Metal/coordination bonds and pseudocenters

[pamod]

Hello,
we are developing a molecular database + electronic lab notebook application (presently in their last beta internal testing stage), using indigo to perform part of the processing  of molecular info and ketcher as a graphic frontend for molecular input or molecule/fragment queries.

Since several users in our institute work with metallorganic compounds, we had to implement them in the database. However, afaik, available open source javascript/html5-based graphic frontends do not manage:

a) metal or coordination bonds and
b) pseudoatoms:
 b1) possibly bringing charges,
 b2) inheriting their definition (i.e. preserving the information about the set of atoms the geometric center of which corresponds to the pseudoatom),
 b3) acting as terminal atoms in bonds.

We found that ChemAxon Marvin program (not open-suorced and freely available for academic users only) manages such informations and saves them using an extension of the mol v3000 format to describe pseudoatoms (with their full description) and coordination bonds (only usable in queries within the standard v3000 version).

Presently, our interim solution requires that users:
I) draw their metallorganic molecules with local versions of Marvin (or, for expert users, generate such info by manual editing of a standard v3000 mol file),
II) save them in the Chemaxon v3000 mol format,
III) do not use the graphic input features of the database, since they can only upload the ChemAxon v3000 mol files.
Then the program skips all the molecular processing/cleaning operations and the calculation of properties not supporting/consistent with the presence of metals and coordination bond, but it is able to preserve, represent and store in a user-readable and modifiable form the corresponding info.

Thus, we wondered if an implementation of such objects and of the ChemAxon extension to mol v3000 format (or a similar, alternative one) could be possible in ketcher/indigo.

Obviously, should you get interested in this subject, we could provide any required info and collaborate at the best of our possibilities to such implementation.

Best regards,
Pietro