Package: gopenmol Version: 2.30 Revision: 4 Description: Molecular visualization and analysis program DescDetail: << With gOpenMol small molecules, and to lesser extent protein structures, as well as the chemical properties, total electron densities and molecule orbitals of small molecules can be visualized and analyzed. Data from a variety of computational chemistry programs such as TurboMole, Gaussian, Gamess, etc., can be analyzed if the output files from these programs have been converted into the .plt-file format understood by gOpenMol. Moreover, dynamics done with, e.g., InsightII can be visualized and a short mpeg animation of the dynamics files generated. Copyright info (from the website): The program is distributed free of charge for academic installations and academic use. If you have used gOpenMol for your publication, please use the following references: * Laaksonen, L. (1992) A graphics program for the analysis and display of molecular dynamics trajectories. J. Mol. Graph. 10: 33-34. * Bergman, D.L., Laaksonen, L., and Laaksonen, A. (1997) Visualization of solvation structures in liquid mixtures. J. Mol. Graph. Model. 15: 301-306. << DescPort: << A bug in the %p/bin/tclsh from tcltk-8.4.1-2 causes tclsh to emit DOS-style line-endings (\r\n) when used in a pipeline. This breaks parsing of its output by configure. Tcl/Tk folks know and are working on it. For now, just patch configure to fix the line-endings (in a way that will continue working when bug is fixed). Darwin has no malloc.h, so discard all #include of it. But malloc() needs sys/types.h for size_t. The recommended replacement for malloc.h is stdlib.h (which brings along size_t for us) so #include that as necessary. Darwin (gcc) cpp doesn't seem to like null parameters to macros, so fix the last param IMPLEMENT_GET_MODIFIABLE_POINTER in trajectory.c to something harmless. OTOH, GOM_PARSER_RETRIEVE_SELECTIONLIST is only a mild warning? But it does cause a cpp-precomp segfault (not necessarily cause/effect). Apple engineers say just -no-cpp-precomp and get on with our life; so be it. I don't understand why when set_show in config.mk causes ": command not found" when show=':', but making it always 'echo' seems to allow the install.mk install-data-dir target to proceed. The build/install process doesn't understand how to install in a temp packaging location for later installation somewhere else, so need to fix the pathnames in some runtime scripts. Package installs lots of docs in its private hierarchies, so move to or make links from the standard share/doc/%n location. Patch install.mk to not install libs that we already have from other Fink packages. Set our Depends for each of those packages >= version that comes in Source tarball. Put libgopenmol.* in lib instead of private bin. Still in its private space since I don't know version info (so leave -avoid-version) so cannot do -shlibs. Patch plugins/config.mk.ac to link plugins as shared libraries (.dylib) instead of bundles (.so), obeying dyld error message given when using default options. Patch data/{gopenmol_guirc,gopenmolrc}.tcl to use the platform-correct lib extension. The "Tools...Plugins...load" routine for the libfilters plugin was removing the menu item for libsymmetry instead of for itself. Patched a mistake in filters.tcl to fix this. Some plugins fail to load because "couldn't find procedure Thing_Init" (during a tcl "load" call for libthing.dylib). These functions all exist in the associated source files and it's not consistent which ones fail. It seems to depend on order loaded, so there may be something weird going on with memory or symbol namespaces. Patch vrml.tcl to fix broken "Tools...Plugins...VRML..." menu item callback. I can't find a make target to use the src/plugins/*/*.tcl instead of (or to first copy these into) data/autotcl/plugins/*.tcl so will manually copy these during PatchScript (so do all patching to src/ not data/). Fix g77 options to allow full-width lines in utility/UHBD/*.f Fix flag passing in utility.mk. Fix read() format in utility/convert.f (my best guess). Many problems while compiling icon8/icon8.f. Add flag to reduce argument-type-difference errors (for MOVLAP(), HUCKEL(), BANGIT()) to warnings and hope for the best. The allocatable:: attribute and allocate() call are F90 things that do not exist in our g77. Fink has a gfortran package that is a (partial) implementation of F95, but using that as the compiler gives other numberous error messages. No default $TMP or $TMPDIR, so set GOM_TEMP in environment.txt to user's own. The rungOpenMol script just sets vars and calls the actual gopenmol, so put the vars in a profile.d and patch install.mk to not bother with the wrapper. Move the actual binary into %p/bin. The internal command is "identify" but the GUI tries to call it as "indentify". Patch parser/p_s_atomc.c to fix (will be fixed in a future version). Utility programs are in %p/lib/gOpenMol-%v/bin so you have to either add that to yout PATH or call the programs using the full pathname. This is so we don't conflict with (for example) imagemagick's convert program. This will eventually be handled automatically via a splitoff for placing these programs in PATH and/or using alternatives. << Homepage: http://www.csc.fi/gopenmol/ License: Restrictive Maintainer: Daniel Macks BuildDepends: dlcompat-dev, tcltk-dev (>= 8.4-1), glut, libjpeg, python23 | python23-nox, g77, x11-dev # gfortran Depends: dlcompat-shlibs, tcltk (>= 8.4-1), tcltk-shlibs (>= 8.4-1), tcllib (>= 1.4-1), bwidget (>= 1.6.0), tclxml (>= 2.6-1), tclexpat (>= 2.6-1), glut-shlibs, libjpeg-shlibs, python23-shlibs | python23-nox-shlibs, x11 #GCC: 3.1 SetCC: gcc3 SetCXX: g++3 Source: http://www.csc.fi/gopenmol/distribute/%n-linux-%v.tar.gz Source-MD5: e988fac98c064d574daba5329055110a SourceDirectory: gOpenMol-%v Patch: %n.patch PatchScript: << perl -pi -e 's/#include\s*//' `find . -name \*.\[hc\]` perl -pi -e 's#__fink_d__#%d#g;s#__fink_p__#%p#g' src/config.mk.ac src/unix/make/install.mk cp -f src/plugins/{ball/ball.tcl,fchk203/fchk.tcl,filters/filters.tcl,sararea/surfarea.tcl,sym602/symmetry.tcl,vrml/vrml.tcl} data/autotcl/plugins << SetCPPFLAGS: -no-cpp-precomp SetMACOSX_DEPLOYMENT_TARGET: 10.2 ConfigureParams: --with-x --enable-shared CompileScript: << cd src; TCLSH=%p/bin/tclsh PYTHON=%p/bin/python2.3 ./configure %c cd src; make all utility << InstallScript: << cd src; make prefix=%i install install-utility mkdir -p -m 0755 %i/share/doc/%n ln -s %p/share/gOpenMol-%v/help %i/share/doc/%n/html mv %i/share/gOpenMol-%v/docs/* %i/share/doc/%n rmdir %i/share/gOpenMol-%v/docs mv %i/share/gOpenMol-%v/utility %i/share/doc/%n rm %i/share/gOpenMol-%v/README-GLUT-win32.txt mv %i/share/gOpenMol-%v/{COPYRIGHT,README.txt} %i/share/doc/%n << RuntimeVars: << GOM_ROOT: %p/lib/gOpenMol-%v <<