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I've downloaded the chemtool-1.6.14.tar.gz from here. Then I extracted its contents into the directory: /home/fusion809/Downloads/chemtool-1.6.14 then I opened terminal, cd'ed to this directory, ran ./configure (with no errors), then ran make from the terminal and received this output:

make  all-recursive
make[1]: Entering directory `/home/fusion809/Downloads/chemtool-1.6.14'
Making all in m4
make[2]: Entering directory `/home/fusion809/Downloads/chemtool-1.6.14/m4'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/fusion809/Downloads/chemtool-1.6.14/m4'
Making all in po
make[2]: Entering directory `/home/fusion809/Downloads/chemtool-1.6.14/po'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/fusion809/Downloads/chemtool-1.6.14/po'
Making all in src-cht
make[2]: Entering directory `/home/fusion809/Downloads/chemtool-1.6.14/src-cht'
gcc -g -O2 cht.c -o cht
make[2]: Leaving directory `/home/fusion809/Downloads/chemtool-1.6.14/src-cht'
make[2]: Entering directory `/home/fusion809/Downloads/chemtool-1.6.14'
gcc -DLOCALEDIR=\"/usr/local/share/locale\" -DHAVE_CONFIG_H -I.  -I. -I.    -g -O2 -c main.c
main.c:18:22: fatal error: gdk/gdkx.h: No such file or directory
 #include <gdk/gdkx.h>
                      ^
compilation terminated.
make[2]: *** [main.o] Error 1
make[2]: Leaving directory `/home/fusion809/Downloads/chemtool-1.6.14'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/fusion809/Downloads/chemtool-1.6.14'
make: *** [all] Error 2

How do I get past this?

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The error messages indicate that you have not installed the development libraries.

Since chemtool is in the repositories (Universe) you just need to install it via software-center

Install chemtool

However - if you do wish to alter the code - then remember to install the dependencies first:

sudo apt-get install build-dep chemtool

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