sdf files merging

I need help for my task, if possible. I want to merge two sdf files on structure.

In details, I have 2 SDF files, every substance has two entries in these files, namely structure and IDNUMBER.

My willing is to:

1. determine the amount of overlap (identical) structures in these files.

2. merge them into one database (in one SDF-file). This database should not contain the same structures.

3. assign new codes to all substances, in addition to existing codes.

4. all variants of their ID Numbers must be preserved for all structures that are found in more than one of these files 

 Example 1: substance А is contained in two files. So I want to get the following entries in new database:

- structure

- IDNUMBER 1 (from 1.sdf)

- IDNUMBER 2 (from 2.sdf)

- IDNUMBER 3 (new code)

Example 2: substance B is contained in the 2.sdf only. Therefore, it should have the following entries in new database:

- structure

- IDNUMBER 2 (from 2.sdf)

- IDNUMBER 3 (new code)

I couldn't do that in Instant JChem because the structure isn't merged at all.

Hello,

please refer to documentation on Overlap Analysis. It should cover most of your needs and can be used as a starting point for your task. For the ID field, this might be more problematic as each entry in an entity in IJC needs to have a unique ID and your description does not necessarily satisfy this limitation. 

Wishing all the best

David