AMIT KUMAR MISHRA
AMIT KUMAR MISHRA
Till now for params like this `-variable_modifications "Oxidation (M)" "Formyl (K)" "Oxidation (P)" "Formyl (S)" "Oxidation (F)" "Palmitoyl (Protein N-term)"` can produce params like following ``` variable_mod01 = 15.9949 MPF...
I tried individually and the results were the following With only Carbamyl (N-term) ``` variable_mod01 = 43.0058 n 0 5 0 2 0 0.0 variable_mod02 = 43.0058 RST 0 5...
yeah sure, [here](https://github.com/OpenMS/OpenMS/commit/b1d593204e8c11de78cd30d1906dbffe72581cf3) it is. I don't think there was any discussion regarding keeping the N-term separate. That's happening because it has a different `term_distance` (in Protein N-term) because then...
So final one should be like this. right? ``` variable_mod01 = 43.0058 n 0 5 0 2 0 0.0 variable_mod02 = 43.0058 n 0 5 0 0 0 0.0 variable_mod03...
I don't know how these params get processed ahead by comet but what I am observing at this point is that we are ignoring [this line](https://github.com/OpenMS/OpenMS/blob/a16568db230876c1e475a73da9b89d5d55e5ebf6/src/topp/CometAdapter.cpp#L394) and [this line](https://github.com/OpenMS/OpenMS/blob/a16568db230876c1e475a73da9b89d5d55e5ebf6/src/topp/CometAdapter.cpp#L397) and...
So we will merge two residues when they are N_term/C_term/Anywhere. But what if we have N_term and C_term? then what will be the `nc_term`(2 or 3)? like here it is...
May you give a example params for Carbamyl(R), Carbamyl(N-Term), Carbamyl(C-Term), assuming this is valid parameter
If we have declarations in VarMod.h and definitions in VarMod.cpp then how do we make definitions available to CometAdapter.cpp ? I got to know that we can do forward declaration...
Nope... It says something like this ``` /usr/bin/ld: OpenMs/src/topp/CometAdapter.cpp:455: undefined reference to `OpenMS::VarMod::merge(OpenMS::VarMod&)' /usr/bin/ld: OpenMs/src/topp/CometAdapter.cpp:463: undefined reference to `OpenMS::VarMod::toCometString() const' ``` It can get the declarations from header because that's...
Maybe that file needs to be included in the build system somehow?