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Chemical Data Processing Library C++ API - Version 1.4.0
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Chemical Data Processing Library C++ API - Version 1.4.0
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Chem::FragmentGenerator preconfigured with the 16 BRICS bond-cleavage rules and the associated exclude patterns for combinatorial fragmentation of organic molecules. More...
#include <BRICSFragmentGenerator.hpp>
Inheritance diagram for CDPL::Chem::BRICSFragmentGenerator:Public Types | |
| typedef std::shared_ptr< BRICSFragmentGenerator > | SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated BRICSFragmentGenerator instances. More... | |
| Public Types inherited from CDPL::Chem::FragmentGenerator | |
| typedef std::shared_ptr< FragmentGenerator > | SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated FragmentGenerator instances. More... | |
| typedef std::function< bool(const MolecularGraph &)> | FragmentFilterFunction |
| Type of a predicate accepting/rejecting a generated fragment. More... | |
| typedef FragmentationRuleList::const_iterator | ConstFragmentationRuleIterator |
| A constant iterator over the registered fragmentation rules. More... | |
| typedef FragmentationRuleList::iterator | FragmentationRuleIterator |
| A mutable iterator over the registered fragmentation rules. More... | |
| typedef ExcludePatternList::const_iterator | ConstExcludePatternIterator |
| A constant iterator over the registered exclude patterns. More... | |
| typedef ExcludePatternList::iterator | ExcludePatternIterator |
| A mutable iterator over the registered exclude patterns. More... | |
| typedef FragmentLinkList::const_iterator | ConstFragmentLinkIterator |
| A constant iterator over the generated fragment links. More... | |
Public Member Functions | |
| BRICSFragmentGenerator () | |
Constructs the BRICSFragmentGenerator instance with the full BRICS rule and exclude-pattern set registered. More... | |
| Public Member Functions inherited from CDPL::Chem::FragmentGenerator | |
| FragmentGenerator () | |
Constructs the FragmentGenerator instance. More... | |
| FragmentGenerator (const FragmentGenerator &gen) | |
Constructs a copy of the FragmentGenerator instance gen. More... | |
| virtual | ~FragmentGenerator () |
| Virtual destructor. More... | |
| FragmentGenerator & | operator= (const FragmentGenerator &gen) |
| Replaces the state of this generator by a copy of the state of gen. More... | |
| void | addFragmentationRule (const MolecularGraph::SharedPointer &match_ptn, unsigned int rule_id) |
| Registers a new fragmentation rule by its SMARTS match pattern and rule ID. More... | |
| void | addFragmentationRule (const FragmentationRule &rule) |
| Appends a copy of the pre-built fragmentation rule rule. More... | |
| const FragmentationRule & | getFragmentationRule (std::size_t idx) const |
| Returns the fragmentation rule at index idx. More... | |
| FragmentationRule & | getFragmentationRule (std::size_t idx) |
| Returns the fragmentation rule at index idx. More... | |
| ConstFragmentationRuleIterator | getFragmentationRulesBegin () const |
| Returns a constant iterator pointing to the first registered fragmentation rule. More... | |
| ConstFragmentationRuleIterator | getFragmentationRulesEnd () const |
| Returns a constant iterator pointing one past the last registered fragmentation rule. More... | |
| FragmentationRuleIterator | getFragmentationRulesBegin () |
| Returns a mutable iterator pointing to the first registered fragmentation rule. More... | |
| FragmentationRuleIterator | getFragmentationRulesEnd () |
| Returns a mutable iterator pointing one past the last registered fragmentation rule. More... | |
| void | removeFragmentationRule (std::size_t idx) |
| Removes the fragmentation rule at index idx. More... | |
| std::size_t | getNumFragmentationRules () const |
| Returns the number of registered fragmentation rules. More... | |
| void | clearFragmentationRules () |
| Removes all registered fragmentation rules. More... | |
| void | addExcludePattern (const MolecularGraph::SharedPointer &match_ptn, unsigned int rule_id) |
| Registers a rule-specific exclude pattern. More... | |
| void | addExcludePattern (const MolecularGraph::SharedPointer &match_ptn) |
| Registers a generic exclude pattern (applies to all fragmentation rules). More... | |
| void | addExcludePattern (const ExcludePattern &excl_ptn) |
| Appends a copy of the pre-built exclude pattern excl_ptn. More... | |
| const ExcludePattern & | getExcludePattern (std::size_t idx) const |
| Returns the exclude pattern at index idx. More... | |
| ExcludePattern & | getExcludePattern (std::size_t idx) |
| Returns the exclude pattern at index idx. More... | |
| ConstExcludePatternIterator | getExcludePatternsBegin () const |
| Returns a constant iterator pointing to the first registered exclude pattern. More... | |
| ConstExcludePatternIterator | getExcludePatternsEnd () const |
| Returns a constant iterator pointing one past the last registered exclude pattern. More... | |
| ExcludePatternIterator | getExcludePatternsBegin () |
| Returns a mutable iterator pointing to the first registered exclude pattern. More... | |
| ExcludePatternIterator | getExcludePatternsEnd () |
| Returns a mutable iterator pointing one past the last registered exclude pattern. More... | |
| void | removeExcludePattern (std::size_t idx) |
| Removes the exclude pattern at index idx. More... | |
| std::size_t | getNumExcludePatterns () const |
| Returns the number of registered exclude patterns. More... | |
| void | clearExcludePatterns () |
| Removes all registered exclude patterns. More... | |
| bool | splitBondsIncluded () const |
| Tells whether the split (cleaved) bonds are retained in the output fragments. More... | |
| void | includeSplitBonds (bool include) |
| Specifies whether the split (cleaved) bonds shall be retained in the output fragments. More... | |
| const FragmentFilterFunction & | getFragmentFilterFunction () const |
| Returns the predicate used to filter the generated fragments. More... | |
| void | setFragmentFilterFunction (const FragmentFilterFunction &func) |
Sets the predicate used to filter the generated fragments (fragments for which the predicate returns false are discarded). More... | |
| void | generate (const MolecularGraph &molgraph, FragmentList &frag_list, bool append=false) |
| Performs the fragmentation of molgraph and writes the resulting fragments to frag_list. More... | |
| std::size_t | getNumFragmentLinks () const |
| Returns the number of fragment links produced by the most recent generate() call. More... | |
| const FragmentLink & | getFragmentLink (std::size_t idx) const |
| Returns the fragment link at index idx. More... | |
| ConstFragmentLinkIterator | getFragmentLinksBegin () const |
| Returns a constant iterator pointing to the first fragment link. More... | |
| ConstFragmentLinkIterator | getFragmentLinksEnd () const |
| Returns a constant iterator pointing one past the last fragment link. More... | |
Chem::FragmentGenerator preconfigured with the 16 BRICS bond-cleavage rules and the associated exclude patterns for combinatorial fragmentation of organic molecules.
The rule and exclude-pattern set follows the original Breaking of Retrosynthetically Interesting Chemical Substructures publication. Each rule has the corresponding Chem::BRICSRuleID value.
| typedef std::shared_ptr<BRICSFragmentGenerator> CDPL::Chem::BRICSFragmentGenerator::SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated BRICSFragmentGenerator instances.
| CDPL::Chem::BRICSFragmentGenerator::BRICSFragmentGenerator | ( | ) |
Constructs the BRICSFragmentGenerator instance with the full BRICS rule and exclude-pattern set registered.
1.9.1