the new combined map

Updating a new map file in this way does not automatically update the .anon.map.cfg file with the new total number of molecules mapped and other statistics.
The create_cfg.py program will automatically generate a new .anon.map.cfg file for the combined map

The create_cfg.py program is located in

/mnt/nfs/ex9/work/smallworld/create_cfg.py

The create_cfg.py script will automatically generate a cfg file for a map that is composed of two existing SmallWorld Maps. Run as follows:
python create_cfg.py first second combined

Note:
first is first.anon.map
second is second.anon.map
combined is combined.anon.map

The program will look for the .anon.map files and the .anon.map.cfg for the first and second before proceeding

The new_cfg.py program is located in

python /mnt/nfs/ex9/work/smallworld/new_cfg.py <combined cfg file name>

This Python program will find all the cfg folders in a directory and combine them into a single combined cfg file

==Step 3: How to Make the New Database Available. Stop the server first!==

First, stop the server. You do not need to restart Tomcat every time you want to restart SmallWorld. The TomCat GUI is available at
http://10.20.9.22:8080/
You need the tunnel to access the private network or this link will not work! Also, the admin username and password is required.

In the Manager App, in the Applications section, use the Stop and Start buttons for the sw-ws app to restart the SmallWorld server

==Step 4: Move the Map File into the /maps directory==

If you followed the example above, your .anon.map file should be located in
/mnt/nfs/ex9/work/smallworld

Now, simply move the map file into the "/sw/maps" directory so it can be recognized by SmallWorld.

mv <your-file-name>.anon.map /mnt/nfs/ex9/work/smallworld/maps

Or, simply
mv <your-file-name>.anon.map maps

==Step 5: Restart the Server==
Again, go to the TomCat manager under applications and click Start once you are finished moving around the map files.

[[Category: SmallWorld]]
[[Category: NextMove]]

Creating Maps on SmallWorld

2020-01-09T00:11:05Z

Jyoung:

How to use Arthor API

2020-01-08T23:42:32Z

Jyoung:

=Introduction=

This information was taken from the Arthor version 2.1.2 documentation. RESTful API: The current server implementation utilizes the Data Tables JS library to display hits. The current API therefore reflects some requirements of this library and all URLs are organised under the /dt/ (for data tables) path, in future there may be new URLs introduced to match other clients (e.g. /jchem/).

==Data Tables==

===/dt/data===
List all available databases and the types of search available, note a “SUB” in idxTypes means both “SUB” and “SMA” search can be performed:

Example command:
curl 'http://arthor.docking.org/dt/data'

Produces the following JSON:
[
{"displayName":"wait-ok.smi","location":"/usr/local/tomcat/arthor_data/wait-ok.smi","urlFormatStr":null,"idxTypes":["SUB"]},
{"displayName":"for-sale.smi","location":"/usr/local/tomcat/arthor_data/for-sale.smi","urlFormatStr":null,"idxTypes":["SUB"]},
{"displayName":"now_bb.smi","location":"/usr/local/tomcat/arthor_data/now_bb.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},
{"displayName":"wait-ok_bb.smi","location":"/usr/local/tomcat/arthor_data/wait-ok_bb.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},
{"displayName":"for-sale_bb.smi","location":"/usr/local/tomcat/arthor_data/for-sale_bb.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},
{"displayName":"in-stock.smi","location":"/usr/local/tomcat/arthor_data/in-stock.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},
{"displayName":"bb-all.smi","location":"/usr/local/tomcat/arthor_data/bb-all.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},
{"displayName":"bb-now.smi","location":"/usr/local/tomcat/arthor_data/bb-now.smi","urlFormatStr":null,"idxTypes": ["SIM","SUB"]},
{"displayName":"interesting.smi","location":"/usr/local/tomcat/arthor_data/interesting.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},
{"displayName":"on-demand.smi","location":"/usr/local/tomcat/arthor_data/on-demand.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]},
{"displayName":"wuxi.smi","location":"/usr/local/tomcat/arthor_data/wuxi.smi","urlFormatStr":null,"idxTypes":["SIM","SUB"]}
]

===/dt/${db_name}/data===
Access information on a single database, the virtual memory status is also reported for Similarity and Substructure indexes:

===/dt/${db_name}/search/===
Search a database with a query SMILES/SMARTS.

${db_name} Required path variable, the database name is specified in the URL path as ${db_name}. For one of the databases above, ‘ChEMBL 23’ would be searched as /dt/ ChEMBL%2023/search.
query=<string> The query to run either a valid SMILES or SMARTS, depending on search type.
type=SUB|SIM|SMA The search type to perform (SUB=Substructure, SMA=SMARTS, SIM=Similarity), these primarily differ by what input is expected in the query= string. Both “SUB” and “SIM” expect a valid SMILES to be provided, “SMA” expects a SMARTS.
The SMILES provided to “SUB” is aromatized to be consistent with the database (if flag provided) and converted to a query with any flags specified.
This parameter is optional, the default is “SIM”.

start=<num> Optional start offset for the result set to allow paging. The default value is 0 mean- ing the result start at the first hit.
length=<num> Optional length of the result set to allow paging. The default is 10.
draw=<num> Echoed value to maintain consistent ordering of asynchronous events. A number is provided to this parameter that is returned with the result set.
If when the response is received by the client the draw value doesn’t match the current draw value the result can be considered “out of date” and should be ignored.
This value is client specific and optional.
qopts=<opts> Specify the query options to run the Substructure or SMARTS search with. For example “qopts=RC” would lock the rings and chains of the query. See Arthor::ParseQuery for more info.
If your query is an MDL file then you must specify “Mdl” in the qopts.

//matches server side constants
let QueryFlags = {
AROMATISE: 0x0100,
LOCK_RINGS: 0x0200,
LOCK_CHAINS: 0x0400,
LOCK_CHARGES: 0x0800
LOCK_ISOTOPES: 0x1000,
LOCK_CONNECTIVITY 0x2000
};

//matches UI
let DEFAULT_FLAGS = QueryFlags.AROMATISE |
QueryFlags.LOCK_CHARGES |
QueryFlags.LOCK_ISOTOPES |
QueryFlags.LOCK_CONNECTIVITY;

To "lock" means don't allow it to change

Response: The search returns a JSON object containing the result set as a data property

==Similarity Search==

curl 'http://arthor.docking.org/dt/In-Stock-19Q4-13.8M/search?query=c1ccccc1&type=SIM&start=0&length=5'

{"query":"c1ccccc1","
data":[
[1,"c1ccccc1\tZINC000000967532","1.000"],
[2,"c1ccccccccccccccccc1\tZINC000100074375","1.000"],
[3,"c1ncncn1\tZINC000001718513","0.498"],
[4,"c1cncnc1\tZINC000000895216","0.427"],
[5,"Ic1cc(I)cc(I)c1\tZINC000057266212","0.373"]],
"draw":0,"recordsFiltered":1649789,"recordsTotal":1649789,"time":79,"hasMore":false,"error":null
}

==Substructure or SMARTS Search==
A substructure or SMARTS search has some additional complexity. A parameter hasMore indicates whether there are more results. When the first page for a query is requested a background counter is spun up to count the total number of hits. The idea is the server can be pooled until the count is finished.

curl 'http://arthor.docking.org/dt/In-Stock-19Q4-13.8M/search?query=c1ccccc1&type=SUB&start=0&length=5'

{"query":"c1:c:c:c:c:c:1","data":[
[1,"C[C@@]1(c2ccccc2)OC(C(=O)O)=CC1=O\tZINC000000000010",""],
[2,"COc1cc(Cc2cnc(N)nc2N)cc(OC)c1N(C)C\tZINC000000000011",""],
[3,"O=C(C[S@@](=O)C(c1ccccc1)c1ccccc1)NO\tZINC000000000012",""],
[4,"CCC[S@](=O)c1ccc2[nH]/c(=N\\C(=O)OC)[nH]c2c1\tZINC000000000017",""],
[5,"C=C(C)CNc1ccc([C@H](C)C(=O)O)cc1\tZINC000000000022",""]],
"draw":0,"recordsFiltered":1162074,"recordsTotal":1162074,"time":1090,"hasMore":false,"error":null
}

After some time the background count will have completed and the hasMore will now be false meaning the hit count is correct. The time taken to do the count is set on the time field.

[[Category:Arthor]]
[[Category:API]]
[[Category: NextMove]]

How to use SmallWorld API

2020-01-08T23:42:09Z

Jyoung:

=Introduction=

The Web Services API for SmallWorld Documentation is found in Section 8.3 of the SmallWorld version 4.0 manual starting from page 30 to 36.
Copyright ©2012-2017 NextMove Software Limited.
I copied the section here, and provided a list of publicly available databases for searching on sw.docking.org and some simple examples.

==8.3 Web Services API Important Entry Points==
Unless stated otherwise all API entry points operate on HTTP GET/POST requests. A search on the server is first submitted (/search/submit), this returns a stream of events that report the hit list id (hlid). You can then use this hlid to fetch results either as JSON (/search/view) or TSV (/ search/export). An example Java client, SwHttpClient.java, shows how this works.

===/search/submit===

Start a new SmallWorld search with topological distance bounded by the provided upper bounds.

{| class="wikitable"
|-
! Parameter
! Type
! Description
|-
| smi
| text
| Query SMILES
|-
| db
| text
| Reference database (see List of available maps)
|-
| dist
| int
| Topological distance upper bound (default: 10)
|-
| tdn
| int
| Topological terminal down distance upper bound (default: 10)
|-
| tup
| int
| Topological terminal up distance upper bound (default: 10)
|-
| rdn
| int
| Topological ring down distance upper bound (default: 10)
|-
| rup
| int
| Topological ring up distance upper bound (default: 10)
|-
| ldn
| int
| Topological linker down distance upper bound (default: 10)
|-
| lup
| int
| Topological linker up distance upper bound (default: 10)
|-
| scores
| text
| List of scoring functions (default : none) - see /search/config
|}

===Example Request===
Suppose you want to search for c1ccccc1 in the ZINC-Interesting-297K Database: There are two steps. The first step which involves /search/submit returns a stream of events that report the hit list id or hlid. This hlid is required to fetch results using the other options such as /search/view

*Change the smi to the SMILES for the molecule you want to query
*Change the db name to the database name from the List of Publicly Available Maps below
Everything else can stay the same

curl 'http://sw.docking.org//search/submit?smi=c1ccccc1&db=ZINC-Interesting-297K&dist=4&tdn=4&tup=4&rdn=4&rup=4&ldn=4&lup=4&maj=4&min=4&sub=4&scores=Atom%20Alignment,ECFP4,Daylight'

The API streams back JSON chunks. Possible status messages are FIRST, MORE, END, and ‘Ground Control to Major Tom’ (hangup ping). Each status contains the hit list id (hlid) which can be used with the export and view API entry points.

From this example:

data:{"status":"FIRST","hlid":5908,"elap":"0.0 s","numEdges":0,"numNodes":0,"numWaveFront":1,"numEdgesPerSec":"NaN"}
data:{"status":"Ground Control to Major Tom","hlid":5908,"elap":"0.0 s","numEdges":0,"numNodes":0,"numWaveFront":0,"numEdgesPerSec":0.0}
data:{"status":"MORE","hlid":5908,"elap":"0.0 s","numEdges":1,"numNodes":2,"numWaveFront":3,"numEdgesPerSec":47.783445425332395}
data:{"status":"MORE","hlid":5908,"elap":"0.0 s","numEdges":7,"numNodes":8,"numWaveFront":14,"numEdgesPerSec":237.99311152737997}
data:{"status":"MORE","hlid":5908,"elap":"0.1 s","numEdges":47,"numNodes":42,"numWaveFront":51,"numEdgesPerSec":583.5923096639136}
data:{"status":"MORE","hlid":5908,"elap":"0.4 s","numEdges":363,"numNodes":216,"numWaveFront":221,"numEdgesPerSec":884.1124840482239}
data:{"status":"Ground Control to Major Tom","hlid":5908,"elap":"0.5 s","numEdges":363,"numNodes":216,"numWaveFront":221,"numEdgesPerSec":700.4466134439543}
data:{"status":"Ground Control to Major Tom","hlid":5908,"elap":"1.0 s","numEdges":441,"numNodes":253,"numWaveFront":224,"numEdgesPerSec":426.04845162109694}
data:{"status":"Ground Control to Major Tom","hlid":5908,"elap":"1.6 s","numEdges":441,"numNodes":253,"numWaveFront":224,"numEdgesPerSec":284.05782226150757}
data:{"status":"Ground Control to Major Tom","hlid":5908,"elap":"2.1 s","numEdges":458,"numNodes":263,"numWaveFront":278,"numEdgesPerSec":223.1371219908375}
data:{"status":"END","hlid":5908,"elap":"2.2 s","numEdges":2417,"numNodes":981,"numWaveFront":885,"numEdgesPerSec":1104.50351038177}

Here the hlid for my request was 5908.

===/search/export===
Export a hit list (given by the id) to a tab-separated value table. The other parameters describe what columns, order, and filters are applied to the hit list. Like /search/view it uses the JQuery DataTables server-side processing parameters - https://www.datatables.net/manual/server-side.

Useful information about column names and values:
'hlid': hlid,

'columns[0][data]': 0,
'columns[0][name]': 'alignment',
'columns[0][searchable]': 'true',
'columns[0][orderable]': 'false',
'columns[0][search][value]': '',
'columns[0][search][regex]': 'false',

'columns[1][data]': 1,
'columns[1][name]': 'dist',
'columns[1][searchable]': 'true',
'columns[1][orderable]': 'true',
'columns[1][search][value]': '0 - 10',
'columns[1][search][regex]': 'false',

'columns[2][data]': 2,
'columns[2][name]': 'ecfp4',
'columns[2][searchable]': 'true',
'columns[2][orderable]': 'true',
'columns[2][search][value]': '',
'columns[2][search][regex]': 'false',

'columns[3][data]': 3,
'columns[3][name]': 'daylight',
'columns[3][searchable]': 'true',
'columns[3][orderable]': 'true',
'columns[3][search][value]': '',
'columns[3][search][regex]': 'false',

'columns[4][data]': 4,
'columns[4][name]': 'topodist',
'columns[4][searchable]': 'true',
'columns[4][orderable]': 'true',
'columns[4][search][value]': '0 - 10',
'columns[4][search][regex]': 'false',

'columns[5][data]': 5,
'columns[5][name]': 'mces',
'columns[5][searchable]': 'true',
'columns[5][orderable]': 'true',
'columns[5][search][value]': '',
'columns[5][search][regex]': 'false',

'columns[6][data]': 6,
'columns[6][name]': 'tdn',
'columns[6][searchable]': 'true',
'columns[6][orderable]': 'true',
'columns[6][search][value]': '0 - 0',
'columns[6][search][regex]': 'false',

'columns[7][data]': 7,
'columns[7][name]': 'tup',
'columns[7][searchable]': 'true',
'columns[7][orderable]': 'true',
'columns[7][search][value]': '0 - 10',
'columns[7][search][regex]': 'false',

'columns[8][data]': 8,
'columns[8][name]': 'rdn',
'columns[8][searchable]': 'true',
'columns[8][orderable]': 'true',
'columns[8][search][value]': '0 - 0',
'columns[8][search][regex]': 'false',

'columns[9][data]': 9,
'columns[9][name]': 'rup',
'columns[9][searchable]': 'true',
'columns[9][orderable]': 'true',
'columns[9][search][value]': '0 - 10',
'columns[9][search][regex]': 'false',

'columns[10][data]': 10,
'columns[10][name]': 'ldn',
'columns[10][searchable]': 'true',
'columns[10][orderable]':

=Important! Once you run the /search/submit the most important value is the hlid=

The columns in the resulting tab separated file are alignment dist ecfp4 daylight topodist mces tdn tup rdn rup ldn lup mut maj min hyb sub
The results are sorted in starting with the highest ECFP4
===Example Request===
*Here you only need to change the hlid!

curl 'http://sw.docking.org//search/export/?hlid=5908&draw=8&columns%5B0%5D%5Bdata%5D=0&columns%5B0%5D%5Bname%5D=alignment&columns%5B0%5D%5Bsearchable%5D=true&columns%5B0%5D%5Borderable%5D=false&columns%5B0%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B0%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B1%5D%5Bdata%5D=1&columns%5B1%5D%5Bname%5D=dist&columns%5B1%5D%5Bsearchable%5D=true&columns%5B1%5D%5Borderable%5D=true&columns%5B1%5D%5Bsearch%5D%5Bvalue%5D=0-10&columns%5B1%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B2%5D%5Bdata%5D=2&columns%5B2%5D%5Bname%5D=ecfp4&columns%5B2%5D%5Bsearchable%5D=true&columns%5B2%5D%5Borderable%5D=true&columns%5B2%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B2%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B3%5D%5Bdata%5D=3&columns%5B3%5D%5Bname%5D=daylight&columns%5B3%5D%5Bsearchable%5D=true&columns%5B3%5D%5Borderable%5D=true&columns%5B3%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B3%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B4%5D%5Bdata%5D=4&columns%5B4%5D%5Bname%5D=topodist&columns%5B4%5D%5Bsearchable%5D=true&columns%5B4%5D%5Borderable%5D=true&columns%5B4%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B4%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B5%5D%5Bdata%5D=5&columns%5B5%5D%5Bname%5D=mces&columns%5B5%5D%5Bsearchable%5D=true&columns%5B5%5D%5Borderable%5D=true&columns%5B5%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B5%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B6%5D%5Bdata%5D=6&columns%5B6%5D%5Bname%5D=tdn&columns%5B6%5D%5Bsearchable%5D=true&columns%5B6%5D%5Borderable%5D=true&columns%5B6%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B6%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B7%5D%5Bdata%5D=7&columns%5B7%5D%5Bname%5D=tup&columns%5B7%5D%5Bsearchable%5D=true&columns%5B7%5D%5Borderable%5D=true&columns%5B7%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B7%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B8%5D%5Bdata%5D=8&columns%5B8%5D%5Bname%5D=rdn&columns%5B8%5D%5Bsearchable%5D=true&columns%5B8%5D%5Borderable%5D=true&columns%5B8%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B8%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B9%5D%5Bdata%5D=9&columns%5B9%5D%5Bname%5D=rup&columns%5B9%5D%5Bsearchable%5D=true&columns%5B9%5D%5Borderable%5D=true&columns%5B9%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B9%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B10%5D%5Bdata%5D=10&columns%5B10%5D%5Bname%5D=ldn&columns%5B10%5D%5Bsearchable%5D=true&columns%5B10%5D%5Borderable%5D=true&columns%5B10%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B10%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B11%5D%5Bdata%5D=11&columns%5B11%5D%5Bname%5D=lup&columns%5B11%5D%5Bsearchable%5D=true&columns%5B11%5D%5Borderable%5D=true&columns%5B11%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B11%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B12%5D%5Bdata%5D=12&columns%5B12%5D%5Bname%5D=mut&columns%5B12%5D%5Bsearchable%5D=true&columns%5B12%5D%5Borderable%5D=true&columns%5B12%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B12%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B13%5D%5Bdata%5D=13&columns%5B13%5D%5Bname%5D=maj&columns%5B13%5D%5Bsearchable%5D=true&columns%5B13%5D%5Borderable%5D=true&columns%5B13%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B13%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B14%5D%5Bdata%5D=14&columns%5B14%5D%5Bname%5D=min&columns%5B14%5D%5Bsearchable%5D=true&columns%5B14%5D%5Borderable%5D=true&columns%5B14%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B14%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B15%5D%5Bdata%5D=15&columns%5B15%5D%5Bname%5D=hyb&columns%5B15%5D%5Bsearchable%5D=true&columns%5B15%5D%5Borderable%5D=true&columns%5B15%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B15%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B16%5D%5Bdata%5D=16&columns%5B16%5D%5Bname%5D=sub&columns%5B16%5D%5Bsearchable%5D=true&columns%5B16%5D%5Borderable%5D=true&columns%5B16%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B16%5D%5Bsearch%5D%5Bregex%5D=false&order%5B0%5D%5Bcolumn%5D=0&order%5B0%5D%5Bdir%5D=asc&start=0&length=18&search%5Bvalue%5D=&search%5Bregex%5D=false&_=1561063193443'

==List of Publicly Available Maps==
* ZINC-Interesting-297K
* BB-Stock-1.5M
* In-Stock-13.9M
* ZINC-All-For-Sale-1.2B
*ZINC-All-1.2B
*BB-all-for-sale-18M
*ZINC-On-Demand-1B
*GDB13-977M
*Wait-OK-1B
*WuXi-58.6M

==The SmallWorld API provides the following additional entry points:==

===/search/view===
Provides data in JSON format.

*Here again you only need to change the hlid

curl 'http://sw.docking.org//search/view/?hlid=5908&draw=8&columns%5B0%5D%5Bdata%5D=0&columns%5B0%5D%5Bname%5D=alignment&columns%5B0%5D%5Bsearchable%5D=true&columns%5B0%5D%5Borderable%5D=false&columns%5B0%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B0%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B1%5D%5Bdata%5D=1&columns%5B1%5D%5Bname%5D=dist&columns%5B1%5D%5Bsearchable%5D=true&columns%5B1%5D%5Borderable%5D=true&columns%5B1%5D%5Bsearch%5D%5Bvalue%5D=0-10&columns%5B1%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B2%5D%5Bdata%5D=2&columns%5B2%5D%5Bname%5D=ecfp4&columns%5B2%5D%5Bsearchable%5D=true&columns%5B2%5D%5Borderable%5D=true&columns%5B2%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B2%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B3%5D%5Bdata%5D=3&columns%5B3%5D%5Bname%5D=daylight&columns%5B3%5D%5Bsearchable%5D=true&columns%5B3%5D%5Borderable%5D=true&columns%5B3%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B3%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B4%5D%5Bdata%5D=4&columns%5B4%5D%5Bname%5D=topodist&columns%5B4%5D%5Bsearchable%5D=true&columns%5B4%5D%5Borderable%5D=true&columns%5B4%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B4%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B5%5D%5Bdata%5D=5&columns%5B5%5D%5Bname%5D=mces&columns%5B5%5D%5Bsearchable%5D=true&columns%5B5%5D%5Borderable%5D=true&columns%5B5%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B5%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B6%5D%5Bdata%5D=6&columns%5B6%5D%5Bname%5D=tdn&columns%5B6%5D%5Bsearchable%5D=true&columns%5B6%5D%5Borderable%5D=true&columns%5B6%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B6%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B7%5D%5Bdata%5D=7&columns%5B7%5D%5Bname%5D=tup&columns%5B7%5D%5Bsearchable%5D=true&columns%5B7%5D%5Borderable%5D=true&columns%5B7%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B7%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B8%5D%5Bdata%5D=8&columns%5B8%5D%5Bname%5D=rdn&columns%5B8%5D%5Bsearchable%5D=true&columns%5B8%5D%5Borderable%5D=true&columns%5B8%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B8%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B9%5D%5Bdata%5D=9&columns%5B9%5D%5Bname%5D=rup&columns%5B9%5D%5Bsearchable%5D=true&columns%5B9%5D%5Borderable%5D=true&columns%5B9%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B9%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B10%5D%5Bdata%5D=10&columns%5B10%5D%5Bname%5D=ldn&columns%5B10%5D%5Bsearchable%5D=true&columns%5B10%5D%5Borderable%5D=true&columns%5B10%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B10%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B11%5D%5Bdata%5D=11&columns%5B11%5D%5Bname%5D=lup&columns%5B11%5D%5Bsearchable%5D=true&columns%5B11%5D%5Borderable%5D=true&columns%5B11%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B11%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B12%5D%5Bdata%5D=12&columns%5B12%5D%5Bname%5D=mut&columns%5B12%5D%5Bsearchable%5D=true&columns%5B12%5D%5Borderable%5D=true&columns%5B12%5D%5Bsearch%5D%5Bvalue%5D=&columns%5B12%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B13%5D%5Bdata%5D=13&columns%5B13%5D%5Bname%5D=maj&columns%5B13%5D%5Bsearchable%5D=true&columns%5B13%5D%5Borderable%5D=true&columns%5B13%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B13%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B14%5D%5Bdata%5D=14&columns%5B14%5D%5Bname%5D=min&columns%5B14%5D%5Bsearchable%5D=true&columns%5B14%5D%5Borderable%5D=true&columns%5B14%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B14%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B15%5D%5Bdata%5D=15&columns%5B15%5D%5Bname%5D=hyb&columns%5B15%5D%5Bsearchable%5D=true&columns%5B15%5D%5Borderable%5D=true&columns%5B15%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B15%5D%5Bsearch%5D%5Bregex%5D=false&columns%5B16%5D%5Bdata%5D=16&columns%5B16%5D%5Bname%5D=sub&columns%5B16%5D%5Bsearchable%5D=true&columns%5B16%5D%5Borderable%5D=true&columns%5B16%5D%5Bsearch%5D%5Bvalue%5D=0-4&columns%5B16%5D%5Bsearch%5D%5Bregex%5D=false&order%5B0%5D%5Bcolumn%5D=0&order%5B0%5D%5Bdir%5D=asc&start=0&length=18&search%5Bvalue%5D=&search%5Bregex%5D=false&_=1561063193443'

===/search/maps===
Lists all available dataset mapfiles. The response is a JSON detailing the map name, id prefix, resolve url

Example Request:
curl 'http://sw.docking.org/search/maps'

===/search/config===
Retrieves the public server configuration as JSON including the list of available score functions. The names of the scoring functions can be provided as a parameter to the /search/submit endpoint.
Example Request:
curl 'http://sw.docking.org/search/config'

[[Category: API]]
[[Category: SmallWorld]]
[[Category: NextMove]]