IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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a python restraint that computes the score for a composite of proteins Authors: G. More...
a python restraint that computes the score for a composite of proteins Authors: G.
Bouvier, R. Pellarin. Pasteur Institute.
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... | |
Restraint * | create_current_decomposition () const |
Decompose this restraint into constituent terms for the current conf. More... | |
Restraint * | create_decomposition () const |
Decompose this restraint into constituent terms. More... | |
virtual ScoringFunction * | create_scoring_function (double weight=1.0, double max=NO_MAX) const |
Create a scoring function with only this restraint. More... | |
virtual RestraintInfo * | get_dynamic_info () const |
virtual double | get_last_score () const |
double | get_score () const |
virtual RestraintInfo * | get_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... | |
Model * | get_model () const |
ModelObjectsTemp | get_outputs () const |
const ScoreStatesTemp & | get_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 () |
def IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint.__init__ | ( | self, | |
m, | |||
slope = 1.0 , |
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theta = 0.0 , |
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plateau = 1e-10 , |
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linear_slope = 0.015 |
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) |
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.
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.