---
name: "cif_guess_AMCSD_atom_types"
section: "1"
platform: "linux"
package: "cod-tools"
version: "3.11.0+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cif_guess_AMCSD_atom_types"
---

# cif\_guess\_AMCSD\_atom\_types(1)

read the CIF file, assuming that it follows AMCSD atom naming conventions, and assign atom types and attached hydrogen counts as follows: - for 'Wat' atoms (with or without a number) assign atom type 'O' and hydrogen count 2. - for 'O-H' atoms assign atom type 'O' and hydrogen count 1. - for 'OH' atoms assign atom type 'O' and hydrogen count 0 (hydrogen atoms are usually given explicitly in such cases). - For other 'O\[a-rt-z\]' matching atoms, assign type 'O' and no attached hydrogens.

## NAME

cif\_guess\_AMCSD\_atom\_types - read the CIF file, assuming that it follows AMCSD atom naming conventions, and assign atom types and attached hydrogen counts as follows: - for 'Wat' atoms (with or without a number) assign atom type 'O' and hydrogen count 2. - for 'O-H' atoms assign atom type 'O' and hydrogen count 1. - for 'OH' atoms assign atom type 'O' and hydrogen count 0 (hydrogen atoms are usually given explicitly in such cases). - For other 'O\[a-rt-z\]' matching atoms, assign type 'O' and no attached hydrogens.

## SYNOPSIS

cif\_guess\_AMCSD\_atom\_types --options input1.cif input\*.cif

## DESCRIPTION

Read the CIF file, assuming that it follows AMCSD atom naming conventions, and assign atom types and attached hydrogen counts as follows:

\- for 'Wat' atoms (with or without a number) assign atom type 'O' and hydrogen count 2.

\- for 'O-H' atoms assign atom type 'O' and hydrogen count 1.

\- for 'OH' atoms assign atom type 'O' and hydrogen count 0 (hydrogen atoms are usually given explicitly in such cases).

\- For other 'O\[a-rt-z\]' matching atoms, assign type 'O' and no attached hydrogens.

## OPTIONS

\--keep-tag-order\
                   Keep the original tag order in CIF file (default).

\--sort-tags\
                   Reorder tags in CIF file according to COD.

\--use-perl-parser\
                   Use Perl parser to parse CIF files.

\--use-c-parser\
                   Use C parser to parse CIF files (default).

\--help, --usage\
                   Output a short usage message (this message) and exit.

\--version\
                   Output version information and exit.

## REPORTING BUGS

Report cif\_guess\_AMCSD\_atom\_types bugs using e-mail: cod-bugs@ibt.lt