jmol Java 3D viewer for chemical structures

14.30.2 science =1 14.30.1Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2008-05-17 23:04:58

Last Update: 2020-02-01 03:32:16

SVN Revision: 524753

Also Listed In: java

License: LGPL21

Description:

Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export). WWW: https://sourceforge.net/projects/jmol/

SVNWeb : Homepage

pkg-plist: as obtained via: make generate-plist

Expand this list (8 items)

1. bin/jmol
2. bin/jmoldata
3. /usr/local/share/java/classes/Jmol.jar
4. /usr/local/share/java/classes/JmolData.jar
5. /usr/local/share/java/classes/JmolLib.jar
6. /usr/local/share/licenses/Jmol-14.30.2/catalog.mk
7. /usr/local/share/licenses/Jmol-14.30.2/LICENSE
8. /usr/local/share/licenses/Jmol-14.30.2/LGPL21

Collapse this list.

Dependency lines:

• Jmol>0:science/jmol

To install the port: cd /usr/ports/science/jmol/ && make install clean

To add the package: pkg install Jmol

PKGNAME: Jmol

Flavors: there is no flavor information for this port.

distinfo:

TIMESTAMP = 1580526458 SHA256 (Jmol-14.30.2-full.tar.gz) = 5348ef99ee526c4f6adb8c6185f1ba0849a19a6f8200ea2b20cc0ebfea651895 SIZE (Jmol-14.30.2-full.tar.gz) = 133544337

Dependencies

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:

1. java : java/openjdk8
2. ant : devel/apache-ant

Runtime dependencies:

1. java : java/openjdk8

There are no ports dependent upon this port

Configuration Options

===> The following configuration options are available for Jmol-14.30.2: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings

Master Sites:

1. http://cytranet.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
2. http://downloads.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
3. http://excellmedia.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
4. http://freefr.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
5. http://jaist.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
6. http://kent.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
7. http://nchc.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
8. http://netcologne.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
9. http://netix.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
10. http://superb-dca2.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
11. http://superb-sea2.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
12. http://ufpr.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
13. http://vorboss.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
14. https://cytranet.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
15. https://downloads.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
16. https://excellmedia.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
17. https://freefr.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
18. https://jaist.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
19. https://kent.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
20. https://nchc.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
21. https://netcologne.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
22. https://netix.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
23. https://superb-dca2.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
24. https://superb-sea2.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
25. https://ufpr.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/
26. https://vorboss.dl.sourceforge.net/project/jmol/Jmol/Version%2014.30/Jmol%2014.30.2/

science/jmol: Update 14.30.1 -> 14.30.2 and unbreak

Code signing certificate which disappearance make this port unfetchable turned
out
to be not required. So I removed it.

Reported by:	portscout

Mark BROKEN again

With hat:	portmgr
Pointy hat:	yuri

science/jmol: Not broken

Erroneously labeled as BROKEN/unfetchable in rev.522132,
which may have been made during a period of intermittent connectivity problems.

Mark a few ports broken (unfetchable)

science/jmol: Update 14.30.0 -> 14.30.1

Reported by:	portscout

science/jmol: Update 14.29.55 -> 14.30.0

Mark a few ports BROKEN (unfetchable)

science/jmol: Update 14.29.54 -> 14.29.55

Reported by:	repology

science/jmol: Update 14.29.53 -> 14.29.54

Reported by:	portscout

science/jmol: Update 14.29.52 -> 14.29.53

Reported by:	portscout

science/jmol: Update 14.29.51 -> 14.29.52

Reported by:	portscout

science/jmol: Update 14.29.50 -> 14.29.51

Reported by:	portscout

science/jmol: Update 14.29.49 -> 14.29.50

Reported by:	portscout

science/jmol: Update 14.29.46 -> 14.29.49

Reported by:	portscout

science/jmol: Update 14.29.42 -> 14.29.46

Reported by:	portscout

science/jmol: Update 14.29.40 -> 14.29.42

Reported by:	portscout

science/jmol: Update to 14.29.38 -> 14.29.40

Reported by:	portscout

science/jmol: Update 14.29.37 -> 14.29.38

Reported by:	portscout

science/jmol: Update 14.29.36 -> 14.29.37

Reported by:	portscout

science/jmol: Update 14.29.34 -> 14.29.36

Reported by:	portscout

science/jmol: Update 14.29.32 -> 14.29.34

Reported by:	portscout

science/jmol: Update 14.29.31 -> 14.29.32

Also add -Djava.awt.headless=true to Jave VM args.

Reported by:	portscout

science/jmol: Add the executable jmoldata for headless operation

Re-add: science/jmol: Java 3D viewer for chemical structures

Remove expired ports without open PRs:
2016-07-04 security/openpgpsdk: Broken for more than 6 months
2016-07-04 security/radiusniff: Broken for more than 6 months
2016-07-04 security/pear-Auth_OpenID: Broken for more than 6 months
2016-07-04 security/sshit: Broken for more than 6 months
2016-07-04 security/ifd-slb_rf60: Broken for more than 6 months
2016-07-04 security/rainbowcrack: Broken for more than 6 months
2016-07-04 security/vlog: Broken for more than 6 months
2016-07-04 security/cryptstring: Broken for more than 6 months
2016-07-04 x11/libdnd: Broken for more than 6 months
2016-07-04 x11/xlupe: Broken for more than 6 months
2016-07-04 x11/xco: Broken for more than 6 months
2016-07-04 x11/xclick: Broken for more than 6 months
2016-07-04 devel/ocfpcsc: Broken for more than 6 months
2016-07-04 devel/dits: Broken for more than 6 months

Deprecate ports broken for more than 6 months

Mark a few ports BROKEN: unfetchable

Remove trailing whitespace from Makefiles, M-X.

Cleanup plist

- Update to version 13.2.3 [1]
- Remove leading article, revise capitalization in COMMENT
- Convert to new options framework
- Support staging
- Add launch script and desktop entry file

PR:		ports/182482 [1]
Submitted by:	Max Sterling <maxclsb@gmail.com> [1]

Add NO_STAGE all over the place in preparation for the staging support (cat:
science)

- Use single space after WWW:

Decommissioning java 1.5 (EOLed since October 2009):
suppress any reference to JAVA_VERSION=	1.5+ (part3)

- Trim Makefile headers
- Reset maintainer to ports@

- Update to 12.2.23

PR:             167297
Submitted by:   Muhammad Moinur Rahman <5u623l20@gmail.com>

 - remove MD5

- Update to 11.8.24

- Update to 11.8.7
- Update my mail address to FreeBSD

Approved by:    miwi(mentor)

- Switch SourceForge ports to the new File Release System: categories starting
with P,R,S

- Update to 11.6.17

PR:             131733
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)

- Update to 11.6

PR:             128047
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)

- Fix a typo

PR:             126647
Submitted by:   Wen heping <wenheping@gmail.com> (maintainer)

- Update to 11.4.6

PR:             126586
Submitted by:   Wen heping <wenheping@gmail.com> (maintainer)

- Update to 11.4.4
- Respect NOPORTEXAMPLE/NOPORTDOCS  [1]

PR:             124695
Submitted by:   Wen heping <wenheping@gmail.com>
                miwi [1]

Bump portrevision due to upgrade of devel/gettext.

The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@
Approved by:    portmgr (pav)

Jmol is a Java molecular viewer for
three-dimensional chemical structures.
Features include reading a variety
of file types and output from quantum
chemistry programs, and animation of
multi-frame files and computed normal
modes from quantum programs.

WWW:  http://sourceforge.net/projects/jmol/

PR:             ports/123631
Submitted by:   Wen heping <wenheping at gmail.com>

14 vulnerabilities affecting 178 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2020-02-14 01:16:43