LOOS  v2.3.2
ENM Namespace Reference

Namespace to encapsulate Elastic Network Model routines. More...

Classes

class  ANM
 Anisotropic network model. More...
 
class  BadSpringFunction
 Bad spring function was requested. More...
 
class  BadSpringParameter
 Unspecified problem with parameters in SpringFunction. More...
 
class  BoundSuperBlock
 Decorator for switching spring functions based on a matrix of flags. More...
 
class  ConstBonded
 Use a spring function that is a constant weight regardless of distance. More...
 
class  DistanceCutoff
 Basic distance cutoff for "traditional" ENM. More...
 
class  DistanceWeight
 Distance weighting (i.e. $r^p$) More...
 
class  ElasticNetworkModel
 Interface for all ENMs. More...
 
class  ExponentialDistance
 Exponential distance weighting (i.e. $\exp(k r)$) More...
 
class  HCA
 HCA method (bimodal distance-based function) More...
 
class  SpringFunction
 Interface for ENM spring functions. More...
 
class  SuperBlock
 This class creates superblocks in a hessian. More...
 
class  SuperBlockDecorator
 SuperBlock decorator base class. More...
 
class  UniformSpringFunction
 Spring functions that are uniform in all directions (ie return a single value) More...
 
class  VSA
 Vibrational subsystem analysis ENM. More...
 

Functions

void copyMasses (loos::AtomicGroup &target, const loos::AtomicGroup &source)
 Map masses from one group onto another... Minimal error checking...
 
void massFromPSF (loos::AtomicGroup &grp, const std::string &name)
 Copy the masses from a PSF onto a group.
 
void massFromOccupancy (loos::AtomicGroup &grp)
 The masses are stored in the occupancy field of a PDB...
 
DoubleMatrix getMasses (const loos::AtomicGroup &grp)
 Build the 3n x 3n diagonal mass matrix for a group.
 
std::vector< std::string > splitCommaSeparatedList (const std::string &s)
 
SpringFunctionspringFactory (const std::string &spring_desc)
 Factory function for generating new SpringFunction instances based on a user string. More...
 
std::vector< std::string > springNames ()
 List of possible names for springFactory()
 

Detailed Description

Namespace to encapsulate Elastic Network Model routines.

Function Documentation

SpringFunction * ENM::springFactory ( const std::string &  spring_desc)

Factory function for generating new SpringFunction instances based on a user string.

Factory function for spring constants. The spring description is the name of the spring function with an optional comma-separated list of parameters to pass to it, i.e. distance distance,15.0 hca,1,2,3,4,5

Will throw in the event of an error.

Definition at line 36 of file spring_functions.cpp.