Command line to go from Latfit output to lattice output

[brspurri]

Is there any documentation or an example on how to use the command line to go from the latfit output file (ie., 1CZ8discretized5.25FuC.pdb) to the lattice output (ie., 1CZ8_VWInLattice.txt).

I am trying to create my own discretized antigens, while desperately trying to avoid the GUI.

Many thanks!

[petouzeman]

Dear Brett,

So, first, mega sorry for the delay, I didn't receive notifications, and this is not the main repository where we develop the program (unexperienced me)

Indeed, we didn't make it possible to run each single step separately for discretization (yet),
And I also realized a confusion in the howto, it is possible to run the discretization by command line (although the GUI will popup), the job is still already done.

Feel free to contact me at probertmontp at gmail.com if you are still interested to do it,

[petouzeman]

Dear Brett again,
So, here is an example how to do from a C++ command, I will add a command line option!

A full discretization without GUI would be:

#include "discretization.h"
discretization a("3ULU","A",5.25, "FuC");
string file1 = a.preparePDB(); // should return file1 = "3ULUdeIns.pdb";
a.initialize();
string file2 = a.discretizeIntoFile(file1,true,25,true); // should return file2 = "3ULU_AdiscretizedFuC5.25.pdb"
string createdOutputInLatticeFile = a.transformDiscretizedFileToLattice(file2);

So you can run only the last step. I will make a commit with a new command line

[petouzeman]

Ok, now what you want is available, normally even in the AbsolutNoLib version,

#1 Selecting the chain and removing insertions
./Absolut discretize_delete_insertions 1ADQ A
output: 1ADQdeIns.pdb

#2 Using latfit to generate a discretized PDB
./Absolut discretize_latfit_to_discrete_pdb 1ADQ A 1ADQdeIns.pdb
output: 1ADQ_AdiscretizedFuC5.25.pdb

or with non-default parameters:
./Absolut discretize_latfit_to_discrete_pdb 1ADQ A 1ADQdeIns.pdb 6 CoM false 40
output: 1ADQ_AdiscretizedCoM6.pdb

#3 and last step, from the latfit output to the inLattice text file
./Absolut discretize_discrete_pdb_to_lattice 1ADQ A 1ADQ_AdiscretizedFuC5.25.pdb
output: 1ADQ_Ainlattice.txt

Will commit now! Thanks for feedback!

[petouzeman]

Commit was updated, I will close the issue!