Chemical Data Processing Library C++ API - Version 1.1.1
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A writer for reaction data in the Daylight SMILES [SMILES] format. More...
#include <SMILESReactionWriter.hpp>
Public Member Functions | |
SMILESReactionWriter (std::ostream &os) | |
Constructs a SMILESReactionWriter instance that will write the reaction data to the output stream os. More... | |
~SMILESReactionWriter () | |
Destructor. More... | |
Base::DataWriter< Reaction > & | write (const Reaction &rxn) |
Writes the reaction rxn to the output stream specified in the constructor. More... | |
operator const void * () const | |
bool | operator! () const |
Public Member Functions inherited from CDPL::Base::DataWriter< Reaction > | |
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< Reaction > | |
typedef std::shared_ptr< DataWriter > | SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated DataWriter instances. More... | |
typedef Reaction | 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< Reaction > | |
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 reaction data in the Daylight SMILES [SMILES] format.
SMILESReactionWriter
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_RXN_WRITE_ATOM_MAPPING_ID | true | 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::SMILESReactionWriter::SMILESReactionWriter | ( | std::ostream & | os | ) |
Constructs a SMILESReactionWriter
instance that will write the reaction data to the output stream os.
os | The output stream to write to. |
CDPL::Chem::SMILESReactionWriter::~SMILESReactionWriter | ( | ) |
Destructor.
Base::DataWriter<Reaction>& CDPL::Chem::SMILESReactionWriter::write | ( | const Reaction & | rxn | ) |
Writes the reaction rxn to the output stream specified in the constructor.
rxn | The reaction to write. |
CDPL::Chem::SMILESReactionWriter::operator const void * | ( | ) | const |
bool CDPL::Chem::SMILESReactionWriter::operator! | ( | ) | const |