Notes
user@computer:~$represents an example terminal prompt name. Actual command/argument input is after the$.- Replace
name@xx.eduwith your email address.\followed by>on the next line represents continued terminal input. You will need to delete the>symbol in order to run the scripts as a copy/paste into terminal.- You should validate your own EDirect scripts and results as there may be unintentional mistakes in these recipes. A convenient method is to compare your EDirect results to the NCBI Web interface search results: https://www.ncbi.nlm.nih.gov/.
It is possible to pipe EDirect results into chemical structure viewers as some cheminformatics toolkits can read chemical file formats (e.g., SMILES) directly from standard input.
For ChemAxon Marvin, we can pipe EDirect compiled SMILES directly into Marvin View (mview). Note that the - is the mview option to read structures from standard input.
user@computer:~$ esearch -email name@xx.edu -db pccompound -query "132427739"[UID] | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles CID InChIKey IUPACName | \
> mview -
If you have multiple molecules to display, you can use the mview standard input option - along with the gridbag option to display the molecules in a matrix:
user@computer:~$ esearch -email name@xx.edu -db pccompound -query "132427739"[UID] | \
> elink -target pccompound -name pccompound_pccompound | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles CID InChIKey IUPACName | \
> mview --gridbag -
tested with ChemAxon MarvinView version 19.27.0.
One really cool feature of using Open Babel is the ability to display molecules as ASCII figures directly in the terminal. Below, we pipe the results to Open Babel using the standard input smiles format, -ismi, and then output in ascii format, -oascii. The -xh 10 is a resizing option.
user@computer:~$ esearch -email name@xx.edu -db pccompound -query "13586"[UID] | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles | \
> openbabel.obabel -ismi -oascii -xh 10
__
__ \__
_/ \__ \_
__/ \_ \_
O ________/ \_
/
/
\ |
\ /
\/
1 molecule convertedThis works for multiple molecules too!
user@computer:~$ esearch -email name@xx.edu -db pccompound -query "132427739"[UID] | \
> elink -target pccompound -name pccompound_pccompound | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles | \
> openbabel.obabel -ismi -oascii -xh 10
\
____
|
__ O_Si__
O\ \__\ |
|\N / \
__O| \__/
/__/ \ OH
| \
/| /
/
/ |
\_ | O ____
\__O___ |____
__Si_O N \\/ \
\ /| /
| \___ __N
\__O ____
O / ___\/ \\
/ /| /
__ __
\_/
| /
| |
/____ O __Si__/
|/ \ | | |
/ \ O\\ ____ _| \
\ ___ | || / \_/ \__
\____/ \\_N \ /
\ | _/ | /
___
/ \/
|| |\
\__
\_O ___
|_N/ \ /
O|/ _\__\_/
/ /_/ O_Si__
\_
\O |
/
_Si/
\ |_
O____O | \
__|Si_ | | ____
/ \_\ __ | |
/ | / \____N__|
\O| | / \_
\O/\___ \
\ | ||
\_ /
___ \
/ \ O_Si_|
|__\ \ \ \ |
/\_O \__\ _\
__N / \/ \
\ / / |
| O \__/
\ ___\
____/
...
24 molecules convertedYou can save depictions in a more classic PNG file using Open Babel with either a single molecule:
user@computer:~$ esearch -email name@xx.edu -db pccompound -query "13586"[UID] | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles CID | \
> openbabel.obabel -ismi -O 13586.png
1 molecule converted
or multiple molecules in a matrix:
user@computer:~$ esearch -email name@xx.edu -db pccompound -query "132427739"[UID] | \
> elink -target pccompound -name pccompound_pccompound | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles CID | \
> openbabel.obabel -ismi -O 132427739_similar.png -xp 1400
24 molecules converted
Tested with Open Babel v3.0.0 installed from Snap. I did receive a Font Configuration error when saving the PNG files, however, the conversion seemed to work fine.
gnuplot is a command-line graphing program that allows plotting data from standard input. In gnuplot, there is an option called "dumb terminal" that creates plots using ASCII characters directly in the terminal window, which is convenient for initial analysis of compiled EDirect data. For example, here is some data related to the number of J Cheminform articles indexed in PubMed by publication date:
user@computer:~$ esearch -email name@xx.edu -db pubmed -query "J Cheminform[JOUR]" | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element PubDate | \
> cut -d " " -f 1 | \
> sort-uniq-count-rank | \
> sort -k2
22 2009
12 2010
54 2011
39 2012
52 2013
71 2014
78 2015
71 2016
67 2017
68 2018
56 2019We can pipe this data directly to gnuplot. In the below script, set term dumb is the gnuplot option to create an ASCII plot, - sets the data input to standard input instead of a file, using 2:1 sets the second column as the x-axis, and the first column as the y-axis, with boxes creates a box plot, and notitle removes the plot legend:
user@computer:~$ esearch -email name@xx.edu -db pubmed -query "J Cheminform[JOUR]" | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element PubDate | \
> cut -d " " -f 1 | \
> sort-uniq-count-rank | \
> sort -k2 | \
> gnuplot -e "set term dumb; plot '-' using 2:1 with boxes notitle"
80 +---------------------------------------------------------------------+
| + + + ******* + + |
| * * |
70 |-+ ******* ******* ******* +-|
| * * * ****** * |
| * * * * * * |
60 |-+ * * * * * * +-|
| ****** * * * * * ******* |
| * * ******* * * * * * * |
50 |-+ * * * * * * * * * *+-|
| * * * * * * * * * * |
40 |-+ * * * * * * * * * *+-|
| * ******* * * * * * * * |
| * * * * * * * * * * |
30 |-+ * * * * * * * * * *+-|
| * * * * * * * * * * |
| * * * * * * * * * * |
20 |-+******* * * * * * * * * * *+-|
| * * * * * * * * * * * * |
| * ******* * + * * + * * + * * + * * |
10 +---------------------------------------------------------------------+
2008 2010 2012 2014 2016 2018 2020
Tested with gnuplot-x11 5.2.8.