Daylight Worksheet - Explore reaction capabilities of contrib programs. -- WITH HINTS

We'll revisit several of the contrib programs. We'll see if they handle reactions as written, and make modifications if necessary for those which don't work correctly.

showparts.c ($DY_ROOT/contrib/src/c/smiles)

1. Build showparts and run it. Try entering reactions. What is the behavior? Does it correctly identify the parts within different reaction molecules?

        % cd
        % pwd
        /home/mug
        % cd jane_doe/toolkit
        % mkdir showparts
        % cd showparts
        % cp $DY_ROOT/contrib/src/c/smiles/showparts.c .
        % cp $DY_ROOT/contrib/src/c/smiles/makefile .
        % make showparts
        % showparts
        C.CO  
        molecule has 2 parts
        part 1  atom C
        part 2  atom C
        part 2  atom O
        part 2 bond C-O
        C.CO>>CCO
        molecule has 3 parts
        part 1  atom C
        part 2  atom C
        part 2  atom O
        part 3  atom C
        part 3  atom C
        part 3  atom O
        part 2 bond C-O
        part 3 bond C-C
        part 3 bond C-O
        ^D
       

2. Modify showparts.c. Include in the output the role of each atom (use dt_getrole() ). Compile and test.

   Add to variable declarations in showparts():

      int role;
       

   Revise the atom loop to:

      while (NULL_OB != (atom = dt_next(atoms))) {
         sy = dt_symbol(&lensy, atom);
         role = dt_getrole(atom,mol);
         printf("part %d  atom %.*s", du_part(atom), lensy, sy);
         if (role == DX_ROLE_REACTANT) printf("(REACTANT)\n");
         else if (role == DX_ROLE_AGENT) printf("(AGENT)\n");
         else if (role == DX_ROLE_PRODUCT) printf("(PRODUCT)\n");
         else printf("(unknown role=%d)\n",role);
      }
       

smarts_filter.c ($DY_ROOT/contrib/src/c/smarts)

1. Build smarts_filter and run it. Give a molecule SMARTS (eg. "CCC") and see the results when entering both molecule and reaction SMILES.

       $ smarts_filter "CCC"
       C1CCCCC1 C1CCCCC1 CO
       C1CCCCC1>>CCCO C1CCCCC1>>CCCO
   
       $ smarts_filter "CCC>>CCO"
       C1CCCCC1
       CO
       C1CCCCC1>>CCCO
       C1CCCCC1>>CCCO
       

2. Add code to identify the number of matches found (use dt_count(pathset,TYP_PATH)). For reaction queries, identify where the matches occur (eg. in the reactant, product, agent, or combination thereof).

   Revise the appropriate section of code to:

      if (NULL_OB != pathset) {
         printf("%s\n", buf);
         printf("\tnumber of matches = %d\n",dt_count(pathset,TYP_PATH));
      }