Toolkit Tutorial: Programming Exercises

... SMILES molecule.
... SMILES reaction.
... SMARTS pattern.
... SMIRKS transform.

Compiling Source Code

The main progran syntax should look something like this:

#include "dt_smiles.h"
#include "dt_smarts.h"

int main() {

  /* toolkit code */

  return 0;
}

Place the portions of source code from the tutorial into the main syntax and compile and run the executable. Compare you output to the results shown in the SMARTS - Pattern and SMIRKS - Transform sections. To compile source code, use the following command:

$ cc -o <filename> <filename>.c -I$DY_ROOT/include -L$DY_ROOT/lib -ldt_smarts -ldt_smiles

Let's explore the "Contrib" code and write some new toolkit code that demonstrate the concepts discussed in this tutorial.

SMILES - Molecule

In the $DY_ROOT/contrib/src/c/smiles directory, browse the makefile and source code, especially for:

cansmi
showmf
rings

In the $DY_ROOT/contrib/src/c/smiles directory, browse the makefile and the source code.

Exercise: Write a program to read SMILES in and determine if the input is a molecule or a reaction. Then, for molecules, stream the molecule for atoms and write their symbols. For reactions, stream the reaction for molecules and write their reaction role and canonical SMILES out.

SMARTS - Pattern

In the $DY_ROOT/contrib/src/c/smarts directory, browse the makefile and source code, especially for:

smartsmatch

In the $DY_ROOT/contrib/src/c/transform directory, browse the makefile and the source code, especially for:

tranfilter

Create an HTML index of "Contrib" software by doing the following:

$ cd $DY_ROOT/contrib
$ make_index -html > index.html

Open the above "index.html" file with a browser. There is a lot of "Contrib" software. Familarize yourself with the breadth of software. Try to locate "Contrib" code that does the following:

• Identify ring systems in input structures.
• Align 2D layout based on a SMARTS query.
• Calculate polar surface area.