MTK++ Latest version: 0.2.0

Public Member Functions | Protected Types | Protected Attributes
MTKpp::stdFrag Class Reference

Container for stdAtoms, stdBond, stdImpropers, stdLoops, stdAlias'. More...

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

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List of all members.

Public Member Functions

 stdFrag (stdGroup *parent=0)
 stdFrag Constructor
 stdFrag (stdFrag *sf, stdGroup *parent=0)
 stdFrag Copy Constructor
virtual ~stdFrag ()
 Standard Fragment Destructor.
stdGroupgetParent ()
 Get group which fragment is apart of.
void setName (const std::string &name)
 Set name of fragment.
std::string getName ()
 Get name of the fragment.
void setSymbol (const std::string &symbol)
 Set symbol of the fragment.
std::string getSymbol ()
 Get symbol of the fragment.
void setCode (const std::string &code)
 Set 8 character code of the fragment.
std::string getCode ()
 Get code of the fragment.
void setCharacter (const std::string &c)
 Set 1 letter character of the fragment.
std::string getCharacter ()
 Get 1 letter character of the fragment.
void setType (const std::string &type)
 Set type of the fragment.
std::string getType ()
 Get type of the fragment.
void setSymmetry (const std::string &sym)
 Set symmetry of the fragment.
std::string getSymmetry ()
 Get symmetry of the fragment.
void setSubGraphs (const std::vector< std::string > &g)
 Set which fragments this fragment is a subgraph of.
std::vector< std::string > getSubGraphs ()
 Get list of fragments related to this one.
std::string getSubGraphStr ()
 Get list of fragments related to this one.
stdAtomaddStdAtom ()
 Add a stdAtom to the fragment.
stdAtomaddStdAtom (stdAtom *s)
 Add a stdAtom to the fragment.
stdAtomgetStdAtom (const int &index)
 Get a stdAtom by atom index.
stdAtomgetStdAtom (const std::string &name)
 Get a stdAtom by name.
bool hasStdAtom (const std::string &name)
 Has a stdAtom by name.
std::vector< stdAtom * > getBondedStdAtoms (stdAtom *sAt)
 Get a list of stdAtoms which are bonded to sAt.
int numStdAtoms ()
 Get number of stdAtoms in fragment.
int numStdHeavyAtoms ()
 Get number of stdAtoms in fragment.
stdBondaddStdBond ()
 Add a stdBond to the fragment.
stdBondaddStdBond (stdBond *b)
 Add a stdBond to the fragment.
stdBondgetStdBond (const int &at1, const int &at2)
 get a stdBond from the fragment based on atom indices
stdBondgetStdBond (const std::string &at1, const std::string &at2)
 get a stdBond from the fragment based on atom indices
stdBondgetStdBond (stdAtom *pAt1, stdAtom *pAt2)
 get a stdBond from the fragment based on atom indices
bool hasStdBond (const int &at1, const int &at2)
 Does the fragment contain a bond.
int numStdBonds ()
 Get the number of stdBonds in the fragment.
int numStdBonds (stdAtom *pStdAtom)
 Get the number of stdBonds which pStdAtom is apart of.
stdImproperaddStdImproper ()
 Add a stdImproper to the fragment.
stdImproperaddStdImproper (stdImproper *i)
 Add a stdImproper to the fragment.
stdLoopaddStdLoop ()
 Add a stdLoop to the fragment.
stdLoopaddStdLoop (stdLoop *l)
 Add a stdLoop to the fragment.
stdLoopgetStdLoop (const int &at1, const int &at2)
 get a stdLoop from the fragment based on atom indices
stdLoopgetStdLoop (stdAtom *pAt1, stdAtom *pAt2)
 get a stdLoop from the fragment based on atom indices
stdAliasaddStdAlias ()
 Add a stdAlias to the fragment.
stdAliasaddStdAlias (stdAlias *a)
 Add a stdAlias to the fragment.
stdRingaddStdRing ()
 Add a stdRing to the fragment.
stdRingaddStdRing (stdRing *r)
 Add a stdRing to the fragment.
stdFeatureaddStdFeature ()
 Add a stdFeature to the fragment.
stdFeatureaddStdFeature (stdFeature *f)
 Add a stdFeature to the fragment.
bool hasStdFeature (stdAtom *a, std::string f)
 Has the stdAtom got a stdFeature matching f.
stdFuncGroupaddStdFuncGroup ()
 Add a stdFuncGroup to the stdMolecule.
stdFuncGroupaddStdFuncGroup (stdFuncGroup *f)
 Add a stdFuncGroup to the stdMolecule.
void addStdConnPts (std::vector< int > &v)
 Add connection points to the fragment.
stdConnTorsionaddStdConnTorsion ()
 Add a stdConnTorsion to the stdMolecule.
stdRotBondaddStdRotBond ()
 Add a stdRotBond to the stdMolecule.
std::vector< stdAtom * > getStdAtomList ()
 Get all stdAtoms in the fragment.
std::vector< stdBond * > getStdBondList ()
 Get all stdBonds in the fragment.
std::vector< stdLoop * > getStdLoopList ()
 Get all stdLoops in the fragment.
std::vector< stdAlias * > getStdAliasList ()
 Get all stdAlias' in the fragment.
std::vector< stdImproper * > getStdImproperList ()
 Get all stdImpropers in the fragment.
std::vector< stdRing * > getStdRingList ()
 Get all stdRings in the fragment.
std::vector< stdFeature * > getStdFeatureList ()
 Get all stdFeatures in the fragment.
std::vector< stdFuncGroup * > getStdFuncGroupList ()
 Get all stdFuncGroups in the fragment.
std::vector< int > getStdConnPtsList ()
 Get all stdConnPts in the fragment.
int getNumStdConnPtsList ()
 Get number of stdConnPts in the fragment.
std::vector< stdConnTorsion * > getStdConnTorList ()
 Get all stdConnTorsion in the fragment.
std::vector< stdRotBond * > getStdRotBondList ()
 Get all stdRotBonds in the fragment.
std::string getAlias (const std::string &name)
 Get stdAlias by name.
int generateCoordinates ()
 Generate fragment coordinates.
int generateCoordinates (vector3d *bd, vector3d *ag, vector3d *tr, const int &forward=1)
 Generate fragment coordinates using known coordinates.
std::vector< vector3d * > getCoordinates ()
 Get fragment coordinates.
void print ()
 Print details of stdFrag.
void generateSimpleFP ()
 Generate simple fingerprint.
std::vector< unsigned int > getSimpleFP ()
 Get simple fingerprint.
int generateAdjMatrix ()
 Generate adjacency matrix.
int generateHeavyAdjMatrix ()
 Generate heavy atom adjacency matrix.
int * getAdjMatrix ()
 Get adjacency matrix.
int * getHeavyAdjMatrix ()
 Get heavy atom adjacency matrix.
int getAdjMatrixSize ()
 Get adjacency matrix size.
int getHeavyAdjMatrixSize ()
 Get heavy atom adjacency matrix size.
int generateAtomSymbols ()
 Generate atom symbols array.
int generateHeavyAtomSymbols ()
 Generate heavy atom symbols array.
char * getAtomSymbols ()
 Get atom symbols array.
char * getHeavyAtomSymbols ()
 Get heavy atom symbols array.
int generateAtomKinds ()
 Generate atom kinds array.
int generateHeavyAtomKinds ()
 Generate heavy atom kinds array.
int * getAtomKinds ()
 Get atom kinds array.
int * getHeavyAtomKinds ()
 Get heavy atom kinds array.
double getCharge ()
 Get charge.
int getStdAtomIndex (stdAtom *a)
 Get index of stdAtom.

Protected Types

typedef std::vector< stdAtom * >
::iterator 
stdAtomIterator
 standard atom iterator
typedef std::vector< stdBond * >
::iterator 
stdBondIterator
 standard bond iterator
typedef std::vector< stdLoop * >
::iterator 
stdLoopIterator
 standard loop iterator
typedef std::vector< stdAlias * >
::iterator 
stdAliasIterator
 standard alias iterator
typedef std::vector
< stdImproper * >::iterator 
stdImproperIterator
 standard improper iterator
typedef std::vector< stdRing * >
::iterator 
stdRingIterator
 standard ring iterator
typedef std::vector
< stdFeature * >::iterator 
stdFeatureIterator
 standard feature iterator
typedef std::vector
< stdFuncGroup * >::iterator 
stdFuncGroupIterator
 standard functional group iterator
typedef std::vector< int >
::iterator 
stdConnPtsIterator
 standard connection points iterator
typedef std::vector
< stdConnTorsion * >::iterator 
stdConnTorsionIterator
 standard connTorsion iterator
typedef std::vector
< stdRotBond * >::iterator 
stdRotBondIterator
 standard rotatable bond iterator

Protected Attributes

std::string itsName
 standard fragment name
std::string itsSymbol
 standard fragment symbol (3 Character)
std::string itsCode
 standard fragment code (8 Character)
std::string itsCharacter
 1 Letter character
std::string itsType
std::string itsSymmetry
std::vector< std::string > itsSubGraphs
 list of 3L code fragments which this fragment is a subgraph of
std::vector< stdAtom * > itsStdAtomList
 standard atom list
std::vector< stdBond * > itsStdBondList
 standard bond list
std::vector< stdLoop * > itsStdLoopList
 standard loop list
std::vector< stdAlias * > itsStdAliasList
 standard alias list
std::vector< stdImproper * > itsStdImproperList
 standard improper list
std::vector< stdRing * > itsStdRingList
 standard ring list
std::vector< stdFeature * > itsStdFeatureList
 standard feature list
std::vector< stdFuncGroup * > itsStdFuncGroupList
 standard functional group list
std::vector< int > itsStdConnPtsList
 standard connection points list
std::vector< stdConnTorsion * > itsStdConnTorsionList
 stdConnTorsion list
std::vector< stdRotBond * > itsStdRotBondList
 stdRotBond list
std::vector< vector3d * > itsCoords
 standard improper list
std::vector< unsigned int > itsSimpleFP
 Simple fingerprint.
std::vector< unsigned int > itsFragmentFP
 Fragment fingerprint.
stdGrouppParent
 standard group which fragment belongs to
stdAtompStdAtom
 standard atom pointer
stdAtompStdAtom1
 standard atom pointer
stdAtompStdAtom2
 standard atom pointer
vector3dpCoords
 vector3d pointer
stdBondpStdBond
 standard bond pointer
stdLooppStdLoop
 standard loop pointer
stdAliaspStdAlias
 standard alias pointer
stdImproperpStdImproper
 standard improper pointer
stdRingpStdRing
 standard ring pointer
stdFeaturepStdFeature
 standard feature pointer
stdFuncGrouppStdFuncGroup
 standard function group pointer
stdConnTorsionpStdConnTorsion
 standard connection torion pointer
stdRotBondpStdRotBond
 standard rotatable bond pointer
int * adjMatrix
 Adjacency Matrix.
int adjMatrixSize
 Adjacency Matrix size.
char * atomSymbols
 Atom symbols.
int * atomKinds
 Atom kinds.
int * heavyAtomAdjMatrix
 Adjacency Matrix.
int heavyAtomAdjMatrixSize
 Adjacency Matrix size.
char * heavyAtomSymbols
 Atom symbols.
int * heavyAtomKinds
 Atom kinds.

Detailed Description

Container for stdAtoms, stdBond, stdImpropers, stdLoops, stdAlias'.


Member Typedef Documentation

typedef std::vector<stdAtom*>::iterator MTKpp::stdFrag::stdAtomIterator [protected]

standard atom iterator

typedef std::vector<stdBond*>::iterator MTKpp::stdFrag::stdBondIterator [protected]

standard bond iterator

typedef std::vector<stdLoop*>::iterator MTKpp::stdFrag::stdLoopIterator [protected]

standard loop iterator

typedef std::vector<stdAlias*>::iterator MTKpp::stdFrag::stdAliasIterator [protected]

standard alias iterator

typedef std::vector<stdImproper*>::iterator MTKpp::stdFrag::stdImproperIterator [protected]

standard improper iterator

typedef std::vector<stdRing*>::iterator MTKpp::stdFrag::stdRingIterator [protected]

standard ring iterator

typedef std::vector<stdFeature*>::iterator MTKpp::stdFrag::stdFeatureIterator [protected]

standard feature iterator

typedef std::vector<stdFuncGroup*>::iterator MTKpp::stdFrag::stdFuncGroupIterator [protected]

standard functional group iterator

typedef std::vector<int>::iterator MTKpp::stdFrag::stdConnPtsIterator [protected]

standard connection points iterator

typedef std::vector<stdConnTorsion*>::iterator MTKpp::stdFrag::stdConnTorsionIterator [protected]

standard connTorsion iterator

typedef std::vector<stdRotBond*>::iterator MTKpp::stdFrag::stdRotBondIterator [protected]

standard rotatable bond iterator


Constructor & Destructor Documentation

MTKpp::stdFrag::stdFrag ( stdGroup parent = 0)
MTKpp::stdFrag::stdFrag ( stdFrag sf,
stdGroup parent = 0 
)
MTKpp::stdFrag::~stdFrag ( ) [virtual]

Member Function Documentation

stdGroup * MTKpp::stdFrag::getParent ( )

Get group which fragment is apart of.

Returns:
stdGroup pointer

References pParent.

Referenced by main(), and MTKpp::protonate::optimizePolarHs().

void MTKpp::stdFrag::setName ( const std::string &  name)

Set name of fragment.

Parameters:
nameName of fragment

References itsName.

Referenced by main(), and MTKpp::prepParser::Read().

std::string MTKpp::stdFrag::getName ( )
void MTKpp::stdFrag::setSymbol ( const std::string &  symbol)

Set symbol of the fragment.

Parameters:
symbolFragment symbol

References itsSymbol.

Referenced by main(), and MTKpp::prepParser::Read().

std::string MTKpp::stdFrag::getSymbol ( )
void MTKpp::stdFrag::setCode ( const std::string &  code)

Set 8 character code of the fragment.

Parameters:
codeFragment symbol

References itsCode.

Referenced by main().

std::string MTKpp::stdFrag::getCode ( )

Get code of the fragment.

Returns:
fragment 8 character code

References itsCode.

Referenced by MTKpp::molecule::addFunctionalGroup(), MTKpp::molecule::delFunctionalGroup(), main(), and stdFrag().

void MTKpp::stdFrag::setCharacter ( const std::string &  c)

Set 1 letter character of the fragment.

Parameters:
ccharacter

References itsCharacter, and itsSymbol.

std::string MTKpp::stdFrag::getCharacter ( )

Get 1 letter character of the fragment.

Returns:
character

References itsCharacter.

Referenced by stdFrag().

void MTKpp::stdFrag::setType ( const std::string &  type)

Set type of the fragment.

Parameters:
typeFragment type

References itsType.

Referenced by main(), and MTKpp::prepParser::Read().

std::string MTKpp::stdFrag::getType ( )
void MTKpp::stdFrag::setSymmetry ( const std::string &  sym)

Set symmetry of the fragment.

Parameters:
symFragment symmetry

References itsSymmetry.

std::string MTKpp::stdFrag::getSymmetry ( )

Get symmetry of the fragment.

Returns:
fragment symmetry

References itsSymmetry.

Referenced by stdFrag().

void MTKpp::stdFrag::setSubGraphs ( const std::vector< std::string > &  g)

Set which fragments this fragment is a subgraph of.

Parameters:
g

References itsSubGraphs.

Referenced by stdFrag().

std::vector< std::string > MTKpp::stdFrag::getSubGraphs ( )

Get list of fragments related to this one.

Returns:
list of fragments related to this one

References itsSubGraphs.

Referenced by stdFrag().

std::string MTKpp::stdFrag::getSubGraphStr ( )

Get list of fragments related to this one.

Returns:
list of fragments related to this one

References itsSubGraphs.

stdAtom * MTKpp::stdFrag::addStdAtom ( )

Add a stdAtom to the fragment.

Returns:
stdAtom

References itsStdAtomList, MTKpp::stdAtom::kind, and pStdAtom.

Referenced by MTKpp::prepParser::readFragment(), and stdFrag().

stdAtom * MTKpp::stdFrag::addStdAtom ( stdAtom s)
stdAtom * MTKpp::stdFrag::getStdAtom ( const int &  index)
stdAtom * MTKpp::stdFrag::getStdAtom ( const std::string &  name)

Get a stdAtom by name.

Parameters:
nameatom name
Returns:
stdAtom

References getAlias(), MTKpp::stdAtom::identity, itsStdAtomList, and pStdAtom.

bool MTKpp::stdFrag::hasStdAtom ( const std::string &  name)

Has a stdAtom by name.

Parameters:
nameatom name
Returns:
stdAtom

References getAlias(), MTKpp::stdAtom::identity, itsStdAtomList, and pStdAtom.

Referenced by MTKpp::proProtonate::addHydrogens(), and MTKpp::prepParser::readFragment().

std::vector< stdAtom * > MTKpp::stdFrag::getBondedStdAtoms ( stdAtom sAt)

Get a list of stdAtoms which are bonded to sAt.

Parameters:
sAtstdAtom pointer
Returns:
list of stdAtoms bonded to sAt

References hasStdBond(), MTKpp::stdAtom::index, itsStdAtomList, and pStdAtom.

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

int MTKpp::stdFrag::numStdAtoms ( )
int MTKpp::stdFrag::numStdHeavyAtoms ( )

Get number of stdAtoms in fragment.

Returns:
number of stdAtoms

References itsStdAtomList.

Referenced by MTKpp::protonate::buildMissingHeavyAtoms(), generateHeavyAdjMatrix(), generateHeavyAtomKinds(), generateHeavyAtomSymbols(), and MTKpp::protonate::runMol().

stdBond * MTKpp::stdFrag::addStdBond ( )

Add a stdBond to the fragment.

Returns:
stdBond

References itsStdBondList, and pStdBond.

Referenced by MTKpp::prepParser::readFragment(), and stdFrag().

stdBond * MTKpp::stdFrag::addStdBond ( stdBond b)
stdBond * MTKpp::stdFrag::getStdBond ( const int &  at1,
const int &  at2 
)
stdBond * MTKpp::stdFrag::getStdBond ( const std::string &  at1,
const std::string &  at2 
)

get a stdBond from the fragment based on atom indices

Parameters:
at1atom 1 name
at2atom 2 name
Returns:
stdBond

References MTKpp::stdBond::atom1, MTKpp::stdBond::atom2, getStdAtom(), MTKpp::stdAtom::index, itsStdBondList, and pStdBond.

stdBond * MTKpp::stdFrag::getStdBond ( stdAtom pAt1,
stdAtom pAt2 
)

get a stdBond from the fragment based on atom indices

Parameters:
pAt1stdAtom 1 pointer
pAt2stdAtom 2 pointer
Returns:
stdBond

References MTKpp::stdBond::atom1, MTKpp::stdBond::atom2, MTKpp::stdAtom::index, itsStdBondList, and pStdBond.

bool MTKpp::stdFrag::hasStdBond ( const int &  at1,
const int &  at2 
)

Does the fragment contain a bond.

Parameters:
at1atom 1 index
at2atom 2 index
Returns:
true/false

References MTKpp::stdBond::atom1, MTKpp::stdLoop::atom1, MTKpp::stdBond::atom2, MTKpp::stdLoop::atom2, itsStdBondList, itsStdLoopList, pStdBond, and pStdLoop.

Referenced by getBondedStdAtoms().

int MTKpp::stdFrag::numStdBonds ( )

Get the number of stdBonds in the fragment.

Returns:
number of bonds

References itsStdBondList.

Referenced by MTKpp::proProtonate::getBestTorsions().

int MTKpp::stdFrag::numStdBonds ( stdAtom pStdAtom)

Get the number of stdBonds which pStdAtom is apart of.

Parameters:
pStdAtomstdAtom pointer
Returns:
number of bonds

References MTKpp::stdBond::atom1, MTKpp::stdLoop::atom1, MTKpp::stdBond::atom2, MTKpp::stdLoop::atom2, MTKpp::stdAtom::index, itsStdBondList, itsStdLoopList, pStdBond, and pStdLoop.

stdImproper * MTKpp::stdFrag::addStdImproper ( )

Add a stdImproper to the fragment.

Returns:
stdImproper

References itsStdImproperList, and pStdImproper.

Referenced by MTKpp::prepParser::readFragment(), and stdFrag().

stdImproper * MTKpp::stdFrag::addStdImproper ( stdImproper i)
stdLoop * MTKpp::stdFrag::addStdLoop ( )

Add a stdLoop to the fragment.

Returns:
stdLoop

References itsStdLoopList, and pStdLoop.

Referenced by MTKpp::prepParser::readFragment(), and stdFrag().

stdLoop * MTKpp::stdFrag::addStdLoop ( stdLoop l)
stdLoop * MTKpp::stdFrag::getStdLoop ( const int &  at1,
const int &  at2 
)

get a stdLoop from the fragment based on atom indices

Parameters:
at1atom 1 index
at2atom 2 index
Returns:
stdLoop

References MTKpp::stdLoop::atom1, MTKpp::stdLoop::atom2, itsStdLoopList, and pStdLoop.

Referenced by generateAdjMatrix(), generateHeavyAdjMatrix(), and main().

stdLoop * MTKpp::stdFrag::getStdLoop ( stdAtom pAt1,
stdAtom pAt2 
)

get a stdLoop from the fragment based on atom indices

Parameters:
pAt1stdAtom 1 pointer
pAt2stdAtom 2 pointer
Returns:
stdLoop

References MTKpp::stdLoop::atom1, MTKpp::stdLoop::atom2, MTKpp::stdAtom::index, itsStdLoopList, and pStdLoop.

stdAlias * MTKpp::stdFrag::addStdAlias ( )

Add a stdAlias to the fragment.

Returns:
stdAlias

References itsStdAliasList, and pStdAlias.

Referenced by MTKpp::prepParser::readFragment(), and stdFrag().

stdAlias * MTKpp::stdFrag::addStdAlias ( stdAlias a)

Add a stdAlias to the fragment.

Parameters:
astdAlias pointer
Returns:
stdAlias

References MTKpp::stdAlias::atom1, MTKpp::stdAlias::atom2, itsStdAliasList, and pStdAlias.

stdRing * MTKpp::stdFrag::addStdRing ( )

Add a stdRing to the fragment.

Returns:
stdRing

References itsStdRingList, and pStdRing.

Referenced by main(), and stdFrag().

stdRing * MTKpp::stdFrag::addStdRing ( stdRing r)
stdFeature * MTKpp::stdFrag::addStdFeature ( )

Add a stdFeature to the fragment.

Returns:
stdFeature

References itsStdFeatureList, and pStdFeature.

Referenced by main(), and stdFrag().

stdFeature * MTKpp::stdFrag::addStdFeature ( stdFeature f)

Add a stdFeature to the fragment.

Parameters:
fstdFeature pointer
Returns:
stdFeature

References MTKpp::stdFeature::atoms, itsStdFeatureList, MTKpp::stdFeature::name, and pStdFeature.

bool MTKpp::stdFrag::hasStdFeature ( stdAtom a,
std::string  f 
)

Has the stdAtom got a stdFeature matching f.

Parameters:
astdAtom pointer
fstdFeature string
Returns:
bool

References MTKpp::stdAtom::index, and itsStdFeatureList.

Referenced by MTKpp::protonate::optimizePolarHs(), and MTKpp::proProtonate::optimizePolarHs().

stdFuncGroup * MTKpp::stdFrag::addStdFuncGroup ( )

Add a stdFuncGroup to the stdMolecule.

Returns:
stdFeature

References itsStdFuncGroupList, and pStdFuncGroup.

Referenced by main(), and stdFrag().

stdFuncGroup * MTKpp::stdFrag::addStdFuncGroup ( stdFuncGroup f)
void MTKpp::stdFrag::addStdConnPts ( std::vector< int > &  v)

Add connection points to the fragment.

Parameters:
vconnection points vector

References itsStdConnPtsList.

stdConnTorsion * MTKpp::stdFrag::addStdConnTorsion ( )

Add a stdConnTorsion to the stdMolecule.

Returns:
stdConnTorsion

References itsStdConnTorsionList, and pStdConnTorsion.

stdRotBond * MTKpp::stdFrag::addStdRotBond ( )

Add a stdRotBond to the stdMolecule.

Returns:
stdRotBond pointer

References itsStdRotBondList, and pStdRotBond.

std::vector< stdAtom * > MTKpp::stdFrag::getStdAtomList ( )
std::vector< stdBond * > MTKpp::stdFrag::getStdBondList ( )

Get all stdBonds in the fragment.

Returns:
vector of stdBonds

References itsStdBondList.

Referenced by main(), and stdFrag().

std::vector< stdLoop * > MTKpp::stdFrag::getStdLoopList ( )

Get all stdLoops in the fragment.

Returns:
vector of stdLoops

References itsStdLoopList.

Referenced by MTKpp::connections::bondByLibrary(), main(), stdFrag(), and MTKpp::prepParser::Write().

std::vector< stdAlias * > MTKpp::stdFrag::getStdAliasList ( )

Get all stdAlias' in the fragment.

Returns:
vector of stdAlias

References itsStdAliasList.

Referenced by stdFrag().

std::vector< stdImproper * > MTKpp::stdFrag::getStdImproperList ( )

Get all stdImpropers in the fragment.

Returns:
vector of stdImpropers

References itsStdImproperList.

Referenced by stdFrag(), and MTKpp::prepParser::Write().

std::vector< stdRing * > MTKpp::stdFrag::getStdRingList ( )

Get all stdRings in the fragment.

Returns:
vector of stdRings

References itsStdRingList.

Referenced by MTKpp::atomTyper::assignStdRings(), and stdFrag().

std::vector< stdFeature * > MTKpp::stdFrag::getStdFeatureList ( )

Get all stdFeatures in the fragment.

Returns:
vector of stdFeatures

References itsStdFeatureList.

Referenced by MTKpp::atomTyper::assignStdHydrophobicGroups(), and stdFrag().

std::vector< stdFuncGroup * > MTKpp::stdFrag::getStdFuncGroupList ( )

Get all stdFuncGroups in the fragment.

Returns:
vector of stdFuncGroups

References itsStdFuncGroupList.

Referenced by MTKpp::atomTyper::assignStdFunctionalGroups(), and stdFrag().

std::vector< int > MTKpp::stdFrag::getStdConnPtsList ( )

Get all stdConnPts in the fragment.

Returns:
vector of stdConnPts (atom indices)

References itsStdConnPtsList.

Referenced by MTKpp::molecule::addFunctionalGroup(), MTKpp::complex::setCoreFragment(), and stdFrag().

int MTKpp::stdFrag::getNumStdConnPtsList ( )

Get number of stdConnPts in the fragment.

Returns:
number of stdConnPts

References itsStdConnPtsList.

Referenced by MTKpp::functionalize::determineSymmetricFrags().

std::vector< stdConnTorsion * > MTKpp::stdFrag::getStdConnTorList ( )

Get all stdConnTorsion in the fragment.

Returns:
vector of stdConnTorsion

References itsStdConnTorsionList.

std::vector< stdRotBond * > MTKpp::stdFrag::getStdRotBondList ( )

Get all stdRotBonds in the fragment.

Returns:
vector of stdRotBond

References itsStdRotBondList.

std::string MTKpp::stdFrag::getAlias ( const std::string &  name)

Get stdAlias by name.

Parameters:
nameatom name
Returns:
stdAtom alias

References MTKpp::stdAlias::atom1, MTKpp::stdAlias::atom2, itsStdAliasList, and pStdAlias.

Referenced by getStdAtom(), and hasStdAtom().

int MTKpp::stdFrag::generateCoordinates ( )
int MTKpp::stdFrag::generateCoordinates ( vector3d bd,
vector3d ag,
vector3d tr,
const int &  forward = 1 
)

Generate fragment coordinates using known coordinates.

Parameters:
bdatom to which the first standard atom is bonded to
agatom to which the first standard atom forms an angle with
tratom to which the first standard atom forms a torsion with
forwardproceed through the fragment in a forward/reverse manner
Returns:
success

References MTKpp::DEG2RAD, getStdAtom(), getStdAtomIndex(), itsCoords, itsStdAtomList, pCoords, and pStdAtom.

std::vector< vector3d * > MTKpp::stdFrag::getCoordinates ( )

Get fragment coordinates.

References itsCoords.

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

void MTKpp::stdFrag::print ( )

Print details of stdFrag.

References itsStdAtomList.

void MTKpp::stdFrag::generateSimpleFP ( )
std::vector< unsigned int > MTKpp::stdFrag::getSimpleFP ( )

Get simple fingerprint.

Returns:
simple fingerprint

References itsSimpleFP.

Referenced by MTKpp::functionalize::run().

int MTKpp::stdFrag::generateAdjMatrix ( )
int MTKpp::stdFrag::generateHeavyAdjMatrix ( )
int * MTKpp::stdFrag::getAdjMatrix ( )

Get adjacency matrix.

Returns:
Adjacency matrix

References adjMatrix.

Referenced by MTKpp::functionalize::determineSymmetricFrags(), and MTKpp::functionalize::run().

int * MTKpp::stdFrag::getHeavyAdjMatrix ( )

Get heavy atom adjacency matrix.

Returns:
heavy atom Adjacency matrix

References heavyAtomAdjMatrix.

int MTKpp::stdFrag::getAdjMatrixSize ( )

Get adjacency matrix size.

Returns:
Adjacency matrix size

References adjMatrixSize.

Referenced by MTKpp::functionalize::determineSymmetricFrags(), and MTKpp::functionalize::run().

int MTKpp::stdFrag::getHeavyAdjMatrixSize ( )

Get heavy atom adjacency matrix size.

Returns:
heavy atom adjacency matrix size

References heavyAtomAdjMatrixSize.

int MTKpp::stdFrag::generateAtomSymbols ( )

Generate atom symbols array.

Returns:
success

References atomSymbols, MTKpp::stdAtom::atSymbol, itsStdAtomList, numStdAtoms(), and pStdAtom.

Referenced by generateAdjMatrix().

int MTKpp::stdFrag::generateHeavyAtomSymbols ( )

Generate heavy atom symbols array.

Returns:
success

References MTKpp::stdAtom::atSymbol, heavyAtomSymbols, itsStdAtomList, numStdHeavyAtoms(), and pStdAtom.

Referenced by getHeavyAtomSymbols().

char * MTKpp::stdFrag::getAtomSymbols ( )

Get atom symbols array.

Returns:
atom symbols array

References atomSymbols.

Referenced by MTKpp::functionalize::determineSymmetricFrags(), and MTKpp::functionalize::run().

char * MTKpp::stdFrag::getHeavyAtomSymbols ( )

Get heavy atom symbols array.

Returns:
heavy atom symbols array

References generateHeavyAtomSymbols(), and heavyAtomSymbols.

int MTKpp::stdFrag::generateAtomKinds ( )

Generate atom kinds array.

Returns:
success

References atomKinds, itsStdAtomList, MTKpp::stdAtom::kind, numStdAtoms(), and pStdAtom.

Referenced by MTKpp::stdLibrary::generateAtomKinds().

int MTKpp::stdFrag::generateHeavyAtomKinds ( )

Generate heavy atom kinds array.

Returns:
success

References MTKpp::stdAtom::atSymbol, heavyAtomKinds, itsStdAtomList, MTKpp::stdAtom::kind, numStdHeavyAtoms(), and pStdAtom.

Referenced by getHeavyAtomKinds().

int * MTKpp::stdFrag::getAtomKinds ( )

Get atom kinds array.

Returns:
atom kinds array

References atomKinds.

Referenced by MTKpp::functionalize::determineSymmetricFrags(), and MTKpp::functionalize::run().

int * MTKpp::stdFrag::getHeavyAtomKinds ( )

Get heavy atom kinds array.

Returns:
atom kinds array

References generateHeavyAtomKinds(), and heavyAtomKinds.

double MTKpp::stdFrag::getCharge ( )
int MTKpp::stdFrag::getStdAtomIndex ( stdAtom a)

Get index of stdAtom.

Parameters:
astdAtom pointer
Returns:
index of standard atom

References itsStdAtomList.

Referenced by generateCoordinates().


Member Data Documentation

std::string MTKpp::stdFrag::itsName [protected]

standard fragment name

Referenced by getName(), setName(), and stdFrag().

std::string MTKpp::stdFrag::itsSymbol [protected]

standard fragment symbol (3 Character)

Referenced by getSymbol(), setCharacter(), setSymbol(), and stdFrag().

std::string MTKpp::stdFrag::itsCode [protected]

standard fragment code (8 Character)

Referenced by getCode(), setCode(), and stdFrag().

std::string MTKpp::stdFrag::itsCharacter [protected]

1 Letter character

Referenced by getCharacter(), setCharacter(), and stdFrag().

std::string MTKpp::stdFrag::itsType [protected]

fragment type Definitions

  • m Independent molecule
  • s terminal (start) chain group
  • e terminal (end) chain group
  • t terminal chain (start/ end) group
  • l chain group

Referenced by getType(), setType(), and stdFrag().

std::string MTKpp::stdFrag::itsSymmetry [protected]

fragment symmetry Definitions

  • C2 C2 symmetric (180 degree rotation results in equivalent geometry)

Referenced by getSymmetry(), setSymmetry(), and stdFrag().

std::vector<std::string> MTKpp::stdFrag::itsSubGraphs [protected]

list of 3L code fragments which this fragment is a subgraph of

Referenced by getSubGraphs(), getSubGraphStr(), and setSubGraphs().

std::vector<stdAtom*> MTKpp::stdFrag::itsStdAtomList [protected]
std::vector<stdBond*> MTKpp::stdFrag::itsStdBondList [protected]
std::vector<stdLoop*> MTKpp::stdFrag::itsStdLoopList [protected]
std::vector<stdAlias*> MTKpp::stdFrag::itsStdAliasList [protected]

standard alias list

Referenced by addStdAlias(), getAlias(), getStdAliasList(), and ~stdFrag().

standard improper list

Referenced by addStdImproper(), getStdImproperList(), and ~stdFrag().

std::vector<stdRing*> MTKpp::stdFrag::itsStdRingList [protected]

standard ring list

Referenced by addStdRing(), generateSimpleFP(), getStdRingList(), and ~stdFrag().

std::vector<stdFeature*> MTKpp::stdFrag::itsStdFeatureList [protected]

standard feature list

Referenced by addStdFeature(), getStdFeatureList(), hasStdFeature(), and ~stdFrag().

standard functional group list

Referenced by addStdFuncGroup(), getStdFuncGroupList(), and ~stdFrag().

std::vector<int> MTKpp::stdFrag::itsStdConnPtsList [protected]

standard connection points list

Referenced by addStdConnPts(), getNumStdConnPtsList(), getStdConnPtsList(), and stdFrag().

std::vector<stdRotBond*> MTKpp::stdFrag::itsStdRotBondList [protected]
std::vector<vector3d*> MTKpp::stdFrag::itsCoords [protected]

standard improper list

Referenced by generateCoordinates(), and getCoordinates().

std::vector<unsigned int> MTKpp::stdFrag::itsSimpleFP [protected]

Simple fingerprint.

Referenced by generateSimpleFP(), and getSimpleFP().

std::vector<unsigned int> MTKpp::stdFrag::itsFragmentFP [protected]

Fragment fingerprint.

standard group which fragment belongs to

Referenced by getParent(), and stdFrag().

standard atom pointer

Referenced by generateSimpleFP().

standard atom pointer

Referenced by generateSimpleFP().

vector3d pointer

Referenced by generateCoordinates().

standard alias pointer

Referenced by addStdAlias(), getAlias(), stdFrag(), and ~stdFrag().

standard improper pointer

Referenced by addStdImproper(), stdFrag(), and ~stdFrag().

standard ring pointer

Referenced by addStdRing(), generateSimpleFP(), stdFrag(), and ~stdFrag().

standard feature pointer

Referenced by addStdFeature(), stdFrag(), and ~stdFrag().

standard function group pointer

Referenced by addStdFuncGroup(), stdFrag(), and ~stdFrag().

standard connection torion pointer

Referenced by addStdConnTorsion(), stdFrag(), and ~stdFrag().

standard rotatable bond pointer

Referenced by addStdRotBond(), stdFrag(), and ~stdFrag().

int* MTKpp::stdFrag::adjMatrix [protected]

Adjacency Matrix.

Referenced by generateAdjMatrix(), getAdjMatrix(), stdFrag(), and ~stdFrag().

Adjacency Matrix size.

Referenced by generateAdjMatrix(), getAdjMatrixSize(), and stdFrag().

char* MTKpp::stdFrag::atomSymbols [protected]

Atom symbols.

Referenced by generateAtomSymbols(), getAtomSymbols(), stdFrag(), and ~stdFrag().

int* MTKpp::stdFrag::atomKinds [protected]

Atom kinds.

Referenced by generateAtomKinds(), getAtomKinds(), and stdFrag().

Adjacency Matrix.

Referenced by generateHeavyAdjMatrix(), getHeavyAdjMatrix(), and stdFrag().

Adjacency Matrix size.

Referenced by generateHeavyAdjMatrix(), getHeavyAdjMatrixSize(), and stdFrag().

Atom symbols.

Referenced by generateHeavyAtomSymbols(), getHeavyAtomSymbols(), and stdFrag().

Atom kinds.

Referenced by generateHeavyAtomKinds(), getHeavyAtomKinds(), and stdFrag().


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

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