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.  | |
| class | ElasticNetworkModel |
| Interface for all ENMs. More... | |
| class | ExponentialDistance |
Exponential distance weighting (i.e.  | |
| 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 (AtomicGroup &grp, const string &name) |
| 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. | |
| void | massFromPSF (loos::AtomicGroup &grp, const std::string &name) |
| Copy the masses from a PSF onto a group. | |
| std::vector< std::string > | splitCommaSeparatedList (const std::string &s) |
| SpringFunction * | springFactory (const std::string &spring_desc) |
| Factory function for generating new SpringFunction instances based on a user string. | |
| std::vector< std::string > | springNames () |
| List of possible names for springFactory() | |
Detailed Description
Namespace to encapsulate Elastic Network Model routines.
Function Documentation
◆ springFactory()
| 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.
