The C++ example does not seem to work

[lopippo]

Greetings, following the COMPILATION instructions, I get the following output:

(ins)rusconi@roma:~/devel/packaging/isospec/tarballs/isospec/Examples/C++$ clang++ -std=c++11 -lIsoSpec++ -L. water.cpp water.cpp:7:5: error: unknown type name 'IsoSpec' IsoSpec iso = IsoSpec::IsoFromFormula("H2O1", 0.9); ^ water.cpp:7:20: error: use of undeclared identifier 'IsoSpec' IsoSpec iso = IsoSpec::IsoFromFormula("H2O1", 0.9); ^ water.cpp:57:15: error: unknown type name 'IsoSpecLayered' iso = new IsoSpecLayered(elementNumber, isotopeNumbers, atomCounts, isotope_masses, probs, 0.9); ^ 3 errors generated.

Further: when I change directory to IsoSpec++ and I run

grep IsoFromFormula *

I do not get any output.

I can build the shared library.

git status in the master branch is ok.

What could I be missing? Thank you very much for providing this library. Filippo

[michalsta]

Hi,

The example has lagged a bit behind the codebase - it targetted the 1.0.X API, while the repo is in 1.9.0alpha stage. I have fixed that though, it should work now.

[lopippo]

Greetings,

thank you for your message.

On Thu, Oct 04, 2018 at 02:35:29PM -0700, michalsta wrote:

The example has lagged a bit behind the codebase - it targetted the 1.0.X API, while the repo is in 1.9.0alpha stage. I have fixed that though, it should work now.

I have git pull'ed now, and in fact the example builds just fine.

When you have some time, it would be wonderful to write some small documentation that I'll eagerly add to the Debian package that I intend to create with your C++ library.

Thank you for providing the community with this work!

Sincerely, Filippo

--

⢀⣴⠾⠻⢶⣦⠀ Filippo Rusconi, PhD ⣾⠁⢠⠒⠀⣿⡁ Scientist at CNRS ⢿⡄⠘⠷⠚⠋⠀ Debian Developer ⠈⠳⣄⠀⠀⠀⠀ http://msxpertsuite.org http://www.debian.org

[michalsta]

Yes, in fact, since there seems to be a flurry of interest lately, I think that we'll try to get the repo in shape to push out the 1.9.0 (stable, non-alpha) release sometime in the next week, and that of course will include some sensible documentation, among other things. Will that be okay with whatever timelines you have to keep?

On Fri, 5 Oct 2018 at 10:23, lopippo notifications@github.com wrote:

Greetings,

thank you for your message.

On Thu, Oct 04, 2018 at 02:35:29PM -0700, michalsta wrote:

The example has lagged a bit behind the codebase - it targetted the 1.0.X API, while the repo is in 1.9.0alpha stage. I have fixed that though, it should work now.

I have git pull'ed now, and in fact the example builds just fine.

When you have some time, it would be wonderful to write some small documentation that I'll eagerly add to the Debian package that I intend to create with your C++ library.

Thank you for providing the community with this work!

Sincerely, Filippo

--

⢀⣴⠾⠻⢶⣦⠀ Filippo Rusconi, PhD ⣾⠁⢠⠒⠀⣿⡁ Scientist at CNRS ⢿⡄⠘⠷⠚⠋⠀ Debian Developer ⠈⠳⣄⠀⠀⠀⠀ http://msxpertsuite.org http://www.debian.org

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/MatteoLacki/IsoSpec/issues/7#issuecomment-427285424, or mute the thread https://github.com/notifications/unsubscribe-auth/AKRphMz-YOF9P2LzfotEjEcEjFVeg624ks5uhxcKgaJpZM4XGrjm .

[lopippo]

Yes, in fact, since there seems to be a flurry of interest lately, I think that we'll try to get the repo in shape to push out the 1.9.0 (stable, non-alpha) release sometime in the next week, and that of course will include some sensible documentation, among other things. Will that be okay with whatever timelines you have to keep?

Thank you very much. That would be perfect. Packaging -at least as C++ lib- should be very straighforward.

Sincerely, Filippo

[michalsta]

Hi,

We have just now tagged and released a 1.9.0, along with documentation and fixed examples (and several bugfixes too). Sorry it took much longer than projected ;)

Anyway, if you still want to package it, now would be a good moment. Of course feel free to contact us if you have any questions/other issues!

[lopippo]

Greetings, Matteo,

On Wed, Nov 07, 2018 at 01:04:27PM -0800, michalsta wrote:

We have just now tagged and released a 1.9.0, along with documentation and fixed examples (and several bugfixes too). Sorry it took much longer than projected ;)

Anyway, if you still want to package it, now would be a good moment. Of course feel free to contact us if you have any questions/other issues!

Thank you so much for this update.

I would be very grateful if you would take some time to write a small manual with some typical usecases (proteins, peptides, small molecules), just show the command line, the formula to crunch, the textual output and how it translates into a super isotopic cluster.

Sorry for asking this, but I find it essential that users (myself in it) can be put at work with nice examples.

Do you know docbook ? If you write that document, I could format it in docbook so that we can generate pdf / html version of it.

Cheers, Filippo

--

⢀⣴⠾⠻⢶⣦⠀ Filippo Rusconi, PhD ⣾⠁⢠⠒⠀⣿⡁ Scientist at CNRS ⢿⡄⠘⠷⠚⠋⠀ Debian Developer ⠈⠳⣄⠀⠀⠀⠀ http://msxpertsuite.org http://www.debian.org

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[MatteoLacki]

Hello Filippo,

We will cook up some small examples, most likely during the weekend. I never heard of docbook. Will simple LaTeX be enough (like, can something like pandoc translate it to docbook)? I can also write something in markdown and put it on github. Actually, there is a webpage already hosted there. We simply would need to update it, because it's no longer valid.

Best,

[lopippo]

Greetings, Matteo, sure LaTeX will be fine. Please, integrate in the examples, at least one detailed example for a typical peptide (15-20 residues-long) and anothe one for a protein (400 residues-long, typically). That will make your soft more appealing to massists doing top/middle-down proteomics (like I'll start doing soon ;-)

Thanks for your hard work! Cheers, Filippo

[MatteoLacki]

Hi Filippo,

I am still working on the description (sorry, IsoSpec is not what they pay me for ;) ). It occurred to me, that you might want to use IsoSpec directly with amino-acids as input. This is not directly supported by IsoSpec for now, but I've cooked up a tool for changing protein fastas into IsoSpec parsable chemical formulas, called aa2atom. Since we still have some important things to do with the software itself, I hope this will offer a solution to the potential problem, or something just I only imagined to be a problem. Anyway, the description of how to call IsoSpec in C++ is coming.

Best wishes,

[lopippo]

Greetings, Matteo,

Thank you so much for the update. That's awesome. I have seen the new man directory, which i'll look deeper into in the next days. I feel like we are approaching the documentation level required by the Debian packaging standards. Looking forward to reading the examples to bootstrap new users right into the use of IsoSpec! Thank you for your hard work! Cheers, Filippo

[MatteoLacki]

Can I say this issue is no longer valid?

[lopippo]

Certainly, I close it right now. Thank you Filippo