COOT(1)

NAME
pyrogen - A crystallographic dictionary restraints generating tool

SYNOPSIS
pyrogen [OPTIONS] file-or-SMILES

OPTIONS
-h, --help show this help message and exit -c FILE, --mmcif=FILE Make restraints from input mmcif FILE -m FILE, --mol=FILE Make restraints from input sdf/mol FILE -r COMP_ID, --residue-type=COMP_ID Create restraints for this type. Default is LIG -4, --quartet-planes Use 4-atom plane restraints, forces --quartet-hydrogens -H, --quartet-hydrogens Use 4-atom hydrogen plane restraints -b, --no-shift-hydrogen-atoms Stop addition or deletion of Hydrogen atoms for formally-charged atoms -n, --no-mogul Don't run CSD Mogul to update bond and angle restraints -N COMPOUND_NAME, --name=COMPOUND_NAME Compound name -S, --smiles Write the SMILES for the input molecule -t, --tautomers Show SMILES for tautomers, don't generate restraints -T MOGUL_DIR, --tmp-directory=MOGUL_DIR Directory into which the tmp files (e.g. for mogul) are written -d OUTPUT_DIR, --directory=OUTPUT_DIR Directory into which the output files (e.g. mmCIF and PDB) are written -o OUTPUT_POSTFIX, --output-postfix=OUTPUT_POSTFIX String to add to output file names, default is "pyrogen" -p, --picture Additionally output a chemical diagram PNG -P, --preserve-input-coordinates Preserve the inputput coordinates (if possible) -v, --version Print version information -a, --no-match-vs-reference-dictionaries Don't match atom names vs. dictionary molecules (default False) -R DICT_FILES_FOR_NAMES_MATCH, --reference-dictionary-files=DICT_FILES_FOR_NAMES_MATCH Try to match the atom names of the output molecule to this dictionary in these files (comma-separated list) -C COMP_ID_LIST_FOR_NAMES_MATCH, --reference-dictionary-comp-ids=COMP_ID_LIST_FOR_NAMES_MATCH Try to match the atom names of the output molecule to these comp-ids (comma-separated list) -w, --wwPDB Fetch the wwPDB ligand definition and use that -f FETCH (Just) fetch from the PDBe the CCD entry for the given compound-id -q, --quiet print less messages

DESCRIPTION
Pyrogen is a command-line tool for the generation of crystallographic dictionary restraints. Pyrogen is based on the RDKit.

AUTHOR
Paul Emsley