---
name: "pyrogen"
section: "1"
platform: "linux"
package: "coot"
version: "1.1.15+dfsg-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pyrogen"
---

# pyrogen(1)

A crystallographic dictionary restraints generating tool

## 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