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
some Maven build ports: pass JAVA_HOME to maven
When a port defines JAVA_VERSION but during the build multiple
jdk versions are installed, Maven does not always use the defined
version if JAVA_HOME is not set in the environment.
PR: 272855
Reviewed-by: https://lists.freebsd.org/archives/freebsd-java/2026-February/003537.html
Approved-by: java@
Mk/**java.mk: Convert bsd.java.mk to USES
The following features have been added or changed:
- Instead of USE_JAVA use USES=java. This defaults to
USES=java:build,run if NO_BUILD is undefined. Else it defaults to
USES=java:run
- Instead of USE_ANT=yes use USES=java:ant which also implies
USES=java:build
- Instead of JAVA_BUILD=yes use USES=java:build. Does not imply run or
extract
- Instead of JAVA_EXTRACT=yes use USES=java:extract does not imply
build or run
- Instead of JAVA_RUN=yes use USES=java:run does not imply extract or
build
- Instead of USE_JAVA=<version> use USES=java and JAVA_VERSION=<version>
Approved by: mat (portmgr), glewis
Differential Revision: https://reviews.freebsd.org/D48201
*/*: properly depend on Maven package
devel/maven and devel/maven39 do not provide mvn(1) from LOCALBASE that
one comes from devel/maven-wrapper instead. Therefore, one should depend
on the package rather than a non-existing executable/script.
Approved by: jrm (mentor), otis (mentor), vvd
Differential Revision: https://reviews.freebsd.org/D44229
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner)
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above )
