checkmol/matchmol, (C) Norbert Haider, University of Vienna, 2003-2013 norbert.haider@univie.ac.at A utility program for functional group analysis of chemical structures and for structure/substructure comparison of two or more molecules. =============================================================================== This software is published under the terms of the GNU General Public License (GPL). For a detailed description of this license, see http://www.gnu.org/copyleft/gpl.html If invoked as "checkmol", this program reads 2D and 3D molecular structure files in various formats (Tripos Alchemy "mol", Tripos SYBYL "mol2", MDL "mol") and describes the molecule either by its functional groups or by a set of descriptors useful for database pre-screening (number of rings, sp2-hybridized carbons, aromatic bonds, etc.). If invoked as "matchmol", the program reads two individual 2D or 3D molecular structure files in various formats (see above) and checks if the first molecule (the "needle") is a substructure of the second one (the "haystack"). "Haystack" can also be a MDL SD-file (containing multiple MOL files); if invoked with "-" as file argument, both "needle" and "haystack" are read as an SD-file from standard input, assuming the first entry in the SDF to be the "needle"; output: entry number + ":F" (false) or ":T" (true) =============================================================================== Quick installation guide Compile with fpc (Free Pascal, see http://www.freepascal.org), using the -Sd or -S2 option (Delphi mode; IMPORTANT!) example for compilation (with optimization) and installation: fpc checkmol.pas -S2 -O3 -Op3 as "root", do the following: cp checkmol /usr/local/bin (or any other directory in your path) cd /usr/local/bin ln checkmol matchmol (ATTENTION: a symbolic link does not work!) Note that checkmol and matchmol are the same executable, but the program behaves differently depending on the name it was invoked with. Of course, you can also copy "checkmol" to "matchmol", but then it takes twice as much disk space (under Windows, this is the only possibility, as there are no hard links available there).