Questions on detecting correct species and reaction route in Ca

[yunjian-hash]

Dear developers,

I am using reacnetgenerator to analyze the system containg Ca ions and SiO4 anions with water molecules. I want to find the reactions between the Ca ion and SiO4 anions. I found that the coordination number of Ca is not correct, which is no more than 4 in the results of the reacnetgenerator. in fact the coordination number of Ca is between the 4 to 7 with an average of 6.

In addition, there is a lot of the reactions between the water molecules, which is not the concerned reactions. Is there any methods to precludes these reactions? The attached is the initial structure. Thanks so much!
Ca_Si_0.67.cif.txt

[njzjz]

We use OpenBabel to detect bonds. Maybe you can modify the following line MaxBnd and recompile openbabel Python library:
https://github.com/openbabel/openbabel/blob/2f34bda337d7ddefa8f2bebfc23931a63e45241f/src/elementtable.h#L59

[yunjian-hash]

Thank you very much！I also have a question on how to realize the function "Depending on the needs of the user, species with specific elements can be selected for analysis, such as the analysis of reactions between all carbon containing species." in your paper.

[njzjz]

You can use --selectatoms. See https://reacnetgenerator.njzjz.win/guide/cli