Tue Nov 3 20:17:59 2020 UTC ()
New package, coordgenlibs-1.4.2.

Part of PR pkg/55755.

This is Schroedinger, Inc's 2D coordinate generation.  It was formerly
proprietary code, but is now released under the BSD license.

The emphasis of these algorithms are on quality of 2D coordinates rather than
speed of generation.  The algorithm distinguishes itself from many others by
doing well with both macrocycles and metal complexes.  It also does extremely
well on typical drug-like small molecules, and has been validated on millions
of compounds.


(bsiegert)
diff -r1.57 -r1.58 pkgsrc/biology/Makefile
diff -r0 -r1.1 pkgsrc/biology/coordgenlibs/DESCR
diff -r0 -r1.1 pkgsrc/biology/coordgenlibs/Makefile
diff -r0 -r1.1 pkgsrc/biology/coordgenlibs/PLIST
diff -r0 -r1.1 pkgsrc/biology/coordgenlibs/buildlink3.mk
diff -r0 -r1.1 pkgsrc/biology/coordgenlibs/distinfo
cvs diff -r1.57 -r1.58 pkgsrc/biology/Makefile (expand / switch to unified diff)

--- pkgsrc/biology/Makefile 2020/11/03 16:41:26 1.57
+++ pkgsrc/biology/Makefile 2020/11/03 20:17:59 1.58
@@ -1,31 +1,32 @@ @@ -1,31 +1,32 @@
1# $NetBSD: Makefile,v 1.57 2020/11/03 16:41:26 bsiegert Exp $ 1# $NetBSD: Makefile,v 1.58 2020/11/03 20:17:59 bsiegert Exp $
2# 2#
3 3
4COMMENT= Software for the biological sciences 4COMMENT= Software for the biological sciences
5 5
6SUBDIR+= R-popbio 6SUBDIR+= R-popbio
7SUBDIR+= arka 7SUBDIR+= arka
8SUBDIR+= azara 8SUBDIR+= azara
9SUBDIR+= bcftools 9SUBDIR+= bcftools
10SUBDIR+= bioperl 10SUBDIR+= bioperl
11SUBDIR+= bodr 11SUBDIR+= bodr
12SUBDIR+= bwa 12SUBDIR+= bwa
13SUBDIR+= canu 13SUBDIR+= canu
14SUBDIR+= cdhit 14SUBDIR+= cdhit
15SUBDIR+= chemical-mime-data 15SUBDIR+= chemical-mime-data
16SUBDIR+= chemtool 16SUBDIR+= chemtool
17SUBDIR+= clustalw 17SUBDIR+= clustalw
18SUBDIR+= coalesce 18SUBDIR+= coalesce
 19SUBDIR+= coordgenlibs
19SUBDIR+= fastDNAml 20SUBDIR+= fastDNAml
20SUBDIR+= fastp 21SUBDIR+= fastp
21SUBDIR+= fluctuate 22SUBDIR+= fluctuate
22SUBDIR+= gabedit 23SUBDIR+= gabedit
23SUBDIR+= genesplicer 24SUBDIR+= genesplicer
24SUBDIR+= glimmer 25SUBDIR+= glimmer
25SUBDIR+= gnome-chemistry-utils 26SUBDIR+= gnome-chemistry-utils
26SUBDIR+= gp 27SUBDIR+= gp
27SUBDIR+= gromacs 28SUBDIR+= gromacs
28SUBDIR+= hisat2 29SUBDIR+= hisat2
29SUBDIR+= hmmer 30SUBDIR+= hmmer
30SUBDIR+= htslib 31SUBDIR+= htslib
31SUBDIR+= kallisto 32SUBDIR+= kallisto
File Added: pkgsrc/biology/coordgenlibs/DESCR
This is Schroedinger, Inc's 2D coordinate generation.  It was formerly
proprietary code, but is now released under the BSD license.

The emphasis of these algorithms are on quality of 2D coordinates rather than
speed of generation.  The algorithm distinguishes itself from many others by
doing well with both macrocycles and metal complexes.  It also does extremely
well on typical drug-like small molecules, and has been validated on millions
of compounds.
File Added: pkgsrc/biology/coordgenlibs/Makefile
# $NetBSD: Makefile,v 1.1 2020/11/03 20:17:59 bsiegert Exp $

GITHUB_TAG=	v${PKGVERSION_NOREV}
DISTNAME=	coordgenlibs-1.4.2
CATEGORIES=	biology
MASTER_SITES=	${MASTER_SITE_GITHUB:=schrodinger/}

MAINTAINER=	bsiegert@NetBSD.org
HOMEPAGE=	https://github.com/schrodinger/coordgenlibs/
COMMENT=	2D coordinate generation for molecules
LICENSE=	modified-bsd

USE_CMAKE=	yes
USE_LANGUAGES=	c c++


.include "../../biology/maeparser/buildlink3.mk"
.include "../../devel/boost-libs/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
File Added: pkgsrc/biology/coordgenlibs/PLIST
@comment $NetBSD: PLIST,v 1.1 2020/11/03 20:17:59 bsiegert Exp $
include/coordgen/CoordgenConfig.hpp
include/coordgen/CoordgenFragmentBuilder.h
include/coordgen/CoordgenFragmenter.h
include/coordgen/CoordgenMacrocycleBuilder.h
include/coordgen/CoordgenMinimizer.h
include/coordgen/sketcherMinimizer.h
include/coordgen/sketcherMinimizerAtom.h
include/coordgen/sketcherMinimizerBendInteraction.h
include/coordgen/sketcherMinimizerBond.h
include/coordgen/sketcherMinimizerClashInteraction.h
include/coordgen/sketcherMinimizerEZConstrainInteraction.h
include/coordgen/sketcherMinimizerFragment.h
include/coordgen/sketcherMinimizerInteraction.h
include/coordgen/sketcherMinimizerMarchingSquares.h
include/coordgen/sketcherMinimizerMaths.h
include/coordgen/sketcherMinimizerMolecule.h
include/coordgen/sketcherMinimizerResidue.h
include/coordgen/sketcherMinimizerResidueInteraction.h
include/coordgen/sketcherMinimizerRing.h
include/coordgen/sketcherMinimizerStretchInteraction.h
lib/cmake/coordgen-config-noconfig.cmake
lib/cmake/coordgen-config.cmake
lib/libcoordgen.so
lib/libcoordgen.so.1
lib/libcoordgen.so.${PKGVERSION}
File Added: pkgsrc/biology/coordgenlibs/buildlink3.mk
# $NetBSD: buildlink3.mk,v 1.1 2020/11/03 20:17:59 bsiegert Exp $

BUILDLINK_TREE+=	coordgenlibs

.if !defined(COORDGENLIBS_BUILDLINK3_MK)
COORDGENLIBS_BUILDLINK3_MK:=

BUILDLINK_API_DEPENDS.coordgenlibs+=	coordgenlibs>=1.4.2
BUILDLINK_PKGSRCDIR.coordgenlibs?=	../../biology/coordgenlibs

.include "../../biology/maeparser/buildlink3.mk"
.include "../../devel/boost-libs/buildlink3.mk"
.endif	# COORDGENLIBS_BUILDLINK3_MK

BUILDLINK_TREE+=	-coordgenlibs
File Added: pkgsrc/biology/coordgenlibs/distinfo
$NetBSD: distinfo,v 1.1 2020/11/03 20:17:59 bsiegert Exp $

SHA1 (coordgenlibs-1.4.2.tar.gz) = cd6b1a6be1e1735324625e21192b53ec475f5667
RMD160 (coordgenlibs-1.4.2.tar.gz) = 15e5d8dbe875fbdadae963b73d66c1070e08c7c3
SHA512 (coordgenlibs-1.4.2.tar.gz) = a1cd2611893cc04e1423fdc32c428a574cfc03d9a76cfb935dd5aa991157f462e78a8460b9f6748f422a2d0d78bed93759e5c3f03e361665331ed8df8cb78fad
Size (coordgenlibs-1.4.2.tar.gz) = 155306 bytes