12.6 ISIS/Draw - 2D molecular editor
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.
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
start ISIS/Draw, you must select Edit
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.
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:
|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
[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.
Due to the MDL mol file format limitation, molecule with more than 999 atoms
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.
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