Port details |
- protomol OO, component based, framework for molecular dynamics (MD) simulations
- 2.0.3_16 biology =2 2.0.3_16Version of this port present on the latest quarterly branch.
- There is no maintainer for this port.
- Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
- Port Added: 2006-05-05 20:12:57
- Last Update: 2024-04-27 12:44:59
- Commit Hash: 98bf258
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv2
- WWW:
- https://protomol.sourceforge.net/
- Description:
- ProtoMol is an object-oriented, component based, framework for molecular
dynamics (MD) simulations. The framework supports the CHARMM 19 and 28a2 force
fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is
designed for high flexibility, easy extendibility and maintenance, and high
performance demands, including parallelization. The technique of multiple
time-stepping is used to improve long-term efficiency. The use of fast
electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME),
and Multigrid (MG) summation further enhances performance. Longer time steps
are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover,
and Langevin integrators. In addition, ProtoMol has been designed to interact
with VMD, a visualization engine developed by the University of Illinois that is
used for displaying large biomolecular systems in three dimensions. ProtoMol is
freely distributed software, and the source code is available.
- ¦ ¦ ¦ ¦
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- protomol>0:biology/protomol
- To install the port:
- cd /usr/ports/biology/protomol/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/protomol
- pkg install protomol
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: protomol
- Flavors: there is no flavor information for this port.
- distinfo:
- SHA256 (protomol-2.0.3-tar.gz) = 52c5faf69c717516a2b071dabbaed089ae7e9944b706e391e74604946a69c183
SIZE (protomol-2.0.3-tar.gz) = 2391568
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- xmu.pc : x11-toolkits/libXmu
- xt.pc : x11-toolkits/libXt
- sm.pc : x11/libSM
- ice.pc : x11/libICE
- xext.pc : x11/libXext
- x11.pc : x11/libX11
- xi.pc : x11/libXi
- Runtime dependencies:
-
- xmu.pc : x11-toolkits/libXmu
- xt.pc : x11-toolkits/libXt
- sm.pc : x11/libSM
- ice.pc : x11/libICE
- xext.pc : x11/libXext
- x11.pc : x11/libX11
- xi.pc : x11/libXi
- Library dependencies:
-
- libpng.so : graphics/png
- libtiff.so : graphics/tiff
- libjpeg.so : graphics/jpeg-turbo
- libglut.so : graphics/freeglut
- There are no ports dependent upon this port
Configuration Options:
- ===> The following configuration options are available for protomol-2.0.3_16:
EXAMPLES=on: Build and/or install examples
GLUT=on: OpenGL Utility Toolkit support
===> Use 'make config' to modify these settings
- Options name:
- biology_protomol
- USES:
- jpeg shebangfix xorg gl
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
Commit | Credits | Log message |
2.0.3_16 27 Apr 2024 12:44:59 |
Tijl Coosemans (tijl) |
graphics/tiff: Update to 4.6.0
PR: 278577
Exp-run by: antoine |
2.0.3_15 01 Nov 2023 22:11:47 |
Rodrigo Osorio (rodrigo) |
*/*: Update WWW to use HTTPS for sourceforge.net projects
Homepage link is permanent redirected to its HTTPS counterpart |
2.0.3_15 28 Jul 2023 17:13:17 |
Daniel Engberg (diizzy) |
*/*: Bump jpeg-turbo users treewide
New major version 3.0.0 |
07 Sep 2022 21:58:51 |
Stefan Eßer (se) |
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) |
2.0.3_14 07 Sep 2022 21:10:59 |
Stefan Eßer (se) |
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 ) |
2.0.3_14 20 Jul 2022 14:20:57 |
Tobias C. Berner (tcberner) |
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above ) |
2.0.3_14 06 Apr 2021 14:31:07 |
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.0.3_14 04 Nov 2019 21:08:20 |
zeising |
Add USES=xorg USES=gl, ports categories b
Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'. |
2.0.3_14 25 Aug 2018 03:47:25 |
tobik |
biology/protomol: Fix doubled USES overwriting the old value
- Make sure shebangfix is actually used |
2.0.3_13 25 Aug 2018 03:45:28 |
tobik |
biology/protomol: Fix build with Clang 6
Report.cpp:208:12: error: invalid operands to binary expression ('std::ostream'
(aka 'basic_ostream<char>') and 'const std::__1::ostream' (aka 'const
basic_ostream<char>'))
*myStream << a;
~~~~~~~~~ ^ ~
/usr/include/c++/v1/ostream:218:20: note: candidate function not viable: no
known conversion from 'const std::__1::ostream' (aka 'const
basic_ostream<char>') to 'const void *' for 1st argument; take the address of
the argument with &
basic_ostream& operator<<(const void* __p);
^
... and so on ...
http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/protomol-2.0.3_13.log |
2.0.3_13 23 May 2017 05:03:16 |
rezny |
Revision bump of all ports with USE_GL after consolidation of mesa-libs
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D10845 |
2.0.3_12 18 Dec 2016 05:34:42 |
marino |
biology/protomol: Support build with C++11 (taken from dports) |
2.0.3_12 01 Apr 2016 13:29:17 |
mat |
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight |
2.0.3_12 19 Aug 2015 13:30:00 |
mat |
Convert ports to use the options helpers in categories [abc]*, and minor fixes.
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D3412? |
2.0.3_12 25 Jun 2015 09:32:19 |
amdmi3 |
- Add LICENSE
- Fix shebangs
Approved by: porgmgr (bapt) |
2.0.3_11 23 Jun 2015 06:58:20 |
bapt |
Convert to COPYTREE_SHARE
Use options helpers |
2.0.3_11 22 Jun 2015 18:33:22 |
antoine |
Convert to USES=jpeg |
2.0.3_11 11 May 2015 18:34:58 |
mat |
Cleanup DIST* variables.
When appropriate:
- Try to use DISTVERSION{SUF,PRE}FIX
- Replace PORTNAME-PORTVERSION by DISTNAME
- Convert MASTER_SITES to use macros
- Other light cleanup
With hat: portmgr
Sponsored by: Absolight |
2.0.3_11 25 Dec 2014 20:54:43 |
bapt |
Bump portrevision after png update |
2.0.3_10 25 Dec 2014 19:04:27 |
antoine |
Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgrade |
2.0.3_10 20 Oct 2014 07:10:48 |
bapt |
Cleanup plist |
2.0.3_10 10 Sep 2014 20:50:37 |
gerald |
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.
Part II, Bump PORTREVISIONs.
PR: 192025
Tested by: antoine (-exp runs)
Approved by: portmgr (implicit) |
2.0.3_9 25 Aug 2014 17:19:31 |
amdmi3 |
- Stagify
- Fix build |
2.0.3_9 23 Jul 2014 16:44:28 |
bapt |
Reset maintainership for ports not staged with no pending PR
With hat: portmgr |
2.0.3_9 16 Apr 2014 18:28:50 |
zeising |
The FreeBSD x11@ and graphics team proudly presents
a zeising, kwm production, with help from dumbbell, bdrewery:
NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE
This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.
This patch also contains updates of libxcb and related ports, pixman, as well (Only the first 15 lines of the commit message are shown above ) |
2.0.3_8 15 Jan 2014 22:51:26 |
bapt |
Reduce over inclusion of bsd.port.mk |
2.0.3_8 11 Dec 2013 14:43:51 |
bapt |
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology |
2.0.3_8 20 Sep 2013 15:55:44 |
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
2.0.3_8 18 Mar 2013 06:54:40 |
jgh |
- adoption of optionsNG
- trim historical header
- fix mixture of DOCS/EXAMPLES -> EXAMPLES
- add shared description for GLUT to bodm
Approved by: portmgr (miwi) |
2.0.3_8 04 Aug 2012 22:52:04 |
kwm |
Switch from libglut to freeglut and retire libglut. Libglut hasn't been
developed in years and has been dropped from the MESA 8.0 distribution.
Freeglut is a rewrite of glut and is actively developed and is used by
many linux distributions instead of libglut.
Bump all ports that directly depend on libglut because of the shlib version
change.
There are some extra items in this patch.
*) Because freeglut doesn't have the same dependancies as libglut, some ports
need extra dependencies added to USE_XORG to make them build.
*) Mark graphics/f90gl broken, f90gl depends on a header that is only shipped
with libglut.
*) Remove option for libglut/freeglut selection in games/cake, only freeglut
remains now.
*) While here fix a png related build issue games/vegastrike.
Thanks to miwi for running the exp-run.
Approved by: portmgr (miwi)
Collaboration with: zeising@
Obtained from: xorg-dev staging area. |
2.0.3_7 01 Jun 2012 05:26:28 |
dinoex |
- update png to 1.5.10 |
2.0.3_6 23 Sep 2011 22:26:39 |
amdmi3 |
- Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS)
- Fix all ports that add {CPP,LD}FLAGS to *_ENV to modify flags instead
PR: 157936
Submitted by: myself
Exp-runs by: pav
Approved by: pav |
2.0.3_6 19 Mar 2011 12:38:54 |
miwi |
- Get Rid MD5 support |
2.0.3_6 28 Mar 2010 06:47:48 |
dinoex |
- update to 1.4.1
Reviewed by: exp8 run on pointyhat
Supported by: miwi |
2.0.3_5 05 Feb 2010 11:46:55 |
dinoex |
- update to jpeg-8 |
2.0.3_4 22 Aug 2009 00:15:15 |
amdmi3 |
- Switch SourceForge ports to the new File Release System: categories starting
with B,C |
2.0.3_4 18 Jul 2009 11:11:29 |
dinoex |
- update to jpeg7
Tested by: pav on pointyhat |
2.0.3_3 23 Jan 2009 16:28:36 |
flz |
- Update X.org ports to 7.4+ (few ports are more recent than the katamari).
- Bump PORTREVISION for all ports depending on libglut since the shlib
version number went from 4 to 3.
- Bump PORTREVISION for all ports depending on libXaw as libXaw.so.8 isn't
installed anymore.
- Couple of ports fixes (mostly missing xorg components added to USE_XORG). |
2.0.3_2 25 Jul 2008 14:34:52 |
pav |
- Remove USE_GCC where it can be satisfied with base compiler on following
FreeBSD versions: 5.3 and up, 6.x, 7.x, 8-CURRENT |
2.0.3_2 19 Apr 2008 17:56:05 |
miwi |
- Remove unneeded dependency from gtk12/gtk20 [1]
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Remove X11BASE support in favor of LOCALBASE or PREFIX
- Use USE_LDCONFIG instead of INSTALLS_SHLIB
- Remove unneeded USE_GCC 3.4+
Thanks to all Helpers:
Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr,
ehaupt, nox, itetcu, flz, pav
PR: 116263
Tested on: pointyhat
Approved by: portmgr (pav) |
2.0.3_2 28 Mar 2008 19:01:48 |
gahr |
- Fix build with GCC 4.2
Approved by: miwi (mentor) |
2.0.3_2 25 Mar 2008 22:44:48 |
miwi |
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION
Approved by: portmgr (xorg cleanup) |
2.0.3_1 02 Oct 2007 09:08:37 |
linimon |
Mark as broken with gcc4.2. |
2.0.3_1 19 May 2007 20:32:57 |
flz |
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}. |
2.0.3 05 May 2006 20:09:55 |
ehaupt |
Add protomol 2.0.3, OO, component based, framework for molecular
dynamics (MD) simulations.
PR: 95123
Submitted by: Sangwoo Shim <sangwoos@gmail.com> |