Toolkit Tutorial: Using Contrib

Introduction

... SMILES molecules.
... SMILES reactions.
... SMARTS patterns.
... SMIRKS transforms.

Using Contrib

Let's begin by creating toolkit programs from freely available source code. "Contrib" software provides working examples of programs that are ready to go. To build "Contrib" software, do the following:

$ cd $DY_ROOT/contrib/src
$ make install

This installs executables, header code, and library objects into:

$DY_ROOT/contrib/bin
$DY_ROOT/contrib/include
$DY_ROOT/contrib/lib

Let's execute the "Contrib" programs that demonstrate the concepts discussed in this tutorial.

SMILES - Molecule

$ echo '[OH-].[H+]' | cansmi
[H+].[OH-]
        in: 1
        out: 1
        changed: 1

$ echo '[OH-].[H+]' | showmf
mf: H2O

$ echo '[OH-].[H+]' | rings
SMILES "[OH-].[H+]" has
        0 SSSR cycle(s) and...
        0 ring-system(s).

SMILES - Reaction

$ echo 'O>>[OH-].[H+]' | cansmi
O>>[H+].[OH-]
        in: 1
        out: 1
        changed: 1

$ echo 'O>>[OH-].[H+]' | showmf
mf: H4O2

$ echo 'O>>[OH-].[H+]' | rings
SMILES "O>>[OH-].[H+]" has
        0 SSSR cycle(s) and...
        0 ring-system(s).

SMARTS - Pattern

$ echo 'Oc1ccc(O)cc1' | smartsmatch -smarts Oa
Reading SMILES from stdin...
Oc1ccc(O)cc1
smartsmatch results: 1 SMILES in, 1 SMILES hit.

SMIRKS - Transform

$ printf "O\nOc1ccc(O)cc1\n" | tranfilter '[O:1][H:2]>>[O-:1].[H+:2]' 0
Input: O
ASmiles: [OH:1][H:2]>>[H+:2].[OH-:1]
USmiles: O>>[H+].[OH-]
Input: Oc1ccc(O)cc1
ASmiles: [H:1][O:2][c:8]1[cH:4][cH:6][c:9]([OH:3])[cH:7][cH:5]1>>[H+:1].[OH:3][c:9]1[cH:6][cH:4][c:8]([O-:2])[cH:5][cH:7]1
USmiles: Oc1ccc(O)cc1>>[H+].Oc1ccc([O-])cc1