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Chemical Data Processing Library C++ API - Version 1.1.1
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Chemical Data Processing Library C++ API - Version 1.1.1
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A writer for molecular graph data in the Daylight SMILES [SMILES] format. More...
#include <SMILESMolecularGraphWriter.hpp>
Inheritance diagram for CDPL::Chem::SMILESMolecularGraphWriter:Public Member Functions | |
| SMILESMolecularGraphWriter (std::ostream &os) | |
Constructs a SMILESMolecularGraphWriter instance that will write data of molecular graphs to the output stream os. More... | |
| ~SMILESMolecularGraphWriter () | |
| Destructor. More... | |
| Base::DataWriter< MolecularGraph > & | write (const MolecularGraph &molgraph) |
| Writes data of the molecular graph molgraph to the output stream specified in the constructor. More... | |
| operator const void * () const | |
| bool | operator! () const |
| Public Member Functions inherited from CDPL::Base::DataWriter< MolecularGraph > | |
| virtual DataWriter & | write (const DataType &obj)=0 |
| Writes the data object obj. More... | |
| virtual void | close () |
| Writes format dependent data (if required) to mark the end of output. More... | |
| virtual | operator const void * () const=0 |
| Returns a pointer whose value indicates the error state of the writer. More... | |
| virtual bool | operator! () const=0 |
| Tells whether the writer is in a bad state. More... | |
| Public Member Functions inherited from CDPL::Base::DataIOBase | |
| std::size_t | registerIOCallback (const IOCallbackFunction &func) |
| Registers an I/O callback target function. More... | |
| void | unregisterIOCallback (std::size_t id) |
| Unregisters the I/O callback function specified by id. More... | |
| void | invokeIOCallbacks (double progress) const |
Invokes all registered I/O callback functions with the argument *this. More... | |
| void | clearIOCallbacks () |
| Clears all registered I/O callback functions. More... | |
| Public Member Functions inherited from CDPL::Base::ControlParameterContainer | |
| std::size_t | getNumParameters () const |
| Returns the number of container entries. More... | |
| template<typename T > | |
| void | setParameter (const LookupKey &key, T &&val) |
| Sets the value of the control-parameter specified by key to val. More... | |
| const Any & | getParameter (const LookupKey &key, bool throw_=false, bool local=false) const |
| Returns the value of the control-parameter specified by key. More... | |
| template<typename T > | |
| const T & | getParameter (const LookupKey &key, bool local=false) const |
Returns the value of the control-parameter specified by key as a const reference to an object of type T. More... | |
| template<typename T > | |
| const T & | getParameterOrDefault (const LookupKey &key, const T &def_val, bool local=false) const |
Returns the value of the control-parameter specified by key as a const reference to an object of type T, or the default value def_val if a stored value does not exist. More... | |
| bool | removeParameter (const LookupKey &key) |
| Removes the entry for the control-parameter specified by key. More... | |
| void | clearParameters () |
| Erases all container entries. More... | |
| bool | isParameterSet (const LookupKey &key, bool local=false) const |
| Tells whether or not a value has been assigned to the control-parameter specified by key. More... | |
| void | addParameters (const ControlParameterContainer &cntnr) |
Adds the control-parameter value entries in the ControlParameterContainer instance cntnr. More... | |
| void | copyParameters (const ControlParameterContainer &cntnr) |
| Replaces the current set of properties by a copy of the entries in cntnr. More... | |
| ConstParameterIterator | getParametersBegin () const |
| Returns a constant iterator pointing to the beginning of the entries. More... | |
| ConstParameterIterator | getParametersEnd () const |
| Returns a constant iterator pointing to the end of the entries. More... | |
| ConstParameterIterator | begin () const |
| Returns a constant iterator pointing to the beginning of the entries. More... | |
| ConstParameterIterator | end () const |
| Returns a constant iterator pointing to the end of the entries. More... | |
| void | setParent (const ControlParameterContainer *cntnr) |
| Sets or removes the parent control-parameter container used to resolve requests for missing entries. More... | |
| const ControlParameterContainer * | getParent () const |
| Returns a pointer to the parent control-parameter container. More... | |
| std::size_t | registerParameterChangedCallback (const ParameterChangedCallbackFunction &func) |
| Registers a callback target function that gets invoked when the value of a control-parameter has changed. More... | |
| void | unregisterParameterChangedCallback (std::size_t id) |
| Unregisters the callback specified by id. More... | |
| std::size_t | registerParameterRemovedCallback (const ParameterRemovedCallbackFunction &func) |
| Registers a callback target function that gets invoked when a control-parameter entry has been removed. More... | |
| void | unregisterParameterRemovedCallback (std::size_t id) |
| Unregisters the callback specified by id. More... | |
| std::size_t | registerParentChangedCallback (const ParentChangedCallbackFunction &func) |
| Registers a callback target function that gets invoked when the parent container has been changed or was detached. More... | |
| void | unregisterParentChangedCallback (std::size_t id) |
| Unregisters the callback specified by id. More... | |
| const ControlParameterContainer & | getParameters () const |
Returns a const reference to itself. More... | |
Additional Inherited Members | |
| Public Types inherited from CDPL::Base::DataWriter< MolecularGraph > | |
| typedef std::shared_ptr< DataWriter > | SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated DataWriter instances. More... | |
| typedef MolecularGraph | DataType |
| The type of the written data objects. More... | |
| Public Types inherited from CDPL::Base::DataIOBase | |
| typedef std::function< void(const DataIOBase &, double)> | IOCallbackFunction |
| A functor class used to wrap I/O callback target functions. More... | |
| Public Types inherited from CDPL::Base::ControlParameterContainer | |
| typedef ParameterMap::value_type | ParameterEntry |
| A Base::LookupKey / Base::Any pair used to store the control-parameter values and associated keys. More... | |
| typedef ParameterMap::const_iterator | ConstParameterIterator |
| A constant iterator used to iterate over the control-parameter entries. More... | |
| typedef std::function< void(const LookupKey &, const Any &)> | ParameterChangedCallbackFunction |
| A functor class that wraps callback target functions which get invoked when the value of a control-parameter has changed. More... | |
| typedef std::function< void(const LookupKey &)> | ParameterRemovedCallbackFunction |
| A functor class that wraps callback target functions which get invoked when a control-parameter entry has been removed. More... | |
| typedef std::function< void()> | ParentChangedCallbackFunction |
| A functor class that wraps callback target functions which get invoked when the parent container has been changed or was detached. More... | |
| Protected Member Functions inherited from CDPL::Base::DataWriter< MolecularGraph > | |
| DataWriter & | operator= (const DataWriter &writer) |
| Assignment operator. More... | |
| Protected Member Functions inherited from CDPL::Base::DataIOBase | |
| DataIOBase () | |
| Default constructor. More... | |
| DataIOBase (const DataIOBase &io_base) | |
| Copy constructor. More... | |
| ~DataIOBase () | |
| Destructor. More... | |
| DataIOBase & | operator= (const DataIOBase &io_base) |
| Assignment operator. More... | |
| Protected Member Functions inherited from CDPL::Base::ControlParameterContainer | |
| ControlParameterContainer () | |
Constructs an empty ControlParameterContainer instance. More... | |
| ControlParameterContainer (const ControlParameterContainer &cntnr) | |
Constructs a copy of the ControlParameterContainer instance cntnr. More... | |
| virtual | ~ControlParameterContainer () |
| Destructor. More... | |
| ControlParameterContainer & | operator= (const ControlParameterContainer &cntnr) |
| Assignment operator. More... | |
A writer for molecular graph data in the Daylight SMILES [SMILES] format.
SMILESMolecularGraphWriter supports the following control-parameters:
| Control-Parameter | Default Value (see Chem::ControlParameterDefault) | Description |
|---|---|---|
| Chem::ControlParameter::STRICT_ERROR_CHECKING | false | Specifies whether non-fatal recoverable errors should be ignored or cause a write operation to fail |
| Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE | true | Specifies whether or not to write explicit ordinary hydrogen atoms |
| Chem::ControlParameter::SMILES_RECORD_FORMAT | "S" | Specifies the data record format |
| Chem::ControlParameter::SMILES_WRITE_CANONICAL_FORM | false | Specifies whether to generate canonical SMILES strings |
| Chem::ControlParameter::SMILES_WRITE_KEKULE_FORM | false | Specifies whether to output aromatic rings as Kekulé structures |
| Chem::ControlParameter::SMILES_WRITE_ATOM_STEREO | true | Specifies whether to output the chirality of tetrahedral stereogenic atoms |
| Chem::ControlParameter::SMILES_WRITE_BOND_STEREO | true | Specifies whether to output directional bonds for the specification of chain double bond geometries |
| Chem::ControlParameter::SMILES_WRITE_RING_BOND_STEREO | true | Specifies whether to output directional bonds for the specification of ring double bond geometries |
| Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE | 8 | Specifies the minimum ring size that is required for the specification of ring double bond geometries |
| Chem::ControlParameter::SMILES_WRITE_ISOTOPE | true | Specifies whether to output the mass of isotopes |
| Chem::ControlParameter::SMILES_MOL_WRITE_ATOM_MAPPING_ID | false | Specifies whether to output reaction atom-atom mapping numbers |
| Chem::ControlParameter::SMILES_WRITE_SINGLE_BONDS | false | Specifies whether to output single bonds |
| Chem::ControlParameter::SMILES_WRITE_AROMATIC_BONDS | false | Specifies whether to output aromatic bonds |
| Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET | false | Specifies whether ordinary C, N, O, S, P, F, Cl, Br and I atoms shall be enclosed in brackets |
| CDPL::Chem::SMILESMolecularGraphWriter::SMILESMolecularGraphWriter | ( | std::ostream & | os | ) |
Constructs a SMILESMolecularGraphWriter instance that will write data of molecular graphs to the output stream os.
| os | The output stream to write to. |
| CDPL::Chem::SMILESMolecularGraphWriter::~SMILESMolecularGraphWriter | ( | ) |
Destructor.
| Base::DataWriter<MolecularGraph>& CDPL::Chem::SMILESMolecularGraphWriter::write | ( | const MolecularGraph & | molgraph | ) |
Writes data of the molecular graph molgraph to the output stream specified in the constructor.
| molgraph | The molecular graph to write. |
| CDPL::Chem::SMILESMolecularGraphWriter::operator const void * | ( | ) | const |
| bool CDPL::Chem::SMILESMolecularGraphWriter::operator! | ( | ) | const |
1.8.20