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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 reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
#include <JMEReactionWriter.hpp>
Inheritance diagram for CDPL::Chem::JMEReactionWriter:Public Member Functions | |
| JMEReactionWriter (std::ostream &os) | |
Constructs a JMEReactionWriter instance that will write the reaction data to the output stream os. More... | |
| ~JMEReactionWriter () | |
| 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 native I/O format of the JME Molecular Editor [JME] java applet.
JMEReactionWriter implements the output of Chem::Reaction objects in the native I/O format used by the JME Molecular Editor applet. The output data are written by means of a std::ostream object that was provided to the JMEReactionWriter constructor.
Atom and bond attributes that get written for a component of the output reaction are defined by the following Chem::Atom, Chem::Bond and Chem::BondContainer properties:
| Chem::Atom Property | Description | Notes |
|---|---|---|
| Chem::AtomProperty::MATCH_CONSTRAINTS | Specifies atom matching constraints | Only written if the constraints have been explicitly assigned and can be expressed by corresponding JME constraints |
| Chem::AtomProperty::COORDINATES_2D | Specifies the 2D position of the atom | - |
| Chem::AtomProperty::TYPE | Specifies the type of the atom (see Chem::AtomType) | Only written if the atom is a query atom and the type is supported by the JME format. |
| Chem::AtomProperty::SYMBOL | Specifies the atom symbol (e.g. element symbol) | Only written if the atom is not a query atom |
| Chem::AtomProperty::FORMAL_CHARGE | Specifies the fromal charge of the atom | Only written if the atom is not a query atom and the specified charge is different from zero |
| Chem::AtomProperty::H_COUNT | Specifies the hydrogen count of the atom | Only written if the atom is a query atom and a corresponding matching constraint has been specified |
| Chem::AtomProperty::RING_FLAG | Tells whether the atom is a member of a ring | Only written if the atom is a query atom and a corresponding matching constraint has been specified |
| Chem::AtomProperty::AROMATICITY_FLAG | Tells whether the atom is a member of an aromatic ring | Only written if the atom is a query atom and a corresponding matching constraint has been specified |
| Chem::AtomProperty::REACTION_ATOM_MAPPING_ID | Specifies the reactant to product atom mapping class | Only written if the specified mapping number is greater than zero |
| Chem::Bond Property | Description | Notes |
|---|---|---|
| Chem::BondProperty::ORDER | Specifies the order of the bond | - |
| Chem::BondProperty::STEREO_FLAG | Specifies the 2D stereo bond type (see Chem::BondStereoFlag) | Either stereo bonds are not supported by the JME format and are written as plain single bonds |
| Chem::BondContainer Property | Description | Notes |
|---|---|---|
| Chem::BondContainerProperty::HEAVY_BOND_COUNT | Specifies the heavy bond count of the atoms | Only written if the atom is a query atom and a corresponding matching constraint has been specified |
Beside the editing of conventional chemical structures, the JME applet allows to some extent the specification of atom matching constraints for the definition of substructure search queries. If an atom of a component of the output reaction specifies any constraints by a Chem::MatchConstraintList data structure that has been assigned to the property Chem::AtomProperty::MATCH_CONSTRAINTS, an attempt is made to convert the contained Chem::MatchConstraint objects to equivalent JME query expression primitives.
Different types of constraints specified by Chem::MatchConstraint instances and the corresponding JME expression primitives are listed in the table below (<n> denotes a positive integer value and <S> the symbol of a chemical element; * the value is either provided by the Chem::MatchConstraint instance (see Chem::MatchConstraint::getValue()) or, if no value has been set, by the property specified in parentheses):
JMEReactionWriter can be configured with 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::COORDINATES_DIMENSION | 2 | Specifies the dimension of atom coordinates |
| Chem::ControlParameter::RECORD_SEPARATOR | "\n" | Specifies the data record separator |
| Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FIX | true | Specifies whether reverse stereo bonds shall be converted to regular stereo bonds by swapping bond start and end atoms |
| Chem::ControlParameter::JME_SEPARATE_COMPONENTS | true | Specifies whether the components of a molecule shall be written separately or combined as a single JME component |
| CDPL::Chem::JMEReactionWriter::JMEReactionWriter | ( | std::ostream & | os | ) |
Constructs a JMEReactionWriter instance that will write the reaction data to the output stream os.
| os | The output stream to write to. |
| CDPL::Chem::JMEReactionWriter::~JMEReactionWriter | ( | ) |
Destructor.
| Base::DataWriter<Reaction>& CDPL::Chem::JMEReactionWriter::write | ( | const Reaction & | rxn | ) |
Writes the reaction rxn to the output stream specified in the constructor.
| rxn | The reaction to write. |
| CDPL::Chem::JMEReactionWriter::operator const void * | ( | ) | const |
| bool CDPL::Chem::JMEReactionWriter::operator! | ( | ) | const |
1.8.20