OBGroupContrib Class Reference

Handle group contribution algorithms. More...

#include <openbabel/groupcontrib.h>

Inheritance diagram for OBGroupContrib:

List of all members.

Public Types
typedef std::map< const char *, OBPlugin *, CharPtrLess >	PluginMapType
typedef PluginMapType::const_iterator	PluginIterator
Public Member Functions
	OBGroupContrib (const char *ID, const char *filename, const char *descr)
virtual const char *	Description ()
virtual OBGroupContrib *	MakeInstance (const std::vector< std::string > &textlines)
virtual double	Predict (OBBase *pOb, std::string *param=NULL)
const char *	TypeID ()
double	PredictAndSave (OBBase *pOb, std::string *param=NULL)
virtual double	GetStringValue (OBBase *pOb, std::string &svalue, std::string *param=NULL)
virtual bool	Compare (OBBase *pOb, std::istream &ss, bool noEval, std::string *param=NULL)
virtual bool	Display (std::string &txt, const char *param, const char *ID=NULL)
virtual bool	Order (double p1, double p2)
virtual bool	Order (std::string s1, std::string s2)
virtual void	Init ()
const char *	GetID () const
virtual PluginMapType &	GetMap () const =0
Static Public Member Functions
static bool	FilterCompare (OBBase *pOb, std::istream &ss, bool noEval)
static void	AddProperties (OBBase *pOb, const std::string &DescrList)
static void	DeleteProperties (OBBase *pOb, const std::string &DescrList)
static std::string	GetValues (OBBase *pOb, const std::string &DescrList)
static std::pair< std::string, std::string >	GetIdentifier (std::istream &optionText)
static OBPlugin *	GetPlugin (const char *Type, const char *ID)
static bool	ListAsVector (const char *PluginID, const char *param, std::vector< std::string > &vlist)
static void	List (const char *PluginID, const char *param=NULL, std::ostream *os=&std::cout)
static std::string	ListAsString (const char *PluginID, const char *param=NULL)
static std::string	FirstLine (const char *txt)
static PluginIterator	Begin (const char *PluginID)
static PluginIterator	End (const char *PluginID)
Static Protected Member Functions
static double	ParsePredicate (std::istream &optionText, char &ch1, char &ch2, std::string &svalue)
static bool	ReadStringFromFilter (std::istream &ss, std::string &result)
static bool	CompareStringWithFilter (std::istream &optionText, std::string &s, bool noEval, bool NoCompOK=false)
static bool	ispunctU (char ch)
static bool	MatchPairData (OBBase *pOb, std::string &s)
static PluginMapType &	PluginMap ()
static PluginMapType &	GetTypeMap (const char *PluginID)
static OBPlugin *	BaseFindType (PluginMapType &Map, const char *ID)
Protected Attributes
const char *	_id

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Detailed Description

Handle group contribution algorithms.

This is the base class for calculations that use the JOELib2 contribution algorithm.

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Member Typedef Documentation

typedef std::map<const char*, OBPlugin*, CharPtrLess> PluginMapType [inherited]

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Constructor & Destructor Documentation

OBGroupContrib	(	const char *	ID,
		const char *	filename,
		const char *	descr
	)		[inline]

constructor. Each instance provides an ID and a datafile.

Predict the logP, MR, TPSA (each instance of OBGroupContrib uses different parameters loaded from its own datafile) for molecule mol using the group contributions algorithm from JOELib2.

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Member Function Documentation

virtual const char* Description

(

)

[virtual]

Required description of a sub-type.

Reimplemented from OBPlugin.

virtual OBGroupContrib* MakeInstance

(

const std::vector< std::string > &

)

[inline, virtual]

Make a new instance of the class. See OpTransform, OBGroupContrib, SmartsDescriptor classes for derived versions. Usually, the first parameter is the classname, the next three are parameters(ID, filename, description) for a constructor, and the rest data.

Reimplemented from OBPlugin.

virtual double Predict	(	OBBase *	,
		std::string *	= NULL
	)		[virtual]

Returns:

the value of a numeric descriptor

Reimplemented from OBDescriptor.

const char* TypeID

(

)

[inline, virtual, inherited]

Redefined by each plugin type: "formats", "fingerprints", etc.

Reimplemented from OBPlugin.

double PredictAndSave	(	OBBase *	pOb,
		std::string *	param = NULL
	)		[inherited]

Returns:

the value of the descriptor and adds it to the object's OBPairData

Referenced by OBDescriptor::AddProperties().

double GetStringValue	(	OBBase *	pOb,
		std::string &	svalue,
		std::string *	param = NULL
	)		[virtual, inherited]

Provides a string value for non-numeric descriptors and returns NaN, or a string representation and returns a numeric value.

This default version provides a string representation of the numeric value.

Referenced by OBDescriptor::GetValues().

bool Compare	(	OBBase *	pOb,
		std::istream &	ss,
		bool	noEval,
		std::string *	param = NULL
	)		[virtual, inherited]

Parses the filter stream for a relational expression and returns its result when applied to the chemical object.

Compare() is a virtual function and can be overridden to allow different comparison behaviour. The default implementation here is suitable for OBDescriptor classes which return a double value. The stringstream is parsed to retrieve a comparison operator, one of > < >= <= = == != , and a numerical value. The function compares this the value returned by Predict() and returns the result. The stringstream is left after the number, and its state reflects whether any errors have occurred. If noEval is true, the parsing is as normal but Predict is not called and the function returns false.

Referenced by OBDescriptor::FilterCompare().

bool Display	(	std::string &	txt,
		const char *	param,
		const char *	ID = NULL
	)		[virtual, inherited]

Write information on a plugin class to the string txt. If the parameter is a descriptor ID, displays the verbose description for that descriptor only e.g. babel -L descriptors HBA1

Reimplemented from OBPlugin.

virtual bool Order	(	double	p1,
		double	p2
	)		[inline, virtual, inherited]

Comparison of the values of the descriptor. Used in sorting. Descriptors may use more complicated ordering than this default (e.g.InChIFilter)

virtual bool Order	(	std::string	s1,
		std::string	s2
	)		[inline, virtual, inherited]

bool FilterCompare	(	OBBase *	pOb,
		std::istream &	optionText,
		bool	noEval
	)		[static, inherited]

Interprets the --filter option string and returns the combined result of all the comparisons it contains.

The string has the form: PropertyID1 predicate1 [booleanOp] PropertyID2 predicate2 ... The propertyIDs are the ID of instances of a OBDescriptor class or the Attributes of OBPairData, and contain only letters, numbers and underscores. The predicates must start with a punctuation character and are interpreted by the Compare function of the OBDescriptor class. The default implementation expects a comparison operator and a number, e.g. >=1.3 Whitespace is optional and is ignored. Each predicate and this OBBase object (usually OBMol) is passed to the Compare function of a OBDescriptor. The result of each comparison is combined in a boolean expression (which can include parentheses) in the normal way. The AND operator can be & or &&, the OR operator can be | or ||, and a unitary NOT is ! The expected operator precedence is achieved using recursive calls of the function. If there is no boolean Op, all the tests have to return true for the function to return true, i.e. the default is AND. If the first operand of an AND is 0, or of an OR is 1, the parsing of the second operand continues but no comparisons are done since the result does not matter.

void AddProperties	(	OBBase *	pOb,
		const std::string &	DescrList
	)		[static, inherited]

Reads list of descriptor IDs and calls PredictAndSave() for each.

void DeleteProperties	(	OBBase *	pOb,
		const std::string &	DescrList
	)		[static, inherited]

Deletes all the OBPairDatas whose attribute names are in the list (if they exist).

string GetValues	(	OBBase *	pOb,
		const std::string &	DescrList
	)		[static, inherited]

Reads list of descriptor IDs and OBPairData names and returns a list of values, each precede by a space or the first character in the list if it is whitespace or punctuation.

pair< string, string > GetIdentifier

(

std::istream &

optionText )

[static, inherited]

Read an identifier and its parameter from the filter string.

double ParsePredicate	(	std::istream &	optionText,
		char &	ch1,
		char &	ch2,
		std::string &	svalue
	)		[static, protected, inherited]

Reads comparison operator and the following string. Return its value if possible else NaN.

bool ReadStringFromFilter	(	std::istream &	ss,
		std::string &	result
	)		[static, protected, inherited]

Reads a string from the filter string optionally preceded by = or !=.

Reads a string from the filter stream, optionally preceded by = or !=

Returns:

false if != operator found, and true otherwise.

On entry the stringstream position should be just after the ID. On exit it is after the string. If there is an error, the stringstream badbit is set. Returns false if != found, to indicate negation. Can be of any of the following forms: mystring =mystring ==mystring [must be terminated by a space or tab] "mystring" 'mystring' ="mystring" ='mystring' [mystring can contain spaces or tabs] !=mystring !="mystring" [Returns false indicating negate] There can be spaces or tabs after the operator = == !=

bool CompareStringWithFilter	(	std::istream &	optionText,
		std::string &	s,
		bool	noEval,
		bool	NoCompOK = false
	)		[static, protected, inherited]

Makes a comparison using the operator and a string read from the filter stream with a provided string.

Returns:

the result of the comparison and true if NoCompOK==true and there is no comparison operator.

static bool ispunctU

(

char

ch )

[inline, static, protected, inherited]

bool MatchPairData	(	OBBase *	pOb,
		std::string &	s
	)		[static, protected, inherited]

Returns:

true if s (with or without _ replaced by spaces) is a PairData attribute. On return s is the form which matches.

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

• groupcontrib.h