IMP Reference Guide
2.7.0
The Integrative Modeling Platform

Score on surfacetoend distance of chain tethered to impenetrable surface. More...
#include <IMP/core/SurfaceTetheredChain.h>
Score on surfacetoend distance of chain tethered to impenetrable surface.
When a flexible linker is represented by the freely jointed chain model with one end tethered to an impenetrable surface, the distance \( z \) of the free end from the surface follows the distribution
\[ p(z  \beta) = 2 \beta z \exp{(\beta z^2)}, \]
where \( \beta = \frac{3}{2 N b^2} \), \( N \) is the number of links, and \( b \) is the average length of a single link. The score reaches its minimum value when \( z = \frac{1}{\sqrt{2 \beta}} \).
See KA Dill, S Bromberg. Molecular Driving Forces. 2nd Edition. 2010. Eq 34.7.
Definition at line 43 of file SurfaceTetheredChain.h.
Public Member Functions  
SurfaceTetheredChain (int link_num, double link_length)  
virtual double  evaluate (double feature) const 
Calculate score with respect to the given feature. More...  
virtual DerivativePair  evaluate_with_derivative (double feature) const 
Calculate score and derivative with respect to the given feature. More...  
double  get_average_distance () const 
Get the average distance from the surface. More...  
double  get_distance_at_minimum () const 
Get the distance at which the score is at its minimum value. More...  
double  get_link_length () const 
Get length of each chain link. More...  
int  get_link_number () const 
Get number of links in chain. More...  
virtual std::string  get_type_name () const 
virtual ::IMP::VersionInfo  get_version_info () const 
Get information about the module and version of the object. More...  
void  set_link_length (double b) 
Set the length of each chain link. More...  
void  set_link_number (int N) 
Set the number of links in chain. More...  
Public Member Functions inherited from IMP::UnaryFunction  
UnaryFunction (std::string name="UnaryFunction%1%")  
Public Member Functions inherited from IMP::Object  
virtual void  clear_caches () 
CheckLevel  get_check_level () const 
LogLevel  get_log_level () const 
void  set_check_level (CheckLevel l) 
void  set_log_level (LogLevel l) 
Set the logging level used in this object. More...  
void  set_was_used (bool tf) const 
void  show (std::ostream &out=std::cout) const 
const std::string &  get_name () const 
void  set_name (std::string name) 
Additional Inherited Members  
Protected Member Functions inherited from IMP::Object  
Object (std::string name)  
Construct an object with the given name. More...  
virtual void  do_destroy () 

virtual 
Calculate score with respect to the given feature.
[in]  feature  Value of feature being tested. 
Reimplemented from IMP::UnaryFunction.
Definition at line 73 of file SurfaceTetheredChain.h.

virtual 
Calculate score and derivative with respect to the given feature.
[in]  feature  Value of feature being tested. 
Reimplemented from IMP::UnaryFunction.
Definition at line 62 of file SurfaceTetheredChain.h.
double IMP::core::SurfaceTetheredChain::get_average_distance  (  )  const 
Get the average distance from the surface.
Definition at line 105 of file SurfaceTetheredChain.h.
double IMP::core::SurfaceTetheredChain::get_distance_at_minimum  (  )  const 
Get the distance at which the score is at its minimum value.
Definition at line 100 of file SurfaceTetheredChain.h.
double IMP::core::SurfaceTetheredChain::get_link_length  (  )  const 
Get length of each chain link.
Definition at line 83 of file SurfaceTetheredChain.h.
int IMP::core::SurfaceTetheredChain::get_link_number  (  )  const 
Get number of links in chain.
Definition at line 80 of file SurfaceTetheredChain.h.

virtual 
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 77 of file SurfaceTetheredChain.h.
void IMP::core::SurfaceTetheredChain::set_link_length  (  double  b  ) 
Set the length of each chain link.
Definition at line 93 of file SurfaceTetheredChain.h.
void IMP::core::SurfaceTetheredChain::set_link_number  (  int  N  ) 
Set the number of links in chain.
Definition at line 86 of file SurfaceTetheredChain.h.