From 34506c3888af23944c86ed23b40d1a7be42130f2 Mon Sep 17 00:00:00 2001
From: Yuri Victorovich <yuri@FreeBSD.org>
Date: Thu, 9 Jan 2020 16:48:21 +0000
Subject: [PATCH] New port: science/cdk: Chemistry Development Kit

---
 science/Makefile      |  1 +
 science/cdk/Makefile  | 54 +++++++++++++++++++++++++++++++++++++++++++
 science/cdk/distinfo  |  5 ++++
 science/cdk/pkg-descr | 13 +++++++++++
 4 files changed, 73 insertions(+)
 create mode 100644 science/cdk/Makefile
 create mode 100644 science/cdk/distinfo
 create mode 100644 science/cdk/pkg-descr

diff --git a/science/Makefile b/science/Makefile
index b5866e1914e4..96bd3e2e7562 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -39,6 +39,7 @@
     SUBDIR += buddy
     SUBDIR += cdcl
     SUBDIR += cdf
+    SUBDIR += cdk
     SUBDIR += cdo
     SUBDIR += cgnslib
     SUBDIR += cgribex
diff --git a/science/cdk/Makefile b/science/cdk/Makefile
new file mode 100644
index 000000000000..6aa6cdeb61fe
--- /dev/null
+++ b/science/cdk/Makefile
@@ -0,0 +1,54 @@
+# $FreeBSD$
+
+PORTNAME=	cdk
+DISTVERSIONPREFIX=	cdk-
+DISTVERSION=	2.3
+CATEGORIES=	science java
+PKGNAMESUFFIX=	-chemistry
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Chemistry Development Kit
+
+LICENSE=	LGPL21
+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
+
+BUILD_DEPENDS=	mvn:devel/maven
+
+USE_JAVA=	yes
+USE_GITHUB=	yes
+
+NO_ARCH=	yes
+
+PLIST_FILES=	${JAVAJARDIR}/${PORTNAME}-${PORTVERSION}.jar
+
+# to rebuild the deps archive:
+#   1. set DEV_UPDATE_MODE=yes
+#   2. make makesum build
+#   3. upload the *-deps archive
+#   4. set DEV_UPDATE_MODE=no
+#   5. make clean makesum
+
+DEV_UPDATE_MODE=	no
+
+.if (${DEV_UPDATE_MODE} == "yes")
+post-build:
+	@cd ${WRKDIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} .m2
+	@${ECHO} "(!!!) Please upload the deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}"
+.else
+MASTER_SITES+=	LOCAL/yuri/:deps
+DISTFILES+=	${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps
+MVN_ARGS=	--offline
+.endif
+
+do-build:
+	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \
+		${LOCALBASE}/bin/mvn ${MVN_ARGS} \
+		-fae install \
+		-Dmaven.test.skip=true \
+		-Duser.home=${WRKDIR} \
+		install
+
+do-install:
+	${INSTALL_DATA} ${WRKSRC}/bundle/target/${PORTNAME}-${PORTVERSION}.jar ${STAGEDIR}${JAVAJARDIR}/${PORTNAME}-${PORTVERSION}.jar
+
+.include <bsd.port.mk>
diff --git a/science/cdk/distinfo b/science/cdk/distinfo
new file mode 100644
index 000000000000..0b8d90bb182f
--- /dev/null
+++ b/science/cdk/distinfo
@@ -0,0 +1,5 @@
+TIMESTAMP = 1578560238
+SHA256 (cdk-2.3-deps.tar.gz) = d3df87bc95d2302f92b60bc1e6fd5172c341aae2f831f263f6508de2f31bcf99
+SIZE (cdk-2.3-deps.tar.gz) = 63038171
+SHA256 (cdk-cdk-cdk-2.3_GH0.tar.gz) = 169772895f6d49c5a66e32da059e1d63f5cd77aa3ffdeed4942dcd76eb8d399d
+SIZE (cdk-cdk-cdk-2.3_GH0.tar.gz) = 26499872
diff --git a/science/cdk/pkg-descr b/science/cdk/pkg-descr
new file mode 100644
index 000000000000..91b69937c2d0
--- /dev/null
+++ b/science/cdk/pkg-descr
@@ -0,0 +1,13 @@
+The CDK is an open-source Java software for cheminformatics and bioinformatics.
+
+Key Features:
+* Molecule and reaction valence bond representation.
+* Read and write file formats: SMILES, SDF, InChI, Mol2, CML, and others.
+* Efficient molecule processing algorithms: Ring Finding, Kekulisation, Aromaticity.
+* Coordinate generation and rendering.
+* Canonical identifiers for fast exact searching.
+* Substructure and SMARTS pattern searching.
+* ECFP, Daylight, MACCS, and other fingerprint methods for similarity searching.
+* QSAR descriptor calculations
+
+WWW: https://cdk.github.io/