Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

https://github.com/PatWalters/rd_filters

A script to run structural alerts using the RDKit and ChEMBL
https://github.com/PatWalters/rd_filters

Last synced: about 1 month ago
JSON representation

A script to run structural alerts using the RDKit and ChEMBL

Lists

README 

        
# rd_filters



This script provides a simple means of applying the 

functional group filters from the ChEMBL database, as well as a number of 

property  filters from the RDKit, to a set 

of compounds.  As of ChEMBL 23,  the database table **structural_alerts**

contains 8 sets of alerts.  ChEMBL doesn't apper to have much in the way of 

documentation on the different alert sets. 



|Rule Set |Number of Alerts|

|---|---:|

|BMS|	180|

|Dundee|	105|

|Glaxo|	55|

|Inpharmatica|	91|

|LINT|	57|

|MLSMR|	116|

|[PAINS](https://pubs.acs.org/doi/abs/10.1021/jm901137j)|	479|

|SureChEMBL|	166|



The SMARTS patterns in a number of these alerts were not compatible with the RDKit

so I edited them.  A complete list of the changes I made is in the file **Notes.txt**. 



## Prerequisite



* At least Python 3.6

* The RDKit, you can find installation instructions [here](https://www.rdkit.org/docs/Install.html).  I'd recommend the conda route.



## Installation



### Directly install from github



`pip install git+https://github.com/PatWalters/rd_filters.git`



### Local install



``` shell

git clone https://github.com/PatWalters/rd_filters

cd rd_filters

pip install .

```



## Usage



The script needs 2 files to operate.



* alert_collection.csv - the set of structural alerts

* rules.json - the configuration file



The script uses the following logic to find alert_collection.csv and rules.json.



1. Use locations specified by the "--alert" (for alerts.csv) and "--rules" (for rules.json) command line arguments.

2. Look in the current directory.

3. Look in the directory pointed to by the FILTER_RULES_DATA environment variable.



I'll provide some examples below to illustrate.  



That's it, at this point you should be good to go. 



### Configuration files



The file **alert_collection.csv** contains alerts.  You shouldn't have to mess with this unless you

want to add your own structural alerts. I think the format is pretty obvious.



The file **rules.json** controls which filters and alerts are used.  You can use the command

below to generate a **rules.json** with the default settings. 



`rd_filters template --out rules.json`



The **rules.json** file looks like this. The values for the properties are the maximum and minimum 

allowed (inclusive).  To set which structural alerts are used, set **true** and **false**. You can 

use multiple alert sets. 

Just edit the file with your [favorite text editor](https://www.gnu.org/software/emacs/).



```javascript

{

    "HBA": [

        0,

        10

    ],

    "HBD": [

        0,

        5

    ],

    "LogP": [

        -5,

        5

    ],

    "MW": [

        0,

        500

    ],

    "Rule_BMS": false,

    "Rule_Dundee": false,

    "Rule_Glaxo": false,

    "Rule_Inpharmatica": true,

    "Rule_LINT": false,

    "Rule_MLSMR": false,

    "Rule_PAINS": false,

    "Rule_SureChEMBL": false,

    "TPSA": [

        0,

        200

    ]

}

```



#### Examples



First off, you're going to want to copy **alert_collection.csv** and 

**rules.json** to a directory and set the FILTER_RULES_DATA environment

variable to point to that directory.  If you are using a bash-ish shell

and the files are in /home/elvis/data that would be:



`export FILTER_RULES_DATA=/home/elvis/data`



If you type



`rd_filters -h`



you'll see this:



``` shell

Usage:

rd_filters filter --in INPUT_FILE --prefix PREFIX [--rules RULES_FILE_NAME] [--alerts ALERT_FILE_NAME][--np NUM_CORES]

rd_filters template --out TEMPLATE_FILE [--rules RULES_FILE_NAME]



Options:

--in INPUT_FILE input file name

--prefix PREFIX prefix for output file names

--rules RULES_FILE_NAME name of the rules JSON file

--alerts ALERTS_FILE_NAME name of the structural alerts file

--np NUM_CORES the number of cpu cores to use (default is all)

--out TEMPLATE_FILE parameter template file name

"""

```



The basic operation is pretty simple. If I want to filter a file called test.smi and 

I want my output files to start with "out", I could do something like this:



`rd_filters filter --in test.smi --prefix out`



This will create 2 files

* **out.smi** - contains the SMILES strings and molecule names for all of the compounds

passing the filters

* **out.csv** - contains calculated property values and a listing alerts triggered

by a molecule



By default, this script runs in parallel and uses all available processors.  To

change this value, use the --np flag. 



`rd_filters filter --in test.smi --prefix out --np 4`



As mentioned above, alternate rules files or alerts files can be specified on

the command line.



``` shell

rd_filters filter --in test.smi --prefix out --rules myrules.json

rd_filters filter --in test.smi --prefix out --alerts myalerts.csv

rd_filters filter --in test.smi --prefix out --rules myrules.json --alerts myalerts.csv

```



A new default rules template file can be generated using the **template** option.



`rdfilters.py template --out myrules.json`



As always please let me know if you have questions, comments, etc. 



Pat Walters, August 2018