Using Mychem

This chapter provides a short tutorial about the usage of Mychem. It will present you a simple way to create a chemical database with Mychem and how to use some functions. More details about each function used in this tutorial are available in the Command Reference.

The Database

A chemical database is composed of one or several tables. The examples presented in this chapter are using a set of four tables, with the following structure:

compounds - a table containing an unique id for each molecule and its name.

+---------+------------------+------+-----+---------------------+----------------+
| Field   | Type             | Null | Key | Default             | Extra          |
+---------+------------------+------+-----+---------------------+----------------+
| id      | int(11) unsigned | NO   | PRI | NULL                | auto_increment |
| name    | varchar(255)     | NO   | MUL | NULL                |                |
| created | timestamp        | NO   |     | 0000-00-00 00:00:00 |                |
+---------+------------------+------+-----+---------------------+----------------+

1D_structures - a table containing an unique reference to the compounds table and several types of 1D molecular descriptors (InChI code and SMILES).

+-------------+------------------+------+-----+---------+-------+
| Field       | Type             | Null | Key | Default | Extra |
+-------------+------------------+------+-----+---------+-------+
| compound_id | int(11) unsigned | NO   | PRI | NULL    |       |
| inchi       | text             | NO   |     | NULL    |       |
| smiles      | text             | NO   |     | NULL    |       |
+-------------+------------------+------+-----+---------+-------+

3D_structures - a table containing an unique reference to the compounds table and the 3D structure in MDL Molfile format.

+-------------+------------------+------+-----+---------+-------+
| Field       | Type             | Null | Key | Default | Extra |
+-------------+------------------+------+-----+---------+-------+
| compound_id | int(11) unsigned | NO   | PRI | NULL    |       |
| molfile     | text             | NO   |     | NULL    |       |
+-------------+------------------+------+-----+---------+-------+

bin_structures - a table containing an unique reference to the compounds table and several types of binary descriptors (fingerprints and serialized OBMol object).

+--------------+------------------+------+-----+---------+-------+
| Field        | Type             | Null | Key | Default | Extra |
+--------------+------------------+------+-----+---------+-------+
| compound_id  | int(11) unsigned | NO   | PRI | NULL    |       |
| fp2          | blob             | YES  |     | NULL    |       |
| obserialized | blob             | YES  |     | NULL    |       |
+--------------+------------------+------+-----+---------+-------+

Such tables can be easily created and populated using mychemdb_manager, a Python script released with Mychem. It can be found in the scripts directory. Its usage is detailed in the Chemical Database Manager chapter.

Examples

Once the database and the tables are created, you can use many chemical functions. Here is a (very) short overview of the possibilities. The dataset used for this example can be freely obtained from the Chemical Structures Project.

Calculate the Molecular Weight

The computation of the molecular weight of a molecule is performed by the MOLWEIGHT function. In the following example, the molecular weight of the amino acid glycine is calculated.

mysql> SELECT MOLWEIGHT(`3D_structures`.`molfile`)
    -> FROM `compounds`,`3D_structures`
    -> WHERE `compounds`.`name`='glycine'
    -> AND `compounds`.`id`=`3D_structures`.`compound_id`;
        -> 75.066600

Search a Substructure

The MATCH_SUBSTRUCTURE function permits to find a substructure and belong to the Molmatch Commands function group. In this example, we are looking for compounds containing a phenol group:

mysql> SELECT `compounds`.`name`
    -> FROM `compounds`,`bin_structures`
    -> WHERE `compounds`.`id`=`bin_structures`.`compound_id`
    -> AND MATCH_SUBSTRUCT('[OH]c1ccccc1',`obserialized`);
    -> LIMIT 10;
+-----------------------------+
| name                        |
+-----------------------------+
| 2,3,4,5,6-Pentachlorophenol |
| 2,3-Dimethylphenol          |
| 2,4,6-Trichlorophenol       |
| 2,4-Dimethylphenol          |
| 2,5-Dimethylphenol          |
| 2,6-Dimethylphenol          |
| 2-Bromophenol               |
| 2-Chloro-5-methylphenol     |
| 2-Chlorophenol              |
| 2-Hydroxybenzaldehyde       |
+-----------------------------+
10 rows in set (0.02 sec)