OBCisTransStereo Class Reference

#include <openbabel/stereo/cistrans.h>

Inheritance diagram for OBCisTransStereo:

Classes
struct	Config

Public Member Functions
	OBCisTransStereo (OBMol *mol)
virtual	~OBCisTransStereo ()
OBGenericData *	Clone (OBBase *mol) const
void	SetAttribute (const std::string &v)
void	SetOrigin (const DataOrigin s)
virtual const std::string &	GetAttribute () const
unsigned int	GetDataType () const
virtual const std::string &	GetValue () const
virtual DataOrigin	GetOrigin () const
Cis/Trans stereochemistry
OBStereo::Type	GetType () const
bool	IsValid () const
void	SetConfig (const Config &config)
Config	GetConfig (OBStereo::Shape shape=OBStereo::ShapeU) const
Config	GetConfig (unsigned long start, OBStereo::Shape shape=OBStereo::ShapeU) const
bool	operator== (const OBCisTransStereo &other) const
bool	operator!= (const OBCisTransStereo &other) const
Query methods to compare stereochemistry.
bool	IsOnSameAtom (unsigned long id1, unsigned long id2) const
bool	IsTrans (unsigned long id1, unsigned long id2) const
bool	IsCis (unsigned long id1, unsigned long id2) const
unsigned long	GetTransRef (unsigned long id) const
unsigned long	GetCisRef (unsigned long id) const
Geniric (for all OBStereo::Type) stereochemistry
OBMol *	GetMolecule () const
void	SetSpecified (bool specified)
bool	IsSpecified () const

Static Public Member Functions
template<typename ConfigType >
static ConfigType	ToConfig (const ConfigType &cfg, unsigned long start, OBStereo::Shape shape=OBStereo::ShapeU)

Protected Attributes
std::string	_attr
unsigned int	_type
DataOrigin	_source

Detailed Description

Class for handling and storing cis/trans stereochemistry.

The OBCisTransStereo class is used to represent cis/trans stereochemistry. Like all OBTetraPlanarStereo subclasses, it uses the OBStereo::Shape parameters to set/get the OBStereo::Ref values in the Config struct. However, since the orientation of the double bond matters, all methods in the "query methods" section check the bonding by actually checking the atoms in the molecule provided through OBStereoBase's constructor. If OBMol::GetAtomById(id) returns 0 for a single id, it will be considered a deleted or implicit hydrogen if the valences confirm this.

The use of OBStereo::Shape is illustarted in the image below.

//
// 3 6 3 6
// \ / | |
// 0===1 = | 0 1 |
// / \ | |
// 4 5 4-------5
//
OBCisTransStereo ct;
ct.SetCenters(0, 1);
ct.SetRefs(OBStereo::MakeRefs(3, 4, 5, 6), OBStereo::ShapeU);

ct.IsTrans(3, 5); // true
ct.IsTrans(3, 4); // false
ct.IsTrans(3, 6); // false

ct.IsCis(3, 6); // true
ct.IsCis(3, 4); // false
ct.IsCis(3, 5); // false

Since

version 2.3

Constructor & Destructor Documentation

OBCisTransStereo()

OBCisTransStereo

(

OBMol *

mol

)

Constructor.

~OBCisTransStereo()

virtual ~OBCisTransStereo ( )

virtual

Destructor.

Member Function Documentation

GetType()

OBStereo::Type GetType ( ) const

inlinevirtual

Get the OBStereo::Type for this object.

Returns

OBStereo::CisTrans

Implements OBStereoBase.

IsValid()

bool IsValid

(

)

const

Returns

True if this object is valid. This object is valid if all these conditions are met:

• begin != OBStereo::NoRef
• end != OBStereo::NoRef
• refs contains 4 elements

Referenced by OpenBabel::CanonicalLabels().

SetConfig()

void SetConfig

(

const Config &

config

)

Set the configuration using a Config struct.

Referenced by OpenBabel::CanonicalLabels(), OBMol::CopySubstructure(), and OBMol::operator+=().

GetConfig() [1/2]

Config GetConfig

(

OBStereo::Shape

shape = OBStereo::ShapeU

)

const

Get the configuration as Config struct.

Referenced by OpenBabel::CanonicalLabels(), OBMol::CopySubstructure(), OBBuilder::CorrectStereoBonds(), OpenBabel::DeleteStereoOnAtom(), OBDepict::DrawMolecule(), OpenBabel::findMetalloceneBonds(), and OBMol::operator+=().

GetConfig() [2/2]

Config GetConfig	(	unsigned long	start,
		OBStereo::Shape	shape = OBStereo::ShapeU
	)		const

Get the configuration as Config struct and ensure refs[0] is equal to start.

operator==()

bool operator==

(

const OBCisTransStereo &

other

)

const

Compare the stereochemistry stored in the Config struct with the stereochemistry specified in the Config struct from other.

Equal to operator. Comparing OBCisTransStereo::Config structs is done using the information stored in the struct's data members (i.e. begin, end, refs and shape).

There are a number of cases resuling in false being returned:

• begin and end don't match (is checked using the 2 combinations)
• One of the Refs lists does not contain 4 elements.
• 2 or more OBStereo::ImplicitRef values in a single Config struct
• (The two refs don't share a single common element)

In the simplest case where both refs contain exactly the same elements (OBStereo::ContainsSameRefs()), coould include OBStereo::ImplicitRef), both Config struct are normalized to OBStereo::ShapeU starting with the same element. After this normalization, there are two possible orientations to overlay the shape on the double bond. From the illustration below, it can be seen only refs[2] has to be checked in order to conclude both Config structs have the same stereochemistry.

 1      4    1      4    1------4
  \    /     |      |           |
   C==C      |      |           |
  /    \     |      |           |
 2      3    2------3    2------3

             1 2 3 4     1 2 3 4
             |   |       |   |      <- in any case, refs[0] & refs[2] remain unchanged
             1 2 3 4     1 4 3 2

When comparing a Config struct with explicit hydrogen(s) to one with implicit hydrogen(s), both refs are also normalized to OBStereo::ShapeU starting with the same common element. This shared element cannot be OBStereo::ImplicitRef. Depending on the position of the OBStereo::ImplicitRef element(s) in the refs, 3 cases are possible:

 refs[2] != OBStereo::ImplicitId:

   (analog to the case above where they contained the same elements )

   1 2 3 4
   |   |      <- refs[0] & refs[2] remain unchanged
   1 H 3 H

 else:

   1 2 3 4
   |     |    <- refs[0] & refs[3] remain unchanged
   1 H H 4

   1 2 3 4
   | |        <- refs[0] & refs[1] remain unchanged
   1 2 H H

In each case, the orientation of the U shape is also defined since there can be only one OBStereo::ImplicitRef for each side of the double bond.

Returns

True if both Config structs represent the stereochemistry.

operator!=()

bool operator!= ( const OBCisTransStereo &  other ) const

inline

Not equal to operator. This is the inverse of the Equal to operator==.

Returns

True if the two Config structs represent a different stereochemistry.

Clone()

OBGenericData* Clone ( OBBase *  mol ) const

virtual

Reimplemented from OBGenericData.

IsOnSameAtom()

bool IsOnSameAtom	(	unsigned long	id1,
		unsigned long	id2
	)		const

Check if the two atoms for id1 & id2 are bonded to the same atom. If the atoms for one of the atoms doesn't exist (anymore), the valence of the begin and end atom is checked. If the exising atom is bonded to the begin atom and end->GetExplicitDegree() == 2, the ids are considered to be on different atoms. The reasoning behind this is that hydrogens may be deleted. However, you can also use OBStereo::ImplicitRef explicitly in code like:

//
// F F F F 0 3
// \ / | | | |
// C===C | C C | | 1 2 |
// / \ | | | |
// (H) (H) (H)----(H) H------H
//
reading smiles F/C=C\F cis-difluorethene
OBCisTransStereo ct(mol);
ct.SetCenters(1, 2);
ct.SetRefs(OBStereo::MakeRefs(0, OBStereo::ImplicitRef, OBStereo::ImplicitRef, 3));
...

Returns

True if id1 and id2 are bonded to the same atom taking implicit hydrogens into account.

IsTrans()

bool IsTrans	(	unsigned long	id1,
		unsigned long	id2
	)		const

Returns

True if the two reference ids are placed trans configuration.

IsCis()

bool IsCis	(	unsigned long	id1,
		unsigned long	id2
	)		const

Returns

True if the two reference ids are placed in a cis configuration.

GetTransRef()

unsigned long GetTransRef

(

unsigned long

id

)

const

Get the reference id trans from reference id.

GetCisRef()

unsigned long GetCisRef

(

unsigned long

id

)

const

Get the reference id cis from reference id.

ToConfig()

static ConfigType ToConfig ( const ConfigType &  cfg, unsigned long  start, OBStereo::Shape  shape = OBStereo::ShapeU  )

inlinestaticinherited

Referenced by OBCisTransConfig::operator==(), and OBSquarePlanarConfig::operator==().

GetMolecule()

OBMol* GetMolecule ( ) const

inlineinherited

Get the molecule. This can be used by subclasses when more information is needed (e.g. OBCisTransStereo::GetCisRef, ...).

SetSpecified()

void SetSpecified ( bool  specified )

inlineinherited

Set whether the stereochemistry is specified. Comparing a specified OBStereoBase derived class (or it's Config struct) with an unspecified one, always returns true.

IsSpecified()

bool IsSpecified ( ) const

inlineinherited

Returns

True if the stereochemistry is specified.

SetAttribute()

void SetAttribute ( const std::string &  v )

inlineinherited

Set the attribute (key), which can be used to retrieve this data.

Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::ComparePairSecond(), OBMol::DoTransformations(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBForceField::GetAtomTypes(), OBMol::GetFormula(), OBMol::GetLSSR(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().

SetOrigin()

void SetOrigin ( const DataOrigin  s )

inlineinherited

Set the origin of this data, which can be used to filter the data.

Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::ComparePairSecond(), OBMol::DoTransformations(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().

GetAttribute()

virtual const std::string& GetAttribute ( ) const

inlinevirtualinherited

Returns

The attribute (key), which can be used to retrieve this data

Referenced by OpenBabel::extract_thermochemistry(), and OBMoleculeFormat::MakeCombinedMolecule().

GetDataType()

unsigned int GetDataType ( ) const

inlineinherited

Returns

the data type for this object as defined in OBGenericDataType

GetValue()

virtual const std::string& GetValue ( ) const

inlinevirtualinherited

Base class returns a default value (the attribute type) but should never be called.

Reimplemented in OBPairData, and OBCommentData.

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), OBDescriptor::FilterCompare(), and OBDescriptor::GetValues().

GetOrigin()

virtual DataOrigin GetOrigin ( ) const

inlinevirtualinherited

Member Data Documentation

_attr

std::string _attr

protectedinherited

attribute tag (e.g., "UnitCell", "Comment" or "Author")

Referenced by OBRotamerList::Clone(), and OBNasaThermoData::OBNasaThermoData().

_type

unsigned int _type

protectedinherited

attribute type – declared for each subclass

Referenced by OBRotamerList::Clone(), and OBNasaThermoData::OBNasaThermoData().

_source

DataOrigin _source

protectedinherited

source of data for accounting

Referenced by OBConformerData::operator=(), OBSymmetryData::operator=(), OBTorsionData::operator=(), and OBAngleData::operator=().

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

• cistrans.h