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|
#! /bin/sh
#------------------------------------------------------------------------------
#$Author: andrius $
#$Date: 2018-08-28 17:09:31 +0300 (An, 28 rugp. 2018) $
#$Revision: 6403 $
#$URL: svn://www.crystallography.net/cod-tools/tags/v2.3/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
#* USAGE: $0 --options --cod-cif cod-input.cif file1.sdf > output.sdf
#* USAGE: $0 --options --cod-cif cod-input.cif < file1.sdf > output.sdf
#**
TMP_DIR="${TMPDIR}"
set -ue
FILES=""
COD_CIF=""
#* OPTIONS:
#* -C, --cod-cif 1000000.cif
#* Provide the original COD CIF to extract structure metadata.
#*
#* --tmp-dir /tmp
#* Use the specified temporary directory (default is /tmp).
#* This option is deprecated and will be removed in
#* future releases.
#*
#* --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
;;
--tmp-dir|--tmp-di|--tmp-d|--tmp|--tm|--t)
TMP_DIR="$2"
shift
;;
--options|--option|--optio|--opti|--opt|--op|--o)
echo "`basename $0`:: The '--options' option is a placehoder."
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 '^\$\$\$\$' ${1+"$@"}
(
DATABASE_ID=$(${cif_values} _cod_database_code $COD_CIF)
test "${DATABASE_ID}" = "?" && \
DATABASE_ID=$(${cif_values} _cod_data_source_block $COD_CIF)
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 $COD_CIF
) \
| ( grep -E -v '^\s*\?' || true ) \
| perl -0777 -pe 's/[ \t]+/ /g; s/^\s*|\s*$//g'
echo ""
echo ""
echo '> <PUBCHEM_SUBSTANCE_COMMENT>'
(
${cif_values} _publ_author_name --value-separator "; " $COD_CIF
echo "("$(${cif_values} _journal_year $COD_CIF)")"
${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
echo $(${cif_values} _journal_page_first $COD_CIF)-$(${cif_values} \
_journal_page_last $COD_CIF)
echo DOI:$(${cif_values} _journal_paper_doi $COD_CIF)
) \
| perl -pe 's/-\?//; s/\(\?\)/?/; s/\?-/?/; s/\?+/?/g' \
| ( grep -Ev '^\?|DOI:\?' || true ) \
| perl -0777 -pe 's/\n(.)/, $1/g; s/[ \t]+/ /g'
echo ""
echo '> <PUBCHEM_EXT_DATASOURCE_URL>'
echo 'http://www.crystallography.net/'
echo ""
echo '> <PUBCHEM_EXT_SUBSTANCE_URL>'
echo "http://www.crystallography.net/cod/${DATABASE_ID}.html"
echo ""
echo '$$$$'
) \
| perl -0777 -pe 's/^> <.*?>\n\s*\n//mg' \
| cif-to-utf8 \
| perl -CS -MUnicode::Normalize -pe \
"# from http://ahinea.com/en/tech/accented-translate.html:
# 2011.12.10
\$_ = NFD(\$_); s/\\pM//g;"
|
