CVS commit: pkgsrc/biology

["Benny Siegert" <bsiegert%netbsd.org@localhost>]

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