Date: Wed, 9 Sep 2009 14:31:36 -0300 From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD GNATS PR Submission <freebsd-gnats-submit@FreeBSD.org> Subject: ports/138670: [new port] science/checkmol Message-ID: <20090909173136.GD15767@iib.unsam.edu.ar> Resent-Message-ID: <200909091740.n89He21V007019@freefall.freebsd.org>
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>Number: 138670 >Category: ports >Synopsis: [new port] science/checkmol >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Wed Sep 09 17:40:00 UTC 2009 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 6.3-RELEASE-p1 i386 >Organization: IIB-UNSAM >Environment: FreeBSD gama.iib.unsam.edu.ar 6.3-RELEASE-p1 FreeBSD 6.3-RELEASE-p1 #0: Wed Apr 2 18:37:14 ART 2008 fernan@gama.iib.unsam.edu.ar:/usr/obj/freebsd/freebsd-6.3/src/sys/GAMA i386 <machine, os, target, libraries (multiple lines)> >Description: <precise description of the problem (multiple lines)> Please add checkmol/matchmol to the FreeBSD ports tree. >How-To-Repeat: <code/input/activities to reproduce the problem (multiple lines)> >Fix: <how to correct or work around the problem, if known (multiple lines)> --- checkmol.shar begins here --- # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # checkmol # checkmol/Makefile # checkmol/distinfo # checkmol/pkg-descr # echo c - checkmol mkdir -p checkmol > /dev/null 2>&1 echo x - checkmol/Makefile sed 's/^X//' >checkmol/Makefile << '70f7de408da5538b11531080bb84d9a2' X# New ports collection makefile for: checkmol X# Date created: 23 Feb 2009 X# Whom: Fernan Aguero <fernan@iib.unsam.edu.ar> X# X# $FreeBSD$ X# X XPORTNAME= checkmol XPORTVERSION= 0.4a XCATEGORIES= science XMASTER_SITES= http://merian.pch.univie.ac.at/pch/download/chemistry/checkmol/ XDISTNAME= ${PORTNAME} XEXTRACT_SUFX= .pas X XMAINTAINER= fernan@iib.unsam.edu.ar XCOMMENT= Analyze molecules for the presence of functional groups X XUSE_FPC= yes XPLIST_FILES= bin/checkmol bin/matchmol X Xdo-extract: X @${RM} -rf ${WRKDIR} X @${MKDIR} ${WRKDIR} X ${CP} ${DISTDIR}/${DISTFILES} ${WRKDIR}/ Xdo-build: X cd ${WRKDIR}; ${LOCALBASE}/bin/fpc ${DISTFILES} -S2 -O3 -Op3 Xdo-install: X ${INSTALL_PROGRAM} ${WRKDIR}/${PORTNAME} ${PREFIX}/bin/ X ${LN} ${PREFIX}/bin/${PORTNAME} ${PREFIX}/bin/matchmol X X.include <bsd.port.mk> 70f7de408da5538b11531080bb84d9a2 echo x - checkmol/distinfo sed 's/^X//' >checkmol/distinfo << '7c360a0d53fa2797cd7278f2e0a7cd4f' XMD5 (checkmol.pas) = 01e7eacacf82e4ead63bf0c1113691e9 XSHA256 (checkmol.pas) = c69bc8dfd99b0735b4359995ce1480883022d6dab0cb751a4fc22685496bd5d7 XSIZE (checkmol.pas) = 443374 7c360a0d53fa2797cd7278f2e0a7cd4f echo x - checkmol/pkg-descr sed 's/^X//' >checkmol/pkg-descr << '3c86ce68abc8324c2f163fa9dbe0e959' XWhat is checkmol/matchmol? X XCheckmol is a command-line utility program which reads molecular Xstructure files in different formats and analyzes the input Xmolecule for the presence of various functional groups and structural Xelements. At present, approx. 200 different functional groups are Xrecognized. This output can be easily placed into a database table, Xpermitting the creation of chemical databases with a functional group Xsearch option. Checkmol also outputs a set of statistical values derived Xfrom a given molecule, which can also be used for quick retrieval from a Xdatabase. These values include: the number of atoms, bonds, and rings, Xthe number of differently hybridized carbon, oxgen, and nitrogen atoms, Xthe number of C=O double bonds, the number of rings of different sizes, Xthe number of rings containing nitrogen, oxygen, sulfur, the number of Xaromatic rings, the number of heterocyclic rings, etc. The combination Xof all of these values for a given molecule represents some kind of X"fingerprint" which is useful for rapid pre-selection in a database Xstructure/substructure search prior to a full atom-by-atom match. X XMatchmol complements the capabilities of checkmol. It compares two (or Xmore) molecular structures and determines whether one of them is a Xsubstructure of the other one. This is done by a full atom-by-atom Xcomparison of the input structures. Thus, matchmol can be used as a Xback-end program for structure/substructure search operations in Xchemical databases. X XThe port installs both checkmol and matchmol. X XWWW: http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html 3c86ce68abc8324c2f163fa9dbe0e959 exit --- checkmol.shar ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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