#include <generalizedBornCase.h>
Public Member Functions | |
| void | clear () throw () |
| bool | setup (const AtomContainer &ac) throw (Exception::FileNotFound) |
| We need an additional optioned version of that piece of code. | |
| void | setScalingFactorFile (const String &filename) throw () |
| ??? This should be done through Options! | |
| void | setScalingFactors (const StringHashMap< float > &scaling_factors) throw () |
| const StringHashMap< float > & | getScalingFactors () const throw () |
| void | setSolventDC (float solvent_dc) throw () |
| ??? Should be done by options | |
| void | setSoluteDC (float solute_dc) throw () |
| ??? Should be done by options | |
| float | calculateEnergy () throw () |
| Compute the total energy of the system. | |
| float | calculateSolvationEnergy () throw () |
| Compoute only the solvation energy (meaning the transfer energy which is a kind of a reaction field energy). | |
| void | calculatePotential (HashMap< const Atom *, float > &p_hash) const throw () |
| Calculate the total potential created by every other atom of the system for every atom and return a hashmap conteining the potential values. | |
| float | calculatePotential (const Atom &atom_i) const throw () |
| Calculate the total potential created by every other atom of the system at the position of atom_i. | |
| bool | readScalingFactors (const String &inifile_name) throw (Exception::FileNotFound) |
This implementation bases on
[1] "Modification of the Generalized Born Model Suitable for Macromolecules" Onufriev, Bashford, Case J. Phys. Chem. B 104:3712-3720, 2000
This paper uses techniques from
[2] "Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics" Still, Tempczyk, Hawley, Hendrickson J. Am. Chem. Soc. 112(16):6127-6129, 1990
[3] "Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt eff¤ects " Srinivasan, Trevathan, Beroza, Case Theor. Chem. Acc. 101(6):426-434, 1999