OELibraryGen

class OELibraryGen

This class represents OELibraryGen that is designed to perform library generation.

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Constructors

OELibraryGen()

Default constructor.

OELibraryGen(const OELibraryGen &rhs)

Copy constructor.

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

Creates a OELibraryGen object with the given SMIRKS reaction. Success of initialization can be tested using the operator OELibraryGen::operator bool method.

Passing a value of false to the second method argument will relax the strict SMIRKS 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.

Atoms in the provided reaction must have unique mapping numbers, otherwise there is ambiguity as to the correspondence of reactant to product atoms. A duplicate mapping number warning message indicates that the SMIRKS must be corrected prior to use.

smirks

The string representing the reaction for library generation.

strictSmirks

The parameter that specifies the interpretation of the SMIRKS semantics.

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operator=

OELibraryGen &operator=(const OELibraryGen &rhs)

Assignment operator.

operator()

bool operator()(OEMolBase &) const

operator bool

operator bool() const

Returns true, if the OELibraryGen object was initialized with no failures using either the constructors or one of the OELibraryGen::Init methods.

The method will return false when the OELibraryGen object has not been properly initialized as it will be unable to apply transform operations to molecules.

AddStartingMaterial

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

Initializes the starting materials corresponding to a reaction component. An iterator over molecules or a single molecule may be passed as the first argument to the overloaded methods. Subsequent calls to the OELibraryGen::AddStartingMaterial methods append to the list of starting materials set in prior calls. The second argument (reacnum) specifies the reactant to which the starting materials correspond. The return value is the number of starting materials that were successfully added for the specified reaction component.

A copy of the starting 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 (umatch) is used to control the pattern matching of the reactant pattern to the starting 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.

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ClearStartingMaterial

void ClearStartingMaterial(unsigned reacnum)

Removes any starting materials previously set by either the OELibraryGen::AddStartingMaterial or the OELibraryGen::SetStartingMaterial methods corresponding to the reactant pattern number (‘reacnum’ ) passed as the argument to the method.

GetAssignMapIdx

bool GetAssignMapIdx() const

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GetClearCoordinates

bool GetClearCoordinates() const

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GetExplicitHydrogens

bool GetExplicitHydrogens() const

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GetProducts

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

Returns an iterator over all the products generated by the library generation.

GetRemoveUnmappedFragments

bool GetRemoveUnmappedFragments() const

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GetStartingMaterial

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

Returns an iterator over all the starting materials that have been successfully added to the OELibraryGen object.

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GetTitleSeparator

const std::string& GetTitleSeparator() const

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GetValenceCorrection

bool GetValenceCorrection() const

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GetValidateKekule

bool GetValidateKekule() const

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Init

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

The first method initializes an OELibraryGen object with the OEQMolBase object. The second method initializes an OELibraryGen object with the ‘smirks’ pattern. By default, the SMIRKS string is interpreted using strict semantics.

Passing a value of false to the second method argument will relax the strict SMIRKS 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.

NumReactants

unsigned int NumReactants() const

Returns the number of separate reactants that the OELibraryGen object 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.

NumPossibleProducts

unsigned int NumPossibleProducts() const

Returns the number of all possible products generated by the library generation. A warning message will be thrown if the number possible combinations exceeds the \(2^{32}\) limit.

SetAssignMapIdx

bool SetAssignMapIdx(bool)

Sets whether the atom mapping of the reaction is transferred to the product. The default setting is false i.e. no mapping will be transferred to the product.

Example of assigning map indices

reaction

product
../../_images/amide-map.svg ../../_images/amide-product-map.svg

SetClearCoordinates

bool SetClearCoordinates(bool clearcoords)

Sets whether the coordinates of a molecule are cleared when the molecule is added to the library generation by calling the OELibraryGen::AddStartingMaterial or OELibraryGen::SetStartingMaterial methods. The default setting is false i.e. the coordinates will be kept.

Note

The OELibraryGen modifies the molecular graph of the reactant(s) to generate products. Generating valid 2D or 3D coordinates for the products is beyond the scope of the OELibraryGen class.

It is recommended to either clear the coordinates by invoking the OELibraryGen::SetClearCoordinates method or regenerate the coordinates of the products afterwards.

SetExplicitHydrogens

bool SetExplicitHydrogens(bool explcitH)

Sets whether to add explicit hydrogens or suppress them when a starting material is added to the library. The default setting is true i.e. explicit hydrogens will be added.

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SetRemoveUnmappedFragments

bool SetRemoveUnmappedFragments(bool remove)

Sets whether unmapped components of the products are removed or kept prior to returning them by the OELibraryGen::GetProducts method. The default setting is false i.e. unmapped components will be kept.

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SetStartingMaterial

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

Initializes the starting materials corresponding to a reaction component. An iterator over molecules or a single molecule may be passed as the first argument to the overloaded methods. Subsequent calls to the OELibraryGen::SetStartingMaterial methods discard the list of starting materials set in prior calls. The second argument (‘reacnum’) specifies the reactant to which the starting materials correspond.

A copy of the starting 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 (‘umatch’) is used to control the pattern matching of the reactant pattern to the starting 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.

See also

SetTitleSeparator

bool SetTitleSeparator(const char *c)

Sets the separator or delimiter used by the OELibraryGen object 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 _.

Note

The title separator must be set prior to calling OELibraryGen::GetProducts. Calling OELibraryGen::SetTitleSeparator after calling OELibraryGen::GetProducts will have no affect on the resultant product molecule titles.

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SetValenceCorrection

bool SetValenceCorrection(bool)

Sets whether valence correction is applied to the products prior to returning them by the OELibraryGen::GetProducts method. The default setting is false i.e. no valence correction will be performed.

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SetValidateKekule

bool SetValidateKekule(bool validate)

Sets whether the generated products are simply returned after a Kekulization attempt, or if the Kekulé form is validated more rigorously. If the extra validation is enabled and an invalid Kekulé form is identified, alternatives are tried by adding and removing implicit hydrogens from aromatic nitrogens to produce a valid Kekulé form. No further attempt is made to return the most reasonable or chemically sensible result. By default, the extra Kekulé validation is enabled. The default setting is true i.e. Kekulé form validation will be performed.

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