We receive structures from a server within our company. Those structures are transferred as MOL files. Some of these structures contain R and/or S groups. Some of the creators of these structures create a really large empty space between the actual structure and the groups. We have currently ~30.000 structures in our database. Around 2.000 of these structures are flawed.
I have attached how such a structure might look at the bottom, as the image is quite large.
What I am trying to do now is to remove that empty space.
The process is currently receiving the MOL files wrapped within an XML file that does have additional information to store along with the structure. That process is written in Java. Up to now we do not have any library within the project to process and manipulate structures, as we have just parsed the MOL as String from the XML file and written it into a CLOB field in the database.
I know that libraries like the CDK exist, but right now I do not know if it can help me with that task.
I have pasted the actual mol file here.
If we open it with a viewer it looks like this: