![\"\"](\"https://wikimedia.org/api/rest_v1/media/math/render/svg/904cf7ff9827a0c354df559b2c9fc64db1f1259b\")
We can use the Karplus equation for 3J coupling constants:
\n\n
where the phi is a dihedral angle. More information is available from https://en.wikipedia.org/wiki/Karplus_equation
\n\n![\"\"](\"https://upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Karplus.svg/768px-Karplus.svg.png\")
We can use the Karplus equation for 3J coupling constants:
\n\n
where the phi is a dihedral angle. More information is available from https://en.wikipedia.org/wiki/Karplus_equation
\n\n
Closed-form solution for this particular type of coupling?
", "rawMarkdown": "Closed-form solution for this particular type of coupling?", "votes": null }, { "id": "539533", "postDate": "05/30/2019 06:58:00", "content": "Haasnoot's 3JHH: http://www.stenutz.eu/conf/haasnoot.php\nPachler's 3JHH : http://www.stenutz.eu/conf/pachler.php\nOther types (3JCOCH, 3JCCCH, etc.): http://www.stenutz.eu/conf/karplus.html
\n\n(Edit)\nThe relationship between proton–proton NMR coupling constants and substituent electronegativities.
", "rawMarkdown": "Haasnoot's 3JHH: http://www.stenutz.eu/conf/haasnoot.php\nPachler's 3JHH : http://www.stenutz.eu/conf/pachler.php\nOther types (3JCOCH, 3JCCCH, etc.): http://www.stenutz.eu/conf/karplus.html\n\n(Edit)\n[The relationship between proton–proton NMR coupling constants and substituent electronegativities.](https://www.researchgate.net/publication/230009488_The_relationship_between_proton-proton_NMR_coupling_constants_and_substituent_electronegativities_II-conformational_analysis_of_the_sugar_ring_in_nucleosides_and_nucleotides_in_solution_using_a_genera)", "votes": null }, { "id": "540002", "postDate": "05/30/2019 20:58:35", "content": "I think you're on to something here. I found some relevant python code to calculate the dihedral angle: https://stackoverflow.com/questions/20305272/dihedral-torsion-angle-from-four-points-in-cartesian-coordinates-in-python
", "rawMarkdown": "I think you're on to something here. I found some relevant python code to calculate the dihedral angle: https://stackoverflow.com/questions/20305272/dihedral-torsion-angle-from-four-points-in-cartesian-coordinates-in-python", "votes": null }, { "id": "540067", "postDate": "05/31/2019 01:02:50", "content": "In another competition, I calculated dihedral angles in a crystalline material using the following kernel:
\n\nhttps://www.kaggle.com/tonyyy/how-to-get-atomic-coordinates
", "rawMarkdown": "In another competition, I calculated dihedral angles in a crystalline material using the following kernel:\n\nhttps://www.kaggle.com/tonyyy/how-to-get-atomic-coordinates", "votes": null }, { "id": "548030", "postDate": "06/08/2019 16:46:50", "content": "I noticed in your kernel you are using the lattice_vector for the calculations, which are not given in our xyz data. Is there a way to calculate this from what we have?
", "rawMarkdown": "I noticed in your kernel you are using the lattice_vector for the calculations, which are not given in our xyz data. Is there a way to calculate this from what we have?", "votes": null }, { "id": "548035", "postDate": "06/08/2019 16:53:02", "content": "That's from a different competition. You'll probably find it easier calculating dihedrals directly from the coordinates given. Take your two target atoms and find the two connected atoms that are also connected to eachother. Something like this:\n![\"\"](\"https://i.stack.imgur.com/rCCmC.png\")
\nFrom these four points, you can calculate a dihedral angle using the stackoverflow post.
Ok, I'll give it a try, thanks.
", "rawMarkdown": "Ok, I'll give it a try, thanks.", "votes": null }, { "id": "548239", "postDate": "06/09/2019 02:59:42", "content": "Open Babel has a function to calculate a dihedral angle GetTorsion. RDKit also has a similar function GetDihedralDeg.
", "rawMarkdown": "Open Babel has a function to calculate a dihedral angle [GetTorsion](http://openbabel.org/dev-api/classOpenBabel_1_1OBMol.shtml#a401a725a0efbc20c49783f176d78e6a7). RDKit also has a similar function [GetDihedralDeg](https://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html#rdkit.Chem.rdMolTransforms.GetDihedralDeg).", "votes": null }, { "id": "548247", "postDate": "06/09/2019 03:25:23", "content": "Thanks Tony! Great addition
", "rawMarkdown": "Thanks Tony! Great addition", "votes": null } ], "comments": [ { "id": 539519, "author_name": "vivaroma", "author_url": "", "post_date": "05/30/2019 06:33:48", "content": "Closed-form solution for this particular type of coupling?
", "votes": null, "replies": [ { "id": 539533, "author_name": "tonyyy", "author_url": "", "post_date": "05/30/2019 06:58:00", "content": "Haasnoot's 3JHH: http://www.stenutz.eu/conf/haasnoot.php\nPachler's 3JHH : http://www.stenutz.eu/conf/pachler.php\nOther types (3JCOCH, 3JCCCH, etc.): http://www.stenutz.eu/conf/karplus.html
\n\n(Edit)\nThe relationship between proton–proton NMR coupling constants and substituent electronegativities.
", "votes": null, "replies": [] } ] }, { "id": 540002, "author_name": "phucco", "author_url": "", "post_date": "05/30/2019 20:58:35", "content": "I think you're on to something here. I found some relevant python code to calculate the dihedral angle: https://stackoverflow.com/questions/20305272/dihedral-torsion-angle-from-four-points-in-cartesian-coordinates-in-python
", "votes": null, "replies": [ { "id": 540067, "author_name": "tonyyy", "author_url": "", "post_date": "05/31/2019 01:02:50", "content": "In another competition, I calculated dihedral angles in a crystalline material using the following kernel:
\n\nhttps://www.kaggle.com/tonyyy/how-to-get-atomic-coordinates
", "votes": null, "replies": [] }, { "id": 548030, "author_name": "taniaj", "author_url": "", "post_date": "06/08/2019 16:46:50", "content": "I noticed in your kernel you are using the lattice_vector for the calculations, which are not given in our xyz data. Is there a way to calculate this from what we have?
", "votes": null, "replies": [] }, { "id": 548035, "author_name": "matthewmasters", "author_url": "", "post_date": "06/08/2019 16:53:02", "content": "That's from a different competition. You'll probably find it easier calculating dihedrals directly from the coordinates given. Take your two target atoms and find the two connected atoms that are also connected to eachother. Something like this:\n\nFrom these four points, you can calculate a dihedral angle using the stackoverflow post.
Ok, I'll give it a try, thanks.
", "votes": null, "replies": [] }, { "id": 548239, "author_name": "tonyyy", "author_url": "", "post_date": "06/09/2019 02:59:42", "content": "Open Babel has a function to calculate a dihedral angle GetTorsion. RDKit also has a similar function GetDihedralDeg.
", "votes": null, "replies": [] }, { "id": 548247, "author_name": "matthewmasters", "author_url": "", "post_date": "06/09/2019 03:25:23", "content": "Thanks Tony! Great addition
", "votes": null, "replies": [] } ] } ], "raw_markdown_by_id": { "539404": "We can use the Karplus equation for 3J coupling constants:\n\n \n\nwhere the phi is a dihedral angle. More information is available from https://en.wikipedia.org/wiki/Karplus_equation\n\n", "539519": "Closed-form solution for this particular type of coupling?", "539533": "Haasnoot's 3JHH: http://www.stenutz.eu/conf/haasnoot.php\nPachler's 3JHH : http://www.stenutz.eu/conf/pachler.php\nOther types (3JCOCH, 3JCCCH, etc.): http://www.stenutz.eu/conf/karplus.html\n\n(Edit)\n[The relationship between proton–proton NMR coupling constants and substituent electronegativities.](https://www.researchgate.net/publication/230009488_The_relationship_between_proton-proton_NMR_coupling_constants_and_substituent_electronegativities_II-conformational_analysis_of_the_sugar_ring_in_nucleosides_and_nucleotides_in_solution_using_a_genera)", "540002": "I think you're on to something here. I found some relevant python code to calculate the dihedral angle: https://stackoverflow.com/questions/20305272/dihedral-torsion-angle-from-four-points-in-cartesian-coordinates-in-python", "540067": "In another competition, I calculated dihedral angles in a crystalline material using the following kernel:\n\nhttps://www.kaggle.com/tonyyy/how-to-get-atomic-coordinates", "548030": "I noticed in your kernel you are using the lattice_vector for the calculations, which are not given in our xyz data. Is there a way to calculate this from what we have?", "548035": "That's from a different competition. You'll probably find it easier calculating dihedrals directly from the coordinates given. Take your two target atoms and find the two connected atoms that are also connected to eachother. Something like this:\n\nFrom these four points, you can calculate a dihedral angle using the stackoverflow post.", "548077": "Ok, I'll give it a try, thanks.", "548239": "Open Babel has a function to calculate a dihedral angle [GetTorsion](http://openbabel.org/dev-api/classOpenBabel_1_1OBMol.shtml#a401a725a0efbc20c49783f176d78e6a7). RDKit also has a similar function [GetDihedralDeg](https://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html#rdkit.Chem.rdMolTransforms.GetDihedralDeg).", "548247": "Thanks Tony! Great addition" }, "source": "meta" }