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Typedefs | Functions | Variables
ddg_monomer.cc File Reference
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <protocols/scoring/Interface.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <basic/options/util.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/ddg.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/database/open.hh>
#include <devel/init.hh>
#include <numeric/xyzVector.hh>
#include <core/pack/task/ResfileReader.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#include <ObjexxFCL/format.hh>
#include <cstdlib>
#include <string>
#include <protocols/ddg/ddGMover.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>

Typedefs

using mutations = utility::vector1< core::chemical::AA >
 
using ddgs = utility::vector1< double >
 

Functions

void print_ddgs (std::string const &ddg_out, std::string const &label, ddgs const &delta_e_components, ddgs const &, double total_ddgs, protocols::ddg::ddGMover &mover, bool print_header, bool min_cst)
 print ddGs More...
 
void read_in_mutations (utility::vector1< mutations > &res_to_mut, std::string filename, pose::Pose &pose)
 The input file is a list of mutation blocks. Usually, this will be a set of point mutations. where each "block" lists a single mutation. However, it is possible to specify multiple mutations together in a single block. More...
 
int main (int argc, char *argv[])
 

Variables

static basic::Tracer TR ("apps.public.ddg.ddg_monomer")
 

Detailed Description

Author
Liz Kellogg ekell.nosp@m.ogg@.nosp@m.u.was.nosp@m.hing.nosp@m.ton.e.nosp@m.du comments by JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)

Typedef Documentation

using ddgs = utility::vector1<double>
using mutations = utility::vector1<core::chemical::AA>

Function Documentation

int main ( int  argc,
char *  argv[] 
)
void print_ddgs ( std::string const &  ddg_out,
std::string const &  label,
ddgs const &  delta_e_components,
ddgs const &  ,
double  total_ddgs,
protocols::ddg::ddGMover &  mover,
bool  print_header,
bool  min_cst 
)

print ddGs

References utility::exit(), ObjexxFCL::format::F(), test.T110_numeric::m, and TR.

Referenced by main().

void read_in_mutations ( utility::vector1< mutations > &  res_to_mut,
std::string  filename,
pose::Pose pose 
)

The input file is a list of mutation blocks. Usually, this will be a set of point mutations. where each "block" lists a single mutation. However, it is possible to specify multiple mutations together in a single block.

The file format is: "total N" followed by N blocks, where each block is "M" specifying followed by M lines of wt/resid/mutaa triples "wtaa resid mutaa" N, M and resid are all supposed to be integers. wtaa, and mutaa are supposed to be 1-letter amino acid codes.

References debug_assert, basic::Tracer::Error, basic::options::OptionKeys::mp::mutate_relax::mutation, clean_pdb_keep_ligand::resnum, runtime_assert, TR, and revert_app::wt.

Referenced by main().

Variable Documentation

basic::Tracer TR("apps.public.ddg.ddg_monomer")
static

Referenced by main(), print_ddgs(), and read_in_mutations().