Rosetta  2021.16
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mmtf_reader.cc File Reference
#include <core/io/mmtf/mmtf_reader.hh>
#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/io/ozstream.hh>
#include <utility/string_util.hh>
#include <utility/string_constants.hh>
#include <utility/io/izstream.hh>
#include <numeric/random/random.hh>
#include <core/pose/PDBInfo.hh>
#include <core/io/pdb/Field.hh>
#include <core/io/HeaderInformation.hh>
#include <core/io/AtomInformation.hh>
#include <core/io/pdb/build_pose_as_is.hh>
#include <core/io/StructFileRep.hh>
#include <core/io/mmtf/ExtraDataEnum.hh>
#include <core/io/mmtf/ExtraDataEnumManager.hh>
#include <core/simple_metrics/SimpleMetricStruct.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfoManager.hh>
#include <core/io/Remarks.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/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

static basic::Tracer TR ("core.io.mmtf.mmtf_reader")
 
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)
 
template<typename T >
bool core::io::mmtf::sort_xbond_func (T const &lhs, T const &rhs)
 
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...
 
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...
 
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...
 
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...
 
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...
 
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...
 
template<typename T >
void core::io::mmtf::map_decode_from_model (::mmtf::MapDecoder const &md, std::string const &map_key, bool const required, core::Size const model_index, T &target)
 
void core::io::mmtf::read_extra_data (core::io::StructFileRepOP &sfr,::mmtf::StructureData const &sd, core::Size const model_index)
 
std::map< core::Size, core::Sizecore::io::mmtf::make_old_to_new_mapping (std::vector< std::vector< core::Size >> const atom_idx_chains, core::Size const starting_index)
 
void core::io::mmtf::update_bond_indices (core::io::StructFileRep &sfr, std::map< core::Size, core::Size > const &old_to_new_idx)
 
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...
 

Function Documentation

static basic::Tracer TR ( "core.io.mmtf.mmtf_reader"  )
static