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#! /bin/sh
#------------------------------------------------------------------------------
#$Author: antanas $
#$Date: 2022-05-12 17:31:05 +0300 (Thu, 12 May 2022) $
#$Revision: 9312 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.7.0/scripts/sdf_add_cod_data $
#------------------------------------------------------------------------------
#*
#* Append COD-specific meta-information to an SDF file in a format
#* suitable for PubChem.
#*
#* USAGE:
#* $0 --options --cod-cif cod-input.cif file1.sdf
#* $0 --options --cod-cif cod-input.cif file1.sdf > output.sdf
#* $0 --options --cod-cif cod-input.cif < file1.sdf > output.sdf
#**
set -ue
FILES=""
COD_CIF=""
#* OPTIONS:
#* -C, --cod-cif 1000000.cif
#* Provide the original COD CIF to extract structure metadata.
#*
#* --help, --usage
#* Output a short help message (this message) and exit.
#* --version
#* Output version information and exit.
#**
while [ $# -gt 0 ]
do
case $1 in
-C|--cod-cif|--cod-ci|--cod-c|--cod|--co|--c)
COD_CIF="$2"
shift
;;
--options|--option|--optio|--opti|--opt|--op|--o)
echo "$(basename "$0"):: The '--options' option is a placeholder."
echo "$(basename "$0"):: It should be replaced by one of the following options:"
awk '/#\* OPTIONS:/,/#\*\*/ {
sub("OPTIONS:", "");
sub("^ *#[*]?[*]?", "");
gsub("\\$0","'"$0"'");
print $0
}' "$0"
exit
;;
--help|--hel|--he|--h|--usage)
awk '/#\*/,/#\*\*/ {
sub("^ *#[*]?[*]?", "");
gsub("\\$0","'"$0"'");
print $0
}' "$0"
exit
;;
--version)
"$(dirname "$0")"/cod-tools-version
exit
;;
-*) echo "$(basename "$0"):: ERROR, unknown option '$1'." >&2 ; exit 1 ;;
*) FILES="$FILES '$1'" ;;
esac
shift
done
eval set -- "${FILES}"
cif_values='cif_values --no-header --no-dataname --no-filename --dont-replace-spaces --tags'
grep -v '^\$\$\$\$' ${1+"$@"}
DATA_BLOCK_CODE=$(cif_values --no-header --dataname "${COD_CIF}" | head -n 1)
DATA_BLOCK_CODE="data_${DATA_BLOCK_CODE}"
(
DATABASE_ID=$(${cif_values} _cod_database_code "${COD_CIF}")
if [ "${DATABASE_ID}" = "?" ]
then
echo "$0: ${COD_CIF} ${DATA_BLOCK_CODE}: WARNING, data item" \
"'_cod_database_code' was not found -- database identifier will" \
"be determined from the '_cod_data_source_block' data item." 1>&2
DATABASE_ID=$(${cif_values} _cod_data_source_block "${COD_CIF}")
fi
if [ "${DATABASE_ID}" = "?" ]
then
echo "$0: ${COD_CIF} ${DATA_BLOCK_CODE}: WARNING, data item" \
"'_cod_data_source_block' was not found -- database identifier" \
"will set to '?'." 1>&2
fi
DATABASE_ID=$(echo "${DATABASE_ID}" | perl -pe 's/^\s+|\s+$//g')
echo '> <PUBCHEM_EXT_DATASOURCE_REGID>'
echo "${DATABASE_ID}"
echo ""
echo '> <PUBCHEM_SUBSTANCE_SYNONYM>'
(
${cif_values} _chemical_name_systematic "${COD_CIF}"
${cif_values} _chemical_name_common "${COD_CIF}"
) \
| ( grep -E -v '^\s*\?' || true ) \
| perl -0777 -pe 's/[ \t]+/ /g; s/^\s*|\s*$//msg;' \
| awk '!a[$0]++'
echo ""
echo '> <PUBCHEM_SUBSTANCE_COMMENT>'
(
${cif_values} _publ_author_name --value-separator "; " "${COD_CIF}" \
| perl -pe 's/^\s+//g; s/^\s*(;\s*)*$//';
journal_year="$(${cif_values} _journal_year "${COD_CIF}" \
| perl -pe 's/^\s+|\s+$//g; s/^\s*$/?/;')"
if [ "${journal_year}" != "?" ]
then
printf "(%s)\n" "${journal_year}"
fi
${cif_values} _publ_section_title "${COD_CIF}"
${cif_values} _journal_name_full "${COD_CIF}"
${cif_values} _journal_volume "${COD_CIF}"
${cif_values} _journal_issue "${COD_CIF}"
page_first="$(${cif_values} _journal_page_first "${COD_CIF}" \
| perl -pe 's/^\s+|\s+$//g; s/^\s*$/?/;')"
if [ "${page_first}" != "?" ]
then
pages="${page_first}";
page_last="$(${cif_values} _journal_page_last "${COD_CIF}" \
| perl -pe 's/^\s+|\s+$//g; s/^\s*$/?/;')"
if [ "${page_last}" != "?" ]
then
pages="${pages}-${page_last}"
fi
printf "%s\n" "${pages}"
fi
doi="$(${cif_values} _journal_paper_doi "${COD_CIF}" \
| perl -pe 's/^\s+|\s+$//g; s/^\s*$/?/;')"
if [ "${doi}" != "?" ]
then
printf "DOI:%s\n" "${doi}"
fi
) \
| ( grep -E -v -e '^\s*[?]?\s*$' || true ) \
| perl -0777 -p \
-e 's/\n(.)/, $1/g;' \
-e 's/[ \t]+/ /g;' \
-e 's/\s+([,;])/$1/g;'
echo ""
echo '> <PUBCHEM_EXT_DATASOURCE_URL>'
echo 'https://www.crystallography.net/cod/'
echo ""
echo '> <PUBCHEM_EXT_SUBSTANCE_URL>'
echo "https://www.crystallography.net/cod/${DATABASE_ID}.html"
echo ""
echo '$$$$'
) \
| perl -0777 -pe 's/^> <.*?>\n\s*\n//mg' \
| cif-to-utf8 \
| perl -CS -MUnicode::Normalize -pe \
"# Remove diacritics from Unicode characters.
# From http://ahinea.com/en/tech/accented-translate.html:
# 2011.12.10
\$_ = NFD(\$_); s/\\pM//g;"
|
