IMP Reference Guide
2.20.2
The Integrative Modeling Platform
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Score on end-to-end distance of freely jointed chain. More...
#include <IMP/misc/FreelyJointedChain.h>
Score on end-to-end distance of freely jointed chain.
A flexible linker can be represented by the freely jointed chain model as a polymer under a Gaussian random walk. The end-to-end distance \( z \) then follows the distribution
\[p(z | \beta) = 4 \pi z^2 (\frac{\beta}{\pi})^{3/2)} \exp{(-\beta z^2)},\]
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 \( z = \frac{1}{\sqrt{\beta}} \).
See KA Dill, S Bromberg. Molecular Driving Forces. 2nd Edition. 2010. Eqs 33.26, 33.27.
Definition at line 41 of file FreelyJointedChain.h.
Public Member Functions | |
FreelyJointedChain (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 override |
virtual ::IMP::VersionInfo | get_version_info () const override |
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 () |
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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 FreelyJointedChain.h.
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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 60 of file FreelyJointedChain.h.
double IMP::misc::FreelyJointedChain::get_average_distance | ( | ) | const |
Get the average distance from the surface.
Definition at line 105 of file FreelyJointedChain.h.
double IMP::misc::FreelyJointedChain::get_distance_at_minimum | ( | ) | const |
Get the distance at which the score is at its minimum value.
Definition at line 100 of file FreelyJointedChain.h.
double IMP::misc::FreelyJointedChain::get_link_length | ( | ) | const |
Get length of each chain link.
Definition at line 83 of file FreelyJointedChain.h.
int IMP::misc::FreelyJointedChain::get_link_number | ( | ) | const |
Get number of links in chain.
Definition at line 80 of file FreelyJointedChain.h.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 77 of file FreelyJointedChain.h.
void IMP::misc::FreelyJointedChain::set_link_length | ( | double | b | ) |
Set the length of each chain link.
Definition at line 93 of file FreelyJointedChain.h.
void IMP::misc::FreelyJointedChain::set_link_number | ( | int | N | ) |
Set the number of links in chain.
Definition at line 86 of file FreelyJointedChain.h.