12.5 ISIS/Draw - 2D molecular editor
12.5.1 Introduction
ISIS/Draw is a well know two dimensional molecular editor mainly used to put the structures in the databases and/or in the documents. The plug-in allows to edit the molecules already present in the VEGA ZZ workspace transferring them in the ISIS/Draw environment. The modified structures are automatically re-transferred in the VEGA ZZ workspace updating the previous structures. If required the structures generated by ISIS/Draw can be converted from 2D to 3D by the AMMP molecular mechanics engine.
12.5.2 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 the Windows version with NT kernel only (Windows NT 4, 2000, XP, XP x64, Vista and Vista x64) only and so the plug-in can't work with Window 95, 98 and Millennium.
12.5.3 ISIS/Draw 2.5 installation
12.5.3 Usage
To
start ISIS/Draw, you must select Edit -> ISIS/Draw
in the 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 in the ISIS/Draw environment, otherwise a blank project is
created.
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:
12.5.4 Configuration file
The file ...\VEGA ZZ\Plugins\plugins.ini 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
In the following table are reported all parameter that the user can change in the configuration file:
Parameter | Range | Default | Description |
CONVERT_TO_3D | 0-1 | 1 | Determinate the status of the 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 the 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:
the [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.
12.5.5 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 any atoms could be overlapped.
12.5.6 Copyright
ISIS/Draw 2.5
Copyright 1990-2008, 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