MTK++ Latest version: 0.2.0

Public Member Functions | Protected Attributes | Friends
MTKpp::connections Class Reference

Class to assign bonds, angles, torsion and improper. More...

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

Collaboration diagram for MTKpp::connections:
Collaboration graph
[legend]

List of all members.

Public Member Functions

 connections ()
 connections Constructor
 connections (collection *parent)
 connections Constructor
virtual ~connections ()
 connections Destructor
void assignBonds ()
 Assigns all Bonds for Every Molecule in the Collection.
void assignBonds (molecule *pMolecule)
 Assigns all Bonds in a Molecule.
void assignDisulfideBonds ()
 Determine all disulfide bonds in the collection.
void assignDisulfideBonds (molecule *pMolecule)
 Determine all disulfide bonds in a molecule.
void assignAngles ()
 Assigns all Angles for Every Molecule in the Collection.
void assignAngles (molecule *pMolecule)
 Assigns all Angles in a Molecule.
void assignAngles (metalCenter *pMetalCenter)
 Assigns all Angles in a metal center.
void assignTorsions ()
 Assigns all Torsions for Every Molecule in the Collection.
void assignTorsions (molecule *pMolecule)
 Assigns all Torsions in a Molecule.
void assignImpropers ()
 Assigns all Impropers for Every Molecule in the Collection.
void assignImpropers (molecule *pMolecule)
 Assigns all Impropers in a Molecule.
void run ()
 Convenience function to carry out assignBonds, assignAngles, assignTorsions, assignImpropers.
void run (collection *pCol)
 Convenience function to carry out assignBonds, assignAngles, assignTorsions, assignImpropers.
void run (molecule *pMol)
 Convenience function to carry out assignBonds, assignAngles, assignTorsions, assignImpropers.
void assignStd ()
 Convenience function to carry out assignStdBonds, assignStdAngles, assignStdTorsions, assignStdImpropers.
void assignStd (molecule *pMol)
 Convenience function to carry out assignStdBonds, assignStdAngles, assignStdTorsions, assignStdImpropers.
void assignStdBondsAngles (molecule *pMol)
 Convenience function to carry out assignStdBonds and assignStdAngles.
void bondByLibrary (molecule *m, submolecule *s1, stdFrag *f1, submolecule *s2, stdFrag *f2)
 Bond by library.
void bondByDistance (molecule *m, submolecule *s1, submolecule *s2)
 Bond by distance.
virtual bool BondExists (double d, atom *a, atom *b)
 Does a bond exist between a and b (used by bondByDistance)
void assignStdBonds ()
 Assign Standard Bonds.
void assignStdBonds (molecule *pMol)
 Assign Standard Bonds.
void assignStdAngles ()
 Assign Standard Angles.
void assignStdAngles (molecule *pMol)
 Assign Standard Angles.
void assignStdTorsions ()
 Assign Standard Torsions.
void assignStdTorsions (molecule *pMol)
 Assign Standard Torsions.
void assignStdImpropers ()
 Assign Standard Impropers.
void assignStdImpropers (molecule *pMol)
 Assign Standard Impropers.

Protected Attributes

collectionpCollection
 collection pointer
moleculepMolecule
 molecule pointer
submoleculepSubMolecule
 submolecule pointer
submoleculepSubMoleculeMinus1
 submolecule pointer
atompAtom
 atom pointer
atompAtom1
 atom pointer
atompAtom2
 atom pointer
atompAtom3
 atom pointer
atompAtom4
 atom pointer
BondpBond
 Bond pointer.
AnglepAngle
 Angle pointer.
TorsionpTorsion
 Torsion pointer.
ImproperpImproper
 Improper pointer.
vector3dcoord1
 coordinate pointer
vector3dcoord2
 coordinate pointer
stdLibrarypStdLibrary
 standard library pointer
stdGrouppStdGroup
 standard group pointer
stdFragpStdFrag
 standard fragment pointer
stdFragpStdFragMinus1
 standard fragment pointer
stdAtompStdAtom
 standard atom pointer
stdAtompStdAtom1
 standard atom pointer
stdAtompStdAtom2
 standard atom pointer
stdLooppStdLoop
 standard loop pointer
std::vector< molecule * > moleculeList
 molecule vector
std::vector< submolecule * > subMoleculeList
 submolecule vector
std::vector< atom * > atomList
 atom vector
std::vector< atom * > atomList2
 atom vector
std::vector< stdLoop * > stdLoopList
 standard loop vector
parameterspParameters
 parameters pointer
int missingBondParams
 Missing bond parameters.
int missingAngleParams
 Missing angle parameters.
int missingTorsionParams
 Missing torsion parameters.
std::string errorMessage
 Error message.

Friends

class protonate

Detailed Description

Class to assign bonds, angles, torsion and improper.

Author:
Martin Peters
Version:
0.1
Date:
2005

Constructor & Destructor Documentation

MTKpp::connections::connections ( )

connections Constructor

Parameters:
parentcollection pointer

References missingAngleParams, missingBondParams, and missingTorsionParams.

MTKpp::connections::connections ( collection parent)

connections Constructor

Parameters:
parentcollection pointer

References missingAngleParams, missingBondParams, and missingTorsionParams.

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

connections Destructor


Member Function Documentation

void MTKpp::connections::assignBonds ( )

Assigns all Bonds for Every Molecule in the Collection.

Todo:
Figure out how to set bond types, stereo, and topology.

References MTKpp::collection::getMoleculeList(), moleculeList, pCollection, and pMolecule.

Referenced by main(), and run().

void MTKpp::connections::assignBonds ( molecule pMolecule)
void MTKpp::connections::assignDisulfideBonds ( )

Determine all disulfide bonds in the collection.

References MTKpp::collection::getMoleculeList(), moleculeList, pCollection, and pMolecule.

Referenced by main(), and run().

void MTKpp::connections::assignDisulfideBonds ( molecule pMolecule)
void MTKpp::connections::assignAngles ( )
void MTKpp::connections::assignAngles ( molecule pMolecule)
void MTKpp::connections::assignAngles ( metalCenter pMetalCenter)
void MTKpp::connections::assignTorsions ( )
void MTKpp::connections::assignTorsions ( molecule pMolecule)
void MTKpp::connections::assignImpropers ( )
void MTKpp::connections::assignImpropers ( molecule pMolecule)
void MTKpp::connections::run ( )
void MTKpp::connections::run ( collection pCol)

Convenience function to carry out assignBonds, assignAngles, assignTorsions, assignImpropers.

References MTKpp::errorLogger, MTKpp::MTK_ERROR, pCollection, run(), and MTKpp::errorHandler::throwError().

void MTKpp::connections::run ( molecule pMol)

Convenience function to carry out assignBonds, assignAngles, assignTorsions, assignImpropers.

Parameters:
pMolmolecule pointer

References assignAngles(), assignBonds(), assignDisulfideBonds(), assignImpropers(), assignStd(), assignTorsions(), MTKpp::errorLogger, MTKpp::INFO, and MTKpp::errorHandler::throwError().

void MTKpp::connections::assignStd ( )

Convenience function to carry out assignStdBonds, assignStdAngles, assignStdTorsions, assignStdImpropers.

References assignStdAngles(), assignStdBonds(), assignStdImpropers(), assignStdTorsions(), MTKpp::errorLogger, MTKpp::INFO, and MTKpp::errorHandler::throwError().

Referenced by MTKpp::protonate::buildMissingHeavyAtoms(), main(), run(), and MTKpp::protonate::runMol().

void MTKpp::connections::assignStd ( molecule pMol)

Convenience function to carry out assignStdBonds, assignStdAngles, assignStdTorsions, assignStdImpropers.

Parameters:
pMolmolecule pointer

References assignStdAngles(), assignStdBonds(), assignStdImpropers(), assignStdTorsions(), MTKpp::errorLogger, MTKpp::INFO, and MTKpp::errorHandler::throwError().

void MTKpp::connections::assignStdBondsAngles ( molecule pMol)

Convenience function to carry out assignStdBonds and assignStdAngles.

Parameters:
pMolmolecule pointer

References assignStdAngles(), assignStdBonds(), MTKpp::errorLogger, MTKpp::INFO, and MTKpp::errorHandler::throwError().

Referenced by main().

void MTKpp::connections::bondByLibrary ( molecule m,
submolecule s1,
stdFrag f1,
submolecule s2,
stdFrag f2 
)
void MTKpp::connections::bondByDistance ( molecule m,
submolecule s1,
submolecule s2 
)
bool MTKpp::connections::BondExists ( double  d,
atom a,
atom b 
) [virtual]

Does a bond exist between a and b (used by bondByDistance)

Parameters:
ddistance between a and b
aatom pointer
batom pointer

References MTKpp::BONDTOLERANCE, MTKpp::element::covalentRadius, MTKpp::d2s(), MTKpp::errorLogger, errorMessage, MTKpp::atom::getElement(), MTKpp::atom::getFileID(), MTKpp::i2s(), MTKpp::INFO, MTKpp::element::symbol, and MTKpp::errorHandler::throwError().

Referenced by bondByDistance().

void MTKpp::connections::assignStdBonds ( )
void MTKpp::connections::assignStdBonds ( molecule pMol)
void MTKpp::connections::assignStdAngles ( )
void MTKpp::connections::assignStdAngles ( molecule pMol)
void MTKpp::connections::assignStdTorsions ( )
void MTKpp::connections::assignStdTorsions ( molecule pMol)
void MTKpp::connections::assignStdImpropers ( )

Assign Standard Impropers.

Referenced by assignStd(), and run().

void MTKpp::connections::assignStdImpropers ( molecule pMol)

Assign Standard Impropers.

Parameters:
pMolmolecule pointer

Friends And Related Function Documentation

friend class protonate [friend]

Member Data Documentation

submolecule pointer

Referenced by assignBonds().

atom pointer

atom pointer

Referenced by assignAngles(), assignImpropers(), and assignTorsions().

atom pointer

Referenced by assignImpropers(), and assignTorsions().

Bond pointer.

Referenced by assignStdBonds(), and bondByLibrary().

Angle pointer.

Referenced by assignAngles(), and assignStdAngles().

Torsion pointer.

Referenced by assignStdTorsions().

Improper pointer.

coordinate pointer

Referenced by assignDisulfideBonds(), bondByDistance(), and bondByLibrary().

coordinate pointer

Referenced by assignDisulfideBonds(), bondByDistance(), and bondByLibrary().

standard library pointer

standard group pointer

standard fragment pointer

Referenced by assignBonds().

standard fragment pointer

Referenced by assignBonds().

standard atom pointer

standard atom pointer

Referenced by bondByLibrary().

standard atom pointer

Referenced by bondByLibrary().

standard loop pointer

Referenced by bondByLibrary().

std::vector<molecule*> MTKpp::connections::moleculeList [protected]
std::vector<atom*> MTKpp::connections::atomList [protected]
std::vector<atom*> MTKpp::connections::atomList2 [protected]

atom vector

Referenced by bondByDistance(), and bondByLibrary().

std::vector<stdLoop*> MTKpp::connections::stdLoopList [protected]

standard loop vector

Referenced by bondByLibrary().

parameters pointer

Referenced by assignStdAngles(), assignStdBonds(), and assignStdTorsions().

Missing bond parameters.

Referenced by assignStdBonds(), and connections().

Missing angle parameters.

Referenced by assignStdAngles(), and connections().

Missing torsion parameters.

Referenced by assignStdTorsions(), and connections().

std::string MTKpp::connections::errorMessage [protected]

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

Generated on Fri Dec 23 2011 09:28:56 for MTK++ by Doxygen 1.7.5.1