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

                                                                                                         COOT(1)