Difference between revisions of "Molecular mechanics dev"
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Latest revision as of 07:20, 2 October 2007
- 1 Introduction
- 2 OBForceField class
- 2.1 Members of OBForceField
- 2.2 Members of OBForceField_FFF_
- 2.3 Functions of OBForceField
- 2.4 Functions of OBForceField_FFF_
- 3 OBFFParameter
- 4 OBFFCalculation
- 5 Current implementations
This page functions as a guide to the force field implementations in openbabel.
This is the base class for all force fields. It contains gerenal functions that can be used by drived OBForceField_FFF_ classes (_FFF_ = MM2, MMFF94, Ghemical, ...). Each OBForceField_FFF_ class should declare the following functions.
Members of OBForceField
Holds the OBMol object we are working with.
Members of OBForceField_FFF_
A vector of OBFFParameter's to hold the parameters read from the parameter files. xxx is the energy term, so ther will be a _ffbondparams, _ffangleparams, ... NOTE: The name _ffxxxparams can be chosen differently, feel free to simple use bondparams etc.
A vector of OBFF_XXX_Calculation_FFF_'s to hold the 'calculations'. (see below) NOTE: again feel free to use other names.
Functions of OBForceField
After a minimization (SteepestDescent, ConjugateGradient or other functions that change the coordinates of the molecule like GenerateCoordinates) the coordinates of the molecule given as parameter to Setup(OBMol &mol) are still unchanged. To update them, call UpdateCoordinates(OBMol &mol)
Functions of OBForceField_FFF_
bool Setup(OBMol &mol)
- Copy the OBMol object (_mol = &mol;)
- Assign atom types
- Open parameter files and store the parameters in OBFFParameter vectors
- Setup the OBFF_XXX_Calculation_FFF_ vectors using the parameters from the corresponding OBFFParameter vector (_XXX_ = Bond, Angle, StrBnd, ...)
Return the total energy. Call the E_Bond(), E_Angle(), E_StrBnd() functions and return the sum of their return values.
Return bond sretching energy.
Return angle bending energy.
double E_StrBnd() [optional]
Since not all force fields implement this energy term, this term is optional. If no E_StrBnd() function is defined by the OBForceField_FFF_ class, the E_StrBnd() function of OBForceField is called wich returns 0.0f. If the function is defined, it should return the stretch-bending enrgy;
Return torsional energy.
double E_OOP() [optional]
Return out-of-plane bending energy. This term is optional.
Return the Van der Waals energy.
Return the electrostatic energy.
The members of this class are used to hold the parameters for the force field. Below is a list of the members and their (possible) use:
- int a, b, c, d: Used to hold the atom types in case the forcefield uses interger atomtypes.
- char *_a, *_b, *_c, *_d: Used to hold the atom types in case the forcefield uses ascii atomtypes.
- double dpar1, dpar2, ..., dpar5: Store force constants, ideal bond lengts and angles, ...
- double ipar1, ipar2, ..., ipar5: Store interger type parameters (bondtype, angletype, ... in MMFF94)
There are no derived classes of the OBFFParameter class, all forcefields use this class in the same way.
To minimize a structure, a large number of energy/gradient calculations have to be performed. To make the time needed for this task as short as possible we have to make sure not to do the same calculations over and over. Each time a E_Bond() function is called it will iterate over a vector of OBFF_XXX_Calcultion_FFF_'s and return the sum of the OBFF_XXX_Calculation_FFF_::GetEnergy() functions. This is the same for the other energy terms.
Members of OBFFCalculation
Some general members are declared by OBFFCalculations itself. Other, more specific variables (and functions) are defined by the derived OBFF_XXX_Calculation_FFF_ classes.
- double energy: Store the energy for the Calculation. This can be acceced later for logging. Note that this energy is the individual energy from a single bond stretch, angle bend, torsional, ... calculation between 2 to 4 atoms.
- OBAtom *a, *b, *c, *d: Hold the atoms for the calculation (normally: 2-4 atoms)
Functions of OBFFCalculation
The GetEnergy() and GetGradient(OBAtom *atom) funtions of OBFFCalculation return 0 and (0,0,0) respectively. Therefore these should be overloaded by functions in the OBFF_XXX_Calculation_FFF_ class which perform the desired calculations. The GetGradient(OBAtom *atom) functions is optional if numerical derivatives are acceptable.
Calculate and return the energy using the atoms (from base class OBFFCalculation) and the parameters (from OBFF_XXX_Calculation_FFF_).
double GetGradient(OBAtom *Atom)
Calculate and return the gradient with respect to the coordinates of atom using the atoms (from base class OBFFCalculation) and the parameters (from OBFF_XXX_Calculation_FFF_).
Setting up the OBFF_XXX_Calculation_FFF_ vectors
For each energy term, a OBFF_XXX_Calculation_FFF_ vector must be filled with atoms and parameters for that term. So for a molecule with n bonds there are n items in the OBFFBondCalculation_FFF_ vector. These atoms are added in the OBForceField_FFF_::Setup(OBMol &mol) function after assigning the atomtypes, reading the parameter files and storing these parameters in OBFFParameter vectors. For example, when we have a bond with atoms that got types C and C assigned to them, we will iterate over the (vector<OBFFParameter>) _ffbondparams vector and find the parameters for that bond with OBForceField::GetParameter(...). When parameters are found we store them in a OBFF_XXX_Calculation_FFF_ together with the asociated atoms and push_back this to the (vector<OBFF_XXX_Calculation_FFF_>) xxxcalculation vector
Currently, the 2.1 development code includes partial implementations of three force fields: