core::io::mmtf Namespace Reference

Classes
class	ExtraDataEnumManager
	Enum string/enum functions for pose extra data we will be storing/retrieving. ALL enums must be defined in mmtf/ExtraDataEnum.hh. More...
struct	sd_index
	storage for indicies to something in a mmtf struct this makes it easier to iterate the struct in relation to AtomInformation vectors More...
struct	ai_cmp
	simple comparator for AtomInformation when grouping by residue/grp More...

Typedefs
typedef utility::pointer::shared_ptr< ExtraDataEnumManager >	ExtraDataEnumManagerOP
typedef utility::pointer::shared_ptr< ExtraDataEnumManager const >	ExtraDataEnumManagerCOP
typedef utility::vector0< core::io::AtomInformation >	aiGroup
typedef utility::vector0< aiGroup >	aiChain
typedef utility::vector0< aiChain >	aiPose
typedef utility::vector0< aiPose >	aiModels

Enumerations
enum	ExtraDataEnum {   pose_cache_string_data = 1 , pose_cache_real_data , pdb_comments , simple_metric_string_data ,   simple_metric_real_data , simple_metric_composite_string_data , simple_metric_composite_real_data , simple_metric_per_residue_string_data ,   simple_metric_per_residue_real_data , simple_metric_per_residue_string_output , simple_metric_per_residue_real_output , ExtraDataEnum_total =simple_metric_per_residue_real_output }
	Enum definitions for pose extra data we will be storing/retrieving. ALL Enums must also have their string equivalents defined in mmtf/ExtraDataEnumManager.cc. More...

Functions
template<typename T >
void	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	sort_xbond_func (T const &lhs, T const &rhs)
void	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	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 >	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	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	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	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	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	map_decode_from_model (::mmtf::MapDecoder const &md, std::string const &map_key, bool const required, core::Size const model_index, T &target)
void	read_extra_data (core::io::StructFileRepOP &sfr, ::mmtf::StructureData const &sd, core::Size const model_index)
std::map< core::Size, core::Size >	make_old_to_new_mapping (std::vector< std::vector< core::Size >> const atom_idx_chains, core::Size const starting_index)
void	update_bond_indices (core::io::StructFileRep &sfr, std::map< core::Size, core::Size > const &old_to_new_idx)
utility::vector1< core::io::StructFileRepOP >	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	read_extra_data (utility::vector1< core::io::StructFileRepOP > &sfrs, ::mmtf::StructureData const &sd)
void	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...
void	read_extra_data (::mmtf::StructureData &sd, core::io::StructFileRep &sfr)
	Read extra data from StructureData into the SFR. More...
bool	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	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	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	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	set_mmtf_default_options (core::io::StructFileRepOptions &options)
	Set StructFileRepOptions defauls for mmtf. More...
::mmtf::GroupType	make_current_group (aiGroup const &ai_group)
bool	is_in_bondAtomList (std::vector< int32_t > const &bondAtomList, core::Size const lower_atom, core::Size const upper_atom)
aiChain	make_chain (utility::vector0< AtomInformation > const &chain_atoms)
	group chain_atoms into groups based on chain_id and resseq More...
aiPose	aiPose_from_sfr (core::io::StructFileRep const &sfr)
	Convert linear sfr to vec0[vec0[vec0[AtomInformation]]]. More...
aiModels	aiModels_from_sfrs (utility::vector1< core::io::StructFileRepOP > const &sfrs)
	Convert linear sfr to vec0[vec0[vec0[vec0[AtomInformation]]]]. More...
void	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	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	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	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 >	make_AIM_to_atom_num (aiModels const &AIM)
void	dump_mmtf (std::ostream &out, utility::vector1< core::io::StructFileRepOP > sfrs, core::io::StructFileRepOptions const &options)
	dump single mmtf function. More...
void	dump_mmtf (std::ostream &out, StructFileRepOP sfr, StructFileRepOptions const &options)
	dump single mmtf function. More...
::mmtf::StructureData	sfr_to_sd (core::io::StructFileRepOP sfr, core::io::StructFileRepOptions const &options)
::mmtf::StructureData	sfrs_to_sd (utility::vector1< core::io::StructFileRepOP > sfrs, core::io::StructFileRepOptions const &options)
template<typename T >
void	resize_and_add_if_not_empty (T const &data, std::vector< T > &destination, core::Size const &data_index, core::Size const &max_size)
	resize_add_if_not_empty – adds T to std::vector< T > if T isn't empty templated to allow us to add a variety of containers More...
std::ostream &	operator<< (std::ostream &os, sd_index const &sd_i)
std::map< core::Size, sd_index >	make_atom_num_to_sd_map (::mmtf::StructureData const &sd)
	use the sd_index struct to make iterating StructureData easier More...

Typedef Documentation

aiChain

typedef utility::vector0<aiGroup> core::io::mmtf::aiChain

aiGroup

typedef utility::vector0<core::io::AtomInformation> core::io::mmtf::aiGroup

aiModels

typedef utility::vector0<aiPose> core::io::mmtf::aiModels

aiPose

typedef utility::vector0<aiChain> core::io::mmtf::aiPose

ExtraDataEnumManagerCOP

typedef utility::pointer::shared_ptr< ExtraDataEnumManager const > core::io::mmtf::ExtraDataEnumManagerCOP

ExtraDataEnumManagerOP

typedef utility::pointer::shared_ptr< ExtraDataEnumManager > core::io::mmtf::ExtraDataEnumManagerOP

Enumeration Type Documentation

ExtraDataEnum

enum core::io::mmtf::ExtraDataEnum

Enum definitions for pose extra data we will be storing/retrieving. ALL Enums must also have their string equivalents defined in mmtf/ExtraDataEnumManager.cc.

Enumerator
pose_cache_string_data
pose_cache_real_data
pdb_comments
simple_metric_string_data
simple_metric_real_data
simple_metric_composite_string_data
simple_metric_composite_real_data
simple_metric_per_residue_string_data
simple_metric_per_residue_real_data
simple_metric_per_residue_string_output
simple_metric_per_residue_real_output
ExtraDataEnum_total

Function Documentation

add_bond_information()

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.

A warning for this function: mmtf has following bond order options Bond-order Resonance Explanation -1 1 kekulized form is unavailable, but resonance is known 1(or 2,3,4) 1 kekulized form is known, and resonance is known and exists 1(or 2,3,4) 0 kekulized form is known, but resonance is nonexistant 1(or 2,3,4) -1 kekulized form is known, but resonance is not known -Warning pt 2- mmtf supports up to 4 bonds, rosetta only up to 3 i set 4x bonds to be 0 (unk) in rosetta

References core::io::AtomInformation::connected_indices, core::io::AtomInformation::connected_orders, core::io::mmtf::sd_index::group_atom_index, core::io::mmtf::sd_index::group_index, and core::chemical::UnknownBond.

Referenced by create_sfrs_from_mmtf_filename().

add_bonds_to_sd()

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
	)

References core::chemical::AromaticBond, core::io::AtomInformation::connected_indices, core::io::AtomInformation::connected_orders, core::chemical::DoubleBond, core::io::mmtf::sd_index::group_atom_index, core::io::mmtf::sd_index::group_index, is_in_bondAtomList(), core::chemical::SingleBond, and core::chemical::TripleBond.

Referenced by sfrs_to_sd().

add_extra_data()

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.

Parameters

utility::vector1<	core::io::StructFileRepOP > const & to get infos from
::mmtf::StructureData	const& the StructureData to add to

References core::io::mmtf::ExtraDataEnumManager::enum_to_string(), core::io::StructFileRepOptions::integration_test_mode(), core::io::StructFileRepOptions::mmtf_extra_data_io(), pdb_comments, pose_cache_real_data, pose_cache_string_data, resize_and_add_if_not_empty(), simple_metric_composite_real_data, simple_metric_composite_string_data, simple_metric_per_residue_real_data, simple_metric_per_residue_real_output, simple_metric_per_residue_string_data, simple_metric_per_residue_string_output, simple_metric_real_data, simple_metric_string_data, core::io::TR(), core::io::StructFileRepOptions::use_pdb_format_HETNAM_records(), and core::io::StructFileRepOptions::write_glycan_pdb_codes().

Referenced by sfrs_to_sd().

add_if_not_empty()

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

Parameters

given_name	The name to use in the data map if not empty
content	The content to add if not empty
target_map	Where to add the content if it's not empty
zone	Required zone to keep msgpack happy

add_link_and_ss_information()

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.

References add_xbond_information(), core::io::AtomInformation::chainID, core::io::StructFileRep::link_map(), core::io::AtomInformation::name, core::io::AtomInformation::resSeq, and core::io::StructFileRep::ssbond_map().

Referenced by create_sfrs_from_mmtf_filename().

add_ters_via_bonds()

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.

References protocols::loops::chainID, protocols::loops::resSeq, and protocols::denovo_design::set_difference().

Referenced by create_sfrs_from_mmtf_filename().

add_xbond_information()

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  )

inline

References core::io::AtomInformation::chainID, core::io::AtomInformation::iCode, core::io::AtomInformation::name, core::io::AtomInformation::resName, core::io::AtomInformation::resSeq, core::id::to_string(), core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

Referenced by add_link_and_ss_information().

aiModels_from_sfrs()

aiModels core::io::mmtf::aiModels_from_sfrs

(

utility::vector1< core::io::StructFileRepOP > const &

sfrs

)

Convert linear sfr to vec0[vec0[vec0[vec0[AtomInformation]]]].

Parameters

core::io::StructFileRep

const& to build aiModels from

References aiPose_from_sfr().

Referenced by sfrs_to_sd().

aiPose_from_sfr()

aiPose core::io::mmtf::aiPose_from_sfr

(

core::io::StructFileRep const &

sfr

)

Convert linear sfr to vec0[vec0[vec0[AtomInformation]]].

Parameters

core::io::StructFileRep

const& to build aiPodel from

References core::io::StructFileRep::chains(), and make_chain().

Referenced by aiModels_from_sfrs().

create_sfr_from_mmtf_filename()

core::io::StructFileRepOP core::io::mmtf::create_sfr_from_mmtf_filename	(	std::string const &	mmtf_filename,
		StructFileReaderOptions const &	options
	)

create sfr from create_sfrs_from_mmtf_filename

References create_sfrs_from_mmtf_filename().

Referenced by core::import_pose::pose_from_file().

create_sfrs_from_mmtf_filename()

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

Note

: mmtf format requires us to iterate completely because order doesn't matter. So it makes more sense to iterate over all and then trim back your selection at the end.

References add_bond_information(), add_link_and_ss_information(), add_ters_via_bonds(), core::io::AtomInformation::chainID, make_all_atom_information(), make_atom_num_to_sd_map(), make_old_to_new_mapping(), read_extra_data(), core::io::StructFileReaderOptions::read_pdb_header(), core::io::TR(), and update_bond_indices().

Referenced by create_sfr_from_mmtf_filename().

dump_mmtf() [1/6]

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.

Dump mmtf to an outstream, optionally passing options and returning a StructFileRep for further processing.

References dump_mmtf(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), core::conformation::membrane::out, and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

dump_mmtf() [2/6]

bool core::io::mmtf::dump_mmtf	(	core::pose::Pose const &	pose,
		std::string const &	file_name,
		StructFileRepOptionsCOP	options
	)

Dump a MMTF from a pose to a file. Return success or failure.

References core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), core::conformation::membrane::out, set_mmtf_default_options(), core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr(), and core::io::TR().

Referenced by core::pose::Pose::dump_file(), dump_mmtf(), core::pose::Pose::dump_mmtf(), protocols::jd2::mmtfJobOutputter::dump_pose(), and protocols::jd3::pose_outputters::mmTFPoseOutputter::write_output().

dump_mmtf() [3/6]

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.

Dump a MMTF from a pose, optionally extracting extra info. NOTE: DEPRECATED. LEGACY JD2 function to use JOB data, which we no longer use in JD3.

References dump_mmtf(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), core::conformation::membrane::out, and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

dump_mmtf() [4/6]

void core::io::mmtf::dump_mmtf	(	std::ostream &	out,
		StructFileRepOP	sfr,
		StructFileRepOptions const &	options
	)

dump single mmtf function.

Note

We sadly have to use this to call the function that dumps a vector of SFRs due to the mmtf file format. It only makes sense because of the compression scheme used.

References core::conformation::membrane::out, and sfr_to_sd().

dump_mmtf() [5/6]

void core::io::mmtf::dump_mmtf	(	std::ostream &	out,
		utility::vector1< core::io::StructFileRepOP >	sfrs,
		core::io::StructFileRepOptions const &	options
	)

dump single mmtf function.

Note

We sadly have to use this to call the function that dumps a vector of SFRs due to the mmtf file format. It only makes sense because of the compression scheme used.

References core::conformation::membrane::out, and sfrs_to_sd().

dump_mmtf() [6/6]

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.

Parameters

file_name	The file name to write the mmtf to
sfr	The StructFileRepOP to build the mmtf from
options	The StructFileRepOptions used to build the sfr

References dump_mmtf(), core::conformation::membrane::out, and core::io::TR().

is_in_bondAtomList()

bool core::io::mmtf::is_in_bondAtomList	(	std::vector< int32_t > const &	bondAtomList,
		core::Size const	lower_atom,
		core::Size const	upper_atom
	)

References protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by add_bonds_to_sd().

load_heterogen_info()

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

make_AIM_to_atom_num()

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

)

make_all_atom_information()

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

References make_atom_information().

Referenced by create_sfrs_from_mmtf_filename().

make_atom_information()

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

References core::io::AtomInformation::altLoc, core::io::AtomInformation::chainID, core::io::AtomInformation::chem_comp_type, core::kinematics::distance(), core::io::AtomInformation::element, core::io::AtomInformation::iCode, core::io::AtomInformation::isHet, core::io::AtomInformation::name, core::io::StructFileReaderOptions::new_chain_order(), core::io::AtomInformation::occupancy, core::io::AtomInformation::resName, core::io::AtomInformation::resSeq, core::io::AtomInformation::segmentID, core::io::AtomInformation::serial, core::io::AtomInformation::temperature, core::io::AtomInformation::terCount, core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

Referenced by make_all_atom_information().

make_atom_num_to_sd_map()

std::map< core::Size, sd_index > core::io::mmtf::make_atom_num_to_sd_map

(

::mmtf::StructureData const &

sd

)

use the sd_index struct to make iterating StructureData easier

Referenced by create_sfrs_from_mmtf_filename(), and sfrs_to_sd().

make_chain()

aiChain core::io::mmtf::make_chain

(

utility::vector0< AtomInformation > const &

chain_atoms

)

group chain_atoms into groups based on chain_id and resseq

Warning

groups (aka residues) are made by grouping together identical ai.{chain,resSeq,resName,iCode} I don't think there's a better way than that.

References core::io::AtomInformation::chainID, core::io::AtomInformation::iCode, core::io::AtomInformation::resName, and core::io::AtomInformation::resSeq.

Referenced by aiPose_from_sfr().

make_current_group()

::mmtf::GroupType core::io::mmtf::make_current_group

(

aiGroup const &

ai_group

)

References protocols::cluster::calibur::aa, core::chemical::aa_from_name(), core::io::AtomInformation::chem_comp_type, protocols::simple_filters::gt, core::chemical::is_aa_name_unknown(), core::chemical::is_canonical_L_aa_or_gly(), core::chemical::oneletter_code_from_aa(), and core::io::AtomInformation::resName.

Referenced by sfrs_to_sd().

make_old_to_new_mapping()

std::map<core::Size, core::Size> core::io::mmtf::make_old_to_new_mapping	(	std::vector< std::vector< core::Size >> const	atom_idx_chains,
		core::Size const	starting_index
	)

Referenced by create_sfrs_from_mmtf_filename().

map_decode_from_model()

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
	)

Warning. This might be inefficient! time will tell We access and decode map_key for every model... that could be expensive... but maybe it's not that bad! otherwise we have to find a way to decode all at once....

Referenced by read_extra_data().

operator<<()

std::ostream & core::io::mmtf::operator<<	(	std::ostream &	os,
		sd_index const &	sd_i
	)

References core::io::mmtf::sd_index::to_string().

read_extra_data() [1/3]

void core::io::mmtf::read_extra_data	(	::mmtf::StructureData &	sd,
		core::io::StructFileRep &	sfr
	)

Read extra data from StructureData into the SFR.

SD non-const as the decode method of mmTF is NOT CONST!

read_extra_data() [2/3]

void core::io::mmtf::read_extra_data	(	core::io::StructFileRepOP &	sfr,
		::mmtf::StructureData const &	sd,
		core::Size const	model_index
	)

References core::simple_metrics::SimpleMetricStruct::composite_real_data_, core::simple_metrics::SimpleMetricStruct::composite_string_data_, core::io::mmtf::ExtraDataEnumManager::enum_to_string(), map_decode_from_model(), pdb_comments, core::simple_metrics::SimpleMetricStruct::per_residue_real_data_, core::simple_metrics::SimpleMetricStruct::per_residue_real_output_, core::simple_metrics::SimpleMetricStruct::per_residue_string_data_, core::simple_metrics::SimpleMetricStruct::per_residue_string_output_, pose_cache_real_data, pose_cache_string_data, core::simple_metrics::SimpleMetricStruct::real_data_, simple_metric_composite_real_data, simple_metric_composite_string_data, simple_metric_per_residue_real_data, simple_metric_per_residue_real_output, simple_metric_per_residue_string_data, simple_metric_per_residue_string_output, simple_metric_real_data, simple_metric_string_data, and core::simple_metrics::SimpleMetricStruct::string_data_.

Referenced by create_sfrs_from_mmtf_filename().

read_extra_data() [3/3]

void core::io::mmtf::read_extra_data	(	utility::vector1< core::io::StructFileRepOP > &	sfrs,
		::mmtf::StructureData const &	sd
	)

resize_and_add_if_not_empty() [1/2]

template<typename T >

void core::io::mmtf::resize_and_add_if_not_empty	(	T const &	data,
		std::vector< T > &	destination,
		core::Size const &	data_index,
		core::Size const &	max_size
	)

resize_add_if_not_empty – adds T to std::vector< T > if T isn't empty templated to allow us to add a variety of containers

Parameters

data	The data to add to destination, if !data.empty()
destination	The destination of the content if !empty
data_index	Where to add the content if !empty (will resize destination)

resize_and_add_if_not_empty() [2/2]

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
	)

Referenced by add_extra_data().

set_mmtf_default_options()

void core::io::mmtf::set_mmtf_default_options

(

core::io::StructFileRepOptions &

options

)

Set StructFileRepOptions defauls for mmtf.

Parameters

core::io::StructFileRepOptions&

options to modify for mmtf

References core::io::StructFileRepOptions::set_write_all_connect_info(), and core::io::StructFileRepOptions::set_write_pdb_link_records().

Referenced by dump_mmtf(), and protocols::jd2::mmtfJobOutputter::dump_pose().

set_model_index_if_not_empty()

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

sfr_to_sd()

mmtf::StructureData core::io::mmtf::sfr_to_sd	(	core::io::StructFileRepOP	sfr,
		core::io::StructFileRepOptions const &	options
	)

References sfrs_to_sd().

Referenced by dump_mmtf().

sfrs_to_sd()

::mmtf::StructureData core::io::mmtf::sfrs_to_sd	(	utility::vector1< core::io::StructFileRepOP >	sfrs,
		core::io::StructFileRepOptions const &	options
	)

References add_bonds_to_sd(), add_extra_data(), aiModels_from_sfrs(), core::io::AtomInformation::chainID, core::io::AtomInformation::connected_indices, core::kinematics::distance(), protocols::simple_filters::gt, core::io::AtomInformation::iCode, make_atom_num_to_sd_map(), make_current_group(), core::io::AtomInformation::occupancy, protocols::loops::resSeq, core::io::AtomInformation::temperature, core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

Referenced by dump_mmtf(), and sfr_to_sd().

sort_xbond_func()

template<typename T >

bool core::io::mmtf::sort_xbond_func	(	T const &	lhs,
		T const &	rhs
	)

update_bond_indices()

void core::io::mmtf::update_bond_indices	(	core::io::StructFileRep &	sfr,
		std::map< core::Size, core::Size > const &	old_to_new_idx
	)

References core::io::StructFileRep::chains().

Referenced by create_sfrs_from_mmtf_filename().