When considering the degree of splitting in the NMR spectrum it is helpful to know dihedral angles, connectivity, etc. Using pre-built packages such as OpenBabel will help process the structure files without having to re-invent the wheel.
\n\nSpecifically, I would favor using Z-Matrix Notation for the structure files (instead of .XYZ)
\n\nSee the following link: http://openbabel.org/wiki/Babel#Examples
", "messages": [ { "id": "571524", "postDate": "07/09/2019 17:37:48", "content": "When considering the degree of splitting in the NMR spectrum it is helpful to know dihedral angles, connectivity, etc. Using pre-built packages such as OpenBabel will help process the structure files without having to re-invent the wheel.
\n\nSpecifically, I would favor using Z-Matrix Notation for the structure files (instead of .XYZ)
\n\nSee the following link: http://openbabel.org/wiki/Babel#Examples
", "rawMarkdown": "When considering the degree of splitting in the NMR spectrum it is helpful to know dihedral angles, connectivity, etc. Using pre-built packages such as OpenBabel will help process the structure files without having to re-invent the wheel.\n\nSpecifically, I would favor using Z-Matrix Notation for the structure files (instead of .XYZ)\n\nSee the following link: [http://openbabel.org/wiki/Babel#Examples](http://openbabel.org/wiki/Babel#Examples)", "votes": null }, { "id": "571527", "postDate": "07/09/2019 17:39:21", "content": "Could you please share a small implementation code snippet as an example.
", "rawMarkdown": "Could you please share a small implementation code snippet as an example.", "votes": null }, { "id": "571538", "postDate": "07/09/2019 17:50:50", "content": "I linked to the example portion of their wiki. I would loop (perhaps in bash*?*) through the structures converting each one into a fenske-hall z-matrix format (.fh) a command such as:
\n\nbabel -ixyz dsgdb9nsd_000790.xyz -ofh dsgdb9nsd_000790.fh
", "rawMarkdown": "I linked to the example portion of their wiki. I would loop (perhaps in bash*?*) through the structures converting each one into a fenske-hall z-matrix format (.fh) a command such as:\n\nbabel -ixyz dsgdb9nsd_000790.xyz -ofh dsgdb9nsd_000790.fh", "votes": null }, { "id": "571559", "postDate": "07/09/2019 18:25:35", "content": "You may use it with python.\nI've done a kernel, a few days ago : https://www.kaggle.com/jmtest/molecule-with-openbabel
", "rawMarkdown": "You may use it with python.\nI've done a kernel, a few days ago : [https://www.kaggle.com/jmtest/molecule-with-openbabel](https://www.kaggle.com/jmtest/molecule-with-openbabel)", "votes": null }, { "id": "571562", "postDate": "07/09/2019 18:30:28", "content": "This is my first time using Kaggle am I able to create a Kernel with the conversion script from xyz to z-matrix??\nEdit: Just looked, there is no support for bash... will use python.
", "rawMarkdown": "This is my first time using Kaggle am I able to create a Kernel with the conversion script from xyz to z-matrix??\nEdit: Just looked, there is no support for bash... will use python.", "votes": null }, { "id": "572177", "postDate": "07/10/2019 15:28:49", "content": "@larsbratholm I was wondering what calculate methods we could use in the CCLIB package. All of them seem like they would be against the rules, but I would like your feedback\nhttps://cclib.github.io/methods.html
", "rawMarkdown": "larsbratholm I was wondering what calculate methods we could use in the CCLIB package. All of them seem like they would be against the rules, but I would like your feedback\nhttps://cclib.github.io/methods.html", "votes": null }, { "id": "590664", "postDate": "08/02/2019 13:06:56", "content": "I'm not too familiar with CCLIB, but it seems like it just takes an output file from a quantum chemistry calculation and does some parsing on it? You don't have the output files, so wouldn't think that it's useful?\nIf there's a specific method in CCLIB that you're worried about, then let me know and I can have a look.
", "rawMarkdown": "I'm not too familiar with CCLIB, but it seems like it just takes an output file from a quantum chemistry calculation and does some parsing on it? You don't have the output files, so wouldn't think that it's useful?\nIf there's a specific method in CCLIB that you're worried about, then let me know and I can have a look.", "votes": null } ], "comments": [ { "id": 571527, "author_name": "ankittomar1", "author_url": "", "post_date": "07/09/2019 17:39:21", "content": "Could you please share a small implementation code snippet as an example.
", "votes": null, "replies": [ { "id": 571538, "author_name": "danielchemie", "author_url": "", "post_date": "07/09/2019 17:50:50", "content": "I linked to the example portion of their wiki. I would loop (perhaps in bash*?*) through the structures converting each one into a fenske-hall z-matrix format (.fh) a command such as:
\n\nbabel -ixyz dsgdb9nsd_000790.xyz -ofh dsgdb9nsd_000790.fh
", "votes": null, "replies": [] }, { "id": 571559, "author_name": "jmtest", "author_url": "", "post_date": "07/09/2019 18:25:35", "content": "You may use it with python.\nI've done a kernel, a few days ago : https://www.kaggle.com/jmtest/molecule-with-openbabel
", "votes": null, "replies": [] }, { "id": 571562, "author_name": "danielchemie", "author_url": "", "post_date": "07/09/2019 18:30:28", "content": "This is my first time using Kaggle am I able to create a Kernel with the conversion script from xyz to z-matrix??\nEdit: Just looked, there is no support for bash... will use python.
", "votes": null, "replies": [] } ] }, { "id": 572177, "author_name": "petersk20", "author_url": "", "post_date": "07/10/2019 15:28:49", "content": "@larsbratholm I was wondering what calculate methods we could use in the CCLIB package. All of them seem like they would be against the rules, but I would like your feedback\nhttps://cclib.github.io/methods.html
", "votes": null, "replies": [ { "id": 590664, "author_name": "larsbratholm", "author_url": "", "post_date": "08/02/2019 13:06:56", "content": "I'm not too familiar with CCLIB, but it seems like it just takes an output file from a quantum chemistry calculation and does some parsing on it? You don't have the output files, so wouldn't think that it's useful?\nIf there's a specific method in CCLIB that you're worried about, then let me know and I can have a look.
", "votes": null, "replies": [] } ] } ], "raw_markdown_by_id": { "571524": "When considering the degree of splitting in the NMR spectrum it is helpful to know dihedral angles, connectivity, etc. Using pre-built packages such as OpenBabel will help process the structure files without having to re-invent the wheel.\n\nSpecifically, I would favor using Z-Matrix Notation for the structure files (instead of .XYZ)\n\nSee the following link: [http://openbabel.org/wiki/Babel#Examples](http://openbabel.org/wiki/Babel#Examples)", "571527": "Could you please share a small implementation code snippet as an example.", "571538": "I linked to the example portion of their wiki. I would loop (perhaps in bash*?*) through the structures converting each one into a fenske-hall z-matrix format (.fh) a command such as:\n\nbabel -ixyz dsgdb9nsd_000790.xyz -ofh dsgdb9nsd_000790.fh", "571559": "You may use it with python.\nI've done a kernel, a few days ago : [https://www.kaggle.com/jmtest/molecule-with-openbabel](https://www.kaggle.com/jmtest/molecule-with-openbabel)", "571562": "This is my first time using Kaggle am I able to create a Kernel with the conversion script from xyz to z-matrix??\nEdit: Just looked, there is no support for bash... will use python.", "572177": "larsbratholm I was wondering what calculate methods we could use in the CCLIB package. All of them seem like they would be against the rules, but I would like your feedback\nhttps://cclib.github.io/methods.html", "590664": "I'm not too familiar with CCLIB, but it seems like it just takes an output file from a quantum chemistry calculation and does some parsing on it? You don't have the output files, so wouldn't think that it's useful?\nIf there's a specific method in CCLIB that you're worried about, then let me know and I can have a look." }, "source": "meta" }