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mmtf_writer.cc File Reference

Functions for MMTF writing. More...

#include <core/io/StructFileRepOptions.hh>
#include <core/io/pose_to_sfr/PoseToStructFileRepConverter.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/io/izstream.hh>
#include <utility/version.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/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 <msgpack.hpp>
#include <mmtf.hpp>
#include <cstdlib>
#include <cstdio>
#include <algorithm>
#include <tuple>
#include <core/io/mmtf/mmtf_writer.hh>

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_writer")
 
bool core::io::mmtf::dump_mmtf (core::pose::Pose const &pose, std::string const &file_name, StructFileRepOptionsCOP options=StructFileRepOptionsCOP(new StructFileRepOptions))
 Dump a MMTF from a pose to a file. Return success or failure. More...
 
core::io::StructFileRepOP core::io::mmtf::dump_mmtf (core::pose::Pose const &pose, std::ostream &out, StructFileRepOptionsCOP options)
 Dump an MMTF from a pose to an ostream. More...
 
core::io::StructFileRepOP core::io::mmtf::dump_mmtf (core::pose::Pose const &pose, std::string const &jd2_job_data, std::ostream &out)
 Dump an MMTF from a pose, optionally extracting extra info. More...
 
bool core::io::mmtf::dump_mmtf (std::string const &file_name, StructFileRepOP sfr, StructFileRepOptions const &options)
 dump_mmtf function. Create the sfr from pose using the PoseToStructFileRepConverter class. Return success or failure. More...
 
void core::io::mmtf::set_mmtf_default_options (core::io::StructFileRepOptions &options)
 Set StructFileRepOptions defauls for mmtf. More...
 
::mmtf::GroupType core::io::mmtf::make_current_group (aiGroup const &ai_group)
 
bool core::io::mmtf::is_in_bondAtomList (std::vector< int32_t > const &bondAtomList, core::Size const lower_atom, core::Size const upper_atom)
 
aiChain core::io::mmtf::make_chain (utility::vector0< AtomInformation > const &chain_atoms)
 group chain_atoms into groups based on chain_id and resseq More...
 
aiPose core::io::mmtf::aiPose_from_sfr (core::io::StructFileRep const &sfr)
 Convert linear sfr to vec0[vec0[vec0[AtomInformation]]]. More...
 
aiModels core::io::mmtf::aiModels_from_sfrs (utility::vector1< core::io::StructFileRepOP > const &sfrs)
 Convert linear sfr to vec0[vec0[vec0[vec0[AtomInformation]]]]. More...
 
void core::io::mmtf::add_bonds_to_sd (::mmtf::StructureData &sd, aiModels const &AIM, std::map< core::Size, sd_index > const &atom_num_to_sd_map)
 
template<typename T >
void core::io::mmtf::add_if_not_empty (std::string const &given_name, T const &content, std::map< std::string, msgpack::object > &target_map, msgpack::zone &zone)
 add_if_not_empty – adds to a sd {string: msgpack::object} templated to allow us to add a variety of containers More...
 
template<typename T >
void core::io::mmtf::resize_and_add_if_not_empty (utility::vector1< core::io::StructFileRepOP > const &sfrs, std::string const &key, std::map< std::string, msgpack::object > &xxxProperties, msgpack::zone &zone, T const &fn)
 
void core::io::mmtf::add_extra_data (::mmtf::StructureData &sd, utility::vector1< core::io::StructFileRepOP > const &sfrs, core::io::StructFileRepOptions const &options)
 Add extra info to the structureData if we are asked to add it includes: heterogen info. More...
 
std::map< std::tuple
< core::Size, core::Size,
core::Size, core::Size >
, core::Size
core::io::mmtf::make_AIM_to_atom_num (aiModels const &AIM)
 
void core::io::mmtf::dump_mmtf (std::ostream &out, utility::vector1< core::io::StructFileRepOP > sfrs, core::io::StructFileRepOptions const &options)
 dump single mmtf function. More...
 
void core::io::mmtf::dump_mmtf (std::ostream &out, StructFileRepOP sfr, StructFileRepOptions const &options)
 dump single mmtf function. More...
 
::mmtf::StructureData core::io::mmtf::sfr_to_sd (core::io::StructFileRepOP sfr, core::io::StructFileRepOptions const &options)
 
::mmtf::StructureData core::io::mmtf::sfrs_to_sd (utility::vector1< core::io::StructFileRepOP > sfrs, core::io::StructFileRepOptions const &options)
 

Detailed Description

Functions for MMTF writing.

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

Function Documentation

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