OBGrid Class Reference
A base grid class. More...
#include <openbabel/grid.h>

Public Member Functions | |
OBGrid () | |
virtual void | Init (OBMol &box) |
double | GetXmin () const |
double | GetYmin () const |
double | GetZmin () const |
double | GetXmax () const |
double | GetYmax () const |
double | GetZmax () const |
bool | PointIsInBox (double x, double y, double z) |
bool | PointIsInBox (double *c) |
bool | PointIsInBox (vector3 v) |
virtual bool | Clear () |
virtual OBBase * | DoTransformations (const std::map< std::string, std::string > *, OBConversion *) |
template<class T > | |
T * | CastAndClear (bool clear=true) |
virtual const char * | GetTitle (bool replaceNewlines=true) const |
virtual void | SetTitle (const char *) |
Generic data handling methods (via OBGenericData) | |
bool | HasData (const std::string &) |
bool | HasData (const char *) |
bool | HasData (const unsigned int type) |
void | DeleteData (unsigned int type) |
void | DeleteData (OBGenericData *) |
void | DeleteData (std::vector< OBGenericData * > &) |
bool | DeleteData (const std::string &s) |
void | SetData (OBGenericData *d) |
void | CloneData (OBGenericData *d) |
size_t | DataSize () const |
OBGenericData * | GetData (const unsigned int type) |
OBGenericData * | GetData (const std::string &) |
OBGenericData * | GetData (const char *) |
std::vector< OBGenericData * > & | GetData () |
std::vector< OBGenericData * > | GetData (DataOrigin source) |
std::vector< OBGenericData * > | GetAllData (const unsigned int type) |
OBDataIterator | BeginData () |
OBDataIterator | EndData () |
Static Public Member Functions | |
static const char * | ClassDescription () |
Protected Attributes | |
double | _xmin |
double | _xmax |
double | _ymin |
double | _ymax |
double | _zmin |
double | _zmax |
std::vector< OBGenericData * > | _vdata |
Detailed Description
A base grid class.
Constructor & Destructor Documentation
OBGrid | ( | ) | [inline] |
Member Function Documentation
void Init | ( | OBMol & | box ) | [virtual] |
Initialize the grid based on a box around the molecule box
Subclasses should overload this method -- this only tracks the dimension of the box itself.
double GetXmin | ( | ) | const [inline] |
- Returns:
- the minimum x point of the grid
double GetYmin | ( | ) | const [inline] |
- Returns:
- the minimum y point of the grid
double GetZmin | ( | ) | const [inline] |
- Returns:
- the minimum z point of the grid
double GetXmax | ( | ) | const [inline] |
- Returns:
- the maximum x point of the grid
double GetYmax | ( | ) | const [inline] |
- Returns:
- the maximum y point of the grid
double GetZmax | ( | ) | const [inline] |
- Returns:
- the maximum z point of the grid
bool PointIsInBox | ( | double | x, |
double | y, | ||
double | z | ||
) | [inline] |
- Returns:
- whether the supplied XYZ coordinates fall within the box
bool PointIsInBox | ( | double * | c ) | [inline] |
- Returns:
- true if the point falls within the box
bool PointIsInBox | ( | vector3 | v ) | [inline] |
- Returns:
- true if the point falls within the box
bool Clear | ( | void | ) | [virtual, inherited] |
Clear any and all data associated with this object.
This method can be called by OBConversion::Read() before reading data. Derived classes should be sure to call OBBase::Clear() to remove inherited generic data.
- Returns:
- Whether the call was successful.
- Since:
- version 2.1.
Reimplemented in OBAtom, OBMol, OBReaction, and OBResidue.
Referenced by OBResidue::Clear().
virtual OBBase* DoTransformations | ( | const std::map< std::string, std::string > * | , |
OBConversion * | |||
) | [inline, virtual, inherited] |
Perform a set of transformations specified by the user
Typically these are program options to filter or modify an object For example, see OBMol::DoTransformations() and OBMol::ClassDescription() Base type does nothing
Reimplemented in OBMol.
static const char* ClassDescription | ( | ) | [inline, static, inherited] |
- Returns:
- A list of descriptions of command-line options for DoTransformations()
Reimplemented in OBMol, and OBReaction.
T* CastAndClear | ( | bool | clear = true ) |
[inline, inherited] |
By default clears the object. Called from ReadMolecule of most format classes.
virtual const char* GetTitle | ( | bool | replaceNewlines = true ) |
const [inline, virtual, inherited] |
Base type does nothing Made virtual around r3535 to simplify code which passes around OBBase*.
Reimplemented in OBMol.
Referenced by OBMoleculeFormat::DoOutputOptions().
virtual void SetTitle | ( | const char * | ) | [inline, virtual, inherited] |
Reimplemented in OBMol.
Referenced by OBMoleculeFormat::DoOutputOptions().
bool HasData | ( | const std::string & | s ) | [inherited] |
- Returns:
- whether the generic attribute/value pair exists
Referenced by OBDepict::DrawMolecule(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBDescriptor::MatchPairData(), OBMol::operator=(), and OBMol::SetEnergies().
bool HasData | ( | const char * | s ) | [inherited] |
- Returns:
- whether the generic attribute/value pair exists
bool HasData | ( | const unsigned int | type ) | [inherited] |
- Returns:
- whether the generic attribute/value pair exists, for a given OBGenericDataType
void DeleteData | ( | unsigned int | type ) | [inherited] |
Delete any data matching the given OBGenericDataType.
Referenced by OpenBabel::CanonicalLabels(), OBDescriptor::DeleteProperties(), and OBMol::RenumberAtoms().
void DeleteData | ( | OBGenericData * | gd ) | [inherited] |
Delete the given generic data from this object.
void DeleteData | ( | std::vector< OBGenericData * > & | vg ) | [inherited] |
Delete all of the given generic data from this object.
bool DeleteData | ( | const std::string & | s ) | [inherited] |
Deletes the generic data with the specified attribute, returning false if not found.
void SetData | ( | OBGenericData * | d ) | [inline, inherited] |
Adds a data object; does nothing if d==NULL.
Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBMoleculeFormat::MakeCombinedMolecule(), OBDescriptor::PredictAndSave(), and OBMol::SetEnergies().
void CloneData | ( | OBGenericData * | d ) | [inherited] |
Adds a copy of a data object; does nothing if d == NULL
- Since:
- version 2.2
size_t DataSize | ( | ) | const [inline, inherited] |
- Returns:
- the number of OBGenericData items attached to this molecule.
OBGenericData * GetData | ( | const unsigned int | type ) | [inherited] |
- Returns:
- the first matching data for a given type from OBGenericDataType or NULL if nothing matches
Referenced by OpenBabel::CalcSignedVolume(), OpenBabel::CorrectChirality(), OBDepict::DrawMolecule(), OBDescriptor::FilterCompare(), OpenBabel::GetAtomSymClass(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBDescriptor::GetValues(), OBMoleculeFormat::MakeCombinedMolecule(), OBMolAngleIter::OBMolAngleIter(), OBMolRingIter::OBMolRingIter(), OBMolTorsionIter::OBMolTorsionIter(), OBMol::operator=(), and OBDescriptor::PredictAndSave().
OBGenericData * GetData | ( | const std::string & | s ) | [inherited] |
- Returns:
- any data matching the given attribute name or NULL if nothing matches
- the value given an attribute name
OBGenericData * GetData | ( | const char * | s ) | [inherited] |
- Returns:
- any data matching the given attribute name or NULL if nothing matches
- the value given an attribute name
std::vector<OBGenericData*>& GetData | ( | ) | [inline, inherited] |
- Returns:
- all data, suitable for iterating
Referenced by OBMol::GetEnergies(), OBMol::GetEnergy(), and OBMol::SetEnergies().
std::vector< OBGenericData * > GetData | ( | DataOrigin | source ) | [inherited] |
- Returns:
- all data with a specific origin, suitable for iterating
std::vector< OBGenericData * > GetAllData | ( | const unsigned int | type ) | [inherited] |
- Returns:
- the all matching data for a given type from OBGenericDataType or an empty vector if nothing matches
- Since:
- version 2.2
Referenced by OpenBabel::CanonicalLabels(), OBBuilder::CorrectStereoAtoms(), and OBBuilder::CorrectStereoBonds().
OBDataIterator BeginData | ( | ) | [inline, inherited] |
- Returns:
- An iterator pointing to the beginning of the data
Referenced by OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().
OBDataIterator EndData | ( | ) | [inline, inherited] |
- Returns:
- An iterator pointing to the end of the data
Referenced by OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().
Member Data Documentation
double _xmin [protected] |
Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().
double _xmax [protected] |
Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().
double _ymin [protected] |
Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().
double _ymax [protected] |
Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().
double _zmin [protected] |
Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().
double _zmax [protected] |
the min/max axes in XYZ axes (i.e., the box)
Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().
std::vector<OBGenericData*> _vdata [protected, inherited] |
Custom data.
Referenced by OBMol::OBMol().
The documentation for this class was generated from the following files: