Daylight Worksheet - Compiling cansmi.c --WITH HINTS

One good way to start learning Daylight Toolkit programming is to work from a simple existing program. If programming in C or Fortran, learning to compile and link, probably with a Makefile, is an essential skill. cansmi.c is a good first program because it links only to the SMILES Toolkit, and performs a simple yet useful function, to canonicalize SMILES.

1. Before compiling cansmi.c, the following must have been done first by the Daylight administrator (user "thor"):

   % cd $DY_ROOT/contrib/src
% make


   This creates the Daylight-user library and also installs the correct machine-dependent include file at $DY_ROOT/contrib/src/makefile_include.

   Note: In this course, if you are using a Daylight distribution on a shared server, this has already been done and is unnecessary.

2. You should be logged in as user "mug". Create a self-named sub-directory, and if you wish, additional sub-directories to organize your work.

   % cd
% pwd
/home/mug
% mkdir jane_doe
% cd jane_doe
% mkdir toolkit
% cd toolkit


3. Copy cansmi.c and its associated makefile to this directory:

   % cp $DY_ROOT/contrib/src/c/smiles/cansmi.c .
% cp $DY_ROOT/contrib/src/c/smiles/makefile .


4. Now compile cansmi.c:

   % make cansmi


5. Test cansmi by entering the command and then a few SMILES:

   % cansmi
OCC
CCO
etc.


Modifying cansmi.c

You have created a "development environment" in which cansmi.c can be modified and recompiled. Or, a new program could be created and compiled by modifying the makefile, which we will try in a subsequent exercise.

1. Let's modify cansmi.c and recompile.

2. Use the function dt_count() to determine the number of atoms and bonds in each molecule. With each SMILES, print these numbers.

   You could try adding...
   

     {
       int atomcount, bondcount;
       acount = dt_count(mol, TYP_ATOM);
       bcount = dt_count(mol, TYP_BOND);
       fprintf(stderr, "atomcount = %d; bondcount = %d...\n", acount, bcount);
     }
   

3. Recompile as before and test.