Expose "hidden options"

I was looking for a way to specify the mmCIF dict file, and found the "hidden options":

Lines 92 to 100 in 32b28bf

    
           hidden_options.add_options() 
        
           	("xyzin,i",				po::value<std::string>(),	"coordinates file") 
        
           	("output,o",            po::value<std::string>(),	"Output to this file") 
        
           	("debug,d",				po::value<int>(),			"Debug level (for even more verbose output)") 
        
           	("compounds",			po::value<std::string>(),	"Location of the components.cif file from CCD") 
        
           	("components",			po::value<std::string>(),	"Location of the components.cif file from CCD, alias") 
        
           	("extra-compounds",		po::value<std::string>(),	"File containing residue information for extra compounds in this specific target, should be either in CCD format or a CCP4 restraints file") 
        
           	("mmcif-dictionary",	po::value<std::string>(),	"Path to the mmcif_pdbx.dic file to use instead of default")

I wonder why these are hidden from the --help considering I just had use for them. Can they not be unhidden?

Could you give a bit more details of what you were trying to do so we can see whether this is a general use-case or a rather specific one?

You are right, these options ended up at the wrong location. I'll fix that. Thanks for reporting.

…

-maarten Op 03-05-2022 om 06:45 schreef Michael Milton:

I was looking for a way to specify the mmCIF dict file, and found the "hidden options": https://github.com/PDB-REDO/dssp/blob/32b28bf23cb2476eeb5ee97de2485337360f37e5/src/mkdssp.cpp#L92-L100 <https://github.com/PDB-REDO/dssp/blob/32b28bf23cb2476eeb5ee97de2485337360f37e5/src/mkdssp.cpp#L92-L100> I wonder why these are hidden from the |--help| considering I just had use for them. Can they not be unhidden? — Reply to this email directly, view it on GitHub <#36>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADNA47DNBI6XK6SY6QUEAJ3VICVOTANCNFSM5U526I7A>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Maarten L. Hekkelman http://www.hekkelman.com/

Well I was trying to install dssp 4.0 into a conda environment, but for whatever reason it wasn't able to find the mmCIF dictionary file, which was actually installed. If it's controlled by an environment variable then it would be great to document that too. But failing that, I had to use this hidden flag.

As a sidenote: it would be great if you guys could submit dssp (and any of your other tools) to bioconda. I've actually already submitted libcifpp there, but I had some trouble getting cif-tools to compile.

Thanks for the suggestion. We'll look into that.

If any of you end up doing that, I'm happy to give you maintainership over the bioconda recipe I made and/or write permissions to my branch for cif-tools to make things easier.

I've updated both libcifpp (version 4.0.1) and dssp (version 4.0.5). This issue should now be solved.

Great, thank you!

	hidden_options.add_options()
	("xyzin,i", po::value<std::string>(), "coordinates file")
	("output,o", po::value<std::string>(), "Output to this file")
	("debug,d", po::value<int>(), "Debug level (for even more verbose output)")

	("compounds", po::value<std::string>(), "Location of the components.cif file from CCD")
	("components", po::value<std::string>(), "Location of the components.cif file from CCD, alias")
	("extra-compounds", po::value<std::string>(), "File containing residue information for extra compounds in this specific target, should be either in CCD format or a CCP4 restraints file")
	("mmcif-dictionary", po::value<std::string>(), "Path to the mmcif_pdbx.dic file to use instead of default")