#include <OrbitalType.hh>

Collaboration diagram for core::chemical::orbitals::OrbitalType:

Public Member Functions
	OrbitalType (std::string &orbital_name, std::string &atom_type_name)
	Constructor that is generally initialized in OrbitalTypeSet.hh. If you add a property, you must initialize that property as false!!!!!!!! More...

void	set_parameter (std::string const &param, core::Real const setting)
	The parameters are the actual headings in the orbital_properties.txt. If you want to add more paramters, you must edit orbital_properties.txt and add another heading. You also need to edit AtomTypeSet.txt so that it recognizes that parameter and parses it. The parameters are different form the properties in that they are Reals/Size and properties are strings. More...

void	set_property (std::string const &property, bool const setting)
	Currently, these properties are not actually in the orbital_properties.txt. I have them here as an example on how to add properties. This is also a place holder as the ligand code will soon be using these properties. The Acceptor/Donor could refer to orbitals that have a lone pair and are donating to a hydrogen, or an electron defficient region. In order to add properties, one must add the properties to the last line of orbital_properties.txt and make a private member variable for that property in the header file. Then do a string match comparision, like seen below. These properties are set via OrbitalTypeSet.hh. More...

std::string	name () const
	returns the name of the orbital type. defined in orbital_properties.txt More...

Real	distance () const
	returns the distance from the atom the orbital comes off. defined in orbital_properties.txt More...

utility::vector1< std::string >	atom_type_name () const
	returns the atom_types associated with the orbital type. defined in orbital_properties.txt More...

std::string	hybridization () const
	returns hybrdiziation of atom the orbital is attached to More...

std::string	orbital_name () const
	returns the orbital associated with the type More...

orbital_type_enum	orbital_enum () const

Private Attributes
bool	is_orbital_acceptor_
	is the orbital an acceptor? More...

bool	is_orbital_donor_
	is the orbital a donor? More...

std::string	orbital_type_name_
	the orbital type name More...

std::string	hybridization_
	hybridization of atom the orbital is attached to More...

std::string	orbital_name_
	orbital name associated with the orbital type More...

utility::vector1< std::string >	atom_type_name_
	atom type associated with a given orbital type More...

core::Real	distance_
	distance of orbital from center of atom More...

orbital_type_enum	orbital_type_enum_

Detailed Description

Definition at line 56 of file OrbitalType.hh.

Constructor & Destructor Documentation

core::chemical::orbitals::OrbitalType::OrbitalType	(	std::string &	orbital_name,
		std::string &	atom_type_name
	)

Constructor that is generally initialized in OrbitalTypeSet.hh. If you add a property, you must initialize that property as false!!!!!!!!

Definition at line 63 of file OrbitalType.cc.

References atom_type_name_, core::chemical::orbitals::OrbitalTypeMapper::get_instance(), core::chemical::orbitals::OrbitalTypeMapper::get_orbital_enum(), hybridization_, orbital_name(), orbital_name_, orbital_type_enum_, and orbital_type_name_.

Member Function Documentation

utility::vector1< std::string > core::chemical::orbitals::OrbitalType::atom_type_name ( ) const

returns the atom_types associated with the orbital type. defined in orbital_properties.txt

Definition at line 151 of file OrbitalType.cc.

References atom_type_name_.

Real core::chemical::orbitals::OrbitalType::distance ( ) const

returns the distance from the atom the orbital comes off. defined in orbital_properties.txt

Definition at line 145 of file OrbitalType.cc.

References distance_.

std::string core::chemical::orbitals::OrbitalType::hybridization ( ) const

returns hybrdiziation of atom the orbital is attached to

Definition at line 157 of file OrbitalType.cc.

References hybridization_.

std::string core::chemical::orbitals::OrbitalType::name ( ) const

returns the name of the orbital type. defined in orbital_properties.txt

Definition at line 132 of file OrbitalType.cc.

References orbital_type_name_.

Referenced by core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), and protocols::features::OrbitalsFeatures::set_OrbOrb_features_data().

orbital_type_enum core::chemical::orbitals::OrbitalType::orbital_enum ( ) const

Definition at line 137 of file OrbitalType.cc.

References orbital_type_enum_.

std::string core::chemical::orbitals::OrbitalType::orbital_name ( ) const

returns the orbital associated with the type

Definition at line 163 of file OrbitalType.cc.

References orbital_name_.

Referenced by OrbitalType().

void core::chemical::orbitals::OrbitalType::set_parameter	(	std::string const &	param,
		core::Real const	setting
	)

The parameters are the actual headings in the orbital_properties.txt. If you want to add more paramters, you must edit orbital_properties.txt and add another heading. You also need to edit AtomTypeSet.txt so that it recognizes that parameter and parses it. The parameters are different form the properties in that they are Reals/Size and properties are strings.

Definition at line 92 of file OrbitalType.cc.

References distance_.

Referenced by core::chemical::orbitals::OrbitalTypeSet::read_file().

void core::chemical::orbitals::OrbitalType::set_property	(	std::string const &	property,
		bool const	setting
	)

Currently, these properties are not actually in the orbital_properties.txt. I have them here as an example on how to add properties. This is also a place holder as the ligand code will soon be using these properties. The Acceptor/Donor could refer to orbitals that have a lone pair and are donating to a hydrogen, or an electron defficient region. In order to add properties, one must add the properties to the last line of orbital_properties.txt and make a private member variable for that property in the header file. Then do a string match comparision, like seen below. These properties are set via OrbitalTypeSet.hh.

Definition at line 114 of file OrbitalType.cc.

References is_orbital_acceptor_, and is_orbital_donor_.

Referenced by core::chemical::orbitals::OrbitalTypeSet::read_file().