Rosetta 3.4
Public Member Functions
core::chemical::orbitals::OrbitalType Class Reference

#include <OrbitalType.hh>

Collaboration diagram for core::chemical::orbitals::OrbitalType:
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List of all members.

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!!!!!!!!
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.
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.
std::string name () const
 returns the name of the orbital type. defined in orbital_properties.txt
Real distance () const
 returns the distance from the atom the orbital comes off. defined in orbital_properties.txt
utility::vector1< std::string > atom_type_name () const
 returns the atom_types associated with the orbital type. defined in orbital_properties.txt
std::string hybridization () const
 returns hybrdiziation of atom the orbital is attached to
std::string orbital_name () const
 returns the orbital associated with the type
orbital_type_enum orbital_enum () const

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!!!!!!!!

References core::chemical::orbitals::OrbitalTypeMapper::get_instance(), core::chemical::orbitals::OrbitalTypeMapper::get_orbital_enum(), and orbital_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

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

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

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

returns hybrdiziation of atom the orbital is attached to

std::string core::chemical::orbitals::OrbitalType::name ( ) const
orbital_type_enum core::chemical::orbitals::OrbitalType::orbital_enum ( ) const
std::string core::chemical::orbitals::OrbitalType::orbital_name ( ) const

returns the orbital associated with the type

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.

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.

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


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