12.6 ISIS/Draw - 2D molecular editor

 

12.6.1 Introduction

ISIS/Draw is a well know two dimensional molecular editor mainly used to put structures in databases and/or in documents. The plug-in allows to edit molecules already present in the current VEGA ZZ workspace transferring them to the ISIS/Draw environment. The modified structures are automatically re-transferred to the VEGA ZZ workspace updating the previous structures. If required, the structures generated by ISIS/Draw can be converted from 2D to 3D by AMMP molecular mechanics engine.

 

12.6.2 Requirements

The plug-in works properly only if the ISIS/Draw 2.5 is correctly installed. The advanced technique to control the ISIS/Draw application (called code injection) is available in Windows versions with NT kernel only (Windows NT 4, 2000, XP, Server 2003, Vista, Server 2008 and 7).

 

12.6.3 ISIS/Draw 2.5 installation

 

12.6.3 Usage

To start ISIS/Draw, you must select Edit ISIS/Draw in main menu. If you start ISIS/Draw from the Windows start menu, the communication with VEGA ZZ is not operative.
If a molecule is present in the current workspace, it will be transferred automatically to the ISIS/Draw environment, otherwise a blank project is created.

 

ISIS/Draw main window

 

To transfer the molecule to VEGA ZZ, you can proceed in two ways:

If the VEGA ZZ Convert to 3D menu item is checked, the structure is automatically converted to 3D during the transfer, following these steps:

 

12.6.4 Configuration file

...\VEGA ZZ\Plugins\plugins.ini file contains the start-up configuration of all plug-ins. The [ISIS/Draw] section allows to change the default parameters used by the ISIS/Draw plug-in. Each line is a parameter in the format:

 

PARAMETER_NAME = VALUE

 

The following table shows all parameters that you can change in the configuration file:

Parameter Range Default Description
CONVERT_TO_3D 0-1 1 Determinate the status of Convert to 3D menu item (0 = unchecked, 1 = checked).
GSDG_STEPS >= 0 15 Number of steps performed by the Guass-Siedel distance geometry algorithm.
FORCE_ADD_H 0-1 0 Determinate the status of Force add hydrog. menu item (0 = unchecked, 1 = checked).
CONJ_STEPS >= 0 3000 Number of conjugate gradients steps.
CONJ_TOLER >= 0 0.01 Conjugate gradients minimization toler value.
STEEP_STEPS >= 0 50 Number of steepest descent steps.
STEEP_TOLER >= 0 1.00 Steepest descent minimization toler value.

Plugin.ini section example:

[ISIS/Draw]
CONVERT_TO_3D=1
FORCE_ADD_H=0
GSDG_STEPS=15
STEEP_STEPS=50
STEEP_TOLER=1.00
CONJ_STEPS=3000
CONJ_TOLER=0.01

 

WARNING:
[ISIS/Draw] section could be not present in the configuration file until the plug-in didn't save them. To force it, you must open ISIS/Draw inside VEGA ZZ, change the configuration (e.g. checking and unchecking the Force add hydrog. menu) and closing ISIS/Draw.

 

12.6.5 Limits

Due to the MDL mol file format limitation, molecule with more than 999 atoms aren't editable.
When you transfer a 3D structure to the 2D ISIS/Draw environment, it could be difficult to edit the molecule because some atoms could be overlapped.

 

12.6.6 Copyright

ISIS/Draw 2.5
Copyright 1990-2017, Elsevier MDL
2440 Camino Ramon, Suite 300
San Ramon, CA 94583
Tel: +1 (925) 543-5400
Fax: +1 (925) 543-5401
E-Mail: info@mdl.com
WWW: www.mdli.com