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)