core::io::pose_from_sfr Namespace Reference

Classes
class	GeometricRenameIsomorphismCallback
class	GeometricRenameVerticiesEquivalent
	Will consider two verticies equivalent if they have the same element. More...
class	GraphvizPropertyWriter
	Callback class for writing graphviz info. More...
class	PoseFromSFRBuilder
	The PoseFromSFRBuilder is responsible for taking a partially-processed representation of a structure file, a structure-file repersentation or StructFileRep, and it constructs a Pose from it. Its primary output is a Pose, but it also keeps track of the "missing atoms:" the set of atoms in the Pose whose coordinates were not given in the original file. More...

Typedefs
using	AtomInfoGraph = boost::undirected_graph< AtomInformation >
using	AIVD = AtomInfoGraph::vertex_descriptor
using	RestypeInfoGraph = boost::undirected_graph< std::pair< std::string, std::string > >
using	RIGVD = RestypeInfoGraph::vertex_descriptor
typedef boost::bimap< std::string, std::string >	NameBimap
typedef utility::pointer::shared_ptr< PoseFromSFRBuilder >	PoseFromSFRBuilderOP
typedef utility::pointer::shared_ptr< PoseFromSFRBuilder const >	PoseFromSFRBuilderCOP

Functions
void	check_and_correct_sister_atoms (core::conformation::ResidueOP &rsd)
	due to differences in different crystallography/NMR/modeling packages, labeling of sister atoms (like OP1 <--> OP2, or H41 <--> H42) in PDBs is totally wacky. This is an attempt to regularize... and it can actually make a difference since sometimes partial charges on sister hydrogens can be different. Right now only set up for nucleic acids, but could probably generalize. More...
void	check_and_correct_sister_atom_based_on_chirality (core::conformation::ResidueOP &rsd, std::string const &sister1_name, std::string const &sister2_name, std::string const &parent_name, std::string const &cousin_name)
void	check_and_correct_sister_atom_based_on_outgroup (core::conformation::ResidueOP &rsd, std::string const &sister1_name, std::string const &sister2_name, std::string const &outgroup_name)
void	flip_atom_xyz (core::conformation::ResidueOP &rsd, std::string const &sister1_name, std::string const &sister2_name)
int	sgn (Real const &x)
int	get_chirality_sign (Vector const &xyz_sister1, Vector const &xyz_sister2, Vector const &xyz_parent, Vector const &xyz_cousin)
int	get_closest_sister (Vector const &xyz_sister1, Vector const &xyz_sister2, Vector const &xyz_outgroup)
core::Real	bonding_distance_threshold (std::string element1, std::string element2)
	Get theshold distance below which two atoms are considered bonded. (1.2*covalent) More...
core::Real	score_mapping (NameBimap const &mapping, ResidueInformation const &rinfo, chemical::ResidueType const &rsd_type)
	Scoring scheme for the heuristic PDB renaming. More...
void	remap_names_on_geometry (NameBimap &mapping, ResidueInformation const &rinfo, chemical::ResidueType const &rsd_type)
	Attempt to use element identity and connectivity to map atom names from the rinfo object onto the rsd_type object names. More...
static basic::Tracer	TR ("core.io.pose_from_sfr.PoseFromSFRBuilder")
bool	missing_O2prime (utility::vector1< core::io::AtomInformation > const &atoms)
core::chemical::ResidueTypeCOP	find_restype (std::string const &name, std::string const &name3, core::chemical::ResidueTypeSet const &restypeset, std::set< std::string > &warned_on_ccd_confusion)
	Utility function to help pass_2_quick_and_dirty_resolve_residue_types() More...
bool	is_connected (core::conformation::Conformation const &conf, core::Size ii, std::string const &ii_atm, core::Size jj, std::string const &jj_atm)
void	show_residue_connections (core::conformation::Conformation const &conf, core::Size i)
std::string	convert_atom_name (std::string const &res_name, std::string const &atom_name)
	for nucleic acids, slightly better mechanism is below (convert_nucleic_acid_residue_info_to_standard) More...
std::string	convert_res_name (std::string const &name)
void	create_working_data (StructFileRepOptions const &options, StructFileRep const &sfr, utility::vector1< core::io::ResidueInformation > &rinfos)
bool	update_atom_information_based_on_occupancy (StructFileRepOptions const &options, AtomInformation &ai)
void	randomize_missing_coords (AtomInformation &ai)
	randomize missing density More...

Typedef Documentation

AIVD

using core::io::pose_from_sfr::AIVD = typedef AtomInfoGraph::vertex_descriptor

AtomInfoGraph

using core::io::pose_from_sfr::AtomInfoGraph = typedef boost::undirected_graph<AtomInformation>

NameBimap

typedef boost::bimap< std::string, std::string > core::io::pose_from_sfr::NameBimap

PoseFromSFRBuilderCOP

typedef utility::pointer::shared_ptr< PoseFromSFRBuilder const > core::io::pose_from_sfr::PoseFromSFRBuilderCOP

PoseFromSFRBuilderOP

typedef utility::pointer::shared_ptr< PoseFromSFRBuilder > core::io::pose_from_sfr::PoseFromSFRBuilderOP

RestypeInfoGraph

using core::io::pose_from_sfr::RestypeInfoGraph = typedef boost::undirected_graph< std::pair< std::string, std::string> >

RIGVD

using core::io::pose_from_sfr::RIGVD = typedef RestypeInfoGraph::vertex_descriptor

Function Documentation

bonding_distance_threshold()

core::Real core::io::pose_from_sfr::bonding_distance_threshold	(	std::string	element1,
		std::string	element2
	)

Get theshold distance below which two atoms are considered bonded. (1.2*covalent)

The closest distance of a non-bonded contact is likely to be something like the opposite atoms cyclobutane. This would be sqrt(2)*covalent bond distance. We thus set the contact distance threshold to 1.2*covalent bond distance to allow bond length flexibility. In initial tests this looks to give a clean decision.

Pass-by-value is deliberate, as we want to strip the elements of whitespace

References core::chemical::Element::CovalentRadius, and core::chemical::orbitals::strip_whitespace().

Referenced by remap_names_on_geometry(), and score_mapping().

check_and_correct_sister_atom_based_on_chirality()

void core::io::pose_from_sfr::check_and_correct_sister_atom_based_on_chirality	(	core::conformation::ResidueOP &	rsd,
		std::string const &	sister1_name,
		std::string const &	sister2_name,
		std::string const &	parent_name,
		std::string const &	cousin_name
	)

References flip_atom_xyz(), get_chirality_sign(), and core::chemical::ResidueType::ideal_xyz().

Referenced by check_and_correct_sister_atoms().

check_and_correct_sister_atom_based_on_outgroup()

void core::io::pose_from_sfr::check_and_correct_sister_atom_based_on_outgroup	(	core::conformation::ResidueOP &	rsd,
		std::string const &	sister1_name,
		std::string const &	sister2_name,
		std::string const &	outgroup_name
	)

References flip_atom_xyz(), get_closest_sister(), and core::chemical::ResidueType::ideal_xyz().

Referenced by check_and_correct_sister_atoms().

check_and_correct_sister_atoms()

void core::io::pose_from_sfr::check_and_correct_sister_atoms

(

core::conformation::ResidueOP &

rsd

)

due to differences in different crystallography/NMR/modeling packages, labeling of sister atoms (like OP1 <--> OP2, or H41 <--> H42) in PDBs is totally wacky. This is an attempt to regularize... and it can actually make a difference since sometimes partial charges on sister hydrogens can be different. Right now only set up for nucleic acids, but could probably generalize.

References check_and_correct_sister_atom_based_on_chirality(), and check_and_correct_sister_atom_based_on_outgroup().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose().

convert_atom_name()

std::string core::io::pose_from_sfr::convert_atom_name	(	std::string const &	res_name,
		std::string const &	atom_name
	)

for nucleic acids, slightly better mechanism is below (convert_nucleic_acid_residue_info_to_standard)

References TR().

Referenced by create_working_data().

convert_res_name()

std::string core::io::pose_from_sfr::convert_res_name

(

std::string const &

name

)

Temporary hacky hack Need better mechanism for this for nucleic acids, slightly better mechanism is below (convert_nucleic_acid_residue_info_to_standard)

References TR().

Referenced by create_working_data().

create_working_data()

void core::io::pose_from_sfr::create_working_data	(	StructFileRepOptions const &	options,
		StructFileRep const &	sfr,
		utility::vector1< core::io::ResidueInformation > &	rinfos
	)

References core::io::StructFileRep::chains(), convert_atom_name(), convert_res_name(), core::io::AtomInformation::name, core::io::AtomInformation::resName, and core::io::pose_from_sfr::PoseFromSFRBuilder::update_atom_information_based_on_occupancy().

Referenced by protocols::ligand_docking::StartFrom::parse_pdb_file(), and core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary().

find_restype()

core::chemical::ResidueTypeCOP core::io::pose_from_sfr::find_restype	(	std::string const &	name,
		std::string const &	name3,
		core::chemical::ResidueTypeSet const &	restypeset,
		std::set< std::string > &	warned_on_ccd_confusion
	)

Utility function to help pass_2_quick_and_dirty_resolve_residue_types()

References core::chemical::ResidueTypeSet::has_name(), core::chemical::ResidueTypeSet::name_mapOP(), and TR().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types().

flip_atom_xyz()

void core::io::pose_from_sfr::flip_atom_xyz	(	core::conformation::ResidueOP &	rsd,
		std::string const &	sister1_name,
		std::string const &	sister2_name
	)

References TR().

Referenced by check_and_correct_sister_atom_based_on_chirality(), and check_and_correct_sister_atom_based_on_outgroup().

get_chirality_sign()

int core::io::pose_from_sfr::get_chirality_sign	(	Vector const &	xyz_sister1,
		Vector const &	xyz_sister2,
		Vector const &	xyz_parent,
		Vector const &	xyz_cousin
	)

References sgn().

Referenced by check_and_correct_sister_atom_based_on_chirality().

get_closest_sister()

int core::io::pose_from_sfr::get_closest_sister	(	Vector const &	xyz_sister1,
		Vector const &	xyz_sister2,
		Vector const &	xyz_outgroup
	)

Referenced by check_and_correct_sister_atom_based_on_outgroup().

is_connected()

bool core::io::pose_from_sfr::is_connected	(	core::conformation::Conformation const &	conf,
		core::Size	ii,
		std::string const &	ii_atm,
		core::Size	jj,
		std::string const &	jj_atm
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::connect_atom(), core::conformation::Residue::is_bonded(), and core::conformation::Conformation::residue().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), and protocols::magnesium::update_mg_hoh_fold_tree().

missing_O2prime()

bool core::io::pose_from_sfr::missing_O2prime

(

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

atoms

)

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::convert_nucleic_acid_residue_info_to_standard().

randomize_missing_coords()

void core::io::pose_from_sfr::randomize_missing_coords

(

AtomInformation &

ai

)

randomize missing density

The missing density regions in the input pdb should have 0.000 in the placeholders this routine puts random coordinates wherever there is 0.000 for mainchain atoms. tex - that's a stupid way of defining missing density, as atoms can be at the origin for other reasons. This has been updated to check for occupancy to define missing density rather than atoms located at the origin.

References core::io::AtomInformation::name, core::io::AtomInformation::occupancy, core::io::AtomInformation::resName, core::io::AtomInformation::resSeq, core::scoring::rg, TR(), core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

Referenced by core::io::StructFileRepOptions::init_from_options(), and core::io::StructFileRepOptions::list_options_read().

remap_names_on_geometry()

void core::io::pose_from_sfr::remap_names_on_geometry	(	NameBimap &	mapping,
		ResidueInformation const &	rinfo,
		chemical::ResidueType const &	rsd_type
	)

Attempt to use element identity and connectivity to map atom names from the rinfo object onto the rsd_type object names.

References protocols::forge::methods::add_vertex(), core::chemical::ResidueType::atom_name(), core::io::ResidueInformation::atoms(), bonding_distance_threshold(), core::chemical::ResidueType::bonds(), core::io::ResidueInformation::chainID(), core::chemical::ResidueType::element_type(), core::io::ResidueInformation::iCode(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::natoms(), core::io::ResidueInformation::resName(), core::io::ResidueInformation::resSeq(), core::chemical::orbitals::strip_whitespace(), TR(), core::chemical::write_graphviz(), and core::io::ResidueInformation::xyz().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map().

score_mapping()

core::Real core::io::pose_from_sfr::score_mapping	(	NameBimap const &	mapping,
		ResidueInformation const &	rinfo,
		chemical::ResidueType const &	rsd_type
	)

Scoring scheme for the heuristic PDB renaming.

References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::bonded_neighbor(), bonding_distance_threshold(), core::chemical::ResidueType::bonds(), core::chemical::ResidueType::element_type(), core::chemical::ResidueType::ideal_xyz(), core::chemical::ResidueType::natoms(), protocols::hybridization::score, and core::io::ResidueInformation::xyz().

Referenced by core::io::pose_from_sfr::GeometricRenameIsomorphismCallback::operator()().

sgn()

int core::io::pose_from_sfr::sgn

(

Real const &

x

)

Referenced by protocols::fldsgn::topology::calc_strand_helix_angle(), core::scoring::func::GaussianChainQuadrupleFunc::dfunc(), core::scoring::func::GaussianChainQuadrupleFunc::func(), core::scoring::func::GaussianChainGeneralFunc::func(), get_chirality_sign(), and protocols::sparta::PDB::getDihedralAngle().

show_residue_connections()

void core::io::pose_from_sfr::show_residue_connections	(	core::conformation::Conformation const &	conf,
		core::Size	i
	)

References core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), core::conformation::Residue::n_non_polymeric_residue_connections(), core::conformation::Residue::n_polymeric_residue_connections(), core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::name(), core::chemical::ResConnID::resid(), core::conformation::Conformation::residue(), core::conformation::Residue::residue_connect_atom_index(), and TR().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

TR()

static basic::Tracer core::io::pose_from_sfr::TR ( "core.io.pose_from_sfr.PoseFromSFRBuilder"  )

static

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_2_temps(), convert_atom_name(), core::io::pose_from_sfr::PoseFromSFRBuilder::convert_nucleic_acid_residue_info_to_standard(), convert_res_name(), core::io::pose_from_sfr::PoseFromSFRBuilder::determine_residue_branching_info(), find_restype(), core::io::pose_from_sfr::PoseFromSFRBuilder::output_ignore_water_warning_once(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_4_redo_termini(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_5_note_discarded_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::pre_process_residue_type_information(), randomize_missing_coords(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::io::pose_from_sfr::PoseFromSFRBuilder::remember_unrecognized_res(), core::io::pose_from_sfr::PoseFromSFRBuilder::setup(), show_residue_connections(), and update_atom_information_based_on_occupancy().

update_atom_information_based_on_occupancy()

bool core::io::pose_from_sfr::update_atom_information_based_on_occupancy	(	StructFileRepOptions const &	options,
		AtomInformation &	ai
	)

References core::io::AtomInformation::chainID, core::io::AtomInformation::iCode, core::io::StructFileRepOptions::ignore_zero_occupancy(), core::io::AtomInformation::name, core::io::AtomInformation::occupancy, core::io::StructFileRepOptions::randomize_missing_coords(), core::io::pose_from_sfr::PoseFromSFRBuilder::randomize_missing_coords(), core::io::AtomInformation::resSeq, and TR().