rdkit.ForceField.rdForceField.ForceField

Package rdkit :: Package ForceField :: Module rdForceField :: Class ForceField |
[hide private]
[frames] | no frames]

# Class ForceField

     object --+
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    ??.instance --+
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                 ForceField

    A force field

Instance Methods | [hide private]
AddDistanceConstraint(...) AddDistanceConstraint( (ForceField)self, (int)idx1, (int)idx2, (float)minLen, (float)maxLen, (float)forceConstant) -> None : Adds a distance constraint to the UFF force field (deprecated, use UFFAddDistanceConstraint instead). |
AddExtraPoint(...) AddExtraPoint( (ForceField)self, (float)x, (float)y, (float)z [, (bool)fixed=True]) -> int : Adds an extra point, this can be useful for adding constraints. |
AddFixedPoint(...) AddFixedPoint( (ForceField)self, (int)idx) -> None : Adds a fixed point to the force field. |
CalcEnergy(...) CalcEnergy( (ForceField)arg1) -> float : Returns the energy (in kcal/mol) of the current arrangement |
GetExtraPointPos(...) GetExtraPointPos( (ForceField)self, (int)idx) -> object : returns the location of an extra point as a tuple |
Initialize(...) Initialize( (ForceField)arg1) -> None : initializes the force field (call this before minimizing) |
MMFFAddAngleConstraint(...) MMFFAddAngleConstraint( (ForceField)self, (int)idx1, (int)idx2, (int)idx3, (bool)relative, (float)minAngleDeg, (float)maxAngleDeg, (float)forceConstant) -> None : Adds an angle constraint to the MMFF force field; if relative == True, then minAngleDeg and maxAngleDeg are intended as relative to the current angle. |
MMFFAddDistanceConstraint(...) MMFFAddDistanceConstraint( (ForceField)self, (int)idx1, (int)idx2, (bool)relative, (float)minLen, (float)maxLen, (float)forceConstant) -> None : Adds a distance constraint to the MMFF force field; if relative == True, then minLen and maxLen are intended as relative to the current distance. |
MMFFAddPositionConstraint(...) MMFFAddPositionConstraint( (ForceField)self, (int)idx, (float)maxDispl, (float)forceConstant) -> None : Adds a position constraint to the MMFF force field. |
MMFFAddTorsionConstraint(...) MMFFAddTorsionConstraint( (ForceField)self, (int)idx1, (int)idx2, (int)idx3, (int)idx4, (bool)relative, (float)minDihedralDeg, (float)maxDihedralDeg, (float)forceConstant) -> None : Adds a dihedral angle constraint to the MMFF force field; if relative == True, then minDihedralDeg and maxDihedralDeg are intended as relative to the current dihedral angle. |
Minimize(...) Minimize( (ForceField)arg1 [, (int)maxIts=200 [, (float)forceTol=0.0001 [, (float)energyTol=1e-06]]]) -> int : Runs some minimization iterations. |
MinimizeTrajectory(...) MinimizeTrajectory( (ForceField)arg1, (int)snapshotFreq [, (int)maxIts=200 [, (float)forceTol=0.0001 [, (float)energyTol=1e-06]]]) -> tuple : Runs some minimization iterations, recording the minimization trajectory every snapshotFreq steps. |
UFFAddAngleConstraint(...) UFFAddAngleConstraint( (ForceField)self, (int)idx1, (int)idx2, (int)idx3, (bool)relative, (float)minAngleDeg, (float)maxAngleDeg, (float)forceConstant) -> None : Adds an angle constraint to the UFF force field; if relative == True, then minAngleDeg and maxAngleDeg are intended as relative to the current angle. |
UFFAddDistanceConstraint(...) UFFAddDistanceConstraint( (ForceField)self, (int)idx1, (int)idx2, (bool)relative, (float)minLen, (float)maxLen, (float)forceConstant) -> None : Adds a distance constraint to the UFF force field; if relative == True, then minLen and maxLen are intended as relative to the current distance. |
UFFAddPositionConstraint(...) UFFAddPositionConstraint( (ForceField)self, (int)idx, (float)maxDispl, (float)forceConstant) -> None : Adds a position constraint to the UFF force field. |
UFFAddTorsionConstraint(...) UFFAddTorsionConstraint( (ForceField)self, (int)idx1, (int)idx2, (int)idx3, (int)idx4, (bool)relative, (float)minDihedralDeg, (float)maxDihedralDeg, (float)forceConstant) -> None : Adds a dihedral angle constraint to the UFF force field; if relative == True, then minDihedralDeg and maxDihedralDeg are intended as relative to the current dihedral angle. |
__init__(...) Raises an exception... |
__reduce__(...) helper for pickle |
Inherited from `unreachable.instance`: `__new__` Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Properties | [hide private]
Inherited from `object`: `__class__`

Method Details | [hide private]

### AddDistanceConstraint(...) |
    AddDistanceConstraint( (ForceField)self, (int)idx1, (int)idx2, (float)minLen, (float)maxLen, (float)forceConstant) -> None :
        Adds a distance constraint to the UFF force field (deprecated, use UFFAddDistanceConstraint instead).

        C++ signature :
            void AddDistanceConstraint(ForceFields::PyForceField*,unsigned int,unsigned int,double,double,double)

### AddExtraPoint(...) |
    AddExtraPoint( (ForceField)self, (float)x, (float)y, (float)z [, (bool)fixed=True]) -> int :
        Adds an extra point, this can be useful for adding constraints.

        C++ signature :
            int AddExtraPoint(ForceFields::PyForceField {lvalue},double,double,double [,bool=True])

### AddFixedPoint(...) |
    AddFixedPoint( (ForceField)self, (int)idx) -> None :
        Adds a fixed point to the force field.

        C++ signature :
            void AddFixedPoint(ForceFields::PyForceField*,unsigned int)

### CalcEnergy(...) |
    CalcEnergy( (ForceField)arg1) -> float :
        Returns the energy (in kcal/mol) of the current arrangement

        C++ signature :
            double CalcEnergy(ForceFields::PyForceField {lvalue})

### GetExtraPointPos(...) |
    GetExtraPointPos( (ForceField)self, (int)idx) -> object :
        returns the location of an extra point as a tuple

        C++ signature :
            _object* GetExtraPointPos(ForceFields::PyForceField*,unsigned int)

### Initialize(...) |
    Initialize( (ForceField)arg1) -> None :
        initializes the force field (call this before minimizing)

        C++ signature :
            void Initialize(ForceFields::PyForceField {lvalue})

### MMFFAddAngleConstraint(...) |
    MMFFAddAngleConstraint( (ForceField)self, (int)idx1, (int)idx2, (int)idx3, (bool)relative, (float)minAngleDeg, (float)maxAngleDeg, (float)forceConstant) -> None :
        Adds an angle constraint to the MMFF force field; if relative == True, then minAngleDeg and maxAngleDeg are intended as relative to the current angle.

        C++ signature :
            void MMFFAddAngleConstraint(ForceFields::PyForceField*,unsigned int,unsigned int,unsigned int,bool,double,double,double)

### MMFFAddDistanceConstraint(...) |
    MMFFAddDistanceConstraint( (ForceField)self, (int)idx1, (int)idx2, (bool)relative, (float)minLen, (float)maxLen, (float)forceConstant) -> None :
        Adds a distance constraint to the MMFF force field; if relative == True, then minLen and maxLen are intended as relative to the current distance.

        C++ signature :
            void MMFFAddDistanceConstraint(ForceFields::PyForceField*,unsigned int,unsigned int,bool,double,double,double)

### MMFFAddPositionConstraint(...) |
    MMFFAddPositionConstraint( (ForceField)self, (int)idx, (float)maxDispl, (float)forceConstant) -> None :
        Adds a position constraint to the MMFF force field.

        C++ signature :
            void MMFFAddPositionConstraint(ForceFields::PyForceField*,unsigned int,double,double)

### MMFFAddTorsionConstraint(...) |
    MMFFAddTorsionConstraint( (ForceField)self, (int)idx1, (int)idx2, (int)idx3, (int)idx4, (bool)relative, (float)minDihedralDeg, (float)maxDihedralDeg, (float)forceConstant) -> None :
        Adds a dihedral angle constraint to the MMFF force field; if relative == True, then minDihedralDeg and maxDihedralDeg are intended as relative to the current dihedral angle.

        C++ signature :
            void MMFFAddTorsionConstraint(ForceFields::PyForceField*,unsigned int,unsigned int,unsigned int,unsigned int,bool,double,double,double)

### Minimize(...) |
    Minimize( (ForceField)arg1 [, (int)maxIts=200 [, (float)forceTol=0.0001 [, (float)energyTol=1e-06]]]) -> int :
        Runs some minimization iterations.

          Returns 0 if the minimization succeeded.

        C++ signature :
            int Minimize(ForceFields::PyForceField {lvalue} [,int=200 [,double=0.0001 [,double=1e-06]]])

### MinimizeTrajectory(...) |
    MinimizeTrajectory( (ForceField)arg1, (int)snapshotFreq [, (int)maxIts=200 [, (float)forceTol=0.0001 [, (float)energyTol=1e-06]]]) -> tuple :
        Runs some minimization iterations, recording the minimization trajectory every snapshotFreq steps.

        Returns a (int, []) tuple; the int is 0 if the minimization succeeded, while the list contains Snapshot objects.

        C++ signature :
            boost::python::tuple MinimizeTrajectory(ForceFields::PyForceField {lvalue},unsigned int [,int=200 [,double=0.0001 [,double=1e-06]]])

### UFFAddAngleConstraint(...) |
    UFFAddAngleConstraint( (ForceField)self, (int)idx1, (int)idx2, (int)idx3, (bool)relative, (float)minAngleDeg, (float)maxAngleDeg, (float)forceConstant) -> None :
        Adds an angle constraint to the UFF force field; if relative == True, then minAngleDeg and maxAngleDeg are intended as relative to the current angle.

        C++ signature :
            void UFFAddAngleConstraint(ForceFields::PyForceField*,unsigned int,unsigned int,unsigned int,bool,double,double,double)

### UFFAddDistanceConstraint(...) |
    UFFAddDistanceConstraint( (ForceField)self, (int)idx1, (int)idx2, (bool)relative, (float)minLen, (float)maxLen, (float)forceConstant) -> None :
        Adds a distance constraint to the UFF force field; if relative == True, then minLen and maxLen are intended as relative to the current distance.

        C++ signature :
            void UFFAddDistanceConstraint(ForceFields::PyForceField*,unsigned int,unsigned int,bool,double,double,double)

### UFFAddPositionConstraint(...) |
    UFFAddPositionConstraint( (ForceField)self, (int)idx, (float)maxDispl, (float)forceConstant) -> None :
        Adds a position constraint to the UFF force field.

        C++ signature :
            void UFFAddPositionConstraint(ForceFields::PyForceField*,unsigned int,double,double)

### UFFAddTorsionConstraint(...) |
    UFFAddTorsionConstraint( (ForceField)self, (int)idx1, (int)idx2, (int)idx3, (int)idx4, (bool)relative, (float)minDihedralDeg, (float)maxDihedralDeg, (float)forceConstant) -> None :
        Adds a dihedral angle constraint to the UFF force field; if relative == True, then minDihedralDeg and maxDihedralDeg are intended as relative to the current dihedral angle.

        C++ signature :
            void UFFAddTorsionConstraint(ForceFields::PyForceField*,unsigned int,unsigned int,unsigned int,unsigned int,bool,double,double,double)

### __init__(...) (Constructor) |
    Raises an exception
    This class cannot be instantiated from Python
Overrides: object.__init__

### __reduce__(...) |
    helper for pickle
Overrides: object.__reduce__ (inherited documentation)