Molecule Class. More...
#include <openbabel/mol.h>
Public Member Functions | |
| template<class T > | |
| T * | CastAndClear (bool clear=true) |
Initialization and data (re)size methods | |
| OBMol () | |
| OBMol (const OBMol &) | |
| virtual | ~OBMol () |
| OBMol & | operator= (const OBMol &mol) |
| OBMol & | operator+= (const OBMol &mol) |
| void | ReserveAtoms (int natoms) |
| virtual OBAtom * | CreateAtom (void) |
| virtual OBBond * | CreateBond (void) |
| virtual OBResidue * | CreateResidue (void) |
| virtual void | DestroyAtom (OBAtom *) |
| virtual void | DestroyBond (OBBond *) |
| virtual void | DestroyResidue (OBResidue *) |
| bool | AddAtom (OBAtom &) |
| bool | InsertAtom (OBAtom &) |
| bool | AddBond (int beginIdx, int endIdx, int order, int flags=0, int insertpos=-1) |
| bool | AddBond (OBBond &) |
| bool | AddResidue (OBResidue &) |
| OBAtom * | NewAtom () |
| OBAtom * | NewAtom (unsigned long id) |
| OBBond * | NewBond () |
| OBBond * | NewBond (unsigned long id) |
| OBResidue * | NewResidue () |
| bool | DeleteAtom (OBAtom *, bool destroyAtom=true) |
| bool | DeleteBond (OBBond *, bool destroyBond=true) |
| bool | DeleteResidue (OBResidue *, bool destroyResidue=true) |
Data retrieval methods | |
| int | GetFlags () |
| const char * | GetTitle (bool replaceNewlines=true) const |
| unsigned int | NumAtoms () const |
| unsigned int | NumBonds () const |
| unsigned int | NumHvyAtoms () |
| unsigned int | NumResidues () const |
| unsigned int | NumRotors () |
| OBAtom * | GetAtom (int idx) const |
| OBAtom * | GetAtomById (unsigned long id) const |
| OBAtom * | GetFirstAtom () const |
| OBBond * | GetBond (int idx) const |
| OBBond * | GetBondById (unsigned long id) const |
| OBBond * | GetBond (int a, int b) const |
| OBBond * | GetBond (OBAtom *bgn, OBAtom *end) const |
| OBResidue * | GetResidue (int idx) const |
| std::vector< OBInternalCoord * > | GetInternalCoord () |
| double | GetTorsion (int, int, int, int) |
| double | GetTorsion (OBAtom *a, OBAtom *b, OBAtom *c, OBAtom *d) |
| double | GetAngle (OBAtom *a, OBAtom *b, OBAtom *c) |
| std::string | GetFormula () |
| std::string | GetSpacedFormula (int ones=0, const char *sp=" ", bool implicitH=true) |
| double | GetEnergy () const |
| double | GetMolWt (bool implicitH=true) |
| double | GetExactMass (bool implicitH=true) |
| int | GetTotalCharge () |
| unsigned int | GetTotalSpinMultiplicity () |
| unsigned short int | GetDimension () const |
| double * | GetCoordinates () |
| std::vector< OBRing * > & | GetSSSR () |
| std::vector< OBRing * > & | GetLSSR () |
| bool | AutomaticFormalCharge () |
| bool | AutomaticPartialCharge () |
Data modification methods | |
| void | SetTitle (const char *title) |
| void | SetTitle (std::string &title) |
| void | SetFormula (std::string molFormula) |
| void | SetEnergy (double energy) |
| void | SetDimension (unsigned short int d) |
| void | SetTotalCharge (int charge) |
| void | SetTotalSpinMultiplicity (unsigned int spinMultiplicity) |
| void | SetInternalCoord (std::vector< OBInternalCoord * > int_coord) |
| void | SetAutomaticFormalCharge (bool val) |
| void | SetAutomaticPartialCharge (bool val) |
| void | SetAromaticPerceived () |
| void | SetSSSRPerceived () |
| void | SetLSSRPerceived () |
| void | SetRingAtomsAndBondsPerceived () |
| void | SetAtomTypesPerceived () |
| void | SetRingTypesPerceived () |
| void | SetChainsPerceived () |
| void | SetChiralityPerceived () |
| void | SetPartialChargesPerceived () |
| void | SetHybridizationPerceived () |
| void | SetImplicitValencePerceived () |
| void | SetKekulePerceived () |
| void | SetClosureBondsPerceived () |
| void | SetHydrogensAdded () |
| void | SetCorrectedForPH () |
| void | SetAromaticCorrected () |
| void | SetSpinMultiplicityAssigned () |
| void | SetFlags (int flags) |
| void | UnsetAromaticPerceived () |
| void | UnsetSSSRPerceived () |
| void | UnsetRingTypesPerceived () |
| void | UnsetPartialChargesPerceived () |
| void | UnsetImplicitValencePerceived () |
| void | UnsetHydrogensAdded () |
| void | UnsetFlag (int flag) |
Molecule utilities and perception methods | |
| void | FindSSSR () |
| void | FindLSSR () |
| void | FindRingAtomsAndBonds () |
| void | FindChiralCenters () |
| void | FindChildren (std::vector< int > &children, int bgnIdx, int endIdx) |
| void | FindChildren (std::vector< OBAtom * > &children, OBAtom *bgn, OBAtom *end) |
| void | FindLargestFragment (OBBitVec &frag) |
| void | ContigFragList (std::vector< std::vector< int > > &) |
| void | Align (OBAtom *, OBAtom *, vector3 &, vector3 &) |
| void | ConnectTheDots () |
| void | PerceiveBondOrders () |
| void | FindAngles () |
| void | FindTorsions () |
| bool | GetGTDVector (std::vector< int > &) |
| void | GetGIVector (std::vector< unsigned int > &) |
| void | GetGIDVector (std::vector< unsigned int > &) |
Methods to check for existence of properties | |
| bool | Has2D (bool Not3D=false) |
| bool | Has3D () |
| bool | HasNonZeroCoords () |
| bool | HasAromaticPerceived () |
| bool | HasSSSRPerceived () |
| bool | HasLSSRPerceived () |
| bool | HasRingAtomsAndBondsPerceived () |
| bool | HasAtomTypesPerceived () |
| bool | HasRingTypesPerceived () |
| bool | HasChiralityPerceived () |
| bool | HasPartialChargesPerceived () |
| bool | HasHybridizationPerceived () |
| bool | HasImplicitValencePerceived () |
| bool | HasKekulePerceived () |
| bool | HasClosureBondsPerceived () |
| bool | HasChainsPerceived () |
| bool | HasHydrogensAdded () |
| bool | HasAromaticCorrected () |
| bool | IsCorrectedForPH () |
| bool | HasSpinMultiplicityAssigned () |
| bool | IsChiral () |
| bool | Empty () |
Multiple conformer member functions | |
| int | NumConformers () |
| void | SetConformers (std::vector< double * > &v) |
| void | AddConformer (double *f) |
| void | SetConformer (int i) |
| void | CopyConformer (double *c, int nconf) |
| void | DeleteConformer (int nconf) |
| double * | GetConformer (int i) |
| void | SetEnergies (std::vector< double > &energies) |
| std::vector< double > | GetEnergies () |
| double | GetEnergy (int ci) |
| double * | BeginConformer (std::vector< double * >::iterator &i) |
| double * | NextConformer (std::vector< double * >::iterator &i) |
| std::vector< double * > & | GetConformers () |
Iterator methods | |
| OBAtomIterator | BeginAtoms () |
| OBAtomIterator | EndAtoms () |
| OBBondIterator | BeginBonds () |
| OBBondIterator | EndBonds () |
| OBResidueIterator | BeginResidues () |
| OBResidueIterator | EndResidues () |
| OBAtom * | BeginAtom (OBAtomIterator &i) |
| OBAtom * | NextAtom (OBAtomIterator &i) |
| OBBond * | BeginBond (OBBondIterator &i) |
| OBBond * | NextBond (OBBondIterator &i) |
| OBResidue * | BeginResidue (OBResidueIterator &i) |
| OBResidue * | NextResidue (OBResidueIterator &i) |
| OBInternalCoord * | BeginInternalCoord (std::vector< OBInternalCoord * >::iterator &i) |
| OBInternalCoord * | NextInternalCoord (std::vector< OBInternalCoord * >::iterator &i) |
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 () |
Protected Member Functions | |
| bool | HasFlag (int flag) |
| void | SetFlag (int flag) |
Internal Kekulization routines -- see kekulize.cpp and NewPerceiveKekuleBonds() | |
| void | start_kekulize (std::vector< OBAtom * > &cycle, std::vector< int > &electron) |
| bool | expand_kekulize (int bond_idx, std::vector< int > &atomState, std::vector< int > &bondState) |
| bool | has_no_leftover_electrons (std::vector< int > &atomState) |
| int | getorden (OBAtom *atom) |
| bool | expandcycle (OBAtom *atom, OBBitVec &avisit, const OBBitVec &potAromBonds) |
Protected Attributes | |
| int | _flags |
| bool | _autoPartialCharge |
| bool | _autoFormalCharge |
| std::string | _title |
| std::vector< OBAtom * > | _vatom |
| std::vector< OBAtom * > | _atomIds |
| std::vector< OBBond * > | _vbond |
| std::vector< OBBond * > | _bondIds |
| unsigned short int | _dimension |
| int | _totalCharge |
| unsigned int | _totalSpin |
| double * | _c |
| std::vector< double * > | _vconf |
| double | _energy |
| unsigned int | _natoms |
| unsigned int | _nbonds |
| std::vector< OBResidue * > | _residue |
| std::vector< OBInternalCoord * > | _internals |
| unsigned short int | _mod |
| std::vector< OBGenericData * > | _vdata |
Molecule modification methods | |
| virtual void | BeginModify (void) |
| virtual void | EndModify (bool nukePerceivedData=true) |
| int | GetMod () |
| void | IncrementMod () |
| void | DecrementMod () |
| virtual OBBase * | DoTransformations (const std::map< std::string, std::string > *pOptions, OBConversion *pConv) |
| bool | Clear () |
| void | RenumberAtoms (std::vector< OBAtom * > &) |
| void | RenumberAtoms (std::vector< int >) |
| void | SetCoordinates (double *c) |
| void | ToInertialFrame (int conf, double *rmat) |
| void | ToInertialFrame () |
| void | Translate (const vector3 &v) |
| void | Translate (const vector3 &v, int conf) |
| void | Rotate (const double u[3][3]) |
| void | Rotate (const double m[9]) |
| void | Rotate (const double m[9], int nconf) |
| void | Center () |
| bool | Kekulize () |
| bool | PerceiveKekuleBonds () |
| void | NewPerceiveKekuleBonds () |
| bool | DeleteHydrogens () |
| bool | DeleteHydrogens (OBAtom *) |
| bool | DeleteNonPolarHydrogens () |
| bool | DeleteHydrogen (OBAtom *) |
| bool | AddHydrogens (bool polaronly=false, bool correctForPH=false, double pH=7.4) |
| bool | AddHydrogens (OBAtom *) |
| bool | AddPolarHydrogens () |
| bool | StripSalts (int threshold=0) |
| std::vector< OBMol > | Separate (int StartIndex=1) |
| bool | GetNextFragment (OpenBabel::OBMolAtomDFSIter &iter, OBMol &newMol) |
| bool | ConvertDativeBonds () |
| bool | CorrectForPH (double pH=7.4) |
| bool | AssignSpinMultiplicity (bool NoImplicitH=false) |
| void | SetIsPatternStructure () |
| vector3 | Center (int nconf) |
| void | SetTorsion (OBAtom *, OBAtom *, OBAtom *, OBAtom *, double ang) |
| static const char * | ClassDescription () |
Molecule Class.
The most important class in Open Babel is OBMol, or the molecule class. The OBMol class is designed to store all the basic information associated with a molecule, to make manipulations on the connection table of a molecule facile, and to provide member functions which automatically perceive information about a molecule. A guided tour of the OBMol class is a good place to start.
An OBMol class can be declared:
OBMol mol;
For example:
#include <iostream.h> #include <openbabel/mol.h> #include <openbabel/obconversion.h> int main(int argc,char **argv) { OBConversion conv(&cin,&cout); if(conv.SetInAndOutFormats("SDF","MOL2")) { OBMol mol; if(conv.Read(&mol)) ...manipulate molecule conv->Write(&mol); } return(1); }
will read in a molecule in SD file format from stdin (or the C++ equivalent cin) and write a MOL2 format file out to standard out. Additionally, The input and output formats can be altered using the OBConversion class
Once a molecule has been read into an OBMol (or created via other methods) the atoms and bonds can be accessed by the following methods:
OBAtom *atom;
atom = mol.GetAtom(5); //random access of an atom
or
OBBond *bond;
bond = mol.GetBond(14); //random access of a bond
or
FOR_ATOMS_OF_MOL(atom, mol) // iterator access (see OBMolAtomIter)
or
FOR_BONDS_OF_MOL(bond, mol) // iterator access (see OBMolBondIter)
It is important to note that atom arrays currently begin at 1 and bond arrays begin at 0. Requesting atom 0 (
OBAtom *atom = mol.GetAtom(0);
will result in an error, but
OBBond *bond = mol.GetBond(0);
is perfectly valid. Note that this is expected to change in the near future to simplify coding and improve efficiency.
The ambiguity of numbering issues and off-by-one errors led to the use of iterators in Open Babel. An iterator is essentially just a pointer, but when used in conjunction with Standard Template Library (STL) vectors it provides an unambiguous way to loop over arrays. OBMols store their atom and bond information in STL vectors. Since vectors are template based, a vector of any user defined type can be declared. OBMols declare vector<OBAtom*> and vector<OBBond*> to store atom and bond information. Iterators are then a natural way to loop over the vectors of atoms and bonds.
A variety of predefined iterators have been created to simplify common looping requests (e.g., looping over all atoms in a molecule, bonds to a given atom, etc.)
#include <openbabel/obiter.h> ... #define FOR_ATOMS_OF_MOL(a,m) for( OBMolAtomIter a(m); a; ++a ) #define FOR_BONDS_OF_MOL(b,m) for( OBMolBondIter b(m); b; ++b ) #define FOR_NBORS_OF_ATOM(a,p) for( OBAtomAtomIter a(p); a; ++a ) #define FOR_BONDS_OF_ATOM(b,p) for( OBAtomBondIter b(p); b; ++b ) #define FOR_RESIDUES_OF_MOL(r,m) for( OBResidueIter r(m); r; ++r ) #define FOR_ATOMS_OF_RESIDUE(a,r) for( OBResidueAtomIter a(r); a; ++a ) ...
These convenience functions can be used like so:
#include <openbabel/obiter.h> #include <openbabel/mol.h> OBMol mol; double exactMass = 0.0; FOR_ATOMS_OF_MOL(a, mol) { exactMass += a->GetExactMass(); }
Note that with these convenience macros, the iterator "a" (or whichever name you pick) is declared for you -- you do not need to do it beforehand.
| OBMol | ( | ) |
Constructor.
Copy constructor, copies atoms,bonds and OBGenericData.
| ~OBMol | ( | ) | [virtual] |
Destructor.
| bool HasFlag | ( | int | flag ) | [inline, protected] |
Referenced by OBMol::operator=().
| void SetFlag | ( | int | flag ) | [inline, protected] |
| void start_kekulize | ( | std::vector< OBAtom * > & | cycle, |
| std::vector< int > & | electron | ||
| ) | [protected] |
Find a consistent assignment of single/double bonds to a Kekule' ring or a set of fused aromatic rings.
The initial electronic state indicates whether each atom can make a double bond or not. The function works recursively to "walk" around the ring or rings and try all possible arrangements of single and double bonds.
| bool expand_kekulize | ( | int | bond_idx, |
| std::vector< int > & | atomState, | ||
| std::vector< int > & | bondState | ||
| ) | [protected] |
Recursively assign single and double bonds according to the electronical state of the atoms.
| bool has_no_leftover_electrons | ( | std::vector< int > & | atomState ) | [protected] |
Check for leftover electrons. This is used during expand_kekulize() to make sure all of the 4n+2 electrons that were available for bonding in the aromatic ring system were actually used during the assignment of single and double bonds.
| int getorden | ( | OBAtom * | atom ) | [protected] |
Give the priority to give two electrons instead of 1
Recursively find the aromatic atoms with an aromatic bond to the current atom
Assignment, copies atoms,bonds and OBGenericData.
Copies atoms and bonds but not OBGenericData.
| void ReserveAtoms | ( | int | natoms ) | [inline] |
Reserve a minimum number of atoms for internal storage This improves performance since the internal atom vector does not grow.
| OBAtom * CreateAtom | ( | void | ) | [virtual] |
Create a new OBAtom pointer. Does no bookkeeping
| OBBond * CreateBond | ( | void | ) | [virtual] |
Create a new OBBond pointer. Does no bookkeeping
| OBResidue * CreateResidue | ( | void | ) | [virtual] |
Create a new OBResidue pointer. Does no bookkeeping
| void DestroyAtom | ( | OBAtom * | atom ) | [virtual] |
Free an OBAtom pointer if defined. Does no bookkeeping
Referenced by OBMol::~OBMol().
| void DestroyBond | ( | OBBond * | bond ) | [virtual] |
Free an OBBond pointer if defined. Does no bookkeeping
Referenced by OBMol::~OBMol().
| void DestroyResidue | ( | OBResidue * | residue ) | [virtual] |
Free an OBResidue pointer if defined. Does no bookkeeping
Referenced by OBMol::~OBMol().
| bool AddAtom | ( | OBAtom & | atom ) |
Add an atom to a molecule.
Add the specified atom to this molecule
Also checks bond_queue for any bonds that should be made to the new atom
Referenced by OpenBabel::addFragment(), and OBMol::GetNextFragment().
| bool InsertAtom | ( | OBAtom & | atom ) |
Add a new atom to this molecule (like AddAtom) Calls BeginModify() before insertion and EndModify() after insertion
| bool AddBond | ( | int | beginIdx, |
| int | endIdx, | ||
| int | order, | ||
| int | flags = 0, |
||
| int | insertpos = -1 |
||
| ) |
Add a new bond to the molecule with the specified parameters
| beginIdx | the atom index of the "start" atom |
| endIdx | the atom index of the "end" atom |
| order | the bond order (see OBBond::GetBO()) |
| flags | any bond flags such as stereochemistry (default = none) |
| insertpos | the position index to insert the bond (default = none) |
Referenced by OpenBabel::addFragment(), OBResidueData::AssignBonds(), OBBuilder::Build(), OBMol::ConnectTheDots(), OBMol::GetNextFragment(), OBAtom::HtoMethyl(), and OBAtom::SetHybAndGeom().
| bool AddBond | ( | OBBond & | bond ) |
Add the specified residue to this molecule and update connections
| bool AddResidue | ( | OBResidue & | residue ) |
Add the specified residue to this molecule and update connections
| OBAtom * NewAtom | ( | ) |
Create a new OBAtom in this molecule and ensure connections (e.g. OBAtom::GetParent(). A new unique id will be assigned to this atom.
Referenced by OBUnitCell::FillUnitCell(), OBAtom::HtoMethyl(), and OBAtom::SetHybAndGeom().
| OBAtom * NewAtom | ( | unsigned long | id ) |
Instantiate a New Atom and add it to the molecule.
Create a new OBAtom in this molecule and ensure connections. (e.g. OBAtom::GetParent(). The id will be assigned to this atom.
Checks bond_queue for any bonds that should be made to the new atom and updates atom indexes.
| OBBond * NewBond | ( | ) |
Create a new OBBond in this molecule and ensure connections (e.g. OBBond::GetParent(). A new unique id will be assigned to this bond.
Referenced by OBBuilder::Connect().
| OBBond * NewBond | ( | unsigned long | id ) |
Instantiate a New Bond and add it to the molecule.
Create a new OBBond in this molecule and ensure connections (e.g. OBBond::GetParent(). The id will be assigned to this bond.
| bool DeleteAtom | ( | OBAtom * | atom, |
| bool | destroyAtom = true |
||
| ) |
Deletes an atom from this molecule and all appropriate bonds. Updates the molecule and atom and bond indexes accordingly.
Referenced by OBChemTsfm::Apply(), OpenBabel::InternalToCartesian(), and OBAtom::SetHybAndGeom().
| bool DeleteBond | ( | OBBond * | bond, |
| bool | destroyBond = true |
||
| ) |
Deletes an bond from this molecule and updates accordingly
Referenced by OBBuilder::Build(), OBMol::ConnectTheDots(), OBBuilder::IsSpiroAtom(), and OBBuilder::Swap().
| bool DeleteResidue | ( | OBResidue * | residue, |
| bool | destroyResidue = true |
||
| ) |
Deletes a residue from this molecule and updates accordingly.
| void BeginModify | ( | void | ) | [virtual] |
Call when making many modifications -- clears conformer/rotomer data. The method "turns off" perception routines, improving performance. Changes in molecular structure will be re-considered after modifications.
Referenced by OBAtom::HtoMethyl(), and OBAtom::SetHybAndGeom().
| void EndModify | ( | bool | nukePerceivedData = true ) |
[virtual] |
Call when done with modificaions -- re-perceive data as needed. This method "turns on" perception routines and re-evaluates molecular structure.
Referenced by OpenBabel::addFragment(), OBAtom::HtoMethyl(), and OBAtom::SetHybAndGeom().
| int GetMod | ( | ) | [inline] |
| void IncrementMod | ( | ) | [inline] |
Increase the number of nested BeginModify calls. Dangerous! Instead, properly use BeginModify as needed.
Referenced by OBAtom::SetHybAndGeom().
| void DecrementMod | ( | ) | [inline] |
Decrease the number of nested BeginModify calls. Dangerous! Instead, properly use EndModify as needed.
Referenced by OBAtom::SetHybAndGeom().
| int GetFlags | ( | ) | [inline] |
Referenced by OBAtomTyper::AssignImplicitValence().
| const char * GetTitle | ( | bool | replaceNewlines = true ) |
const [virtual] |
| replaceNewlines | whether to replace any newline characters with spaces |
Reimplemented from OBBase.
Referenced by OBBuilder::CorrectStereoAtoms(), OBMoleculeFormat::DeferMolOutput(), OBMoleculeFormat::MakeCombinedMolecule(), OBMol::operator+=(), OBMol::operator=(), OBMoleculeFormat::ReadChemObjectImpl(), OBMoleculeFormat::ReadNameIndex(), OBMoleculeFormat::WriteChemObjectImpl(), and OpenBabel::WriteTitles().
| unsigned int NumAtoms | ( | ) | const [inline] |
Referenced by OBRingSearch::AddRingFromClosure(), OpenBabel::alternate(), OBChemTsfm::Apply(), patty::assign_types(), OBAromaticTyper::AssignAromaticFlags(), OBGastChrg::AssignPartialCharges(), OBRotorList::AssignTorVals(), OpenBabel::CalcSignedVolume(), OpenBabel::CartesianToInternal(), OBMol::Center(), OpenBabel::CompileMoleculeQuery(), OBBuilder::Connect(), OBMol::ConnectTheDots(), OpenBabel::construct_c_matrix(), OpenBabel::construct_g_matrix(), OBMol::CopyConformer(), OBRotamerList::CreateConformerList(), OpenBabel::DetermineFRJ(), OBDepict::DrawMolecule(), OBSmartsMatcher::FastSingleMatch(), OBChargeModel::FillChargeVectors(), OpenBabel::FindAutomorphisms(), OBRotorList::FindRotors(), OpenBabel::generateDiagram(), OBForceField::GetAtomTypes(), OpenBabel::GetChirality(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OpenBabel::GetDFFVector(), OBAtom::GetNextAtom(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBSpectrophore::GetSpectrophore(), OpenBabel::GraphPotentials(), OBAtom::HtoMethyl(), OBBond::IsClosure(), OBStericConformerFilter::IsGood(), OBForceField::IsSetupNeeded(), OBMoleculeFormat::MakeCombinedMolecule(), OpenBabel::MinimumPairRMS(), OBMolAtomBFSIter::OBMolAtomBFSIter(), OBMolAtomDFSIter::OBMolAtomDFSIter(), OBSSMatch::OBSSMatch(), OBMol::operator=(), OBMoleculeFormat::ReadChemObjectImpl(), OBRotorList::RemoveSymVals(), OBMol::RenumberAtoms(), OBMol::Rotate(), OBEnergyConformerScore::Score(), OBRMSDConformerScore::Score(), OBAromaticTyper::SelectRootAtoms(), OBMol::Separate(), OBRotamerList::SetBaseCoordinateSets(), OBForceField::SetConformers(), OBMol::SetCoordinates(), OBForceField::SetCoordinates(), OBAlign::SetRefMol(), OBRotorList::SetRotAtoms(), OBAlign::SetTargetMol(), OBProxGrid::Setup(), OBForceField::Setup(), OBSmartsMatcher::SetupAtomMatchTable(), OBMol::Translate(), OBAlign::UpdateCoords(), OpenBabel::visitRing(), and OBMoleculeFormat::WriteChemObjectImpl().
| unsigned int NumBonds | ( | ) | const [inline] |
Referenced by OpenBabel::alternate(), OBBuilder::Build(), OpenBabel::DetermineFRJ(), OBDepict::DrawMolecule(), OpenBabel::get_bonds_of_ring(), OBForceField::IsSetupNeeded(), OBMoleculeFormat::MakeCombinedMolecule(), OBMolBondBFSIter::OBMolBondBFSIter(), OBMol::operator=(), and OpenBabel::visitRing().
| unsigned int NumHvyAtoms | ( | ) |
| unsigned int NumResidues | ( | ) | const [inline] |
Referenced by OBMol::operator=().
| unsigned int NumRotors | ( | ) |
| OBAtom * GetAtom | ( | int | idx ) | const |
idx or NULL if it does not exist. Returns a pointer to the atom after a safety check 0 < idx <= NumAtoms
Referenced by OpenBabel::alternate(), OBChemTsfm::Apply(), OpenBabel::ApplyRotMatToBond(), OBBondTyper::AssignFunctionalGroupBonds(), OBAtomTyper::AssignHyb(), OBAtomTyper::AssignImplicitValence(), OBPhModel::AssignSeedPartialCharge(), OBRingTyper::AssignTypes(), OBAtomTyper::AssignTypes(), OBBuilder::Build(), OpenBabel::BuildOBRTreeVector(), OpenBabel::CalcSignedVolume(), OpenBabel::CartesianToInternal(), OBBuilder::Connect(), OBMol::ConnectTheDots(), OpenBabel::CorrectBadResonanceForm(), OBBuilder::CorrectStereoAtoms(), OBDepict::DrawMolecule(), AliasData::Expand(), OBSmartsMatcher::FastSingleMatch(), OpenBabel::FindAutomorphisms(), OBRing::findCenterAndNormal(), OpenBabel::FindRings(), OpenBabel::generateDiagram(), OpenBabel::get_bonds_of_ring(), OBAtom::GetAngle(), OBForceField::GetAtomTypes(), OBForceField::GetCoordinates(), OpenBabel::GetDFFVector(), OBAtom::GetDistance(), OBAtom::GetNextAtom(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBRing::GetRootAtom(), OBRotorRules::GetRotorIncrements(), OpenBabel::groupRedraw(), OBRing::IsAromatic(), OBStericConformerFilter::IsGood(), OBForceField::IsSetupNeeded(), OBBuilder::IsSpiroAtom(), OBSmartsMatcher::match(), OBAtom::MatchesSMARTS(), OpenBabel::MinimumPairRMS(), OBMolAtomBFSIter::operator++(), OBMolAtomDFSIter::operator++(), OBMol::PerceiveBondOrders(), OpenBabel::potentialAromaticBonds(), OBMol::RenumberAtoms(), OBAromaticTyper::SelectRootAtoms(), OBRotorList::SetEvalAtoms(), OBBond::SetLength(), OBAlign::SetRefMol(), OBAlign::SetTargetMol(), OBRotamerList::Setup(), OBFFConstraints::Setup(), and OBBuilder::Swap().
| OBAtom * GetAtomById | ( | unsigned long | id ) | const |
id or NULL if it does not exist. Referenced by OpenBabel::CanonicalLabels(), OBBuilder::CorrectStereoAtoms(), OBBuilder::CorrectStereoBonds(), and OBBuilder::IsSpiroAtom().
| OBAtom * GetFirstAtom | ( | ) | const |
| OBBond * GetBond | ( | int | idx ) | const |
idx or NULL if it does not exist. Returns a pointer to the bond after a safety check 0 <= idx < NumBonds
Referenced by OpenBabel::addNbrs(), OpenBabel::alternate(), OBChemTsfm::Apply(), OpenBabel::atomRingToBondRing(), OBBuilder::Build(), OpenBabel::CanonicalLabels(), OBBuilder::CorrectStereoAtoms(), OBBuilder::CorrectStereoBonds(), OBDepict::DrawMolecule(), OpenBabel::expandKekulize(), OBSmartsMatcher::FastSingleMatch(), OpenBabel::findMetalloceneBonds(), OpenBabel::FindRings(), OBMolBondBFSIter::operator++(), OBMol::PerceiveBondOrders(), OpenBabel::potentialAromaticBonds(), and OBBuilder::Swap().
| OBBond * GetBondById | ( | unsigned long | id ) | const |
id or NULL if it does not exist. | OBBond * GetBond | ( | int | a, |
| int | b | ||
| ) | const |
a and b or NULL if none exists. bgn and end or NULL if none exists | OBResidue * GetResidue | ( | int | idx ) | const |
idx, or NULL if none exists Referenced by OBMol::operator=().
| std::vector< OBInternalCoord * > GetInternalCoord | ( | ) |
| double GetTorsion | ( | int | a, |
| int | b, | ||
| int | c, | ||
| int | d | ||
| ) |
Referenced by OBBuilder::CorrectStereoBonds(), OBRotorRules::GetRotorIncrements(), and OBMol::PerceiveBondOrders().
a, b, c, and d) WARNING: SetTorsion takes an angle in radians while GetTorsion returns it in degrees a, b and c (where a-> b (vertex) -> c ) | string GetFormula | ( | ) |
Stochoimetric formula (e.g., C4H6O). This is either set by OBMol::SetFormula() or generated on-the-fly using the "Hill order" -- i.e., C first if present, then H if present all other elements in alphabetical order.
| string GetSpacedFormula | ( | int | ones = 0, |
| const char * | sp = " ", |
||
| bool | implicitH = true |
||
| ) |
Stochoimetric formula in spaced format e.g. C 4 H 6 O 1 No pair data is stored. Normally use without parameters: GetSpacedFormula()
Referenced by OBMoleculeFormat::MakeCombinedMolecule().
| double GetEnergy | ( | ) | const [inline] |
Referenced by OBMol::operator=().
| double GetMolWt | ( | bool | implicitH = true ) |
| double GetExactMass | ( | bool | implicitH = true ) |
| int GetTotalCharge | ( | ) |
Returns the total molecular charge -- if it has not previously been set it is calculated from the atomic formal charge information. (This may or may not be correct!) If you set atomic charges with OBAtom::SetFormalCharge() you really should set the molecular charge with OBMol::SetTotalCharge()
Referenced by OBMol::operator=().
| unsigned int GetTotalSpinMultiplicity | ( | ) |
Returns the total spin multiplicity -- if it has not previously been set It is calculated from the atomic spin multiplicity information assuming the high-spin case (i.e. it simply sums the number of unpaired electrons assuming no further pairing of spins.
Referenced by OBMol::operator=().
| unsigned short int GetDimension | ( | ) | const [inline] |
Referenced by OBBuilder::Build(), OpenBabel::CanonicalLabels(), OBPhModel::CorrectForPH(), OBMol::GetNextFragment(), OBMoleculeFormat::MakeCombinedMolecule(), OBMol::operator+=(), and OBMol::operator=().
| double* GetCoordinates | ( | ) | [inline] |
Referenced by OBScoreGrid::Eval(), OBRotorList::RemoveSymVals(), OBEnergyConformerScore::Score(), OBRotamerList::SetCurrentCoordinates(), OBProxGrid::Setup(), and OBConformerSearch::Setup().
| vector< OBRing * > & GetSSSR | ( | ) |
Implements blue-obelisk:findSmallestSetOfSmallestRings.
Referenced by OBRingTyper::AssignTypes(), OBDepict::DrawMolecule(), OBBond::FindSmallestRing(), OBAtom::IsInRingSize(), OBAtom::MemberOfRingCount(), OBAtom::MemberOfRingSize(), OBMol::PerceiveBondOrders(), and OBAromaticTyper::SelectRootAtoms().
| vector< OBRing * > & GetLSSR | ( | ) |
Referenced by OpenBabel::potentialAromaticBonds().
| bool AutomaticFormalCharge | ( | ) | [inline] |
Get the current flag for whether formal charges are set with pH correction.
Referenced by OBPhModel::CorrectForPH().
| bool AutomaticPartialCharge | ( | ) | [inline] |
Get the current flag for whether partial charges are auto-determined.
Referenced by OBPhModel::AssignSeedPartialCharge().
| void SetTitle | ( | const char * | title ) | [virtual] |
Set the title of this molecule to title.
Reimplemented from OBBase.
Referenced by OBMoleculeFormat::MakeCombinedMolecule().
| void SetTitle | ( | std::string & | title ) |
Set the title of this molecule to title.
| void SetFormula | ( | std::string | molFormula ) |
Set the stochiometric formula for this molecule.
| void SetEnergy | ( | double | energy ) | [inline] |
Set the heat of formation for this molecule (in kcal/mol)
| void SetDimension | ( | unsigned short int | d ) | [inline] |
Set the dimension of this molecule (i.e., 0, 1 , 2, 3)
Referenced by OBBuilder::Build(), and OBMol::GetNextFragment().
| void SetTotalCharge | ( | int | charge ) |
Set the total charge of this molecule to charge.
| void SetTotalSpinMultiplicity | ( | unsigned int | spinMultiplicity ) |
Set the total spin multiplicity of this molecule to spinMultiplicity Overrides the calculation from spin multiplicity of OBAtoms
| void SetInternalCoord | ( | std::vector< OBInternalCoord * > | int_coord ) | [inline] |
Set the internal coordinates to int_coord (Does not call InternalToCartesian to update the 3D cartesian coordinates)
| void SetAutomaticFormalCharge | ( | bool | val ) | [inline] |
Set the flag for determining automatic formal charges with pH (default=true)
| void SetAutomaticPartialCharge | ( | bool | val ) | [inline] |
Set the flag for determining partial charges automatically (default=true)
| void SetAromaticPerceived | ( | ) | [inline] |
Mark that aromaticity has been perceived for this molecule (see OBAromaticTyper)
Referenced by OBAromaticTyper::AssignAromaticFlags(), and OBAtomTyper::AssignImplicitValence().
| void SetSSSRPerceived | ( | ) | [inline] |
Mark that Smallest Set of Smallest Rings has been run (see OBRing class)
| void SetLSSRPerceived | ( | ) | [inline] |
Mark that Largest Set of Smallest Rings has been run (see OBRing class)
| void SetRingAtomsAndBondsPerceived | ( | ) | [inline] |
Mark that rings have been perceived (see OBRing class for details)
| void SetAtomTypesPerceived | ( | ) | [inline] |
Mark that atom types have been perceived (see OBAtomTyper for details)
Referenced by OBAtomTyper::AssignTypes().
| void SetRingTypesPerceived | ( | ) | [inline] |
Mark that ring types have been perceived (see OBRingTyper for details)
Referenced by OBRingTyper::AssignTypes().
| void SetChainsPerceived | ( | ) | [inline] |
Mark that chains and residues have been perceived (see OBChainsParser)
| void SetChiralityPerceived | ( | ) | [inline] |
Mark that chirality has been perceived.
| void SetPartialChargesPerceived | ( | ) | [inline] |
Mark that partial charges have been assigned.
Referenced by OBPhModel::AssignSeedPartialCharge().
| void SetHybridizationPerceived | ( | ) | [inline] |
Mark that hybridization of all atoms has been assigned.
Referenced by OBAtomTyper::AssignHyb(), OBBuilder::Build(), and OBMol::PerceiveBondOrders().
| void SetImplicitValencePerceived | ( | ) | [inline] |
Mark that the implicit hydrogen valence of all atoms has been assigned.
Referenced by OBAtomTyper::AssignImplicitValence().
| void SetKekulePerceived | ( | ) | [inline] |
Mark that Kekule forms have been assigned by Kekulize()
| void SetClosureBondsPerceived | ( | ) | [inline] |
Mark that ring closure bonds have been assigned by graph traversal.
Referenced by OBBond::IsClosure().
| void SetHydrogensAdded | ( | ) | [inline] |
Mark that explicit hydrogen atoms have been added.
| void SetCorrectedForPH | ( | ) | [inline] |
Referenced by OBPhModel::CorrectForPH().
| void SetAromaticCorrected | ( | ) | [inline] |
Referenced by OBAtomTyper::CorrectAromaticNitrogens().
| void SetSpinMultiplicityAssigned | ( | ) | [inline] |
| void SetFlags | ( | int | flags ) | [inline] |
Referenced by OBAtomTyper::AssignImplicitValence().
| void UnsetAromaticPerceived | ( | ) | [inline] |
| void UnsetSSSRPerceived | ( | ) | [inline] |
| void UnsetRingTypesPerceived | ( | ) | [inline] |
| void UnsetPartialChargesPerceived | ( | ) | [inline] |
| void UnsetImplicitValencePerceived | ( | ) | [inline] |
Referenced by OBChemTsfm::Apply().
| void UnsetHydrogensAdded | ( | ) | [inline] |
| void UnsetFlag | ( | int | flag ) | [inline] |
Referenced by OBMol::RenumberAtoms().
| OBBase * DoTransformations | ( | const std::map< std::string, std::string > * | , |
| OBConversion * | |||
| ) | [virtual] |
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 from OBBase.
Referenced by OBMoleculeFormat::ReadChemObjectImpl().
| const char * ClassDescription | ( | ) | [static] |
Reimplemented from OBBase.
| bool Clear | ( | void | ) | [virtual] |
Clear all information from a molecule except OB_PATTERN_STRUCTURE left unchanged.
Reimplemented from OBBase.
Referenced by OpenBabel::addFragment(), OBMoleculeFormat::ReadNameIndex(), OBMol::Separate(), and OBAlign::SetRefMol().
| void RenumberAtoms | ( | std::vector< OBAtom * > & | v ) |
Renumber the atoms of this molecule according to the order in the supplied vector.
Renumber the atoms in this molecule according to the order in the supplied vector. This will return without action if the supplied vector is empty or does not have the same number of atoms as the molecule.
Referenced by OBMol::RenumberAtoms().
| void RenumberAtoms | ( | std::vector< int > | v ) |
Renumber the atoms of this molecule using the initial indexes in the supplied vector.
Renumber the atoms according to the order of indexes in the supplied vector This with assemble an atom vector and call RenumberAtoms(vector<OBAtom*>) It will return without action if the supplied vector is empty or does not have the same number of atoms as the molecule.
| void SetCoordinates | ( | double * | c ) |
Set the coordinates for all atoms in this conformer.
| void ToInertialFrame | ( | int | conf, |
| double * | rmat | ||
| ) |
Translate one conformer and rotate by a rotation matrix (which is returned) to the inertial frame-of-reference.
| void ToInertialFrame | ( | ) |
Translate all conformers to the inertial frame-of-reference.
| void Translate | ( | const vector3 & | v ) |
Translates all conformers in the molecule by the supplied vector.
this method adds the vector v to all atom positions in all conformers
| void Translate | ( | const vector3 & | v, |
| int | nconf | ||
| ) |
Translates one conformer in the molecule by the supplied vector.
this method adds the vector v to all atom positions in the conformer nconf. If nconf == OB_CURRENT_CONFORMER, then the atom positions in the current conformer are translated.
| void Rotate | ( | const double | u[3][3] ) |
Rotate all conformers using the supplied matrix u (a 3x3 array of double)
Referenced by OBMol::Rotate().
| void Rotate | ( | const double | m[9] ) |
Rotate all conformers using the supplied matrix m (a linear 3x3 row-major array of double)
| void Rotate | ( | const double | m[9], |
| int | nconf | ||
| ) |
Rotate a specific conformer nconf using the supplied rotation matrix m.
| void Center | ( | ) |
Translate to the center of all coordinates (for this conformer)
| bool Kekulize | ( | ) |
Transform to standard Kekule bond structure (presumably from an aromatic form)
Referenced by OBMol::PerceiveBondOrders().
| bool PerceiveKekuleBonds | ( | ) |
| void NewPerceiveKekuleBonds | ( | ) |
Kekulize aromatic rings without using implicit valence.
This new perceive kekule bonds function has been designed to handle molecule files without explicit hydrogens such as pdb or xyz. (It can, of course, easily handle explicit hydrogens too.) The function does not rely on GetImplicitValence function The function looks for groups of aromatic cycle For each group it tries to guess the number of electrons given by each atom in order to satisfy the huckel (4n+2) rule If the huckel rule cannot be satisfied the algorithm try with its best alternative guess Then it recursively walk on the atoms of the cycle and assign single and double bonds
| bool DeleteHydrogens | ( | ) |
| bool DeleteHydrogens | ( | OBAtom * | atom ) |
Delete all hydrogens from the supplied atom
| bool DeleteNonPolarHydrogens | ( | ) |
Delete all hydrogen atoms connected to a non-polar atom
| bool DeleteHydrogen | ( | OBAtom * | atom ) |
Delete the supplied atom if it is a hydrogen (Helper function for DeleteHydrogens)
| bool AddHydrogens | ( | bool | polaronly = false, |
| bool | correctForPH = false, |
||
| double | pH = 7.4 |
||
| ) |
Add hydrogens to the entire molecule to fill out implicit valence spots
| polaronly | Whether to add hydrogens only to polar atoms (i.e., not to C atoms) |
| correctForPH | Whether to call CorrectForPH() first |
| pH | The pH to use for CorrectForPH() modification |
Referenced by OBSmartsPattern::Match().
| bool AddHydrogens | ( | OBAtom * | atom ) |
Add hydrogens only to the supplied atom to fill out implicit valence.
| bool AddPolarHydrogens | ( | ) |
Add only polar hydrogens (i.e., attached to polar atoms, not C)
| bool StripSalts | ( | int | threshold = 0 ) |
If threshold is not specified or is zero, remove all but the largest contiguous fragment. If threshold is non-zero, remove any fragments with fewer than threshold atoms.
| vector< OBMol > Separate | ( | int | StartIndex = 1 ) |
Copies each disconnected fragment as a separate OBMol.
Referenced by OBBuilder::IsSpiroAtom(), and OBMoleculeFormat::ReadChemObjectImpl().
| bool GetNextFragment | ( | OpenBabel::OBMolAtomDFSIter & | iter, |
| OBMol & | newMol | ||
| ) |
Iterative component of Separate to copy one fragment at a time.
Referenced by OBMol::Separate().
| bool ConvertDativeBonds | ( | ) |
Converts the charged form of coordinate bonds, e.g.[N+]([O-])=O to N(=O)=O.
Converts for instance [N+]([O-])=O to N(=O)=O.
| bool CorrectForPH | ( | double | pH = 7.4 ) |
Correct for pH by applying the OBPhModel transformations.
| bool AssignSpinMultiplicity | ( | bool | NoImplicitH = false ) |
set spin multiplicity for H-deficient atoms
If NoImplicitH is true then the molecule has no implicit hydrogens. Individual atoms on which ForceNoH() has been called also have no implicit hydrogens. If NoImplicitH is false (the default), then if there are any explicit hydrogens on an atom then they constitute all the hydrogen on that atom. However, a hydrogen atom with its _isotope!=0 is not considered explicit hydrogen for this purpose. In addition, an atom which has had ForceImplH()called for it is never considered hydrogen deficient, e.g. unbracketed atoms in SMILES. Any discrepancy with the expected atom valency is interpreted as the atom being a radical of some sort and iits _spinMultiplicity is set to 2 when it is one hydrogen short and 3 when it is two hydrogens short and similarly for greater hydrogen deficiency.
So SMILES C[CH] is interpreted as methyl carbene, CC[H][H] as ethane, and CC[2H] as CH3CH2D.
Referenced by OpenBabel::alternate(), and OBMol::PerceiveBondOrders().
| void SetIsPatternStructure | ( | ) | [inline] |
| vector3 Center | ( | int | nconf ) |
nconf Set the torsion defined by these atoms, rotating bonded neighbors
Referenced by OBBuilder::Connect(), and OBBuilder::CorrectStereoBonds().
| void FindSSSR | ( | ) |
Find Smallest Set of Smallest Rings (see OBRing class for more details)
Referenced by OBAtom::IsInRingSize(), OBAtom::MemberOfRingCount(), OBAtom::MemberOfRingSize(), OBMolRingIter::OBMolRingIter(), and OBMol::PerceiveBondOrders().
| void FindLSSR | ( | ) |
Find Largest Set of Smallest Rings.
| void FindRingAtomsAndBonds | ( | ) |
Find all ring atoms and bonds. Does not need to call FindSSSR().
Referenced by OBRotorList::FindRotors(), OBBond::IsInRing(), and OBAtom::IsInRing().
| void FindChiralCenters | ( | ) | [inline] |
Find all chiral atom centers. See OBAtom::IsChiral() for more details
| void FindChildren | ( | std::vector< int > & | children, |
| int | first, | ||
| int | second | ||
| ) |
locates all atoms for which there exists a path to 'second' without going through 'first' children must not include 'second'
Referenced by OpenBabel::ApplyRotMatToBond(), OBRotorList::AssignTorVals(), OBBond::SetLength(), OBRotorList::SetRotAtoms(), OBRotorList::SetRotAtomsByFix(), and OBRotamerList::Setup().
locates all atoms for which there exists a path to 'end' without going through 'bgn' children must not include 'end'
| void FindLargestFragment | ( | OBBitVec & | frag ) |
Find the largest fragment in OBMol (which may include multiple non-connected fragments)
| frag | Return (by reference) a bit vector indicating the atoms in the largest fragment |
| void ContigFragList | ( | std::vector< std::vector< int > > & | cfl ) |
Sort a list of contig fragments by size from largest to smallest Each vector<int> contains the atom numbers of a contig fragment
Referenced by OpenBabel::DetermineFRJ().
Aligns atom a on p1 and atom b along p1->p2 vector.
| void ConnectTheDots | ( | void | ) |
Adds single bonds based on atom proximity.
This method adds single bonds between all atoms closer than their combined atomic covalent radii, then "cleans up" making sure bonded atoms are not closer than 0.4A and the atom does not exceed its valence. It implements blue-obelisk:rebondFrom3DCoordinates.
| void PerceiveBondOrders | ( | ) |
Attempts to perceive multiple bonds based on geometries.
This method uses bond angles and geometries from current connectivity to guess atom types and then filling empty valences with multiple bonds. It currently has a pass to detect some frequent functional groups. It still needs a pass to detect aromatic rings to "clean up." AssignSpinMultiplicity(true) is called at the end of the function. The true states that there are no implict hydrogens in the molecule.
| void FindAngles | ( | ) |
Fills out an OBAngleData with angles from the molecule.
Referenced by OBMolAngleIter::OBMolAngleIter().
| void FindTorsions | ( | ) |
Fills out an OBTorsionData with angles from the molecule.
Referenced by OBMolTorsionIter::OBMolTorsionIter().
| bool GetGTDVector | ( | std::vector< int > & | gtd ) |
Calculates the graph theoretical distance (GTD) of each atom.
Creates a vector (indexed from zero) containing, for each atom in the molecule, the number of bonds plus one to the most distant non-H atom.
For example, for the molecule H3CC(=O)Cl the GTD value for C1 would be 3, as the most distant non-H atom (either Cl or O) is 2 bonds away.
Since the GTD measures the distance to non-H atoms, the GTD values for terminal H atoms tend to be larger than for non-H terminal atoms. In the example above, the GTD values for the H atoms are all 4.
Referenced by OBRotorList::FindRotors().
| void GetGIVector | ( | std::vector< unsigned int > & | vid ) |
Calculates a set of graph invariant indexes using the graph theoretical distance, number of connected heavy atoms, aromatic boolean, ring boolean, atomic number, and summation of bond orders connected to the atom. Vector is indexed from zero.
| void GetGIDVector | ( | std::vector< unsigned int > & | vgid ) |
Calculates a set of symmetry identifiers for a molecule. Atoms with the same symmetry ID are symmetrically equivalent. Vector is indexed from zero.
| bool Has2D | ( | bool | Not3D = false ) |
Are there non-zero coordinates in two dimensions (i.e. X and Y)- and, if Not3D is true, no Z coordinates?
| bool Has3D | ( | ) |
Are there non-zero coordinates in all three dimensions (i.e. X, Y, Z)?
Referenced by OpenBabel::CalcSignedVolume().
| bool HasNonZeroCoords | ( | ) |
Are there any non-zero coordinates?
| bool HasAromaticPerceived | ( | ) | [inline] |
Has aromatic perception been performed?
Referenced by OBAromaticTyper::AssignAromaticFlags(), OBBond::IsAromatic(), and OBAtom::IsAromatic().
| bool HasSSSRPerceived | ( | ) | [inline] |
Has the smallest set of smallest rings (FindSSSR) been performed?
Referenced by OBAtom::IsInRingSize(), OBAtom::MemberOfRingCount(), OBAtom::MemberOfRingSize(), OBMolRingIter::OBMolRingIter(), and OBMol::PerceiveBondOrders().
| bool HasLSSRPerceived | ( | ) | [inline] |
Has the largest set of smallest rings (FindLSSR) been performed?
| bool HasRingAtomsAndBondsPerceived | ( | ) | [inline] |
Have ring atoms and bonds been assigned?
Referenced by OBBond::IsInRing(), and OBAtom::IsInRing().
| bool HasAtomTypesPerceived | ( | ) | [inline] |
Have atom types been assigned by OBAtomTyper?
Referenced by OBAtom::GetType().
| bool HasRingTypesPerceived | ( | ) | [inline] |
Have ring types been assigned by OBRingTyper?
Referenced by OBRing::GetType().
| bool HasChiralityPerceived | ( | ) | [inline] |
Has atom chirality been assigned?
Referenced by OpenBabel::CanonicalLabels(), and OBMol::operator=().
| bool HasPartialChargesPerceived | ( | ) | [inline] |
Have atomic Gasteiger partial charges been assigned by OBGastChrg?
| bool HasHybridizationPerceived | ( | ) | [inline] |
Has atomic hybridization been assigned by OBAtomTyper?
Referenced by OBAtom::GetHyb().
| bool HasImplicitValencePerceived | ( | ) | [inline] |
Has implicit hydrogen valence been assigned by OBAtomTyper?
Referenced by OBAtomTyper::AssignImplicitValence(), OBAtom::GetImplicitValence(), and OBAtom::ImplicitHydrogenCount().
| bool HasKekulePerceived | ( | ) | [inline] |
Has aromaticity and Kekule forms been assigned by Kekulize?
| bool HasClosureBondsPerceived | ( | ) | [inline] |
Have ring "closure" bonds been assigned? (e.g., OBBond::IsClosure())
Referenced by OBBond::IsClosure().
| bool HasChainsPerceived | ( | ) | [inline] |
Have biomolecule chains and residues been assigned by OBChainsParser?
| bool HasHydrogensAdded | ( | ) | [inline] |
Have hydrogens been added to the molecule?
| bool HasAromaticCorrected | ( | ) | [inline] |
Have aromatic nitrogens been "corrected?" (deprecated)
Referenced by OBAtomTyper::AssignImplicitValence(), and OBAtomTyper::CorrectAromaticNitrogens().
| bool IsCorrectedForPH | ( | ) | [inline] |
Has the molecule been corrected for pH by CorrectForPH?
Referenced by OBPhModel::CorrectForPH().
| bool HasSpinMultiplicityAssigned | ( | ) | [inline] |
Has total spin multiplicity been assigned?
| bool IsChiral | ( | ) |
Is this molecule chiral?
| bool Empty | ( | ) | [inline] |
Are there any atoms in this molecule?
Referenced by OBMol::ConnectTheDots(), OBSSMatch::OBSSMatch(), OBMol::PerceiveBondOrders(), and OBMol::RenumberAtoms().
| int NumConformers | ( | ) | [inline] |
Referenced by OBMoleculeFormat::DoOutputOptions(), OBMol::operator=(), OBMol::RenumberAtoms(), OBMol::Rotate(), OBForceField::SetConformers(), and OBMol::Translate().
| void SetConformers | ( | std::vector< double * > & | v ) |
Set the entire set of conformers for this molecule to v.
Referenced by OBForceField::GetConformers(), and OBConformerSearch::GetConformers().
| void AddConformer | ( | double * | f ) | [inline] |
Add a new set of coordinates f as a new conformer.
| void SetConformer | ( | int | i ) |
Set the molecule's current conformer to i Does nothing if i is less than 0 or i is larger than NumConformers()
Referenced by OBMol::Center(), OBMoleculeFormat::DoOutputOptions(), and OBForceField::GetConformers().
| void CopyConformer | ( | double * | c, |
| int | nconf | ||
| ) |
Copy the conformer nconf into the array c
c is large enough | void DeleteConformer | ( | int | nconf ) |
Delete the conformer nconf.
| double* GetConformer | ( | int | i ) | [inline] |
i Referenced by OBMol::operator=(), OBMol::RenumberAtoms(), OBMol::Rotate(), OBForceField::SetConformers(), and OBMol::Translate().
| void SetEnergies | ( | std::vector< double > & | energies ) |
Set the entire set of conformer energies.
| vector< double > GetEnergies | ( | ) |
Set the entire set of conformer energies.
| double GetEnergy | ( | int | ci ) |
Get the energy for conformer ci
| double* BeginConformer | ( | std::vector< double * >::iterator & | i ) | [inline] |
Set the iterator to the beginning of the conformer list
| double* NextConformer | ( | std::vector< double * >::iterator & | i ) | [inline] |
Advance the iterator to the next confomer, if possible
| std::vector<double*>& GetConformers | ( | ) | [inline] |
Referenced by OBRotamerList::SetBaseCoordinateSets().
| OBAtomIterator BeginAtoms | ( | ) | [inline] |
| OBAtomIterator EndAtoms | ( | ) | [inline] |
| OBBondIterator BeginBonds | ( | ) | [inline] |
| OBBondIterator EndBonds | ( | ) | [inline] |
| OBResidueIterator BeginResidues | ( | ) | [inline] |
| OBResidueIterator EndResidues | ( | ) | [inline] |
| OBAtom * BeginAtom | ( | OBAtomIterator & | i ) |
Set the iterator i to the beginning of the atom list
Referenced by OBAromaticTyper::AssignAromaticFlags(), OBResidueData::AssignBonds(), OBAtomTyper::AssignHyb(), OBAtomTyper::AssignImplicitValence(), OBGastChrg::AssignPartialCharges(), OBAtomTyper::AssignTypes(), OpenBabel::CalcSignedVolume(), OpenBabel::CartesianToInternal(), OBMol::Center(), OBMol::ConnectTheDots(), OpenBabel::construct_c_matrix(), OpenBabel::construct_g_matrix(), OBMol::ConvertDativeBonds(), OBDepict::DrawMolecule(), OBAromaticTyper::ExcludeSmallRing(), OBSmartsMatcher::FastSingleMatch(), OBChargeModel::FillChargeVectors(), OpenBabel::GetChirality(), OpenBabel::GetDFFVector(), OBAtom::GetPartialCharge(), OBMol::Has2D(), OBMol::Has3D(), OBMol::HasNonZeroCoords(), OBGrid::Init(), OpenBabel::InternalToCartesian(), OBMol::IsChiral(), OBBond::IsClosure(), OBMolAtomIter::OBMolAtomIter(), OBMolPairIter::OBMolPairIter(), OBMolPairIter::operator++(), OBMol::operator+=(), OBMol::operator=(), OBMol::PerceiveBondOrders(), OBMol::RenumberAtoms(), OBMol::SetCoordinates(), OBProxGrid::Setup(), OBSmartsMatcher::SetupAtomMatchTable(), and OBMol::~OBMol().
| OBAtom * NextAtom | ( | OBAtomIterator & | i ) |
Advance the iterator i to the next atom in the molecule
Referenced by OBAromaticTyper::AssignAromaticFlags(), OBResidueData::AssignBonds(), OBAtomTyper::AssignHyb(), OBAtomTyper::AssignImplicitValence(), OBGastChrg::AssignPartialCharges(), OBAtomTyper::AssignTypes(), OpenBabel::CalcSignedVolume(), OpenBabel::CartesianToInternal(), OBMol::Center(), OBMol::ConnectTheDots(), OpenBabel::construct_c_matrix(), OpenBabel::construct_g_matrix(), OBMol::ConvertDativeBonds(), OBDepict::DrawMolecule(), OBAromaticTyper::ExcludeSmallRing(), OBSmartsMatcher::FastSingleMatch(), OBChargeModel::FillChargeVectors(), OpenBabel::GetChirality(), OpenBabel::GetDFFVector(), OBAtom::GetPartialCharge(), OBMol::Has2D(), OBMol::Has3D(), OBMol::HasNonZeroCoords(), OBGrid::Init(), OpenBabel::InternalToCartesian(), OBMol::IsChiral(), OBBond::IsClosure(), OBMolPairIter::OBMolPairIter(), OBMolPairIter::operator++(), OBMol::operator+=(), OBMol::operator=(), OBMol::PerceiveBondOrders(), OBMol::RenumberAtoms(), OBMol::SetCoordinates(), OBProxGrid::Setup(), OBSmartsMatcher::SetupAtomMatchTable(), and OBMol::~OBMol().
| OBBond * BeginBond | ( | OBBondIterator & | i ) |
Set the iterator i to the beginning of the bond list
Referenced by OBAromaticTyper::AssignAromaticFlags(), OBGastChrg::AssignPartialCharges(), OpenBabel::DetermineFRJ(), OBDepict::DrawMolecule(), OBRotorList::FindRotors(), OBBond::IsClosure(), OBMolBondIter::OBMolBondIter(), OBMol::operator+=(), OBMol::operator=(), OBAromaticTyper::SelectRootAtoms(), and OBMol::~OBMol().
| OBBond * NextBond | ( | OBBondIterator & | i ) |
Advance the iterator i to the next bond in the molecule
Referenced by OBAromaticTyper::AssignAromaticFlags(), OBGastChrg::AssignPartialCharges(), OpenBabel::DetermineFRJ(), OBDepict::DrawMolecule(), OBRotorList::FindRotors(), OBBond::IsClosure(), OBMolBondIter::operator++(), OBMol::operator+=(), OBMol::operator=(), OBAromaticTyper::SelectRootAtoms(), and OBMol::~OBMol().
| OBResidue* BeginResidue | ( | OBResidueIterator & | i ) | [inline] |
Set the iterator i to the beginning of the resdiue list
Referenced by OBResidueIter::OBResidueIter(), OBMol::operator+=(), and OBMol::~OBMol().
| OBResidue* NextResidue | ( | OBResidueIterator & | i ) | [inline] |
Advance the iterator i to the next residue in the molecule
Referenced by OBResidueIter::operator++(), OBMol::operator+=(), and OBMol::~OBMol().
| OBInternalCoord* BeginInternalCoord | ( | std::vector< OBInternalCoord * >::iterator & | i ) | [inline] |
Set the iterator to the beginning of the internal coordinate list
| OBInternalCoord* NextInternalCoord | ( | std::vector< OBInternalCoord * >::iterator & | i ) | [inline] |
Advance the iterator to the next internal coordinate record
| T* CastAndClear | ( | bool | clear = true ) |
[inline, inherited] |
By default clears the object. Called from ReadMolecule of most format classes.
| bool HasData | ( | const std::string & | s ) | [inherited] |
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] |
| bool HasData | ( | const unsigned int | type ) | [inherited] |
| 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
| size_t DataSize | ( | ) | const [inline, inherited] |
| OBGenericData * GetData | ( | const unsigned int | type ) | [inherited] |
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] |
| OBGenericData * GetData | ( | const char * | s ) | [inherited] |
| std::vector<OBGenericData*>& GetData | ( | ) | [inline, inherited] |
Referenced by OBMol::GetEnergies(), OBMol::GetEnergy(), and OBMol::SetEnergies().
| std::vector< OBGenericData * > GetData | ( | DataOrigin | source ) | [inherited] |
| std::vector< OBGenericData * > GetAllData | ( | const unsigned int | type ) | [inherited] |
Referenced by OpenBabel::CanonicalLabels(), OBBuilder::CorrectStereoAtoms(), and OBBuilder::CorrectStereoBonds().
| OBDataIterator BeginData | ( | ) | [inline, inherited] |
Referenced by OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().
| OBDataIterator EndData | ( | ) | [inline, inherited] |
Referenced by OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().
int _flags [protected] |
bitfield of flags
Referenced by OBMol::OBMol(), and OBMol::PerceiveBondOrders().
bool _autoPartialCharge [protected] |
Assign partial charges automatically.
Referenced by OBMol::OBMol().
bool _autoFormalCharge [protected] |
Assign formal charges automatically.
Referenced by OBMol::OBMol().
std::string _title [protected] |
Molecule title.
Referenced by OBMol::OBMol().
vector of atoms
Referenced by OBMol::BeginAtom(), OBMol::NextAtom(), OBMol::OBMol(), and OBMol::RenumberAtoms().
vector of atoms indexed by id
Referenced by OBMol::OBMol().
vector of bonds
Referenced by OBMol::BeginBond(), OBMol::NextBond(), and OBMol::OBMol().
vector of bonds
Referenced by OBMol::OBMol().
unsigned short int _dimension [protected] |
Dimensionality of coordinates.
Referenced by OBMol::ConnectTheDots(), OBMol::OBMol(), and OBMol::PerceiveBondOrders().
int _totalCharge [protected] |
Total charge on the molecule.
Referenced by OBMol::OBMol().
unsigned int _totalSpin [protected] |
Total spin on the molecule (if not specified, assumes lowest possible spin)
double* _c [protected] |
coordinate array
Referenced by OBMol::ConnectTheDots(), OBMol::OBMol(), OBMol::Rotate(), OBMol::SetConformer(), OBMol::SetConformers(), OBMol::SetCoordinates(), and OBMol::Translate().
std::vector<double*> _vconf [protected] |
vector of conformers
Referenced by OBMol::Center(), OBMol::ConnectTheDots(), OBMol::CopyConformer(), OBMol::DeleteConformer(), OBMol::OBMol(), OBMol::SetConformer(), OBMol::SetConformers(), OBMol::SetCoordinates(), and OBMol::~OBMol().
double _energy [protected] |
heat of formation
Referenced by OBMol::OBMol().
unsigned int _natoms [protected] |
Number of atoms.
Referenced by OBMol::ConnectTheDots(), and OBMol::OBMol().
unsigned int _nbonds [protected] |
Number of bonds.
Referenced by OBMol::OBMol().
std::vector<OBInternalCoord*> _internals [protected] |
Internal Coordinates (if applicable)
unsigned short int _mod [protected] |
Number of nested calls to BeginModify()
Referenced by OBMol::OBMol().
std::vector<OBGenericData*> _vdata [protected, inherited] |
Custom data.
Referenced by OBMol::OBMol().
This file is part of the documentation for Open Babel, version 2.3.
1.7.2.