{
  "id": 95040,
  "title": "List of chemistry tool kits for chem information processing",
  "url": "/competitions/champs-scalar-coupling/discussion/95040",
  "author_name": "",
  "post_date": "2019-06-09T13:54:05.269790200Z",
  "votes": 4,
  "comment_count": 1,
  "views": 0,
  "content": "<p>Hello,</p>\n\n<p>As I am learning new things, I stumbled across these resources and I thought of sharing these with the wider community.</p>\n\n<p><strong>Chemistry Development Kit</strong>:\n- Language: Java\n- Link: <a href=\"https://cdk.github.io/\">https://cdk.github.io/</a>\n- Description: It is a collection of modular Java libraries for processing chemical information \n- JavaDoc: This page contains description of what each function does in this library. <a href=\"http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/qsar/descriptors/atomic/package-summary.html\">http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/qsar/descriptors/atomic/package-summary.html</a> </p>\n\n<p><strong>Chemistry Toolkit Rosetta</strong>:\n- Contains examples in Python\n- Link: <a href=\"https://ctr.fandom.com/wiki/Chemistry_Toolkit_Rosetta_Wiki\">https://ctr.fandom.com/wiki/Chemistry_Toolkit_Rosetta_Wiki</a>\n- Description: It is a wiki for sharing how to use different chemistry toolkits for the same set of common tasks. The main focus is on chemical informatics, with toolkits that handle molecular structures, depiction, databases, property analysis, nomenclature, and the like. This includes 3D structure visualization especially as applied to docking and small molecule conformation generation, but the visualization should support bond types.</p>",
  "messages": [
    {
      "id": "548510",
      "postDate": "06/09/2019 13:54:05",
      "content": "<p>Hello,</p>\n\n<p>As I am learning new things, I stumbled across these resources and I thought of sharing these with the wider community.</p>\n\n<p><strong>Chemistry Development Kit</strong>:\n- Language: Java\n- Link: <a href=\"https://cdk.github.io/\">https://cdk.github.io/</a>\n- Description: It is a collection of modular Java libraries for processing chemical information \n- JavaDoc: This page contains description of what each function does in this library. <a href=\"http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/qsar/descriptors/atomic/package-summary.html\">http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/qsar/descriptors/atomic/package-summary.html</a> </p>\n\n<p><strong>Chemistry Toolkit Rosetta</strong>:\n- Contains examples in Python\n- Link: <a href=\"https://ctr.fandom.com/wiki/Chemistry_Toolkit_Rosetta_Wiki\">https://ctr.fandom.com/wiki/Chemistry_Toolkit_Rosetta_Wiki</a>\n- Description: It is a wiki for sharing how to use different chemistry toolkits for the same set of common tasks. The main focus is on chemical informatics, with toolkits that handle molecular structures, depiction, databases, property analysis, nomenclature, and the like. This includes 3D structure visualization especially as applied to docking and small molecule conformation generation, but the visualization should support bond types.</p>",
      "rawMarkdown": "Hello,\n\nAs I am learning new things, I stumbled across these resources and I thought of sharing these with the wider community.\n\n**Chemistry Development Kit**:\n- Language: Java\n- Link: https://cdk.github.io/\n- Description: It is a collection of modular Java libraries for processing chemical information \n- JavaDoc: This page contains description of what each function does in this library. http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/qsar/descriptors/atomic/package-summary.html \n\n**Chemistry Toolkit Rosetta**:\n- Contains examples in Python\n- Link: https://ctr.fandom.com/wiki/Chemistry_Toolkit_Rosetta_Wiki\n- Description: It is a wiki for sharing how to use different chemistry toolkits for the same set of common tasks. The main focus is on chemical informatics, with toolkits that handle molecular structures, depiction, databases, property analysis, nomenclature, and the like. This includes 3D structure visualization especially as applied to docking and small molecule conformation generation, but the visualization should support bond types.",
      "votes": null
    },
    {
      "id": "550926",
      "postDate": "06/12/2019 06:26:25",
      "content": "<p>Tools to calculate features like bond angles, bending angles, dihedral angles, dipole moments, coupling partners and so on? (from another discussion)</p>\n\n<p>1) <strong>MolMod</strong> can read XYZ, calculate connection matrices, bond and dihedral angles and more <a href=\"https://github.com/molmod/molmod\">https://github.com/molmod/molmod</a> and documentation <a href=\"https://molmod.github.io/molmod/tutorial/internal_coordinates.html\">https://molmod.github.io/molmod/tutorial/internal_coordinates.html</a></p>\n\n<p>2) <strong>OpenBabel</strong> to to read and convert XYZ <a href=\"https://github.com/openbabel\">https://github.com/openbabel</a></p>\n\n<p>3) <strong>RDkit</strong> can do many many things <a href=\"https://github.com/rdkit/rdkit\">https://github.com/rdkit/rdkit</a>\nUse search function for dihedral angle such as <a href=\"http://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html?highlight=dihedral#rdkit.Chem.rdMolTransforms.GetDihedralDeg\">http://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html?highlight=dihedral#rdkit.Chem.rdMolTransforms.GetDihedralDeg</a></p>",
      "rawMarkdown": "Tools to calculate features like bond angles, bending angles, dihedral angles, dipole moments, coupling partners and so on? (from another discussion)\n\n1) **MolMod** can read XYZ, calculate connection matrices, bond and dihedral angles and more https://github.com/molmod/molmod and documentation https://molmod.github.io/molmod/tutorial/internal_coordinates.html\n\n2) **OpenBabel** to to read and convert XYZ https://github.com/openbabel\n\n3) **RDkit** can do many many things https://github.com/rdkit/rdkit\nUse search function for dihedral angle such as http://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html?highlight=dihedral#rdkit.Chem.rdMolTransforms.GetDihedralDeg",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 550926,
      "author_name": "tobikaggle",
      "author_url": "",
      "post_date": "06/12/2019 06:26:25",
      "content": "<p>Tools to calculate features like bond angles, bending angles, dihedral angles, dipole moments, coupling partners and so on? (from another discussion)</p>\n\n<p>1) <strong>MolMod</strong> can read XYZ, calculate connection matrices, bond and dihedral angles and more <a href=\"https://github.com/molmod/molmod\">https://github.com/molmod/molmod</a> and documentation <a href=\"https://molmod.github.io/molmod/tutorial/internal_coordinates.html\">https://molmod.github.io/molmod/tutorial/internal_coordinates.html</a></p>\n\n<p>2) <strong>OpenBabel</strong> to to read and convert XYZ <a href=\"https://github.com/openbabel\">https://github.com/openbabel</a></p>\n\n<p>3) <strong>RDkit</strong> can do many many things <a href=\"https://github.com/rdkit/rdkit\">https://github.com/rdkit/rdkit</a>\nUse search function for dihedral angle such as <a href=\"http://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html?highlight=dihedral#rdkit.Chem.rdMolTransforms.GetDihedralDeg\">http://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html?highlight=dihedral#rdkit.Chem.rdMolTransforms.GetDihedralDeg</a></p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "548510": "Hello,\n\nAs I am learning new things, I stumbled across these resources and I thought of sharing these with the wider community.\n\n**Chemistry Development Kit**:\n- Language: Java\n- Link: https://cdk.github.io/\n- Description: It is a collection of modular Java libraries for processing chemical information \n- JavaDoc: This page contains description of what each function does in this library. http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/qsar/descriptors/atomic/package-summary.html \n\n**Chemistry Toolkit Rosetta**:\n- Contains examples in Python\n- Link: https://ctr.fandom.com/wiki/Chemistry_Toolkit_Rosetta_Wiki\n- Description: It is a wiki for sharing how to use different chemistry toolkits for the same set of common tasks. The main focus is on chemical informatics, with toolkits that handle molecular structures, depiction, databases, property analysis, nomenclature, and the like. This includes 3D structure visualization especially as applied to docking and small molecule conformation generation, but the visualization should support bond types.",
    "550926": "Tools to calculate features like bond angles, bending angles, dihedral angles, dipole moments, coupling partners and so on? (from another discussion)\n\n1) **MolMod** can read XYZ, calculate connection matrices, bond and dihedral angles and more https://github.com/molmod/molmod and documentation https://molmod.github.io/molmod/tutorial/internal_coordinates.html\n\n2) **OpenBabel** to to read and convert XYZ https://github.com/openbabel\n\n3) **RDkit** can do many many things https://github.com/rdkit/rdkit\nUse search function for dihedral angle such as http://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html?highlight=dihedral#rdkit.Chem.rdMolTransforms.GetDihedralDeg"
  },
  "source": "meta"
}