Open
Conversation
Test-wise addition for / about nitrogen. Tested on the example of pyridine by openbabel from the SMILES string (`c1ccncc1`), and diethylamine (`CCNCC`).
Tested for the examples of diethylether (`CCOCC`), THF (`C1COCC1`), and propan-2-ol (`C(C)(O)(C)`) in .xyz files generated by obabel.
Tested with openbabel generated .xyz about diethyl thioether (`CCSCC`) and furfural (`O=Cc1cccs1`). However, contrasting to e.g., the depiction with openbabel generated .pov, the C-S bonds no longer are visible.
Tested with openbabel SMILES string of fluoroethane (`CCF`). The .pov/.ini and subsequent generation of .png seem fine.
Introduction of chlorine. Tested with an .xyz about chloroethane (`CCCl`) generated by openbabel, the chlorine atom is depicted as sphere, separated from the backbone of the molecule. Because of a similar observation for compounds with C-S bonds, and because the analogue CCF was rendered well, perhaps the assignment where to draw a bond faces an obstacle here.
The previous approach requires four lines each for every atom type as an instance of class Atom. I think an approach which uses the element symbol as key to a the corresponding values of mass, radiosity, and rgb coordinates in a dictionary is - in comparison to this one - easier to read, and to maintain. Lacking any better inspiration, atoms with atom types not yet explicitly defined in said dictionary default to hydrogen. In such an instance, the conversion will not stop for good, however is going to issue one warning for each atom not fully defined (yet).
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The previously explicit color definition about carbon and hydrogen
was reorganized to host now all elements up and including Nd (i.e.,
element number 60) by a dictionary-like approach. Reference for
the scheme is the one deployed e.g., by Jmol. In case of an atom
typ still unknown to the program, there is an explicit note that
(and which) definition is missing. As in earlier versions, atom
types unkwown to the script are going to be processed as hydrogen.