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CVS commit: pkgsrc/biology
Module Name: pkgsrc
Committed By: bsiegert
Date: Tue Nov 3 20:17:59 UTC 2020
Modified Files:
pkgsrc/biology: Makefile
Added Files:
pkgsrc/biology/coordgenlibs: DESCR Makefile PLIST buildlink3.mk
distinfo
Log Message:
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.
To generate a diff of this commit:
cvs rdiff -u -r1.57 -r1.58 pkgsrc/biology/Makefile
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/coordgenlibs/DESCR \
pkgsrc/biology/coordgenlibs/Makefile pkgsrc/biology/coordgenlibs/PLIST \
pkgsrc/biology/coordgenlibs/buildlink3.mk \
pkgsrc/biology/coordgenlibs/distinfo
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Modified files:
Index: pkgsrc/biology/Makefile
diff -u pkgsrc/biology/Makefile:1.57 pkgsrc/biology/Makefile:1.58
--- pkgsrc/biology/Makefile:1.57 Tue Nov 3 16:41:26 2020
+++ pkgsrc/biology/Makefile Tue Nov 3 20:17:59 2020
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.57 2020/11/03 16:41:26 bsiegert Exp $
+# $NetBSD: Makefile,v 1.58 2020/11/03 20:17:59 bsiegert Exp $
#
COMMENT= Software for the biological sciences
@@ -16,6 +16,7 @@ SUBDIR+= chemical-mime-data
SUBDIR+= chemtool
SUBDIR+= clustalw
SUBDIR+= coalesce
+SUBDIR+= coordgenlibs
SUBDIR+= fastDNAml
SUBDIR+= fastp
SUBDIR+= fluctuate
Added files:
Index: pkgsrc/biology/coordgenlibs/DESCR
diff -u /dev/null pkgsrc/biology/coordgenlibs/DESCR:1.1
--- /dev/null Tue Nov 3 20:17:59 2020
+++ pkgsrc/biology/coordgenlibs/DESCR Tue Nov 3 20:17:59 2020
@@ -0,0 +1,8 @@
+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.
Index: pkgsrc/biology/coordgenlibs/Makefile
diff -u /dev/null pkgsrc/biology/coordgenlibs/Makefile:1.1
--- /dev/null Tue Nov 3 20:17:59 2020
+++ pkgsrc/biology/coordgenlibs/Makefile Tue Nov 3 20:17:59 2020
@@ -0,0 +1,19 @@
+# $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@localhost
+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"
Index: pkgsrc/biology/coordgenlibs/PLIST
diff -u /dev/null pkgsrc/biology/coordgenlibs/PLIST:1.1
--- /dev/null Tue Nov 3 20:17:59 2020
+++ pkgsrc/biology/coordgenlibs/PLIST Tue Nov 3 20:17:59 2020
@@ -0,0 +1,26 @@
+@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}
Index: pkgsrc/biology/coordgenlibs/buildlink3.mk
diff -u /dev/null pkgsrc/biology/coordgenlibs/buildlink3.mk:1.1
--- /dev/null Tue Nov 3 20:17:59 2020
+++ pkgsrc/biology/coordgenlibs/buildlink3.mk Tue Nov 3 20:17:59 2020
@@ -0,0 +1,15 @@
+# $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
Index: pkgsrc/biology/coordgenlibs/distinfo
diff -u /dev/null pkgsrc/biology/coordgenlibs/distinfo:1.1
--- /dev/null Tue Nov 3 20:17:59 2020
+++ pkgsrc/biology/coordgenlibs/distinfo Tue Nov 3 20:17:59 2020
@@ -0,0 +1,6 @@
+$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
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