Subsections

8.16 OELibaryGen

class OELibraryGen

8.16.1 Constructors

OELibraryGen()

Default constructor.

OELibraryGen(const char *smirks, bool strictSmirks=true)

Initialize an OELibraryGen instance with a SMIRKS pattern. Success of initialization can be tested using the operator bool method. The second constructor argument is used to specify whether the SMIRKS string should be interpreted using strict SMIRKS semantics. Here strict means in full compliance with the SMIRKS language defined by its originator, Daylight CIS, Inc. If the default value of true is used, the SMIRKS string must have corresponding reaction mapped reactant and product atoms. Mapped product atoms that do not have corresponding mapped reactant atoms are considered invalid SMIRKS and will result in a failure to initialize the OELibraryGen instance. Strict SMIRKS also requires unmapped reactant atoms to be destroyed in the reaction. Passing a boolean value of false to the second method argument will relax both of the strict SMIRKS restrictions.

OELibraryGen(const OELibraryGen &rhs)

Copy constructor. Constructs a copy of the OELibraryGen instance given as the argument to the constructor.

8.16.2 AddStartingMaterial

unsigned int AddStartingMaterial(OESystem::OEIter<OEMolBase>&,
                                 unsigned int reacnum,
                                 bool umatch=true)
unsigned int AddStartingMaterial(OESystem::OEIterBase<OEMolBase>*,
                                 unsigned int reacnum,
                                 bool umatch=true)
unsigned int AddStartingMaterial(const OEMolBase &mol,
                                 unsigned int reacnum,
                                 bool umatch = true)

The AddStartingMaterial methods are used to initialize the starting materials corresponding to a reaction component (reactant). An iterator over molecules or a single molecule may be passed as the first argument to the overloaded methods. Subsequent calls to the AddStartingMaterial methods append to the list of starting materials set in prior calls. The second argument specifies the reactant to which the starting materials correspond. A copy of the staring material molecules are stored internally with the atom maps from the reactant pattern. This is done for efficiency, as each product molecule requires very little computational work to be done because of the starting material preprocessing. The final argument is used to control the pattern matching of the reactant pattern to the staring material. If the value passed is true, only matches that contain a unique set of atoms relative to previously identified matches are used. If the value is false, every possible match including those related by symmetry will be used. Reactant patterns are unique matched by default.

8.16.3 operator()

bool operator()(OEMolBase &mol) const

This method applies the set of transformations stored in the OELibraryGen instance to the molecule passed as the only argument to the method. The passed molecule must be composed of one reactant molecule per reactant specified in the reaction with which the OELibraryGen instance was initialized. The passed molecule should be constructed by taking molecules retrieved using the GetReactants method and concatenating them together using either the OEAddMols function or the OEMolBase::operator+= method. Although this interface may be useful, it is not intended to be the primary interface for molecule construction using the OELibraryGen method. The GetProducts method provides a more natural means for iterating or randomly accessing product molecules.

8.16.4 operator bool

operator bool() const

This method returns boolean true if the OELibraryGen instance has been initialized correctly. If the OELibraryGen instance has not been initialized properly this method will return boolean false.

8.16.5 ClearStartingMaterial

void ClearStartingMaterial(unsigned reacnum)

This methods removes any starting materials previously set by either the AddStartingMaterial and SetStartingMaterial methods corresponding to the reactant pattern number passed as the argument to the method.

8.16.6 GetExplicitHydrogens

bool GetExplicitHydrogens() const

This method returns current state of the variable that controls the behavior of the OELibraryGen instance with respect to handling hydrogens during application of reaction transforms. See SetExplicitHydrogens for a more complete explanation of possible hydrogen handling modes.

8.16.7 GetProducts

OESystem::OEIterBase<OEMolBase> *GetProducts() const

This method is the primary interface for generating a library of products from a reaction and a set of reactants. The pointer to an iterator base class over molecules must be assigned to an iterator over molecules. The following is an example assignment:

OEIter<OEMolBase> iter = libgen.GetProducts();

The returned iterator may be used to generate reaction products in sequence, or by random access using the OEIter<OEMolBase>::operator+= and OEIter<OEMolBase>::operator-= methods.

8.16.8 GetReactants

OESystem::OEIterBase<OEMolBase> *GetReactants(unsigned int rnum) const

The GetReactants method takes an integer corresponding to the reactant component number as specified in the reaction with which the OELibraryGen instance was initialized. Reactants are numbered starting from zero, and incremented by one when a reactant atom is found that is disconnected from the first component. For example, in a SMIRKS string the reactants are numbered starting from zero for the leftmost reactant, and increasing by one for every dot disconnection that isn't grouped with a previous part using parentheses.

8.16.9 GetTitleSeparator

bool GetTitleSeparator(const char *cptr) const

The GetTitleSeparator method retrieves the string used to separate molecule titles in product molecules generated by the OELibraryGen class. The titles of product molecules are created by concatenating reactant molecule titles with a delimiter or separator inserted between the reactant molecule titles. The default separator is the underscore character ``_''. The title separator string may be changed by calling the SetTitleSeparator method. The method always returns true.

8.16.10 GetValenceCorrection

bool GetValenceCorrection() const

The GetValenceCorrection method returns the current valence correction state of the parent OELibraryGen instance. See SetValenceCorrection for a description of possible valence correction modes.

8.16.11 Init

bool Init(const char *smirks, bool strictSmirks=true)

This method is used to initialize an OELibraryGen instance with a SMIRKS pattern passed as a pointer to a constant character string given as the first argument to the method. If the OELibraryGen instance is initialized successfully the method will return boolean true. If the SMIRKS string is invalid or initialization fails the method will return boolean false. The second argument to the method is used to specify whether the SMIRKS string should be interpreted using strict SMIRKS semantics. By default, the SMIRKS string is interpreted using strict semantics. Here strict means in full compliance with the SMIRKS language defined by its originator, Daylight CIS, Inc. SMIRKS requires that reactant atoms that are mapped must appear and have corresponding mapped atoms on the product side. In addition, unmapped reactant atoms are destroyed as part of the reaction. Passing a boolean value of false to the second method argument relaxes both of these restrictions. A mapped reactant atom that does not have a corresponding mapped product atom is valid, and will be destroyed as part of the reaction. Unmapped reactant atoms will be used to match the reactant pattern, but are not destroyed when the reaction is applied. The resulting SMIRKS like reactions may therefore be more easily readable by humans as fewer atoms may be required to be mapped.

bool Init(const OEQMolBase &qmol, bool strictSmirks=true)

This method initializes an OELibraryGen instance with a query molecule. If query molecule is created using the OEParseSmirks function, and if the reaction is desired to be interpreted using strict SMIRKS semantics (see Init(const char*, bool strictSmirks for explanation of strict SMIRKS) then the default value for the second argument to the method should be used. Passing a boolean value of false to the second argument will relax the restrictions imposed by strict SMIRKS semantics.

8.16.12 NumReactants

unsigned int NumReactants() const

The NumReactants method returns the number of separate reactants that the OELibraryGen instance perceived during initialization. The value returned will be equal to the number of graphically disconnected reactants that are not grouped together using the SMIRKS parts primitive.

8.16.13 SetExplicitHydrogens

bool SetExplicitHydrogens(bool)

This variable sets the hydrogen handling mode for the OELibraryGen instance. OELibraryGen instance are constructed by default with the explicit hydrogen mode set to true. Reactions may be executed using either implicit or explicit hydrogens represented in the starting materials for a reaction. If the value is true, the OELibraryGen instance will add explicit hydrogens to reactant molecules when they are initialized using either of the SetStartingMaterial methods. If the value is false, then both of the SetStartingMaterial methods will suppress any explict hydrogens in the reactant molecules, and simply retain the implicit hydrogen counts for remaining non-hydrogen atoms. The hydrogen handling mode must be assigned prior to calling SetStartingMaterial. Calling SetExplicitHydrogens after SetStartingMaterial will have not effect. Note that the explicit hydrogen setting in effect modifies the semantics of smirks. If the programmer wishes to implement strict SMIRKS according to the Daylight standard, in full, explicit hydrogens should be set on.

8.16.14 SetStartingMaterial

unsigned int SetStartingMaterial(OESystem::OEIter<OEMolBase> &moliter,
                                 unsigned int reacnum,
                                 bool umatch=true)
unsigned int SetStartingMaterial(OESystem::OEIterBase<OEMolBase> *moliter,
                                 unsigned int reacnum,
                                 bool umatch=true)
unsigned int SetStartingMaterial(const OEMolBase &mol,
                                 unsigned int reacnum,
                                 bool umatch = true)

The SetStartingMaterial methods are used to initialize the starting materials corresponding to a reaction component (reactant). An iterator over molecules or a single molecule may be passed as the first argument to the overloaded methods. Subsequent calls to the SetStartingMaterial methods discard starting materials set in prior calls. The second argument specifies the reactant to which the starting materials correspond. A copy of the staring material molecules are stored internally with the atom maps from the reactant pattern. This is done for efficiency, as each product molecule requires very little computational work to be done because of the starting material preprocessing. The final argument is used to control the pattern matching of the reactant pattern to the staring material. If the value passed is true, only matches that contain a unique set of atoms relative to previously identified matches are used. If the value is false, every possible match including those related by symmetry will be used. Reactant patterns are unique matched by default.

8.16.15 SetTitleSeparator

bool SetTitleSeparator(const char *cptr)

The SetTitleSeparator method is used to alter the separator or delimiter used by the OELibraryGen class to compose product molecule titles. Product molecule titles are created by concatenating reactant molecule titles separated by a title separator or delimiter. The default separator is the underscore character ``_''. This method allows the title separator to be modified. The method will store the new title separator passed to the method, and return true for any valid C style string. The method will return false if a null pointer is passed as the calling argument. The title separator must be set prior to calling GetProducts. Calling SetTitleSeparator after calling GetProducts will have no affect on the resultant product molecule titles.

8.16.16 SetValenceCorrection

bool SetValenceCorrection(bool)

The SetValenceCorrection method controls the valence correction mode setting of an OELibraryGen instance. OELibraryGen instances are constructed by default with the valence correction mode set to false. Valence correction mode can be turned on by passing a boolean true value to an OELibraryGen instance using this method. When valence correction mode is enabled, the OELibraryGen instance will attempt to adjust the hydrogen count on atoms in the product molecule that are involved in the reaction to match the original valence state of the reactant. For product atoms that do not undergo a nuclear reaction (atomic number is retained) the hydrogen count is either increased or decreased to match the initial valence state of the corresponding reactant atom. Formal charge is taken into account during the hydrogen count adjustment. Note that valence correction in effect modifies the semantics of smirks. Thus, if the programmer wishes to implement strict SMIRKS according to the Daylight standard, in full, valence correction should be set off.

				OEChem - API Manual

				OEChem - API Manual