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.

6 files changed, 76 insertions, 1 deletions

diff --git a/biology/Makefile b/biology/Makefile
index d6c8e22ef9c..a7224f2c37e 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -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
diff --git a/biology/coordgenlibs/DESCR b/biology/coordgenlibs/DESCR
new file mode 100644
index 00000000000..a08540e3438
--- /dev/null
+++ b/biology/coordgenlibs/DESCR
@@ -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.
diff --git a/biology/coordgenlibs/Makefile b/biology/coordgenlibs/Makefile
new file mode 100644
index 00000000000..ef43c95aced
--- /dev/null
+++ b/biology/coordgenlibs/Makefile
@@ -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
+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"
diff --git a/biology/coordgenlibs/PLIST b/biology/coordgenlibs/PLIST
new file mode 100644
index 00000000000..de8a0d39563
--- /dev/null
+++ b/biology/coordgenlibs/PLIST
@@ -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}
diff --git a/biology/coordgenlibs/buildlink3.mk b/biology/coordgenlibs/buildlink3.mk
new file mode 100644
index 00000000000..63786968a62
--- /dev/null
+++ b/biology/coordgenlibs/buildlink3.mk
@@ -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
diff --git a/biology/coordgenlibs/distinfo b/biology/coordgenlibs/distinfo
new file mode 100644
index 00000000000..c747a9fe93f
--- /dev/null
+++ b/biology/coordgenlibs/distinfo
@@ -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