protocols::pockets::GenPharmacophore Class Reference

#include <GenPharmacophore.hh>

Inheritance diagram for protocols::pockets::GenPharmacophore:

Public Member Functions
bool	is_buried_ring (core::conformation::Residue const &rsd, core::Real const &ring_sasa, core::Real const &sasa_cutoff)
core::Real	get_RNAring_sasa (core::conformation::Residue const &rsd, int const &rsdno, core::id::AtomID_Map< core::Real > const &pose_atom_sasa)
void	get_ideal_hydrogenBond_atoms (core::pose::Pose const &protein_pose)
void	cluster_KeyFeatures (std::string const &input_filename, std::string const &output_filename) const
std::string	extract_rna_rings_from_protein_rna_complex (core::pose::Pose const &protein_pose, core::pose::Pose const &rna_pose)
std::string	extract_Hbond_atoms_from_protein_rna_complex (core::pose::Pose const &protein_pose, core::pose::Pose const &rna_pose)
std::string	make_compatible_with_ROCS_custom_ForceField (std::string &input_filename)
void	print_string_to_PDBfile (std::string const &input_filename, std::string const &output_filename) const
std::string	ReplaceString (std::string subject, const std::string &search, const std::string &replace)

Member Function Documentation

cluster_KeyFeatures()

void protocols::pockets::GenPharmacophore::cluster_KeyFeatures	(	std::string const &	input_filename,
		std::string const &	output_filename
	)		const

References core::pose::motif::a(), protocols::pockets::SmallMol::add_atom(), protocols::match::upstream::b, protocols::loops::chainID, core::sequence::end, protocols::pockets::SmallMol::get_root(), protocols::loops::resSeq, protocols::pockets::SmallMol::set_name(), and core::id::to_string().

extract_Hbond_atoms_from_protein_rna_complex()

std::string protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex	(	core::pose::Pose const &	protein_pose,
		core::pose::Pose const &	rna_pose
	)

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_name(), core::scoring::hbonds::HBondSet::clear(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::hbonds::HBondDatabase::get_database(), core::scoring::get_score_function(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbonds::identify_hbonds_1way(), core::conformation::Residue::is_RNA(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), core::conformation::Residue::seqpos(), core::pose::Pose::size(), core::scoring::Energies::tenA_neighbor_graph(), and core::conformation::Atom::xyz().

extract_rna_rings_from_protein_rna_complex()

std::string protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex	(	core::pose::Pose const &	protein_pose,
		core::pose::Pose const &	rna_pose
	)

References core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::scoring::calc_per_atom_sasa(), core::pose::Pose::clear(), core::pose::initialize_atomid_map(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_purine(), core::conformation::Residue::is_RNA(), core::chemical::rna::RNA_Info::is_RNA_base_atom(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::conformation::Residue::RNA_info(), core::conformation::Residue::seqpos(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

get_ideal_hydrogenBond_atoms()

void protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms

(

core::pose::Pose const &

protein_pose

)

References protocols::cluster::calibur::aa, core::conformation::Residue::abase2(), core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), core::pose::Pose::conformation(), core::conformation::Residue::Hpos_polar(), core::chemical::AtomType::hybridization(), core::pose::metrics::CalculatorFactory::Instance(), core::pose::Pose::metric(), core::conformation::Residue::natoms(), core::conformation::membrane::out, core::pose::metrics::CalculatorFactory::register_calculator(), core::pose::Pose::residue(), core::conformation::Conformation::residue(), core::chemical::RING_HYBRID, core::pose::Pose::size(), core::chemical::SP2_HYBRID, core::chemical::SP3_HYBRID, core::kinematics::Stub::spherical(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

get_RNAring_sasa()

core::Real protocols::pockets::GenPharmacophore::get_RNAring_sasa	(	core::conformation::Residue const &	rsd,
		int const &	rsdno,
		core::id::AtomID_Map< core::Real > const &	pose_atom_sasa
	)

References core::conformation::Residue::is_RNA(), core::chemical::rna::RNA_Info::is_RNA_base_atom(), core::conformation::Residue::nheavyatoms(), and core::conformation::Residue::RNA_info().

is_buried_ring()

bool protocols::pockets::GenPharmacophore::is_buried_ring	(	core::conformation::Residue const &	rsd,
		core::Real const &	ring_sasa,
		core::Real const &	sasa_cutoff
	)

References core::conformation::Residue::name3().

make_compatible_with_ROCS_custom_ForceField()

std::string protocols::pockets::GenPharmacophore::make_compatible_with_ROCS_custom_ForceField

(

std::string &

input_filename

)

print_string_to_PDBfile()

void protocols::pockets::GenPharmacophore::print_string_to_PDBfile	(	std::string const &	input_filename,
		std::string const &	output_filename
	)		const

References core::conformation::membrane::out.

ReplaceString()

std::string protocols::pockets::GenPharmacophore::ReplaceString	(	std::string	subject,
		const std::string &	search,
		const std::string &	replace
	)

References protocols::forge::methods::replace().

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

• src/protocols/pockets/GenPharmacophore.hh
• src/protocols/pockets/GenPharmacophore.cc