mmtf_reader.hh File Reference

#include <core/io/StructFileReaderOptions.hh>
#include <core/io/pdb/pdb_reader.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/Patch.hh>
#include <core/chemical/ResidueConnection.hh>
#include <utility/string_util.hh>
#include <iosfwd>
#include <numeric/random/random.hh>
#include <core/pose/PDBInfo.hh>
#include <core/io/pdb/Field.hh>
#include <core/io/AtomInformation.hh>
#include <core/io/HeaderInformation.hh>
#include <core/io/pdb/build_pose_as_is.hh>
#include <core/io/StructFileRep.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfoManager.hh>
#include <core/io/Remarks.hh>
#include <core/io/mmtf/util.hh>
#include <core/types.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/mp.OptionKeys.gen.hh>
#include <basic/options/keys/inout.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <numeric/xyzVector.hh>
#include <utility/string_constants.hh>
#include <utility/vector1.hh>
#include <utility/tools/make_map.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/format.hh>
#include <mmtf.hpp>
#include <cstdlib>
#include <cstdio>
#include <algorithm>

Namespaces
	core
	A class for reading in the atom type properties.
	core::io
	core::io::mmtf

Functions
template<typename T >
void	core::io::mmtf::add_xbond_information (std::map< std::string, utility::vector1< T > > &xbond_map, core::io::AtomInformation const &atm_1, core::io::AtomInformation const &atm_2)
void	core::io::mmtf::add_link_and_ss_information (::mmtf::StructureData const &sd, core::io::StructFileRep &sfr, std::vector< core::io::AtomInformation > const &all_AIs, std::vector< core::Size > const &ai_to_model, core::Size const &current_model)
	This distributes what type of bonds to make based on the mmtf bonds via add_xbond_information. More...
void	core::io::mmtf::add_bond_information (::mmtf::StructureData const &sd, std::vector< core::io::AtomInformation > &all_AIs, std::map< core::Size, sd_index > const &atom_num_to_sd_map)
	This adds actuals bonds from the mmtf object to connected_indicies/connected_orders. More...
void	core::io::mmtf::add_ters_via_bonds (std::vector< core::io::AtomInformation > &all_AIs, std::vector< core::Size > const &ai_to_model)
	This adds TERs based on what is bound to the C of each AA. More...
template<typename T >
void	core::io::mmtf::set_model_index_if_not_empty (core::Size const model_index, std::string const &info_tag, std::vector< T > const &all_model_data, T &target_data)
	set_model_index_if_not_empty does what the name says :p useful for loading various datas from modelProperties More...
void	core::io::mmtf::read_extra_data (utility::vector1< core::io::StructFileRepOP > &sfrs,::mmtf::StructureData const &sd)
void	core::io::mmtf::load_heterogen_info (::mmtf::MapDecoder const &md, core::io::StructFileRep &sfr, core::Size const model_index)
	load heterogen data: heterogen_names && residue_type_base_names More...
std::vector < core::io::AtomInformation >	core::io::mmtf::make_all_atom_information (::mmtf::StructureData const &sd, std::vector< core::Size > &model_indexes, std::map< core::Size, core::Size > &model_index_to_starting_index, StructFileReaderOptions const &options)
	makes a linear vector of all AtomInformation from the mmtf data More...
core::io::AtomInformation	core::io::mmtf::make_atom_information (::mmtf::StructureData const &sd,::mmtf::GroupType const &group, int const groupAtomIndex, core::Size const atomIndex, core::Size const atomSerial, core::Size const groupIndex, core::Size const chainIndex, utility::vector1< char > &known_chainIDs, core::io::StructFileReaderOptions const &options)
	makes a single AtomInformation from the mmtf data More...
core::io::StructFileRepOP	core::io::mmtf::create_sfr_from_mmtf_filename (std::string const &mmtf_filename, core::io::StructFileReaderOptions const &options)
	create sfr from create_sfrs_from_mmtf_filename More...
utility::vector1 < core::io::StructFileRepOP >	core::io::mmtf::create_sfrs_from_mmtf_filename (std::string const &mmtf_filename, core::io::StructFileReaderOptions const &options, utility::vector1< core::Size > const &model_indexes)
	master sfr creator More...
void	core::io::mmtf::read_extra_data (::mmtf::StructureData &sd, core::io::StructFileRep &sfr)
	Read extra data from StructureData into the SFR. More...

Detailed Description

Author

Daniel Farrell (danpf.nosp@m.@uw..nosp@m.edu)