From its pymolwiki page: === psico is a python module which extends PyMOL with many commands. Some of the provided commands are already in the PyMOLWiki Script Library, but it contains also many new stuff. === Some of its functions require additional python modules. It also includes some wrappers for external tools. I looked for what needs to be installed to meet the requirements in its README: Python modules: -------------- * numpy: dev-python/numpy * Bio (biopython): sci-biology/biopython * MMTK: sci-libs/mmtk External tools: -------------- * dssp: sci-chemistry/dssp * stride: sci-biology/stride * TMalign: http://zhanglab.ccmb.med.umich.edu/TM-align/ * TMscore: http://zhanglab.ccmb.med.umich.edu/TM-score/ * MMalign: http://zhanglab.ccmb.med.umich.edu/MM-align/ * theseus: sci-chemistry/theseus from the dberkholz overlay * needle: dev-ruby/needle ???? * DynDom: dyndom command in sci-chemistry/ccp4-apps * qdelaunay: command from media-libs/qhull * mencoder: media-video/mplayer * pdbmat: http://ecole.modelisation.free.fr/modes.html * diagrtb: http://ecole.modelisation.free.fr/modes.html
I will take a look into it. Seems to be very cool
+*pymol-plugins-psico-3.0 (21 Mar 2012) + + 21 Mar 2012; Justin Lecher <jlec@gentoo.org> +pymol-plugins-psico-3.0.ebuild, + +metadata.xml: + New addition, written by me, #408995 + I needed to add some more deps.
Thanks Justin. Impressive work. One question, though, out of curiosity. DynDom is also provided by the sci-chemistry/ccp4-apps packages, which has a stable version. It is the same program as the one in http://fizz.cmp.uea.ac.uk/dyndom/, as revealed by the /usr/share/doc/ccp4-apps-6.1.3-r10/html/dyndom.html file. Why not use this, with sci-chemistry/ccp4-apps as a dependency, instead of telling the user to download and compile DynDom by himself? License reasons? Version number? Related to this, whenever I try to compile dyndom by following its directions, I get this error with m_inv.f: === $ make gcc -c -O2 DynDom.f gcc -c -O2 bstft.f gcc -c -O2 svd.f gcc -c -O2 modcbeta.f gcc -c -O2 det.f gcc -c -O2 inoutputR.f gcc -c -O2 spaceremove.f gcc -c -O2 stringlength.f gcc -c -O2 extcomp2.f gcc -c -O2 m_inv.f m_inv.f:10.23: SMALLREAL=1.0E-90 1 Warning: Real constant underflows its kind at (1) m_inv.f:11.22: LARGEREAL=1.0E90 1 Error: Real constant overflows its kind at (1) make: *** [m_inv.o] Error 1 === LARGEREAL and SMALLREAL are REAL*8 type variables in m_inv.f, which seem too small for a 1e90 value. Have you been able to solve this?
cool, i didn't remember, that dyndom was in ccp4-apps already. The problem is that the license of the standalone version is "lets call it bad". I will attach a patch later to solve the issue during compilation. I have the patch at home.
+ 24 Mar 2012; Justin Lecher <jlec@gentoo.org> pymol-plugins-psico-3.0.ebuild: + Add sci-chemistry/ccp4-apps to DEPs for dyndom, thanks urcindalo pointing me + to this +
Created attachment 306497 [details, diff] dyndom build patch Here the patch
