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IMP Reference Guide  develop.af393bce43,2020/02/22
The Integrative Modeling Platform
IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint Class Reference

a python restraint that computes the score for a composite of proteins Authors: G. More...

+ Inheritance diagram for IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint:

Detailed Description

a python restraint that computes the score for a composite of proteins Authors: G.

Bouvier, R. Pellarin. Pasteur Institute.

Note
This class is only available in Python.

Definition at line 627 of file pmi1/restraints/proteomics.py.

Public Member Functions

def __init__
 input a list of particles, the slope and theta of the sigmoid potential theta is the cutoff distance for a protein-protein contact More...
 
def get_full_graph
 get the full graph of distances between every particle pair More...
 
def get_minimum_spanning_tree
 return the minimum spanning tree More...
 
def sigmoid
 a sigmoid function that scores the probability of a contact between two proteins More...
 
- Public Member Functions inherited from IMP::Restraint
 Restraint (Model *m, std::string name)
 
void add_score_and_derivatives (ScoreAccumulator sa) const
 Perform the actual restraint scoring. More...
 
Restraintcreate_current_decomposition () const
 Decompose this restraint into constituent terms for the current conf. More...
 
Restraintcreate_decomposition () const
 Decompose this restraint into constituent terms. More...
 
virtual ScoringFunctioncreate_scoring_function (double weight=1.0, double max=NO_MAX) const
 Create a scoring function with only this restraint. More...
 
virtual RestraintInfoget_dynamic_info () const
 
virtual double get_last_score () const
 
double get_score () const
 
virtual RestraintInfoget_static_info () const
 
bool get_was_good () const
 
void set_weight (Float weight)
 
Float get_weight () const
 
double get_maximum_score () const
 
void set_maximum_score (double s)
 
- Public Member Functions inherited from IMP::ModelObject
 ModelObject (Model *m, std::string name)
 
bool get_has_dependencies () const
 Return whether this object has dependencies computed. More...
 
bool get_has_required_score_states () const
 Return whether score states are computed. More...
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 Get the interacting sets induced by this ModelObject. More...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_required_score_states () const
 Get the score states that are ancestors of this in the dependency graph. More...
 
void set_has_dependencies (bool tf)
 Either invalidate the dependencies or ensure they are correct. More...
 
void set_has_required_score_states (bool tf)
 Compute the required score states. More...
 
- Public Member Functions inherited from IMP::Object
virtual void clear_caches ()
 
CheckLevel get_check_level () const
 
LogLevel get_log_level () const
 
virtual VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
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)
 
virtual std::string get_type_name () const
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) const
 A restraint should override this to compute the score and derivatives. More...
 
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
- Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemp do_get_inputs () const =0
 
virtual ModelObjectsTemps do_get_interactions () const
 
virtual void handle_set_has_required_score_states (bool)
 
- Protected Member Functions inherited from IMP::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
virtual void do_destroy ()
 

Constructor & Destructor Documentation

def IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint.__init__ (   self,
  m,
  slope = 1.0,
  theta = 0.0,
  plateau = 1e-10,
  linear_slope = 0.015 
)

input a list of particles, the slope and theta of the sigmoid potential theta is the cutoff distance for a protein-protein contact

Definition at line 634 of file pmi1/restraints/proteomics.py.

Member Function Documentation

def IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint.get_full_graph (   self)

get the full graph of distances between every particle pair

Definition at line 661 of file pmi1/restraints/proteomics.py.

def IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint.get_minimum_spanning_tree (   self)

return the minimum spanning tree

Definition at line 673 of file pmi1/restraints/proteomics.py.

def IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint.sigmoid (   self,
  x 
)

a sigmoid function that scores the probability of a contact between two proteins

Definition at line 681 of file pmi1/restraints/proteomics.py.


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