IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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#include <IMP/npctransport/FGChain.h>
a chain with a root
root - root of hierarchy beads - fine chain particles
Public Member Functions | |
FGChain (IMP::Particle *root, double backbone_k=0.0, double rest_length_factor=1.0, std::string name="chain %1%") | |
double | get_backbone_k () const |
get the force constant between consecutive chain beads More... | |
IMP::Particle * | get_bead (unsigned int i) const |
get the i'th bead in the chain (assume valid root) More... | |
IMP::ParticleIndex | get_bead_index (unsigned int i) const |
get the i'th bead index in the chain (assume valid root) More... | |
IMP::ParticlesTemp | get_beads () const |
get the beads of the chain (assume valid root) More... | |
virtual Restraints | get_chain_restraints (Scoring const *scoring_manager) |
unsigned int | get_number_of_beads () const |
get the number of beads in the chain (assume valid root) More... | |
double | get_rest_length_factor () const |
atom::Hierarchy | get_root () const |
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_backbone_k (double k) |
void | set_rest_length_factor (double rlf) |
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) |
Protected Member Functions | |
void | set_root (Particle *p) |
void | set_root (atom::Hierarchy root) |
Protected Member Functions inherited from IMP::Object | |
Object (std::string name) | |
Construct an object with the given name. More... | |
virtual void | do_destroy () |
IMP::npctransport::FGChain::FGChain | ( | IMP::Particle * | root, |
double | backbone_k = 0.0 , |
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double | rest_length_factor = 1.0 , |
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std::string | name = "chain %1%" |
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initialized an FG chain with given backbone k and rest length factor, and a specified root whose leaves are the beads of the chain.
root | root of the chain (leaves are assumed beads). can be null = to be added later |
backbone_k | force constant between consecutive chain beads |
rest_length_factor | equilibrium distance factor between consecutive beads relative to the sum of their radii |
name | chain object name |
double IMP::npctransport::FGChain::get_backbone_k | ( | ) | const |
IMP::Particle* IMP::npctransport::FGChain::get_bead | ( | unsigned int | i | ) | const |
IMP::ParticleIndex IMP::npctransport::FGChain::get_bead_index | ( | unsigned int | i | ) | const |
IMP::ParticlesTemp IMP::npctransport::FGChain::get_beads | ( | ) | const |
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virtual |
Returns a restraint associated with internal interactions by this chain. Once this method has been called once, it is assumed that the chain topology remains static (the behavior of the restraint if the chain topology changes is undefined, e.g. if beads are added)
unsigned int IMP::npctransport::FGChain::get_number_of_beads | ( | ) | const |
double IMP::npctransport::FGChain::get_rest_length_factor | ( | ) | const |
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virtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
void IMP::npctransport::FGChain::set_backbone_k | ( | double | k | ) |
set the force constant between consecutive chain beads
void IMP::npctransport::FGChain::set_rest_length_factor | ( | double | rlf | ) |
set the equilibrium distance factor between consecutive beads relative to the sum of their radii
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protected |
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protected |