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Convert PDB → Coarse Grained XYZ files\n\n`pdb2xyz` is a small tool to convert atomistic protein structures to coarse grained representations where residues\nare reduced to one or two interactions siters.\nMeant to construct models for use with the Calvados force field in the Duello and Faunus software.\n\n## Features\n\n- Convert PDB to XYZ\n- Optional off-center sites for ionizable side-chains\n- N and C terminal handling\n- SS-bond handling\n- Partial charge approximation according to pH using\n[average residue pKa values](https://doi.org/10.1093/database/baz024)\n- Create Calvados3 topology for [Duello](https://github.com/mlund/duello)\n\n## Install\n\n```sh\npip install pdb2xyz\n```\n\n## Usage\n\nIt is recommended that you fix your atomistic PDB file before converting\nusing e.g. [pdbfixer](https://github.com/openmm/pdbfixer?tab=readme-ov-file).\n\n```sh\nusage: pdb2xyz [-h] -i INFILE -o OUTFILE [-t TOP] [--pH PH] [--alpha ALPHA] [--sidechains]\n\nConvert PDB files to XYZ format\n\noptions:\n  -h, --help            show this help message and exit\n  -i INFILE, --infile INFILE\n                        Input PDB file path\n  -o OUTFILE, --outfile OUTFILE\n                        Output XYZ file path\n  -t TOP, --top TOP     Output topology path (default: topology.yaml)\n  --pH PH               pH value (default: 7.0)\n  --alpha ALPHA         Excess polarizability (default: 0.0)\n  --sidechains          Off-center ionizable sidechains (default: disabled)\n  --chains [CHAINS ...]\n                        List of chain IDs to include (default: all chains)\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmlund%2Fpdb2xyz","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmlund%2Fpdb2xyz","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmlund%2Fpdb2xyz/lists"}