Re: [DIYbio] Protein Shop Help!

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Hey Tim!

Below is my original mail outlining the progress I made before losing
heart. It refers to "attached", but here's a link instead to the
archive, as I can't attach it through google groups:
https://anonfiles.com/file/a4c961f31541d7f38575c534ff20a5d1
(Yes, a zip rather than tar.gz, because bizarrely anonfiles.com doesn't
like gzip?)

--- Original Message ---
Hey John!
Welcome to Linux! Sorry you're having trouble already, but looking at
Protein Shop, that's not surprising. I tried to come up with a
comprehensive guide to getting it running, considering that the
developers don't offer compiled programs but rather only the source
code. Worse, it's got big dependencies; OpenGL and FLTK, plus others.
That'd be ok if it was pre-built, because you could just install OpenGL
and FLTK afterwards, but you need to install the "dev" versions of
those, and then build this.

So I tried. I installed all the dependencies and wrote a big email
explaining how, then downloaded the source code, uncompressed it, and
tried to build. Then I found that the source code bundles "Geometry"
and it doesn't compile, so I replaced "Geometry" with the newest
version, and that fixed that. I had to fix a bug where it was using the
"isnan" function as if it was in Math (i.e. Math::isNan), but I think
that must have been deprecated at some point; changed to read "isnan"
because that's now part of C++ standard lib.

And now I've got this new, exciting, bizzarre bug I don't have the
heart to solve, where it says this of compiling "EnergyRenderer.cpp":

g++ -c -o EnergyRenderer.o -D__LINUX__ -D__LITTLE_ENDIAN=1234
-D__BIG_ENDIAN=4321 -DFLTK_NEW -DFLTK_DOUBLE -DGL_GLEXT_PROTOTYPES
-ffriend-injection -I. -g0 -O3 -DNDEBUG -I/usr/include
EnergyRenderer.cpp In file included from EnergyRenderer.cpp:33:0:
ColorFunction.h:70:27: error: expected ';' at end of member declaration
ColorFunction.h:70:37: error: expected ')' before 'number'
ColorFunction.h:86:27: error: expected ';' at end of member declaration
ColorFunction.h:86:40: error: expected ')' before 'number'
EnergyRenderer.cpp: In member function 'AtomClassifier*
EnergyRenderer::getClassifier()': EnergyRenderer.cpp:639:61: error:
'ColorFunction::get' cannot be used as a function
make: *** [EnergyRenderer.o] Error 1

..I don't even know where to start with this crap. I don't code in C++,
I'm barely able to read it! :)

So, with my condolences, you've picked the most troublesome piece of
software I've seen in ages as your first use-case for Linux, which is
sad. I was sort of hoping this would be a case of "it's easy, just pop
up the software center and click install", as things usually are for
Linux these days.. :P

I'm attaching the modified source code I have so far that includes the
functioning version of Geometry and the "isnan" changes, if anyone else
who knows more about C++ wants to have a go at getting this to compile..

Best,
Cathal

On Thu, 19 Sep 2013 11:27:04 -1000
William Heath <wgheath@gmail.com> wrote:

> Hi All,
>
> I used to teach c++ and programmed in it for over 5 years etc... I
> also specialize in linux. I will see what I can do :>
>
> -Tim BCSE, MSCS, MBA
>
>
> On Thu, Sep 19, 2013 at 9:29 AM, Cathal Garvey
> <cathalgarvey@cathalgarvey.me
> > wrote:
>
> > Lol, ignore last message a minute, the preceding message failed to
> > deliver because Google Groups didn't like the attachments. Will post
> > later.
> >
> > I'm afraid it's bad news, John; ProteinShop is either a very buggy
> > or very outdated codebase, and won't compile for me. Perhaps
> > someone with better C++ chops can pick up where I've left off and
> > make it work.
> >
> > On Thu, 19 Sep 2013 05:46:59 -0700 (PDT)
> > John Dohnal <johnhdohnal@aol.com> wrote:
> >
> > > I have never used a Linux OS before, but I downloaded the latest
> > > version of Ubuntu in order to run Protein Shop. I downloaded the
> > > latest version of Protein Shop, but I don't know how to start
> > > it. I know nothing about using Linux, so any explicit, basic
> > > instructions would be most helpful. In the readme file, it
> > > mentions some other files that may need to be installed, but I
> > > don't even know where to begin. Please help!
> > > Thanks,
> > > John
> > >
> >
> >
>