A class to convert a pose to a StructFileRep. More...

#include <PoseToStructFileRepConverter.hh>

Inheritance diagram for core::io::pose_to_sfr::PoseToStructFileRepConverter:

Public Member Functions
	PoseToStructFileRepConverter ()
	Constructor. More...

	PoseToStructFileRepConverter (StructFileRepOptions const &options_in)
	Constructor with options input. More...

	~PoseToStructFileRepConverter () override
	Destructor. More...

core::io::StructFileRepOP	new_sfr ()
	Resets the PoseToStructFileRepConverter object, and reinitializes it with a fresh StruftFileRep object, returning an owning pointer to the new object. More...

void	init_from_pose (core::pose::Pose const &pose)
	Fill StructFileRep object using information from given Pose object. More...

void	init_from_pose (core::pose::Pose const &pose, StructFileRepOptions const &options)
	Fill StructFileRep object using information from given Pose object and a set of options. More...

void	init_from_pose (core::pose::Pose const &pose, utility::vector1< core::Size > const &residue_indices)
	Fill StructFileRep object using information from given Pose object, for a specified subset of residues. More...

void	init_from_pose (core::pose::Pose const &pose, id::AtomID_Mask const &mask)
	Fill StructFileRep object using information from given Pose object, for a specified subset of residues and atoms. More...

void	init_from_pose (core::pose::Pose const &pose, id::AtomID_Mask const &mask, StructFileRepOptions const &options)
	Fill StructFileRep object using information from given Pose object, for a specified subset of residues and atoms. More...

void	grab_additional_pose_data (core::pose::Pose const &pose)
	Get additional pose data. More...

void	append_residue_to_sfr (pose::Pose const &pose, core::Size const resnum)
	Append pdb information to StructFileRep for a single residue. More...

void	append_residue_to_sfr (pose::Pose const &pose, core::Size const resnum, core::Size &new_atom_num, core::Size const new_tercount)
	Start atom numbering from given n. Increments N. More...

void	get_connectivity_annotation_info (core::pose::Pose const &pose)
	Get connectivity annotation information from the Pose object and create LinkInformation and SSBondInformation data as appropriate. More...

LinkInformation	get_link_record (core::pose::Pose const &pose, core::Size ii, core::Size conn)

SSBondInformation	get_ssbond_record (core::pose::Pose const &pose, core::Size ii, core::Size conn)

void	get_parametric_info (core::io::RemarksOP remarks, core::pose::Pose const &pose)
	Get parametric information from the Pose object and add it to the PDB remarks. More...

void	grab_pose_energies_table (core::pose::Pose const &pose)
	Grab all the data that makes the pose energies table. More...

void	grab_pose_cache_data (core::pose::Pose const &pose)
	Grab all the data that is in pose datacache as string/value pairs Arbitrary Float data Arbitrary String data. More...

void	grab_simple_metric_data (core::pose::Pose const &pose)
	Grab RAW simple_metric data for SM IO. More...

StructFileRepOP	sfr ()
	Non-const access to the StructFileRep object. More...

Private Member Functions
void	determine_atom_indices (pose::Pose const &pose)
	Determines the atom indices, which are needed for CONECT info. More...

bool	add_atom_to_sfr (pose::Pose const &pose, conformation::Residue const &rsd, core::Size atom_index) const
	Should this atom be [added]? More...

void	recalculate_new_chainIDs (pose::Pose const &pose)

bool	use_pdb_info_for_num (pose::Pose const &pose, Size resnum) const

void	append_residue_info_to_sfr (ResidueInformation const &res_info, core::conformation::Residue const &rsd)
	Append just residue-based info to StructFileRep For now, it is only HETNAM Data. More...

bool	append_atom_info_to_sfr (core::pose::Pose const &pose, ResidueInformation const &res_info, core::conformation::Residue const &rsd, core::Size const atom_index)
	Append just atom-based info to StructFileRep. New atom number will be detected from current SFR or start from 1. Returns True if successfully added to SFR. More...

bool	append_atom_info_to_sfr (core::pose::Pose const &pose, ResidueInformation const &res_info, core::conformation::Residue const &rsd, core::Size const atom_index, core::Size const new_atom_num, core::Size const new_tercount)
	Append just atom-based info to StructFileRep Specify the new atom to start from. Returns True if successfully added to SFR. More...

std::string	get_chem_comp_type (core::conformation::Residue const &rsd) const
	Determine chem_comp_type via ResidueType and VariantType combinations http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.type.html. More...

core::Size	get_new_atom_serial_num () const

void	generate_default_title_section (rcsb::ExperimentalTechnique const technique)
	Create a default PDB-format title section. More...

void	generate_default_remarks (rcsb::ExperimentalTechnique const technique)
	Create default PDB remarks, which provide the date and Rosetta version number. More...

void	set_fold_tree_io (bool const setting)
	Set whether to write the fold tree, in the StructFileRepOptions object (options_). More...

void	grab_membrane_info (core::pose::Pose const &pose, bool const normalize_to_thk)
	Get the membrane information from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot. More...

void	grab_conect_records_for_atom (core::pose::Pose const &pose, core::Size const res_index, core::Size const atom_index_in_rsd, core::io::AtomInformation &ai)
	Get the conect record information from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot. More...

void	grab_foldtree (core::pose::Pose const &pose, bool const output_foldtree)
	Get the foldtree from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot. More...

void	grab_pdb_parents (core::pose::Pose const &pose, bool const output_parents)
	Get the pdb parents from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot. More...

void	grab_pdb_comments (core::pose::Pose const &pose, bool const output_comments)
	Get the pdb comments from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot. More...

void	grab_torsion_records (core::pose::Pose const &pose, bool const output_torsions)
	Get the torsion information from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot. More...

void	grab_pdbinfo_labels (core::pose::Pose const &pose)
	Get the pdbinfo labels from the pose and store them in the StructFileRep for output to pdbs/mmCIF/whatnot. More...

core::Size	total_sfr_atoms (StructFileRep const &sfr) const
	Get the total number of atoms in the SFR. More...

core::Size	total_sfr_atoms (StructFileRep const &sfr, core::Size const chain_num) const
	Get the total number of atoms in a chain in the SFR. More...

ResidueInformation	get_residue_information (core::pose::Pose const &pose, core::uint const seqpos, core::Size const new_tercount=0) const
	Return the PDB resName, chainID, resSeq, and iCode for the given Rosetta sequence position. More...

void	generate_secondary_structure_informations (core::pose::Pose const &pose)
	fills HELIXInformation and SHEETInformation for SFR More...

void	generate_HELIXInformation (ResidueInformation const &start_info, ResidueInformation const &stop_info, core::Size const index, core::Size const length)
	fills one HELIXInformation into SFR More...

void	generate_SHEETInformation (ResidueInformation const &start_info, ResidueInformation const &stop_info, core::Size const index)
	fills one SHEETInformation into SFR More...

Private Attributes
StructFileRepOP	sfr_
	Owning pointer to the StructFileRep object, copied in during object construction. More...

StructFileRepOptions	options_
	The StructFileRepOptions object. More...

id::AtomID_Map< Size >	atom_indices_
	The index for every atom in the Pose – used for generating CONECT records. More...

bool	atom_indices_initialized_

utility::vector1< char >	new_chainIDs_

Friends
class	::PoseToStructFileRepConverterTests

std::ostream &	operator<< (std::ostream &os, StructFileRep const &)
	Debug printing. More...

Detailed Description

A class to convert a pose to a StructFileRep.

The StructFileRep is a data structure that serves as an intermediate between Protein Databank file formats (PDB and mmCIF) and Rosetta objects (poses). This was implemented at the 2016 Chemical XRW (eXtreme Rosetta Workshop), at which this class was popularly referred to as the "pose unbuilder".

Constructor & Destructor Documentation

◆ PoseToStructFileRepConverter() [1/2]

core::io::pose_to_sfr::PoseToStructFileRepConverter::PoseToStructFileRepConverter ( )

Constructor.

Creates the StructFileRep object, which is subsequently accessible by owning pointer (using the sfr() object). The options_ object is created and initialized from the options system.

References new_sfr().

◆ PoseToStructFileRepConverter() [2/2]

core::io::pose_to_sfr::PoseToStructFileRepConverter::PoseToStructFileRepConverter ( StructFileRepOptions const & options_in )

Constructor with options input.

Creates the StructFileRep object, which is subsequently accessible by owning pointer (using the sfr() object). The options_ object is duplicated from the input options object.

References new_sfr().

◆ ~PoseToStructFileRepConverter()

core::io::pose_to_sfr::PoseToStructFileRepConverter::~PoseToStructFileRepConverter ( )

inlineoverride

Destructor.

Member Function Documentation

◆ add_atom_to_sfr()

bool core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr	(	pose::Pose const &	pose,
		conformation::Residue const &	rsd,
		core::Size	atom_index
	)		const

private

Should this atom be [added]?

References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::chemical::AtomType::is_virtual(), core::io::StructFileRepOptions::no_output_cen(), options_, core::io::StructFileRepOptions::output_virtual(), core::pose::Pose::pdb_info(), core::conformation::Residue::seqpos(), core::io::StructFileRepOptions::suppress_zero_occ_pdb_output(), and use_pdb_info_for_num().

Referenced by append_atom_info_to_sfr().

◆ append_atom_info_to_sfr() [1/2]

bool core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr	(	core::pose::Pose const &	pose,
		ResidueInformation const &	res_info,
		core::conformation::Residue const &	rsd,
		core::Size const	atom_index
	)

private

Append just atom-based info to StructFileRep. New atom number will be detected from current SFR or start from 1. Returns True if successfully added to SFR.

References core::pose::Pose::chain(), get_new_atom_serial_num(), and core::conformation::Residue::seqpos().

Referenced by append_residue_to_sfr(), and init_from_pose().

◆ append_atom_info_to_sfr() [2/2]

bool core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr	(	core::pose::Pose const &	pose,
		ResidueInformation const &	res_info,
		core::conformation::Residue const &	rsd,
		core::Size const	atom_index,
		core::Size const	new_atom_num,
		core::Size const	new_tercount
	)

private

Append just atom-based info to StructFileRep Specify the new atom to start from. Returns True if successfully added to SFR.

◆ append_residue_info_to_sfr()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr	(	ResidueInformation const &	res_info,
		core::conformation::Residue const &	rsd
	)

private

Append just residue-based info to StructFileRep For now, it is only HETNAM Data.

Append just residue-based info to StructFileRep.

References core::chemical::ResidueTypeBase::base_name(), protocols::vip::base_name(), core::chemical::ResidueType::is_membrane(), core::conformation::Residue::is_NA(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::name3(), options_, core::io::ResidueInformation::resid(), sfr_, core::conformation::Residue::type(), and core::io::StructFileRepOptions::write_glycan_pdb_codes().

Referenced by append_residue_to_sfr(), and init_from_pose().

◆ append_residue_to_sfr() [1/2]

void core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_to_sfr	(	pose::Pose const &	pose,
		core::Size const	resnum
	)

Append pdb information to StructFileRep for a single residue.

References core::pose::Pose::chain(), and get_new_atom_serial_num().

Referenced by core::io::pdb::dump_pdb_residue().

◆ append_residue_to_sfr() [2/2]

void core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_to_sfr	(	pose::Pose const &	pose,
		core::Size const	resnum,
		core::Size &	new_atom_num,
		core::Size const	new_tercount
	)

Start atom numbering from given n. Increments N.

Append pdb information to StructFileRep for a single residue.

Start atom numbering from given n

References append_atom_info_to_sfr(), append_residue_info_to_sfr(), get_residue_information(), core::conformation::Residue::natoms(), and core::pose::Pose::residue().

◆ determine_atom_indices()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::determine_atom_indices ( pose::Pose const & pose )

private

Determines the atom indices, which are needed for CONECT info.

References atom_indices_, atom_indices_initialized_, core::chemical::ResidueType::atom_type(), core::pose::initialize_atomid_map(), core::chemical::AtomType::is_virtual(), core::chemical::ResidueType::natoms(), options_, core::io::StructFileRepOptions::output_virtual(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by grab_conect_records_for_atom().

◆ generate_default_remarks()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_default_remarks ( rcsb::ExperimentalTechnique const technique )

private

Create default PDB remarks, which provide the date and Rosetta version number.

This function adds the following to structure files generated by Rosetta:
REMARK 220
REMARK 220 EXPERIMENTAL DETAILS
REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING
REMARK 220 DATE OF DATA COLLECTION : xx-MMM-xx
REMARK 220
REMARK 220 REMARK: MODEL GENERATED BY ROSETTA
REMARK 220 VERSION 000000000000000000000000000000000000000000000000000000000000
If the -write_pdb_parametric_info option is set to true, the REMARK 250 is used instead. If this pose was the result of crystal- or electron-density-refinement, REMARK 3 records are output instead.

Note: 220 is an obsolete REMARK code from an earlier version of the .pdb format. It was used for theoretical models, which at that time were permitted. Technically, REMARK 225 would also have been mandatory, but 225 is a blanket statement that simply explains that any CRYST1 and SCALE records are meaningless. Since a theoretical model can no longer be submitted to the PDB, it is pointless to include RECORD 225.

Author: Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References core::io::StructFileRepOptions::integration_test_mode(), core::io::RemarkInfo::num, options_, core::io::StructFileRepOptions::pdb_author(), sfr_, core::io::rcsb::THEORETICAL_MODEL, core::io::rcsb::UNKNOWN_EXPDTA, core::io::RemarkInfo::value, and core::io::StructFileRepOptions::write_pdb_parametric_info().

Referenced by init_from_pose().

◆ generate_default_title_section()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_default_title_section ( rcsb::ExperimentalTechnique const technique )

private

Create a default PDB-format title section.

This function adds the following to structure files generated by Rosetta:
HEADER xx-MMM-xx XXXX
EXPDTA THEORETICAL MODEL
AUTHOR
If the pose contains electron density, EXPDTA is blanked, since this is technically no longer a theoretical model.

Author: Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References core::io::StructFileRepOptions::integration_test_mode(), options_, core::io::StructFileRepOptions::pdb_author(), and sfr_.

Referenced by init_from_pose().

◆ generate_HELIXInformation()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_HELIXInformation	(	ResidueInformation const &	start_info,
		ResidueInformation const &	stop_info,
		core::Size const	index,
		core::Size const	length
	)

private

fills one HELIXInformation into SFR

Author: Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om

References core::io::ResidueInformation::chainID(), protocols::loops::loop_closure::ccd::helix, core::chemical::element::I, core::io::ResidueInformation::iCode(), core::io::ResidueInformation::resName(), core::io::ResidueInformation::resSeq(), and sfr_.

Referenced by generate_secondary_structure_informations().

◆ generate_secondary_structure_informations()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_secondary_structure_informations ( core::pose::Pose const & pose )

private

fills HELIXInformation and SHEETInformation for SFR

fills HELIXInformation and SHEETInformation for SFR - wrappers for individual functions

Author: Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om, but cribbed from code of Yifan Song as part of Cyrus Biotechnology option dependencies in this function: options_.output_secondary_structure() controls if it runs at all, options_.per_chain_renumbering() is used with ResidueInformation, and it also calls get_residue_information()

References core::conformation::Residue::chain(), core::pose::Pose::chain(), core::io::StructFileRepOptions::do_not_autoassign_SS(), generate_HELIXInformation(), generate_SHEETInformation(), core::scoring::dssp::Dssp::get_dssp_secstruct(), get_residue_information(), options_, core::io::StructFileRepOptions::output_secondary_structure(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::size(), and core::io::pose_to_sfr::TR().

Referenced by init_from_pose().

◆ generate_SHEETInformation()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_SHEETInformation	(	ResidueInformation const &	start_info,
		ResidueInformation const &	stop_info,
		core::Size const	index
	)

private

fills one SHEETInformation into SFR

Author: Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om

References core::io::ResidueInformation::chainID(), core::chemical::element::I, core::io::ResidueInformation::iCode(), core::io::ResidueInformation::resName(), core::io::ResidueInformation::resSeq(), sfr_, and core::scoring::sheet.

Referenced by generate_secondary_structure_informations().

◆ get_chem_comp_type()

std::string core::io::pose_to_sfr::PoseToStructFileRepConverter::get_chem_comp_type ( core::conformation::Residue const & rsd ) const

private

Determine chem_comp_type via ResidueType and VariantType combinations http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.type.html.

References core::chemical::BETA_AA, core::chemical::CARBOHYDRATE, core::chemical::D_AA, core::chemical::DNA, core::chemical::L_AA, core::chemical::L_RNA, core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::OLIGOUREA, core::chemical::PEPTOID, core::chemical::POLYMER, core::chemical::RNA, core::conformation::Residue::type_ptr(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by append_atom_info_to_sfr().

◆ get_connectivity_annotation_info()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info ( core::pose::Pose const & pose )

Get connectivity annotation information from the Pose object and create LinkInformation and SSBondInformation data as appropriate.

Get connectivity annotation information from the Pose object and create LinkInformation and SSBondInformation data as appropriate. Will update chain IDs if -output_ligands_as_separate_chains was set.

References core::chemical::ResidueType::atom_index(), core::conformation::Residue::connected_residue_at_resconn(), core::chemical::DISULFIDE_BONDED, core::chemical::ResidueTypeBase::get_disulfide_atom_name(), get_link_record(), get_ssbond_record(), core::conformation::Residue::has_lower_connect(), core::chemical::ResidueTypeBase::has_property(), core::conformation::Residue::has_upper_connect(), core::chemical::ResidueType::is_carbohydrate(), core::io::link_in_vector(), core::chemical::ResidueType::lower_connect_id(), core::conformation::Residue::n_possible_residue_connections(), core::io::LinkInformation::name1, core::io::LinkInformation::resID1, core::io::SSBondInformation::resID1, core::io::LinkInformation::resID2, core::pose::Pose::residue(), core::chemical::ResidueType::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), core::pose::Pose::residue_type(), sfr_, core::chemical::SIDECHAIN_THIOL, core::pose::Pose::size(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().

Referenced by init_from_pose().

◆ get_link_record()

LinkInformation core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record	(	core::pose::Pose const &	pose,
		core::Size	ii,
		core::Size	conn
	)

Referenced by get_connectivity_annotation_info().

◆ get_new_atom_serial_num()

core::Size core::io::pose_to_sfr::PoseToStructFileRepConverter::get_new_atom_serial_num ( ) const

private

References sfr_, and total_sfr_atoms().

Referenced by append_atom_info_to_sfr(), and append_residue_to_sfr().

◆ get_parametric_info()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::get_parametric_info	(	core::io::RemarksOP	remarks,
		core::pose::Pose const &	pose
	)

Get parametric information from the Pose object and add it to the PDB remarks.

Note: REMARK 250, reserved for "other kinds of studies", is used and appended to the REMARK 250 lines generated by generate_default_remarks().

References core::pose::Pose::conformation(), core::conformation::Conformation::n_parameters_sets(), core::io::RemarkInfo::num, core::conformation::Conformation::parameters_set(), and core::io::RemarkInfo::value.

Referenced by init_from_pose().

◆ get_residue_information()

ResidueInformation core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information	(	core::pose::Pose const &	pose,
		core::uint const	seqpos,
		core::Size const	new_tercount = `0`
	)		const

private

Return the PDB resName, chainID, resSeq, and iCode for the given Rosetta sequence position.

Output is res_info.

References core::pose::Pose::chain(), core::conformation::Conformation::chain_endings(), core::io::ResidueInformation::chainID(), chr_chains(), core::chemical::chr_chains(), core::pose::Pose::conformation(), core::io::ResidueInformation::iCode(), core::chemical::ResidueTypeBase::name3(), new_chainIDs_, options_, core::pose::Pose::pdb_info(), core::io::StructFileRepOptions::per_chain_renumbering(), core::pose::Pose::residue_type(), core::io::ResidueInformation::resName(), core::io::ResidueInformation::resSeq(), core::io::ResidueInformation::segmentID(), core::io::ResidueInformation::terCount(), core::io::pose_to_sfr::TR(), and use_pdb_info_for_num().

Referenced by append_residue_to_sfr(), generate_secondary_structure_informations(), get_link_record(), get_ssbond_record(), and init_from_pose().

◆ get_ssbond_record()

SSBondInformation core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record	(	core::pose::Pose const &	pose,
		core::Size	ii,
		core::Size	conn
	)

Referenced by get_connectivity_annotation_info().

◆ grab_additional_pose_data()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_additional_pose_data ( core::pose::Pose const & pose )

Get additional pose data.

This is rewritten from the old core/io/pdb/file_data.cc:write_additional_pdb_data() function. This was a catch-all for dumping out all sorts of protocol-specific stuff (e.g. membrane info).

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::io::StructFileRepOptions::fold_tree_io(), grab_foldtree(), grab_membrane_info(), grab_pdb_comments(), grab_pdb_parents(), grab_pdbinfo_labels(), grab_torsion_records(), core::io::StructFileRepOptions::normalize_to_thk(), options_, core::io::StructFileRepOptions::output_torsions(), and core::io::StructFileRepOptions::pdb_parents().

Referenced by init_from_pose().

◆ grab_conect_records_for_atom()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom	(	core::pose::Pose const &	pose,
		core::Size const	res_index,
		core::Size const	atom_index_in_rsd,
		core::io::AtomInformation &	ai
	)

private

Get the conect record information from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot.

Parameters

[in]	pose	The pose, for determining what's bonded to what.
[in]	atom_index_in_pose	The index (in the whole pose) of the atom that we're setting up.
[in]	res_index	The current residue index.
[in]	atom_index_rsd	The index (in the residue) of the atom that we're setting up.
[in]	dist_cutoff	The atom separation, above which a CONECT record is written.
[in]	write_virtuals	Are virtual atoms being written out?
	[in/out]	ai The AtomInformation object that's being set up. Modified by this function

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Parameters

[in]	pose	The pose, for determining what's bonded to what.
[in]	atom_index_in_pose	The index (in the whole pose) of the atom that we're setting up.
[in]	res_index	The current residue index.
[in]	atom_index_rsd	The index (in the residue) of the atom that we're setting up.
[in]	dist_cutoff	The atom separation, above which a CONECT record is written.
[in]	write_virtuals	Are virtual atoms being written out?
	[in/out]	ai The AtomInformation object that's being set up. Modified by this function

References atom_indices_, atom_indices_initialized_, core::chemical::ResidueType::atom_type(), core::chemical::ResidueType::bond_type(), core::conformation::Conformation::bonded_neighbor_all_res(), core::pose::Pose::conformation(), core::io::StructFileRepOptions::connect_info_cutoff(), core::io::AtomInformation::connected_indices, core::io::AtomInformation::connected_orders, determine_atom_indices(), core::chemical::ResidueType::is_canonical(), core::chemical::ResidueType::is_solvent(), core::chemical::AtomType::is_virtual(), core::chemical::ResidueType::is_virtual_residue(), core::conformation::Residue::natoms(), options_, core::io::StructFileRepOptions::output_virtual(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::id::AtomID::rsd(), core::chemical::SingleBond, core::pose::Pose::size(), core::io::StructFileRepOptions::skip_connect_info(), core::io::StructFileRepOptions::write_all_connect_info(), and core::pose::Pose::xyz().

Referenced by append_atom_info_to_sfr().

◆ grab_foldtree()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_foldtree	(	core::pose::Pose const &	pose,
		bool const	output_foldtree
	)

private

Get the foldtree from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot.

References core::pose::Pose::fold_tree(), and sfr_.

Referenced by grab_additional_pose_data().

◆ grab_membrane_info()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info	(	core::pose::Pose const &	pose,
		bool const	normalize_to_thk
	)

private

Get the membrane information from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot.

Parameters

[in]	pose	The pose.
[in]	normalize_to_thk	Normalized MEM lines, useful for visualizing the boundaries of the membrane by coupling the NORM and THK coordinates. Added by Rebecca.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by grab_additional_pose_data().

◆ grab_pdb_comments()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pdb_comments	(	core::pose::Pose const &	pose,
		bool const	output_comments
	)

private

Get the pdb comments from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot.

References core::pose::get_all_comments(), and sfr_.

Referenced by grab_additional_pose_data().

◆ grab_pdb_parents()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pdb_parents	(	core::pose::Pose const &	pose,
		bool const	output_parents
	)

private

Get the pdb parents from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot.

References core::pose::get_comment(), and sfr_.

Referenced by grab_additional_pose_data().

◆ grab_pdbinfo_labels()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pdbinfo_labels ( core::pose::Pose const & pose )

private

Get the pdbinfo labels from the pose and store them in the StructFileRep for output to pdbs/mmCIF/whatnot.

This also abuses REMARK lines, and should be rewritten.

References core::conformation::membrane::out, core::pose::Pose::pdb_info(), and sfr_.

Referenced by grab_additional_pose_data().

◆ grab_pose_cache_data()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_cache_data ( core::pose::Pose const & pose )

Grab all the data that is in pose datacache as string/value pairs Arbitrary Float data Arbitrary String data.

Simple Metric data

References core::io::raw_data::ScoreMap::get_arbitrary_score_data_from_pose(), core::io::raw_data::ScoreMap::get_arbitrary_string_data_from_pose(), and sfr_.

Referenced by init_from_pose().

◆ grab_pose_energies_table()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table ( core::pose::Pose const & pose )

Grab all the data that makes the pose energies table.

References core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), core::scoring::n_score_types, core::conformation::Residue::name(), core::scoring::name_from_score_type(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), core::io::pose_to_sfr::restrict_prec(), protocols::hybridization::score, sfr_, core::pose::Pose::size(), core::id::to_string(), core::scoring::Energies::total_energies(), and core::scoring::Energies::weights().

Referenced by init_from_pose().

◆ grab_simple_metric_data()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_simple_metric_data ( core::pose::Pose const & pose )

Grab RAW simple_metric data for SM IO.

References core::simple_metrics::get_sm_data(), core::simple_metrics::has_sm_data(), and sfr_.

Referenced by init_from_pose().

◆ grab_torsion_records()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_torsion_records	(	core::pose::Pose const &	pose,
		bool const	output_torsions
	)

private

Get the torsion information from the pose and store it in the StructFileRep for output to pdbs/mmCIF/whatnot.

This is an incredibly ugly way to handle the output of these records. This abuses the REMARK lines in the PDB format, and should be refactored. Keeping as-is for now to preserve legacy behaviour (VKM 29 January 2016, Chemical XRW).

References core::pose::Pose::chain(), core::scoring::dssp::Dssp::dssp_reduced(), core::chemical::element::F, core::chemical::element::I, core::chemical::ResidueType::is_carbohydrate(), core::pose::is_ideal_pose(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::name1(), core::pose::Pose::omega(), core::conformation::membrane::out, core::pose::Pose::pdb_info(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), sfr_, core::pose::Pose::size(), and core::io::pose_to_sfr::TR().

Referenced by grab_additional_pose_data().

◆ init_from_pose() [1/5]

void core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose ( core::pose::Pose const & pose )

Fill StructFileRep object using information from given Pose object.

Read atoms/residue information from Pose object and put it in StructFileRep object.

References options_.

Referenced by protocols::constel::create_constel_records_from_sfr(), core::io::mmcif::dump_cif(), core::io::mmtf::dump_mmtf(), core::io::pdb::dump_pdb(), core::import_pose::PDBSilentStruct::fill_struct(), init_from_pose(), and core::io::pose_from_pose().

◆ init_from_pose() [2/5]

void core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose	(	core::pose::Pose const &	pose,
		id::AtomID_Mask const &	mask
	)

Fill StructFileRep object using information from given Pose object, for a specified subset of residues and atoms.

References init_from_pose(), and options_.

◆ init_from_pose() [3/5]

void core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose	(	core::pose::Pose const &	pose,
		id::AtomID_Mask const &	mask,
		StructFileRepOptions const &	options
	)

Fill StructFileRep object using information from given Pose object, for a specified subset of residues and atoms.

◆ init_from_pose() [4/5]

void core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose	(	core::pose::Pose const &	pose,
		StructFileRepOptions const &	options
	)

Fill StructFileRep object using information from given Pose object and a set of options.

Read atoms/residue information from Pose object and put it in StructFileRep object using options defined in StructFileRepOptions.

References init_from_pose(), core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::set(), and core::pose::Pose::size().

◆ init_from_pose() [5/5]

void core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	residue_indices
	)

Fill StructFileRep object using information from given Pose object, for a specified subset of residues.

A lightweight, direct way of limiting pose pdb output to a subset of residues.

Note: The alternative of constructing new subposes for output only would be unnecessary/less efficient (?)

References init_from_pose(), core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::set(), and core::pose::Pose::size().

◆ new_sfr()

core::io::StructFileRepOP core::io::pose_to_sfr::PoseToStructFileRepConverter::new_sfr ( )

Resets the PoseToStructFileRepConverter object, and reinitializes it with a fresh StruftFileRep object, returning an owning pointer to the new object.

References atom_indices_initialized_, and sfr_.

Referenced by init_from_pose(), and PoseToStructFileRepConverter().

◆ recalculate_new_chainIDs()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::recalculate_new_chainIDs ( pose::Pose const & pose )

private

References core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), protocols::loops::chainID, core::chemical::chr_chains(), core::pose::Pose::conformation(), core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), core::pose::PDBInfo::empty_record(), core::conformation::Residue::is_carbohydrate(), core::conformation::Residue::is_protein(), new_chainIDs_, core::pose::Pose::num_chains(), options_, core::io::StructFileRepOptions::output_ligands_as_separate_chains(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::io::pose_to_sfr::TR().

Referenced by init_from_pose().

◆ set_fold_tree_io()

void core::io::pose_to_sfr::PoseToStructFileRepConverter::set_fold_tree_io ( bool const setting )

private

Set whether to write the fold tree, in the StructFileRepOptions object (options_).

References options_, and core::io::StructFileRepOptions::set_fold_tree_io().

◆ sfr()

StructFileRepOP core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr ( )

Non-const access to the StructFileRep object.

References sfr_.

Referenced by protocols::constel::create_constel_records_from_sfr(), core::io::mmcif::dump_cif(), core::io::mmtf::dump_mmtf(), core::io::pdb::dump_pdb(), core::io::pdb::dump_pdb_residue(), core::import_pose::PDBSilentStruct::fill_struct(), core::io::pose_from_pose(), and total_sfr_atoms().

◆ total_sfr_atoms() [1/2]

core::Size core::io::pose_to_sfr::PoseToStructFileRepConverter::total_sfr_atoms ( StructFileRep const & sfr ) const

private

Get the total number of atoms in the SFR.

References sfr(), and protocols::analysis::total.

Referenced by get_new_atom_serial_num().

◆ total_sfr_atoms() [2/2]

core::Size core::io::pose_to_sfr::PoseToStructFileRepConverter::total_sfr_atoms	(	StructFileRep const &	sfr,
		core::Size const	chain_num
	)		const

private

Get the total number of atoms in a chain in the SFR.

References sfr().

◆ use_pdb_info_for_num()

bool core::io::pose_to_sfr::PoseToStructFileRepConverter::use_pdb_info_for_num	(	pose::Pose const &	pose,
		Size	resnum
	)		const

private

References options_, core::pose::Pose::pdb_info(), and core::io::StructFileRepOptions::renumber_pdb().

Referenced by add_atom_to_sfr(), append_atom_info_to_sfr(), and get_residue_information().

Friends And Related Function Documentation

◆ ::PoseToStructFileRepConverterTests

friend class ::PoseToStructFileRepConverterTests

friend

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		StructFileRep const &
	)

friend

Debug printing.

Member Data Documentation

◆ atom_indices_

id::AtomID_Map< Size > core::io::pose_to_sfr::PoseToStructFileRepConverter::atom_indices_

private

The index for every atom in the Pose – used for generating CONECT records.

Referenced by determine_atom_indices(), and grab_conect_records_for_atom().

◆ atom_indices_initialized_

bool core::io::pose_to_sfr::PoseToStructFileRepConverter::atom_indices_initialized_

private

Referenced by determine_atom_indices(), grab_conect_records_for_atom(), and new_sfr().

◆ new_chainIDs_

utility::vector1< char > core::io::pose_to_sfr::PoseToStructFileRepConverter::new_chainIDs_

private

Referenced by get_residue_information(), and recalculate_new_chainIDs().

◆ options_

StructFileRepOptions core::io::pose_to_sfr::PoseToStructFileRepConverter::options_

private

The StructFileRepOptions object.

Created at PoseToStructFileRepConverter object creation; not read-accessible outside of this object.

Referenced by add_atom_to_sfr(), append_atom_info_to_sfr(), append_residue_info_to_sfr(), determine_atom_indices(), generate_default_remarks(), generate_default_title_section(), generate_secondary_structure_informations(), get_link_record(), get_residue_information(), grab_additional_pose_data(), grab_conect_records_for_atom(), init_from_pose(), recalculate_new_chainIDs(), set_fold_tree_io(), and use_pdb_info_for_num().

◆ sfr_

StructFileRepOP core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr_

private

Owning pointer to the StructFileRep object, copied in during object construction.

Referenced by append_atom_info_to_sfr(), append_residue_info_to_sfr(), generate_default_remarks(), generate_default_title_section(), generate_HELIXInformation(), generate_SHEETInformation(), get_connectivity_annotation_info(), get_new_atom_serial_num(), grab_foldtree(), grab_membrane_info(), grab_pdb_comments(), grab_pdb_parents(), grab_pdbinfo_labels(), grab_pose_cache_data(), grab_pose_energies_table(), grab_simple_metric_data(), grab_torsion_records(), init_from_pose(), new_sfr(), and sfr().

The documentation for this class was generated from the following files:

src/core/io/pose_to_sfr/PoseToStructFileRepConverter.hh
src/core/io/pose_to_sfr/PoseToStructFileRepConverter.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ PoseToStructFileRepConverter() [1/2]

◆ PoseToStructFileRepConverter() [2/2]

◆ ~PoseToStructFileRepConverter()

Member Function Documentation

◆ add_atom_to_sfr()

◆ append_atom_info_to_sfr() [1/2]

◆ append_atom_info_to_sfr() [2/2]

◆ append_residue_info_to_sfr()

◆ append_residue_to_sfr() [1/2]

◆ append_residue_to_sfr() [2/2]

◆ determine_atom_indices()

◆ generate_default_remarks()

◆ generate_default_title_section()

◆ generate_HELIXInformation()

◆ generate_secondary_structure_informations()

◆ generate_SHEETInformation()

◆ get_chem_comp_type()

◆ get_connectivity_annotation_info()

◆ get_link_record()

◆ get_new_atom_serial_num()

◆ get_parametric_info()

◆ get_residue_information()

◆ get_ssbond_record()

◆ grab_additional_pose_data()

◆ grab_conect_records_for_atom()

◆ grab_foldtree()

◆ grab_membrane_info()

◆ grab_pdb_comments()

◆ grab_pdb_parents()

◆ grab_pdbinfo_labels()

◆ grab_pose_cache_data()

◆ grab_pose_energies_table()

◆ grab_simple_metric_data()

◆ grab_torsion_records()

◆ init_from_pose() [1/5]

◆ init_from_pose() [2/5]

◆ init_from_pose() [3/5]

◆ init_from_pose() [4/5]

◆ init_from_pose() [5/5]

◆ new_sfr()

◆ recalculate_new_chainIDs()

◆ set_fold_tree_io()

◆ sfr()

◆ total_sfr_atoms() [1/2]

◆ total_sfr_atoms() [2/2]

◆ use_pdb_info_for_num()

Friends And Related Function Documentation

◆ ::PoseToStructFileRepConverterTests

◆ operator<<

Member Data Documentation

◆ atom_indices_

◆ atom_indices_initialized_

◆ new_chainIDs_

◆ options_

◆ sfr_