Molden is a package for displaying Molecular Density from the Ab Initio packages
GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac,
it also supports a number of other programs via the Molden Format. Molden reads
all the required information from the GAMESS / GAUSSIAN outputfile. Molden is
capable of displaying Molecular Orbitals, the electron density and the Molecular
minus Atomic density. Either the spherically averaged atomic density or the
oriented ground state atomic density can be subtracted for a number of standard
basis sets. Molden supports contour plots, 3-d grid plots with hidden lines and
a combination of both. It can write a variety of graphics instructions;
postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and
Figure. Both Xwindows and OpenGL versions of Molden are also capable of
importing and displaying of chemx, PDB, and a variety of mopac/ampac files and
lots of other formats. Molden also can animate reaction paths and molecular
vibrations. It can calculate and display the true or Multipole Derived
Electrostatic Potential and atomic charges can be fitted to the Electrostatic
Potential calculated on a Connolly surface. Molden also features an stand alone
forcefield program ambfor, which can optimise geometries with the combined Amber
(protein) and GAFF (small molecules) force fields. Atom typing can be done
automatically and interactively from within Molden, as well as firing
optimisation jobs. Molden has a powerful Z-matrix editor which give full control
over the geometry and allows you to build molecules from scratch, including
polypeptides.
===> The following configuration options are available for molden-7.3,1:
DATA=on: Install data files
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
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 )
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 )
biology/molden: Unbreak build; Correct WWW
For unbreak:
- pass FFLAGS to the build
- fix several errors in C
- remove the failing 'ex' command from makefile
Reported by: fallout
Approved by: portmgr (unbreak)
graphics/mesa-libs: Bump reverse deps for libglvnd
Per discussion with bapt on helping pkg handle the changing of these
deps and avoiding impossible upgrade senarios.
PR: 246767
Reviewed by: manu, bapt
Approved by: x11
Differential Revision: https://reviews.freebsd.org/D30824
Deorbit RESTRICTED && NO_CDROM, part one.
For ports that already use the licenses framwork, merge the content of
RESTRICTED/NO_CDROM/LEGAL* entries into LICENSEs.
Approved by: rene
Differential Revision: https://reviews.freebsd.org/D30010
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330
Related to revision 499061 bump ports with USES=fortran to have them
benefit from the improved situation where libgcc_s is only used when
absolutely necessary.
Suggested by: tijl
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.
PR: 231590
biology/molden: Unbreak: fix the problem that it can't find libgcc_s.so from gcc
Add $(LDFLAGS) to makefile.
While here, add USES=gl.
Approved by: portmgr
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.
This includes ports
- featuring USE_GCC=yes or USE_GCC=any,
- featuring USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and those
- with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.
PR: 222542
biolog/molden: unbreak after at least two intransparent distfile updates
Reviewed by: zeising (mentor)
Approved by: zeising (mentor)
Differential Revision: https://reviews.freebsd.org/D15333
Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 under most circumstances.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang,
c++14-lang, c++0x, c11, or gcc-c++11-lib.
PR: 219275
Chase next distfile update. Upstream contacted whether we would be allowed to
host a distfile copy.
Reviewed by: swills (mentor)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D11586
Revision bump of all ports with USE_GL after consolidation of mesa-libs
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D10845
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using using Mk/bsd.octave.mk which in turn has USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
c++11-lang, c++0x, c11, or gcc-c++11-lib.
PR: 216707
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms), part II.
The first part covered ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.
This adds ports with USES=fortran and ports using Mk/bsd.octave.mk
which in turn has USES=fortran.
PR: 214965
Reported by: thierry
biology/molden: 5.4 -> 5.7
- Adds editable text fields that are longer than the visible string
and introduces a new way of selecting a range of amino acids.
- introduces interfaces to the open source packages openbabel and pharmer.
Openbabel is used to create 2D images of the molecules in a .sdf
file. It is also used to do 2D fingerprint searching.
Pharmer is used to pharmacophore (3D) searching against indexed
databases of .sdf files.
biology/molden: 5.0.7 -> 5.4
Changes:
- Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally.
- Pdb files can now be clipped.
- Fixes missing residues. Introduces an alternative way of generating rotamers,
without using z-matrices. This potentially a faster algorithm.
- Supports Movie making through avconv/ffmpeg.
- calculates the Electron Localization Function (ELF).
- Updated code of ambfor/ambmd to speed up optimisations/MD of proteins
solvated in water (Jan, 2014).
PR: 204341
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)
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3. This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.
Part II, Bump PORTREVISIONs.
PR: 182136
Supported by: Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by: bdrewery (two -exp runs)
Update to libmpc version 1.0.1 which brings the following fixes:
- Switched to automake 1.11.6, see CVE-2012-3386.
- #14669: Fixed extraction of CC from gmp.h.
- Fixed case of intermediate zero real or imaginary part in mpc_fma,
found by hydra with GMP_CHECK_RANDOMIZE=1346362345.
This is on top of the following changes from version 1.0
- Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
invariant sections) for the documentation.
- 100% of all lines are covered by tests
- Renamed functions
. mpc_mul_2exp to mpc_mul_2ui
. mpc_div_2exp to mpc_div_2ui
(Only the first 15 lines of the commit message are shown above )
- Adjust "Created by" tag to include more complete submitter's information
- Mute MKDIRs, remove trailing dot from RESTRICTED, drop leading indefinite
article from COMMENT where appropriate
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.
The vast majority of pkg-descr files had the following format when they
had both lines:
Author: ...
WWW: ....
So standardize on that, and move them to the end of the file when necessary.
Also fix some more whitespace, and remove more "signature tags" of varying
forms, like -- name, etc.
s/AUTHOR/Author/
A few other various formatting issues
- Roll back to 4.6 as 4.7 is the development version and is constantly being
re-rolled.
- Move post-patch target into files/patch-xwin.c to remove sed invocation.
- Respect NOPORTDATA and DATADIR.
- Bring files/patch-aa back (to preserve history) and retire patch-makefile.
- Fixup files/patch-xwin.c so it applies cleanly to this version.
- Update graphics/libglut to 6.4.1.
- Shared lib version and PORTREVISION bumb for all affected ports.
While I'm here:
- Remove USE_MESA knob where it was (35 ports).
It marked as depricated for 2 years.
PR: ports/90247
Submitted by: Ermal Lu?i <eri--@albabsd.org>
enhancement, build and install the opengl viewer, moldenogl.
update to 3.9, not 3.8, which is newer :)
Committed by maintainer timeout:
> Sat Apr 5 17:46:57 EST 2003 - edwin - informed maintainer
PR: 47177
Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
