Chemical Data Processing Library C++ API - Version 1.1.1
Public Member Functions | Friends | List of all members
CDPL::Chem::MOLMoleculeReader Class Reference

A reader for molecule data in the MDL Mol-File [CTFILE] format. More...

#include <MOLMoleculeReader.hpp>

+ Inheritance diagram for CDPL::Chem::MOLMoleculeReader:

Public Member Functions

 MOLMoleculeReader (std::istream &is)
 Constructs a MOLMoleculeReader instance that will read the molecule data from the input stream is. More...
 
 ~MOLMoleculeReader ()
 Destructor. More...
 
- Public Member Functions inherited from CDPL::Util::StreamDataReader< Molecule, MOLMoleculeReader >
Base::DataReader< Molecule > & read (Molecule &obj, bool overwrite=true)
 Reads the data record at the current record index and stores the read data in obj. More...
 
Base::DataReader< Molecule > & read (std::size_t idx, Molecule &obj, bool overwrite=true)
 Reads the data record at index idx and stores the read data in obj. More...
 
Base::DataReader< Molecule > & skip ()
 Skips the data record at the current record index. More...
 
bool hasMoreData ()
 Tells if there are any data records left to read. More...
 
std::size_t getRecordIndex () const
 
void setRecordIndex (std::size_t idx)
 Sets the index of the current data record to idx. More...
 
std::size_t getNumRecords ()
 Returns the total number of available data records. More...
 
 operator const void * () const
 
bool operator! () const
 
- Public Member Functions inherited from CDPL::Base::DataReader< Molecule >
virtual DataReaderread (DataType &obj, bool overwrite=true)=0
 Reads the data record at the current record index and stores the read data in obj. More...
 
virtual DataReaderread (std::size_t idx, DataType &obj, bool overwrite=true)=0
 Reads the data record at index idx and stores the read data in obj. More...
 
virtual void close ()
 Performs a reader specific shutdown operation (if required). 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 AnygetParameter (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 ControlParameterContainergetParent () 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 ControlParameterContainergetParameters () const
 Returns a const reference to itself. More...
 

Friends

class Util::StreamDataReader< Molecule, MOLMoleculeReader >
 

Additional Inherited Members

- Public Types inherited from CDPL::Base::DataReader< Molecule >
typedef Molecule DataType
 The type of the read data objects. More...
 
typedef std::shared_ptr< DataReaderSharedPointer
 A reference-counted smart pointer [SHPTR] for dynamically allocated DataReader instances. 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::Util::StreamDataReader< Molecule, MOLMoleculeReader >
 StreamDataReader (std::istream &is)
 Constructs a StreamDataReader instance that will read from the input stream is. More...
 
- Protected Member Functions inherited from CDPL::Base::DataReader< Molecule >
DataReaderoperator= (const DataReader &reader)
 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...
 
DataIOBaseoperator= (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...
 
ControlParameterContaineroperator= (const ControlParameterContainer &cntnr)
 Assignment operator. More...
 

Detailed Description

A reader for molecule data in the MDL Mol-File [CTFILE] format.

MOLMoleculeReader 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 read operation to fail
Chem::ControlParameter::MULTI_CONF_IMPORT true Specifies whether to check for and import multi-conformer molecules
Chem::ControlParameter::MULTI_CONF_INPUT_PROCESSOR pointer to a Chem::DefaultMultiConfMoleculeInputProcessor instance Specifies an instance of Chem::MultiConfMoleculeInputProcessor that implements the logic of multi-conformer molecule detection and conformational data processing
Chem::ControlParameter::MDL_IGNORE_PARITY false Specifies whether the stereo parity of atoms shall be ignored
Chem::ControlParameter::MDL_TRIM_STRINGS true Specifies whether to remove leading and trailing whitespace from string values
Chem::ControlParameter::MDL_TRIM_LINES false Specifies whether to remove leading and trailing whitespace from data lines
Chem::ControlParameter::MDL_IGNORE_LINE_LENGTH_LIMIT true Specifies whether to check if data lines exceed the maximum allowed line length

Constructor & Destructor Documentation

◆ MOLMoleculeReader()

CDPL::Chem::MOLMoleculeReader::MOLMoleculeReader ( std::istream &  is)

Constructs a MOLMoleculeReader instance that will read the molecule data from the input stream is.

Parameters
isThe input stream to read from.

◆ ~MOLMoleculeReader()

CDPL::Chem::MOLMoleculeReader::~MOLMoleculeReader ( )

Destructor.

Friends And Related Function Documentation

◆ Util::StreamDataReader< Molecule, MOLMoleculeReader >


The documentation for this class was generated from the following file: