mapping problem

[saeid-lab]

Hello,

First, I need to thank you for developing this amazing tool. It really helps to work with complex systems.

I've been working with AutoMapper for a couple of months and everything's working smoothly. Recently I've noticed an issue in the mapping process.
In the following example:
A + B -> C
I have molecules A and B in "pre_system.data" and C in "post_system.data"
Cleaning and mapping go perfectly fine and I'm able to run the fix bond/react in lammps.

In the second scenario, exactly the same reaction, and components exist in the datafile, in presence of one water molecule, one Cl, and one Na ion. All the topological and ff parameters were carefully selected, the only difference(s) is the presence of new molecules (water and ions) in the "pre" and "post" datafile that are not involved in the reaction.

Here is the command and the error:

python3 ./../AutoMapper.py . map cleanedsystem_pre.data cleanedsystem_post.data --save_name pre_molecule.data post_molecule.data --ba 75 558 75 558 --ebt H H H H C C C C C C C N O O O O O H H C C O O H O Na Cl O C H

Note: Pre-bond atomID 134 has been assigned by inference to post-bond atomID 134. The potential choices were ['134', '135']. Please check this is correct.
.... [Few more notes here like above]
Traceback (most recent call last):
File "./../AutoMapper.py", line 92, in
map_processor(directory, args.data_files[0], args.data_files[1], args.save_name[0], args.save_name[1], args.ba[:2], args.ba[2:], args.da, args.ebt, args.ca, args.debug)
File "/home/saeid/Softwares/AutoMapper/MapProcessor.py", line 153, in map_processor
lammps_to_molecule(directory, postDataFileName, postMoleculeFileName, postBondingAtoms, deleteAtoms=postDeleteAtoms, validIDSet=postPartialAtomsSet, renumberedAtomDict=postRenumberedAtomDict)
File "/home/saeid/Softwares/AutoMapper/LammpsToMolecule.py", line 40, in lammps_to_molecule
atoms = refine_data(atoms, 0, validIDSet, renumberedAtomDict)
File "/home/saeid/Softwares/AutoMapper/LammpsTreatmentFuncs.py", line 98, in refine_data
row[index] = newAtomIDs[row[index]]
KeyError: '588'

Thank you so much in advance,
Please let me know if more details are required.
Saeid