Getting Started JChem PostgreSQL Cartridge

{warning} This online page relates to the latest released JChem PostgreSQL Cartridge. Find the version specific documentation in your installed package in /opt/jchem-psql/doc/ directory.

This guide will serve as a basic introduction to installing and using JChem PostgreSQL Cartridge (JPC).

See also Installation and Administration and API Usage pages for detailed description of administration and API use cases.

System requirement

CentOS, RedHat, Debian or Ubuntu operating system x86_64 version.

Find information for cases of other linux systems

postgreSQL 9.4 relational database (preferred download page) for JPC versions up to 2.0
postgreSQL 9.5 relational database for JPC versions starting from 2.1

See help to upgrade of postgreSQL 9.4 to postgreSQL 9.5

postgreSQL 10 relational database for JPC versions starting from 3.0
postgreSQL 12 relational database for JPC versions starting from 5.0
availability of hstore extension of postgresql (e.g., contrib package)
Java8 runtime environment. We support AdoptOpenJDK 8 as well. In the case of AdoptOpenJDK libfontconfig package must be included.

Installation and Setup

Install PostgreSQL Cartridge

Download the latest version of PostgreSQL Cartridge from here. In order to install the latest version, change x.y (version information) in the following statement to the current one:

In CentOS:


sudo yum localinstall jchem-psql-x.y.x86_64.rpm

In RedHat or Debian:


sudo dpkg -i jchem-psql-x.y.x86_64.deb

Before the first use

Install your license file

Copy a valid ChemAxon license to /etc/chemaxon/license.cxl. Required license in the license file is 'Postgres Cartridge'. The jchem-psql user should have read access to the license file.
Initialize index directory
```
sudo service jchem-psql init
```
{primary} If you encounter a problem in your java installation, set your JAVA_HOME in the file /etc/default/jchem-psql.
First start
```
sudo service jchem-psql manual-start
```

Using the extension in a database

Create postgres user and database


sudo su postgres
createuser testuser
createdb testdb -O testuser

Install the extensions


psql testdb
testdb> CREATE EXTENSION chemaxon_type;
testdb> CREATE EXTENSION hstore;
testdb> CREATE EXTENSION chemaxon_framework;

Checking JChem-psql cartridge installation

If jchem-psql service is running, the following query can be executed without any problem:
```
testdb> SELECT 'C'::Molecule('sample') |<| 'CC'::Molecule;
```

Service

The service can be started/stopped using


sudo service jchem-psql manual-start
sudo service jchem-psql stop

By default, the service starts on system boot. This can be switched off by setting ENABLED=0 in the /etc/default/jchem-psql file.

BASIC API Usage

CREATE TABLE


CREATE TABLE table_name (structure_column_name MOLECULE('molecule_type_name'));

Example:


CREATE TABLE ttest (mol MOLECULE('sample'));

Import data

Import from sdf/mol file (located on your local machine):


 et variable_name `cat sdf_file_name`
CREATE TABLE table_name AS 
    SELECT molSrc::molecule('molecule_type_name') AS (structure_column_name)[, props ->'sdf_field_name' AS column_name] FROM parse_sdf(:'variable_name');

Example:


 et content `cat ~/a.sdf`
CREATE TABLE mysdftable AS 
    SELECT molSrc::molecule('sample') AS mol,
        props -> 'Molformula' AS formula 
    FROM parse_sdf(:'content');

Import from local smiles/cxsmiles/smarts/cxsmarts files:


\COPY table_name (structure_column_name) FROM 'file_name' (FORMAT csv);

Example:


\COPY ttest(mol) FROM '/home/posgresuser/targetfiles/nci-pubchem_1m_unique.smiles' (FORMAT csv);

CREATE INDEX

Indextype named chemindex has to be used when indexing a column that contains chemical structures.


CREATE INDEX index_name ON table_name USING chemindex(structure_column_name);

Example:


  CREATE INDEX ttest_idx ON ttest USING chemindex(mol);

SELECT

Substructure search


SELECT * FROM table_name WHERE 'query_structure' |<| structure_column_name;

Examples:


    SELECT * FROM ttest WHERE '<?xml version="1.0" encoding="windows-1250"?>
    <cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/help/formats/schema/mrvSchema_6_1_0.xsd" version="ChemAxon file format v6.1, generated by v6.1.3">
    <MDocument>
    <MChemicalStruct>
    <molecule molID="m1">
    <atomArray atomID="a1" elementType="C" x2="3.4100000858306885" y2="3.740000009536743"/>
    <bondArray/>
    </molecule>
    </MChemicalStruct>
    </MDocument>
    </cml>' |<| mol;
 
    SELECT * FROM ttest WHERE 'c1ccccc1' |<| mol;
 
    SELECT * FROM ttest WHERE '[#6]-[#6]' |<| mol;

Full fragment (exact fragment) search


SELECT * FROM table_name WHERE query_transform('query_structure', 'fullfragment') |<| structure_column_name;

Example:


SELECT * FROM ttest WHERE query_transform('CC', 'fullfragment') |<| mol;

Superstructure search


SELECT * FROM table_name WHERE 'query_structure' |>| structure_column_name;

Example:


SELECT * FROM ttest WHERE 'CCC' |>| mol;

Duplicate search


SELECT * FROM table_name WHERE 'query_structure' |=| structure_column_name;

Example:


SELECT * FROM ttest WHERE 'CCC' |=| mol;