protocols::antibody::design::CDRGraftDesignOptions Class Reference

Class that holds CDRGraftDesign Options. Now that GraftDesign is not a separate 'thing', this should be split into CDRGraftOptions and CDRMinOptions eventually. More...

#include <CDRGraftDesignOptions.hh>

Inheritance diagram for protocols::antibody::design::CDRGraftDesignOptions:

Public Member Functions
	CDRGraftDesignOptions ()
	CDRGraftDesignOptions (CDRNameEnum cdr)
	CDRGraftDesignOptions (CDRGraftDesignOptions const &src)
	~CDRGraftDesignOptions () override
void	set_cdr (CDRNameEnum cdr)
	Set the CDR type for this instance of options. More...
void	design (bool design)
	Should this CDR be designed? More...
bool	design () const
	Should this CDR be designed? More...
void	weight (core::Real weight)
	Set the weight we will use for choosing this particular CDR for design. More...
core::Real	weight () const
	Return the weight we will use for choosing this particular CDR for design. More...
void	mintype (MinTypeEnum mintype)
	Options are: relax, minimize, repack, dualspace. Default is repack for time, but relax is the best. More...
MinTypeEnum	mintype () const
void	min_neighbor_sc (bool min_neighbor_sc)
	Minimize neighbor sidechains? More...
bool	min_neighbor_sc () const
void	min_sc (bool min_sc)
	Minimize sidechains during minimization (relax/min/etc) (default True? More...
bool	min_sc () const
void	min_rb (bool min_rb)
	Use rigid body optimization during minimization of the CDR (Minimize jump bt antigen and antibody)? More...
bool	min_rb () const
void	neighbor_min (utility::vector1< CDRNameEnum > neighbor_min)
	Set other CDRs to minimize when this CDR is minimized. More...
void	neighbor_min_add (CDRNameEnum cdr)
void	neighbor_min_clear ()
utility::vector1< CDRNameEnum >	neighbor_min () const
CDRGraftDesignOptionsOP	clone () const
void	set_defaults ()
	Set defaults - !!! these are not the defaults from the database default instruction file. Use the parser to parse those instructions if you wish. More...

Private Attributes
bool	cdr_
bool	design_
MinTypeEnum	mintype_
bool	min_neighbor_sc_
bool	min_sc_
bool	min_rb_
utility::vector1< CDRNameEnum >	neighbor_min_
core::Real	cdr_weight_

Detailed Description

Class that holds CDRGraftDesign Options. Now that GraftDesign is not a separate 'thing', this should be split into CDRGraftOptions and CDRMinOptions eventually.

Constructor & Destructor Documentation

protocols::antibody::design::CDRGraftDesignOptions::CDRGraftDesignOptions

(

)

References set_defaults().

protocols::antibody::design::CDRGraftDesignOptions::CDRGraftDesignOptions

(

CDRNameEnum

cdr

)

References set_defaults().

protocols::antibody::design::CDRGraftDesignOptions::CDRGraftDesignOptions ( CDRGraftDesignOptions const &  src )

default

protocols::antibody::design::CDRGraftDesignOptions::~CDRGraftDesignOptions ( )

overridedefault

Member Function Documentation

CDRGraftDesignOptionsOP protocols::antibody::design::CDRGraftDesignOptions::clone

(

)

const

void protocols::antibody::design::CDRGraftDesignOptions::design

(

bool

design

)

Should this CDR be designed?

References design(), and design_.

bool protocols::antibody::design::CDRGraftDesignOptions::design ( ) const

inline

Should this CDR be designed?

References design_.

Referenced by design().

void protocols::antibody::design::CDRGraftDesignOptions::min_neighbor_sc

(

bool

min_neighbor_sc

)

Minimize neighbor sidechains?

References min_neighbor_sc(), and min_neighbor_sc_.

bool protocols::antibody::design::CDRGraftDesignOptions::min_neighbor_sc ( ) const

inline

References min_neighbor_sc_.

Referenced by min_neighbor_sc().

void protocols::antibody::design::CDRGraftDesignOptions::min_rb

(

bool

min_rb

)

Use rigid body optimization during minimization of the CDR (Minimize jump bt antigen and antibody)?

Does nothing if repacking the cdr. Default False.

References min_rb(), and min_rb_.

bool protocols::antibody::design::CDRGraftDesignOptions::min_rb ( ) const

inline

References min_rb_.

Referenced by min_rb().

void protocols::antibody::design::CDRGraftDesignOptions::min_sc

(

bool

min_sc

)

Minimize sidechains during minimization (relax/min/etc) (default True?

References min_sc(), and min_sc_.

bool protocols::antibody::design::CDRGraftDesignOptions::min_sc ( ) const

inline

References min_sc_.

Referenced by min_sc().

void protocols::antibody::design::CDRGraftDesignOptions::mintype

(

MinTypeEnum

mintype

)

Options are: relax, minimize, repack, dualspace. Default is repack for time, but relax is the best.

References mintype(), and mintype_.

MinTypeEnum protocols::antibody::design::CDRGraftDesignOptions::mintype ( ) const

inline

References mintype_.

Referenced by mintype().

void protocols::antibody::design::CDRGraftDesignOptions::neighbor_min

(

utility::vector1< CDRNameEnum >

neighbor_min

)

Set other CDRs to minimize when this CDR is minimized.

References neighbor_min(), and neighbor_min_.

utility::vector1<CDRNameEnum> protocols::antibody::design::CDRGraftDesignOptions::neighbor_min ( ) const

inline

References neighbor_min_.

Referenced by neighbor_min().

void protocols::antibody::design::CDRGraftDesignOptions::neighbor_min_add

(

CDRNameEnum

cdr

)

References neighbor_min_.

void protocols::antibody::design::CDRGraftDesignOptions::neighbor_min_clear

(

)

References neighbor_min_.

void protocols::antibody::design::CDRGraftDesignOptions::set_cdr

(

CDRNameEnum

cdr

)

Set the CDR type for this instance of options.

References cdr_.

void protocols::antibody::design::CDRGraftDesignOptions::set_defaults

(

)

Set defaults - !!! these are not the defaults from the database default instruction file. Use the parser to parse those instructions if you wish.

References cdr_weight_, design_, min_neighbor_sc_, min_rb_, min_sc_, protocols::antibody::design::minimize, mintype_, and neighbor_min_.

Referenced by CDRGraftDesignOptions().

void protocols::antibody::design::CDRGraftDesignOptions::weight

(

core::Real

weight

)

Set the weight we will use for choosing this particular CDR for design.

References cdr_weight_, and weight().

core::Real protocols::antibody::design::CDRGraftDesignOptions::weight ( ) const

inline

Return the weight we will use for choosing this particular CDR for design.

References cdr_weight_.

Referenced by weight().

Member Data Documentation

bool protocols::antibody::design::CDRGraftDesignOptions::cdr_

private

Referenced by set_cdr().

core::Real protocols::antibody::design::CDRGraftDesignOptions::cdr_weight_

private

Referenced by set_defaults(), and weight().

bool protocols::antibody::design::CDRGraftDesignOptions::design_

private

Referenced by design(), and set_defaults().

bool protocols::antibody::design::CDRGraftDesignOptions::min_neighbor_sc_

private

Referenced by min_neighbor_sc(), and set_defaults().

bool protocols::antibody::design::CDRGraftDesignOptions::min_rb_

private

Referenced by min_rb(), and set_defaults().

bool protocols::antibody::design::CDRGraftDesignOptions::min_sc_

private

Referenced by min_sc(), and set_defaults().

MinTypeEnum protocols::antibody::design::CDRGraftDesignOptions::mintype_

private

Referenced by mintype(), and set_defaults().

utility::vector1<CDRNameEnum> protocols::antibody::design::CDRGraftDesignOptions::neighbor_min_

private

Referenced by neighbor_min(), neighbor_min_add(), neighbor_min_clear(), and set_defaults().

---

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

• src/protocols/antibody/design/CDRGraftDesignOptions.hh
• src/protocols/antibody/design/CDRGraftDesignOptions.cc