I've recently begun experimenting with drawing molecules from smiles expressions for use in an educational website. I am looking for a way to create simple representations of various molecules in metabolic pathways (Kreb's cycle, Gluconeogenesis, etc) in right-angle notation, as is often encountered in text books, for example the molecule Citrate:

Since I'm creating my website in python I tried using rdkit but so far have only been able to create drawings with 110° angles.

The smiles formula I used here is courtesy of pubchem:

C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O

Is there any open source tool (preferably in python) that I could use to create images in the right-angle notation? Or is there a "trick" of how to do this with rdkit? I would be grateful for any help and please excuse if I have botched any of the terminology in question. Thanks!

I've recently begun experimenting with drawing molecules from smiles expressions for use in an educational website. I am looking for a way to create simple structural representations of various molecules in metabolic pathways (Kreb's cycle, Gluconeogenesis, etc) in what I believe is Fisher projections (or similar?), as is often encountered in text books, for example the molecule Citrate:

Since I'm creating my website in python I tried using rdkit but so far have only been able to create drawings with 110° angles.

The smiles formula I used here is courtesy of pubchem:

C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O

Is there any open source tool (preferably in python) that I could use to create images of the Fischer projections? Or is there a "trick" of how to do this with rdkit? I would be grateful for any help and please excuse if I have botched any of the terminology in question. Thanks!

I've recently begun experimenting with drawing molecules from smiles expressions for use in an educational website. I am looking for a way to create simple representations of various molecules in metabolic pathways (Kreb's cycle, Gluconeogenesis, etc) in right-angle notation, as is often encountered in text books, for example the molecule Citrate:

Since I'm creating my website in python I tried using rdkit but so far have only been able to create drawings with 110° angles.

The smiles formula I used here is courtesy of pubchem:

C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O

Is there any open source tool (preferably in python) that I could use to create images in the right-angle notation? Or is there a "trick" of how to do this with rdkit? I would be grateful for any help and I please excuse if I have botched any of the terminology in question. Thanks!

I've recently begun experimenting with drawing molecules from smiles expressions for use in an educational website. I am looking for a way to create simple representations of various molecules in metabolic pathways (Kreb's cycle, Gluconeogenesis, etc) in right-angle notation, as is often encountered in text books, for example the molecule Citrate:

Since I'm creating my website in python I tried using rdkit but so far have only been able to create drawings with 110° angles.

The smiles formula I used here is courtesy of pubchem:

C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O

Is there any open source tool (preferably in python) that I could use to create images in the right-angle notation? Or is there a "trick" of how to do this with rdkit? I would be grateful for any help and please excuse if I have botched any of the terminology in question. Thanks!