Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Attributes | List of all members
core::chemical::orbitals::OrbitalType Class Reference

#include <OrbitalType.hh>

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_
 

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 atom_type_name_, 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

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

References distance_.

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

returns hybrdiziation of atom the orbital is attached to

References hybridization_.

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

References orbital_type_enum_.

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

returns the orbital associated with the type

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.

References distance_.

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.

References is_orbital_acceptor_, and is_orbital_donor_.

Member Data Documentation

utility::vector1<std::string> core::chemical::orbitals::OrbitalType::atom_type_name_
private

atom type associated with a given orbital type

Referenced by atom_type_name(), and OrbitalType().

core::Real core::chemical::orbitals::OrbitalType::distance_
private

distance of orbital from center of atom

Referenced by distance(), and set_parameter().

std::string core::chemical::orbitals::OrbitalType::hybridization_
private

hybridization of atom the orbital is attached to

Referenced by hybridization(), and OrbitalType().

bool core::chemical::orbitals::OrbitalType::is_orbital_acceptor_
private

is the orbital an acceptor?

Referenced by set_property().

bool core::chemical::orbitals::OrbitalType::is_orbital_donor_
private

is the orbital a donor?

Referenced by set_property().

std::string core::chemical::orbitals::OrbitalType::orbital_name_
private

orbital name associated with the orbital type

Referenced by orbital_name(), and OrbitalType().

orbital_type_enum core::chemical::orbitals::OrbitalType::orbital_type_enum_
private

Referenced by orbital_enum(), and OrbitalType().

std::string core::chemical::orbitals::OrbitalType::orbital_type_name_
private

the orbital type name

Referenced by name(), and OrbitalType().


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