MTK++ Latest version: 0.2.0

Public Member Functions | Protected Attributes
MTKpp::conformers Class Reference

This class creates and operators on conformers, however, the conformers are stored in molecule. More...

#include <mtkpp/src/Molecule/conformer.h>

Collaboration diagram for MTKpp::conformers:
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List of all members.

Public Member Functions

 conformers (molecule *parent=0)
 conformers Constructor
virtual ~conformers ()
 conformers Destructor.
void addRotatableTorsion (int a, int b, int c, int d)
 Set rotatable bonds.
void determineAtomList ()
 Determine atom list.
void getConformerCoordinates (conformer *c, std::vector< vector3d > &newCoords)
 Get the coordinates of the conformer.
void getConformerCoordinates (conformer *c, double coords[][3])
 Get all atomic coordinates.
void centerOfMass (std::vector< vector3d > coords, double center[3])
 Get the center of mass.

Protected Attributes

moleculepParent
 molecule pointer
std::vector< atom * >::iterator atomIterator
 atom iterator
std::vector< Bond * >::iterator bondIterator
std::vector< int >::iterator intIterator
atompAtom1
 atom pointer
atompAtom2
 atom pointer
BondpBond
 Bond pointer.
std::vector< vector3ditsCoords
 parent molecule coordinates
std::vector< std::vector< int > > itsRotatableTorsions
 rotatable torsions
std::vector< std::vector
< unsigned int > > 
rhsAtomList
 vector of atom vectors

Detailed Description

This class creates and operators on conformers, however, the conformers are stored in molecule.

Author:
Martin Peters

Constructor & Destructor Documentation

MTKpp::conformers::conformers ( molecule parent = 0)

conformers Constructor

Parameters:
parentmolecule pointer

References MTKpp::molecule::getCoordinates(), itsCoords, and pParent.

MTKpp::conformers::~conformers ( ) [virtual]

conformers Destructor.


Member Function Documentation

void MTKpp::conformers::addRotatableTorsion ( int  a,
int  b,
int  c,
int  d 
)

Set rotatable bonds.

Parameters:
aatom1 index
batom2 index
catom3 index
datom4 index

References itsRotatableTorsions.

Referenced by MTKpp::molecule::setTorsion(), and MTKpp::molecule::setupConformers().

void MTKpp::conformers::determineAtomList ( )
void MTKpp::conformers::getConformerCoordinates ( conformer c,
std::vector< vector3d > &  newCoords 
)

Get the coordinates of the conformer.

Parameters:
cconformer to be considered
newCoordsconformer coordinates to be returned

References itsCoords, itsRotatableTorsions, rhsAtomList, and MTKpp::conformer::torsions.

Referenced by MTKpp::molecule::setTorsion().

void MTKpp::conformers::getConformerCoordinates ( conformer c,
double  coords[][3] 
)

Get all atomic coordinates.

Parameters:
cconformer pointer
coordsdouble array of coordinates

References itsCoords, itsRotatableTorsions, rhsAtomList, and MTKpp::conformer::torsions.

void MTKpp::conformers::centerOfMass ( std::vector< vector3d coords,
double  center[3] 
)

Get the center of mass.

Parameters:
coordsconformer coordinates to be considered
centerconformer center of mass

Member Data Documentation

molecule pointer

Referenced by conformers(), and determineAtomList().

std::vector<atom*>::iterator MTKpp::conformers::atomIterator [protected]

atom iterator

std::vector<Bond*>::iterator MTKpp::conformers::bondIterator [protected]
std::vector<int>::iterator MTKpp::conformers::intIterator [protected]

atom pointer

Referenced by determineAtomList().

atom pointer

Referenced by determineAtomList().

Bond pointer.

std::vector< vector3d > MTKpp::conformers::itsCoords [protected]

parent molecule coordinates

Referenced by conformers(), and getConformerCoordinates().

std::vector< std::vector<int> > MTKpp::conformers::itsRotatableTorsions [protected]

rotatable torsions

Referenced by addRotatableTorsion(), determineAtomList(), and getConformerCoordinates().

std::vector< std::vector<unsigned int> > MTKpp::conformers::rhsAtomList [protected]

vector of atom vectors

  • For each torsion we will only rotate on the rhs, 4, X, etc
                    2 -- 3     X
                  /       \  /
                1          4
    
  • We need to make a list of these atoms for each torsion

Referenced by determineAtomList(), and getConformerCoordinates().


The documentation for this class was generated from the following files:

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