mol.h File Reference

#include <openbabel/babelconfig.h>
#include <math.h>
#include <float.h>
#include <vector>
#include <string>
#include <map>
#include <openbabel/base.h>

Go to the source code of this file.

Classes
class	OBMol
struct	max_value< T, size >
struct	max_value< T, 0 >

Namespaces
	OpenBabel
	OpenBabel::detail

Macros
#define	THREAD_LOCAL
#define	OB_SSSR_MOL   (1<<1)
#define	OB_RINGFLAGS_MOL   (1<<2)
#define	OB_AROMATIC_MOL   (1<<3)
#define	OB_ATOMTYPES_MOL   (1<<4)
#define	OB_CHIRALITY_MOL   (1<<5)
#define	OB_PCHARGE_MOL   (1<<6)
#define	OB_HYBRID_MOL   (1<<8)
#define	OB_CLOSURE_MOL   (1<<11)
#define	OB_H_ADDED_MOL   (1<<12)
#define	OB_PH_CORRECTED_MOL   (1<<13)
#define	OB_CHAINS_MOL   (1<<15)
#define	OB_TCHARGE_MOL   (1<<16)
#define	OB_TSPIN_MOL   (1<<17)
#define	OB_RINGTYPES_MOL   (1<<18)
#define	OB_PATTERN_STRUCTURE   (1<<19)
#define	OB_LSSR_MOL   (1<<20)
#define	OB_ATOMSPIN_MOL   (1<<21)
#define	OB_REACTION_MOL   (1<<22)
#define	SET_OR_UNSET_FLAG(X)
#define	OB_CURRENT_CONFORMER   -1
#define	BUFF_SIZE   32768
#define	EQ(a, b)   (!strcmp((a), (b)))
#define	EQn(a, b, n)   (!strncmp((a), (b), (n)))
#define	SQUARE(x)   ((x)*(x))
#define	IsUnsatType(x)   (EQ(x,"Car") || EQ(x,"C2") || EQ(x,"Sox") || EQ(x,"Sac") || EQ(x,"Pac") || EQ(x,"So2"))

Typedefs
typedef std::vector< OBResidue * >::iterator	OBResidueIterator

Enumerations
enum	HydrogenType { AllHydrogen, PolarHydrogen, NonPolarHydrogen }

Functions
void	ThrowError (char *str)
void	ThrowError (std::string &str)
void	CartesianToInternal (std::vector< OBInternalCoord *> &, OBMol &)
void	InternalToCartesian (std::vector< OBInternalCoord *> &, OBMol &)
std::string	NewExtension (string &src, char *ext)
void	get_rmat (double *, double *, double *, int)
void	ob_make_rmat (double mat[3][3], double rmat[9])
void	qtrfit (double *r, double *f, int size, double u[3][3])
double	superimpose (double *, double *, int)

Variables
static const unsigned long	NoId = detail::max_value<unsigned long>::result

Detailed Description

Handle molecules. Declarations of OBMol, OBAtom, OBBond, OBResidue. (the main header for Open Babel)

Macro Definition Documentation

THREAD_LOCAL

#define THREAD_LOCAL

OB_SSSR_MOL

#define OB_SSSR_MOL   (1<<1)

Smallest Set of Smallest Rings (SSSR) done. See OBRing and OBMol::FindSSSR.

Referenced by OBMol::AddNewHydrogens(), OBMol::HasSSSRPerceived(), OBMol::RenumberAtoms(), and OBMol::SetSSSRPerceived().

OB_RINGFLAGS_MOL

#define OB_RINGFLAGS_MOL   (1<<2)

Ring flags have been set: See OBRing::FindRingAtomsAndBonds.

Referenced by OBMol::FindRingAtomsAndBonds(), OBMol::HasRingAtomsAndBondsPerceived(), and OBMol::SetRingAtomsAndBondsPerceived().

OB_AROMATIC_MOL

#define OB_AROMATIC_MOL   (1<<3)

Aromatic flags have been set for atoms and bonds.

Referenced by OBMol::AddNewHydrogens(), OBMol::CopySubstructure(), OBMol::EndModify(), OBMol::HasAromaticPerceived(), OBMol::operator=(), OBMol::PerceiveBondOrders(), and OBMol::SetAromaticPerceived().

OB_ATOMTYPES_MOL

#define OB_ATOMTYPES_MOL   (1<<4)

Atom typing has been performed. See OBAtomTyper.

Referenced by OBMol::AddNewHydrogens(), OBMol::HasAtomTypesPerceived(), OBMol::PerceiveBondOrders(), and OBMol::SetAtomTypesPerceived().

OB_CHIRALITY_MOL

#define OB_CHIRALITY_MOL   (1<<5)

Chirality detection has been performed.

Referenced by OBMol::HasChiralityPerceived(), and OBMol::SetChiralityPerceived().

OB_PCHARGE_MOL

#define OB_PCHARGE_MOL   (1<<6)

Partial charges have been set or percieved.

Referenced by OBMol::AddNewHydrogens(), OBMol::HasPartialChargesPerceived(), OBMol::operator=(), and OBMol::SetPartialChargesPerceived().

OB_HYBRID_MOL

#define OB_HYBRID_MOL   (1<<8)

Atom hybridizations have been set. See OBAtomTyper.

Referenced by OBMol::AddNewHydrogens(), OBMol::HasHybridizationPerceived(), OBMol::operator=(), OBMol::PerceiveBondOrders(), and OBMol::SetHybridizationPerceived().

OB_CLOSURE_MOL

#define OB_CLOSURE_MOL   (1<<11)

Ring "closure" bonds have been set. See OBBond::IsClosure.

Referenced by OBMol::HasClosureBondsPerceived(), and OBMol::SetClosureBondsPerceived().

OB_H_ADDED_MOL

#define OB_H_ADDED_MOL   (1<<12)

Hyrdogen atoms have been added where needed. See OBMol::AddHydrogens.

Referenced by OBMol::HasHydrogensAdded(), and OBMol::SetHydrogensAdded().

OB_PH_CORRECTED_MOL

#define OB_PH_CORRECTED_MOL   (1<<13)

pH correction for hydrogen addition has been performed.

Referenced by OBMol::IsCorrectedForPH(), and OBMol::SetCorrectedForPH().

OB_CHAINS_MOL

#define OB_CHAINS_MOL   (1<<15)

Biomolecular chains and residues have been set. See OBChainsParser.

Referenced by OBMol::CopySubstructure(), OBMol::HasChainsPerceived(), OBMol::operator=(), and OBMol::SetChainsPerceived().

OB_TCHARGE_MOL

#define OB_TCHARGE_MOL   (1<<16)

Total charge on this molecule has been set. See OBMol::SetTotalCharge.

Referenced by OBMol::GetTotalCharge(), OBMol::operator=(), and OBMol::SetTotalCharge().

OB_TSPIN_MOL

#define OB_TSPIN_MOL   (1<<17)

Total spin on this molecule has been set. See OBMol::SetTotalSpinMultiplicity.

Referenced by OBMol::GetTotalSpinMultiplicity(), OBMol::operator=(), and OBMol::SetTotalSpinMultiplicity().

OB_RINGTYPES_MOL

#define OB_RINGTYPES_MOL   (1<<18)

Ring typing has been performed. See OBRingTyper.

Referenced by OBMol::HasRingTypesPerceived(), and OBMol::SetRingTypesPerceived().

OB_PATTERN_STRUCTURE

#define OB_PATTERN_STRUCTURE   (1<<19)

A pattern, not a complete molecule.

Referenced by OBMol::Clear(), OBMol::operator=(), and OBMol::SetIsPatternStructure().

OB_LSSR_MOL

#define OB_LSSR_MOL   (1<<20)

Largest Set of Smallest Rings (LSSR) done. See OBRing and OBMol::FindLSSR.

Referenced by OBMol::HasLSSRPerceived(), OBMol::RenumberAtoms(), and OBMol::SetLSSRPerceived().

OB_ATOMSPIN_MOL

#define OB_ATOMSPIN_MOL   (1<<21)

SpinMultiplicities on atoms have been set in OBMol::AssignSpinMultiplicity()

Referenced by OBMol::HasSpinMultiplicityAssigned(), and OBMol::SetSpinMultiplicityAssigned().

OB_REACTION_MOL

#define OB_REACTION_MOL   (1<<22)

Treat as reaction.

Referenced by OBMol::EndModify(), OBMol::IsReaction(), and OBMol::SetIsReaction().

SET_OR_UNSET_FLAG

#define SET_OR_UNSET_FLAG

(

X

)

Value:

if (value) SetFlag(X); \
  else     UnsetFlag(X);

Referenced by OBMol::SetAromaticPerceived(), OBMol::SetAtomTypesPerceived(), OBMol::SetChainsPerceived(), OBMol::SetChiralityPerceived(), OBMol::SetClosureBondsPerceived(), OBMol::SetCorrectedForPH(), OBMol::SetHybridizationPerceived(), OBMol::SetHydrogensAdded(), OBMol::SetIsPatternStructure(), OBMol::SetIsReaction(), OBMol::SetLSSRPerceived(), OBMol::SetPartialChargesPerceived(), OBMol::SetRingAtomsAndBondsPerceived(), OBMol::SetRingTypesPerceived(), OBMol::SetSpinMultiplicityAssigned(), and OBMol::SetSSSRPerceived().

OB_CURRENT_CONFORMER

#define OB_CURRENT_CONFORMER   -1

Referenced by OBMol::Rotate(), and OBMol::Translate().

BUFF_SIZE

#define BUFF_SIZE   32768

Referenced by patty::assign_rules(), OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBForceField::DistanceGeometry(), OBBuilder::GetFragmentCoord(), OBRotorRules::GetRotorIncrements(), OBMol::GetSpacedFormula(), OBGlobalDataBase::Init(), OpenBabel::intToStr(), OBBuilder::LoadFragments(), OBRotorRules::ParseLine(), OBForceField::PrintFormalCharges(), OBForceField::PrintPartialCharges(), OBForceField::PrintTypes(), OBForceField::PrintVelocities(), OBForceField::RandomRotorSearchInitialize(), OBForceField::RandomRotorSearchNextConformer(), patty::read_rules(), OBRotorList::Setup(), OBForceField::SteepestDescentInitialize(), OBForceField::SteepestDescentTakeNSteps(), OBForceField::SystematicRotorSearchInitialize(), OBForceField::SystematicRotorSearchNextConformer(), OBForceField::ValidateConjugateGradients(), OBForceField::ValidateSteepestDescent(), OBForceField::WeightedRotorSearch(), and OBChainsParser::~OBChainsParser().

EQ

#define EQ	(		a,
			b
	)		(!strcmp((a), (b)))

Referenced by OBGastChrg::AssignPartialCharges().

EQn

#define EQn	(		a,
			b,
			n
	)		(!strncmp((a), (b), (n)))

Referenced by OBAtomTyper::ParseLine(), OBRingTyper::ParseLine(), OBRotorRules::ParseLine(), and OBPhModel::ParseLine().

SQUARE

#define SQUARE

(

x

)

((x)*(x))

Referenced by OpenBabel::calc_rms(), OBRotor::CalcBondLength(), OBRotor::CalcTorsion(), OBBond::GetLength(), OBRotor::SetRotor(), OpenBabel::SetRotorToAngle(), OBMol::SetTorsion(), OBProxGrid::Setup(), and OBForceField::UpdatePairsSimple().

IsUnsatType

#define IsUnsatType

(

x

)

(EQ(x,"Car") || EQ(x,"C2") || EQ(x,"Sox") || EQ(x,"Sac") || EQ(x,"Pac") || EQ(x,"So2"))