Checkmol is a command-line utility program which reads molecular

structure files in different formats and analyzes the input
molecule for the presence of various functional groups and structural
elements. At present, approx. 200 different functional groups are
recognized. This output can be easily placed into a database table,
permitting the creation of chemical databases with a functional group
search option. Checkmol also outputs a set of statistical values derived
from a given molecule, which can also be used for quick retrieval from a
database. These values include: the number of atoms, bonds, and rings,
the number of differently hybridized carbon, oxgen, and nitrogen atoms,
the number of C=O double bonds, the number of rings of different sizes,
the number of rings containing nitrogen, oxygen, sulfur, the number of
aromatic rings, the number of heterocyclic rings, etc. The combination
of all of these values for a given molecule represents some kind of
"fingerprint" which is useful for rapid pre-selection in a database
structure/substructure search prior to a full atom-by-atom match.

WWW: http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html

PR:		ports/138670
Feature safe:yes
Submitted by:	Fernan Aguero <fernan at iib.unsam.edu.ar>

4 files changed, 62 insertions, 0 deletions

diff --git a/science/Makefile b/science/Makefile
index 74a8bbaacb72..caaab18f9b80 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -19,6 +19,7 @@
     SUBDIR += cdf
     SUBDIR += cdo
     SUBDIR += cgnslib
+    SUBDIR += checkmol
     SUBDIR += chemical-mime-data
     SUBDIR += chemtool
     SUBDIR += chemtool-devel
diff --git a/science/checkmol/Makefile b/science/checkmol/Makefile
new file mode 100644
index 000000000000..614a4c2728aa
--- /dev/null
+++ b/science/checkmol/Makefile
@@ -0,0 +1,31 @@
+# New ports collection makefile for:	checkmol
+# Date created:		23 Feb 2009
+# Whom:	      		Fernan Aguero <fernan@iib.unsam.edu.ar>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	checkmol
+PORTVERSION=	0.4a
+CATEGORIES=	science
+MASTER_SITES=	http://merian.pch.univie.ac.at/pch/download/chemistry/checkmol/
+DISTNAME=	${PORTNAME}
+EXTRACT_SUFX=	.pas
+
+MAINTAINER=	fernan@iib.unsam.edu.ar
+COMMENT=	Analyze molecules for the presence of functional groups
+
+USE_FPC=	yes
+PLIST_FILES=	bin/checkmol bin/matchmol
+
+do-extract:
+	@${RM} -rf ${WRKDIR}
+	@${MKDIR} ${WRKDIR}
+	${CP} ${DISTDIR}/${DISTFILES} ${WRKDIR}/
+do-build:
+	cd ${WRKDIR}; ${LOCALBASE}/bin/fpc ${DISTFILES} -S2 -O3 -Op3
+do-install:
+	${INSTALL_PROGRAM} ${WRKDIR}/${PORTNAME} ${PREFIX}/bin/
+	${LN} ${PREFIX}/bin/${PORTNAME} ${PREFIX}/bin/matchmol
+
+.include <bsd.port.mk>
diff --git a/science/checkmol/distinfo b/science/checkmol/distinfo
new file mode 100644
index 000000000000..0d3f6287739f
--- /dev/null
+++ b/science/checkmol/distinfo
@@ -0,0 +1,3 @@
+MD5 (checkmol.pas) = 01e7eacacf82e4ead63bf0c1113691e9
+SHA256 (checkmol.pas) = c69bc8dfd99b0735b4359995ce1480883022d6dab0cb751a4fc22685496bd5d7
+SIZE (checkmol.pas) = 443374
diff --git a/science/checkmol/pkg-descr b/science/checkmol/pkg-descr
new file mode 100644
index 000000000000..8a25fdab05b4
--- /dev/null
+++ b/science/checkmol/pkg-descr
@@ -0,0 +1,27 @@
+Checkmol is a command-line utility program which reads molecular
+structure files in different formats and analyzes the input
+molecule for the presence of various functional groups and structural
+elements. At present, approx. 200 different functional groups are
+recognized. This output can be easily placed into a database table,
+permitting the creation of chemical databases with a functional group
+search option. Checkmol also outputs a set of statistical values derived
+from a given molecule, which can also be used for quick retrieval from a
+database. These values include: the number of atoms, bonds, and rings,
+the number of differently hybridized carbon, oxgen, and nitrogen atoms,
+the number of C=O double bonds, the number of rings of different sizes,
+the number of rings containing nitrogen, oxygen, sulfur, the number of
+aromatic rings, the number of heterocyclic rings, etc. The combination
+of all of these values for a given molecule represents some kind of
+"fingerprint" which is useful for rapid pre-selection in a database
+structure/substructure search prior to a full atom-by-atom match.
+
+Matchmol complements the capabilities of checkmol. It compares two (or
+more) molecular structures and determines whether one of them is a
+substructure of the other one. This is done by a full atom-by-atom
+comparison of the input structures. Thus, matchmol can be used as a
+back-end program for structure/substructure search operations in
+chemical databases.
+
+The port installs both checkmol and matchmol.
+
+WWW: http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html