1. Files needed for running EdiSDF.

The following files must be placed in the main EdiSDF directory:

EdiSDF.exe
EdChemS.exe
Edchems.hlp
EdChemS.MOL
FromISIS.MOL
ECSTemplates.sdf
RINGS.SDF
AromaticTPL.SDF
CyclicTPL.SDF
ECSTemplates.sdf
ISISDraw.REF

RGroups sub-directory

The RGroups sub-directory must contain ( i ) *.SDF files corresponding to the lists of potential substituents, and ( ii ) the RGListF.TXT file containing the list of names (without extension, one name per line) of the above *.SDF files.

2. Input files: *.SDF, *.MOL

3. Running EdiSDF.

3.1 Main modes.

• Select drive, directory, and file.
• Use View mode to visualize structure and data or Edit mode to modify any field.

NB: Only structures can be modified in View mode.

NB: ECSTemplates.sdf, RINGS.SDF, AromaticTPL.SDF, CyclicTPL.SDF and ECSTemplates.sdf files must not be edited.

3.2 Manipulations with *.SDF files

When the file and the mode are selected, the program opens the “Structure Data File Viewer” window which visualize the structure and all fields of a given *.SDF file.

The following options are available:

• EDIT , to edit structure with EdChems or ISISDraw programs.

(If using ISISDraw : ( i) the ISISDraw.REF file must contain the path for the executable file of ISISDraw; ( ii ) when the structure is modified, it should be exported as the FromISIS.MOL file in the main directory of EdiSDF.)

• REPLACE MOL , to replace the current 2D or 3D structure with another structure in *.MOL format.
• EXTRACT MOL , to save the current structure as *.MOL file.
• ADD RECORD , the program copies a given record (structure and data) and adds it to the end of the file. Then, the content of the record can be modified.
• DEL RECORD , to delete the current record.
• SAVE , to save the current *.SDF file. If the file is saved under the same name, the program also keep an initial (unmodified) file as *.BAK.
• NEW SD FILE , to create a new empty SD file, containing only fields' names for the data block and no structure. The user can define the names of data fields (one per line) in the dialog window “Construction of blank SD file”. Since that new file is created and saved, the user can open and fill it.
• Structures can be rotated along X, Y and Z axis using Cntrl+x , Cntrl+y and Cntrl+z , respectively.

FILE menu

Load CLUSTERs option to visualize different classes of molecules for a given *.SDF file. When using that option, the program reads an *.FCL file containing the numbers of molecules corresponding to the loaded *.SDF file. The content of a given class can be visualized in the “Structure Data File Viewer” window using the “ Cluster navigator ” window. To pass from one class to another one, use the CLUSTERS list on the main form. To save the content of a given class as *.SDF file, use Save set option in the “ Cluster navigator ” window (Figure 1).

In the The *.FCL file, each class is represented by the sequence of numbers separated by space. There is no limitation for the number of classes and the molecules in each class. The *.FCL file can be created either manually by user or automatically by SMF-clustering program.

Figure 1. Visualization of classes with EdiSDF.

EDIT menu

The Get Bookmark option allows user to set a bookmark at the current record. That record can be found using the Goto Bookmark option.

The MOL Editor option launches the EdChems program.

OPTIONS menu

The Settings option switches ( i ) hydrogen atoms labels, ( ii ) colour for atoms, ( iii ) spacing for double, triple and aromatic bonds, and ( iv ) numbering of atoms.

The Font option selects the character set used for atoms' labels.

The Mols to SDF option prepares a *.SDF file from several *.MOL files and the textual file ontaining property values for those molecules. Both *.MOL and *.TXT files must be placed at the same directory. The property values in the *.TXT file (one per line) should correspond to the order of *.MOL files sorted by name.

The CODESSA Mols and Props to SDF option serves to transform input data prepared for CODESSA PRO program into a *.SDF file. User selects the names of directories containing *.MOL files and *.PRP files of CODESSA PRO, as well as the path for an output file. The property values in the *.PRP file should correspond to the order of *.MOL files sorted by name.

The Convert SDF to implicit H atoms option excludes all H atoms in all structures in a given *.SDF file. The new file is saved under the same name as the initial file. However, the initial file is kept under as an *.SD~ file.

The Tranform BONDs option modifies bond types for all structures in a given *.SDF file using templates. In the Bond transformer window, user selects the name of *.SDF file to be modified, the names of *.SDF files containing template structures and the bond types. If user wants to change several bond types, the modifications should be performed step by step, selecting ONLY one case in Apply option in the Bond transformer window.

Since all above options are selected, the program performs a sub-structural search using template as a query, then replacing bonds in the found structure as selected in the Bond transformer window.

NB: in the “standard” AromaticTPL.SDF and CyclicTPL.SDF files containing templates for normalisation of aromatic bonds and cyclic bonds, respectively, only single, double and triple bonds and are used ( e.g., benzene fragment is represented as Kekule structure). Those files should not be modified ! However, the user can prepare his own files containing any template structures.

The Search option is used for sub-substructural search. Visualization and saving of retrieved structures is performed using Sub-structural search navigator.

The operations with the lists (AND, OR, NOT) are not available yet.