# qiskit-xyz2pdb
This program is designed primarily to convert XYZ files from the results of [Qiskit's protein folding algorithm](https://qiskit-research.github.io/qiskit-research/protein_folding/protein_folding.html), but may also work with other similar XYZ files for protein coordinates. There are two options for the output: 1) a hetero atom (HETATM) format with connect records (CONECT), and 2) a conventional alpha carbon trace protein pdb format. In both outputs, each set of coordinates corresponds to the alpha carbon of each residue in the sequence.
## Install
The `qiskit-xyz2pdb` package is available on the Python Package Index and Conda and can be installed with the following command line:
```
# Install the package through PyPI
$ pip install qiskit-xyz2pdb
# Install the package through the Conda package manage
$ conda install qiskit-xyz2pdb
```
## Features
The hetero atom format is most useful for quick visualization, using a program such as NGL viewer. Note: this option assumes that the XYZ coordinates are all consecutively bound forming a continous single chain; it assumes that there are no side chains, and the CONECT records reflect this. How to run with this option:
```
$ qiskit-xyz2pdb --in-xyz inputfile.xyz --out-pdb outputfile.pdb --hetero-atoms
```
The conventional alpha carbon trace format is more versatile and can be used for further research beyond visualization - such as reconstructing the full backbone and sidechains, adding a force field, and then performing molecular dynamics simulations. How to run with this option:
```
$ qiskit-xyz2pdb --in-xyz inputfile.xyz --out-pdb outputfile.pdb --alpha-c-traces
```
Raw data
{
"_id": null,
"home_page": "http://github.com/thepineapplepirate/qiskit-xyz2pdb",
"name": "qiskit-xyz2pdb",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.6",
"maintainer_email": "",
"keywords": "bioinformatics,chemistry,pdb,proteins,qiskit,quantum",
"author": "Bryan Raubenolt",
"author_email": "raubenb@ccf.org",
"download_url": "https://files.pythonhosted.org/packages/ef/f6/6e3961288045609738be4c349a2c21b55c940765b589c22afe63d77c7f36/qiskit-xyz2pdb-0.1.2.tar.gz",
"platform": null,
"description": "# qiskit-xyz2pdb\n\nThis program is designed primarily to convert XYZ files from the results of [Qiskit's protein folding algorithm](https://qiskit-research.github.io/qiskit-research/protein_folding/protein_folding.html), but may also work with other similar XYZ files for protein coordinates. There are two options for the output: 1) a hetero atom (HETATM) format with connect records (CONECT), and 2) a conventional alpha carbon trace protein pdb format. In both outputs, each set of coordinates corresponds to the alpha carbon of each residue in the sequence. \n\n## Install\n\nThe `qiskit-xyz2pdb` package is available on the Python Package Index and Conda and can be installed with the following command line:\n\n```\n# Install the package through PyPI\n$ pip install qiskit-xyz2pdb\n\n# Install the package through the Conda package manage\n$ conda install qiskit-xyz2pdb\n```\n\n## Features\n\nThe hetero atom format is most useful for quick visualization, using a program such as NGL viewer. Note: this option assumes that the XYZ coordinates are all consecutively bound forming a continous single chain; it assumes that there are no side chains, and the CONECT records reflect this. How to run with this option:\n\n```\n$ qiskit-xyz2pdb --in-xyz inputfile.xyz --out-pdb outputfile.pdb --hetero-atoms\n```\n\nThe conventional alpha carbon trace format is more versatile and can be used for further research beyond visualization - such as reconstructing the full backbone and sidechains, adding a force field, and then performing molecular dynamics simulations. How to run with this option:\n\n```\n$ qiskit-xyz2pdb --in-xyz inputfile.xyz --out-pdb outputfile.pdb --alpha-c-traces\n```\n\n\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "A simple Python package to convert XYZ files from Qiskit output into PDB structures",
"version": "0.1.2",
"project_urls": {
"Download": "https://pypi.org/project/qiskit-xyz2pdb/",
"Homepage": "http://github.com/thepineapplepirate/qiskit-xyz2pdb",
"Issues": "https://github.com/thepineapplepirate/qiskit-xyz2pdb/issues",
"Source": "https://github.com/thepineapplepirate/qiskit-xyz2pdb"
},
"split_keywords": [
"bioinformatics",
"chemistry",
"pdb",
"proteins",
"qiskit",
"quantum"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "eff66e3961288045609738be4c349a2c21b55c940765b589c22afe63d77c7f36",
"md5": "69df2f425a2e06662d65fb35de21ddc5",
"sha256": "04fd1e61c614f1e76d2e5ac3b79eada20244c36d3193730297cae75fd0c51f43"
},
"downloads": -1,
"filename": "qiskit-xyz2pdb-0.1.2.tar.gz",
"has_sig": false,
"md5_digest": "69df2f425a2e06662d65fb35de21ddc5",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.6",
"size": 6602,
"upload_time": "2023-06-23T21:36:27",
"upload_time_iso_8601": "2023-06-23T21:36:27.943912Z",
"url": "https://files.pythonhosted.org/packages/ef/f6/6e3961288045609738be4c349a2c21b55c940765b589c22afe63d77c7f36/qiskit-xyz2pdb-0.1.2.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-06-23 21:36:27",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "thepineapplepirate",
"github_project": "qiskit-xyz2pdb",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"lcname": "qiskit-xyz2pdb"
}
JSON
