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As far as I know, opening the .com files as .txt files (with a text editor like simple notepad) yields a nicely formatted table of (atom) (x) (y) (z) values that can then be worked with. The problem is that this data has no information about what atom is connected to what. But within the actual Gaussview software, there seems to be a data set with more detailed information. Is there any way to easily extract that data via code?

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To my knowledge, neither .xyz nor .com format preserve connectivity information by default. Gaussview (and many other programs) makes an educated guess based on atomic covalent radii and positions of atoms. Gauss .com may also store a set of internal coordinates used for optimization that gaussview derive from connectivity information. Gaussian .com may contain connectivity information if geom=connectivity option was used, but you cannot expect it. The format of connectivity section is documented in geom=connectivity suboption part of Gaussian input docs.

That said, some other formats like .pdb allow to store that data explicitly and are well documented. Also, Gaussian can be used to perform various forms of population analysis printing a lot of nice tables, some of them might be interpreted as connectivity information (then again, some cannot).

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  • $\begingroup$ The Xmol format cannot store connectivity information at all (at least in its initial definition). It's funny that the simplest, an probably most recognised format in computational chemistry, cannot be exported by Gaussian anyway. $\endgroup$ – Martin - マーチン Jun 7 at 17:24
  • $\begingroup$ Just to extend on that a bit, Gaussview can export to .mol and .mol2 and .pdb, all of which store connection data. None of these formats are meant to be read by humans though, and depending on the molecule, they will not be helpful either. $\endgroup$ – Martin - マーチン Jun 7 at 17:38

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