[pkgsrc/trunk]: pkgsrc/biology New package, coordgenlibs-1.4.2.

[bsiegert <bsiegert%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/cc64c8d87b41
branches:  trunk
changeset: 441418:cc64c8d87b41
user:      bsiegert <bsiegert%pkgsrc.org@localhost>
date:      Tue Nov 03 20:17:59 2020 +0000

description:
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.

diffstat:

 biology/Makefile                   |   3 ++-
 biology/coordgenlibs/DESCR         |   8 ++++++++
 biology/coordgenlibs/Makefile      |  19 +++++++++++++++++++
 biology/coordgenlibs/PLIST         |  26 ++++++++++++++++++++++++++
 biology/coordgenlibs/buildlink3.mk |  15 +++++++++++++++
 biology/coordgenlibs/distinfo      |   6 ++++++
 6 files changed, 76 insertions(+), 1 deletions(-)

diffs (111 lines):

diff -r 4b0154c570ac -r cc64c8d87b41 biology/Makefile
--- a/biology/Makefile  Tue Nov 03 18:44:13 2020 +0000
+++ b/biology/Makefile  Tue Nov 03 20:17:59 2020 +0000
@@ -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+=       chemtool
 SUBDIR+=       clustalw
 SUBDIR+=       coalesce
+SUBDIR+=       coordgenlibs
 SUBDIR+=       fastDNAml
 SUBDIR+=       fastp
 SUBDIR+=       fluctuate
diff -r 4b0154c570ac -r cc64c8d87b41 biology/coordgenlibs/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/coordgenlibs/DESCR        Tue Nov 03 20:17:59 2020 +0000
@@ -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 -r 4b0154c570ac -r cc64c8d87b41 biology/coordgenlibs/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/coordgenlibs/Makefile     Tue Nov 03 20:17:59 2020 +0000
@@ -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"
diff -r 4b0154c570ac -r cc64c8d87b41 biology/coordgenlibs/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/coordgenlibs/PLIST        Tue Nov 03 20:17:59 2020 +0000
@@ -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 -r 4b0154c570ac -r cc64c8d87b41 biology/coordgenlibs/buildlink3.mk
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/coordgenlibs/buildlink3.mk        Tue Nov 03 20:17:59 2020 +0000
@@ -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 -r 4b0154c570ac -r cc64c8d87b41 biology/coordgenlibs/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/coordgenlibs/distinfo     Tue Nov 03 20:17:59 2020 +0000
@@ -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