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

A reader for molecule data in the PSD-format of the CDPL. More...

#include <PSDMoleculeReader.hpp>

+ Inheritance diagram for CDPL::Pharm::PSDMoleculeReader:

Public Member Functions

 PSDMoleculeReader (std::istream &is)
 Constructs a PSDMoleculeReader instance that will read the molecule data from the input stream is. More...
 
 PSDMoleculeReader (const std::string &file_name)
 Constructs a PSDMoleculeReader instance that will read the molecule data from the input file file_name. More...
 
 ~PSDMoleculeReader ()
 
PSDMoleculeReaderread (Chem::Molecule &mol, bool overwrite=true)
 Reads the data record at the current record index and stores the read data in obj. More...
 
PSDMoleculeReaderread (std::size_t idx, Chem::Molecule &mol, bool overwrite=true)
 Reads the data record at index idx and stores the read data in obj. More...
 
PSDMoleculeReaderskip ()
 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< Chem::Molecule >
virtual std::size_t getRecordIndex () const=0
 Returns the index of the current data record. More...
 
virtual operator const void * () const=0
 Returns a pointer whose value indicates the error state of the reader. More...
 
virtual bool operator! () const=0
 Tells whether the reader is in a bad state. 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...
 

Additional Inherited Members

- Public Types inherited from CDPL::Base::DataReader< Chem::Molecule >
typedef Chem::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::Base::DataReader< Chem::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 PSD-format of the CDPL.

Constructor & Destructor Documentation

◆ PSDMoleculeReader() [1/2]

CDPL::Pharm::PSDMoleculeReader::PSDMoleculeReader ( std::istream &  is)

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

Parameters
isThe input stream to read from.

◆ PSDMoleculeReader() [2/2]

CDPL::Pharm::PSDMoleculeReader::PSDMoleculeReader ( const std::string &  file_name)

Constructs a PSDMoleculeReader instance that will read the molecule data from the input file file_name.

Parameters
file_nameThe input file to read from.

◆ ~PSDMoleculeReader()

CDPL::Pharm::PSDMoleculeReader::~PSDMoleculeReader ( )

Member Function Documentation

◆ read() [1/2]

PSDMoleculeReader& CDPL::Pharm::PSDMoleculeReader::read ( Chem::Molecule obj,
bool  overwrite = true 
)
virtual

Reads the data record at the current record index and stores the read data in obj.

If the read operation was successful, the record index is incremented by 1.

Parameters
objThe object storing the read data.
overwriteSpecifies whether any existing data in obj shall be replaced by the newly read data or if the read data should be appended (if supported by the reader and data type).
Returns
A reference to itself.
Exceptions
Base::IOErrorif an I/O error occurred.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ read() [2/2]

PSDMoleculeReader& CDPL::Pharm::PSDMoleculeReader::read ( std::size_t  idx,
Chem::Molecule obj,
bool  overwrite = true 
)
virtual

Reads the data record at index idx and stores the read data in obj.

If the read operation was successful, the record index is set to idx + 1.

Parameters
idxThe zero-based index of the data record to read.
objThe object storing the read data.
overwriteSpecifies whether any existing data in obj shall be replaced by the newly read data or if the read data should be appended (if supported by the reader and data type).
Returns
A reference to itself.
Exceptions
Base::IndexErrorif idx is greater or equal to the number of records. Base::IOError if an I/O error occurred.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ skip()

PSDMoleculeReader& CDPL::Pharm::PSDMoleculeReader::skip ( )
virtual

Skips the data record at the current record index.

If the operation was successful, the record index is incremented by 1.

Returns
A reference to itself.
Exceptions
Base::IOErrorif an I/O error occurred.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ hasMoreData()

bool CDPL::Pharm::PSDMoleculeReader::hasMoreData ( )
virtual

Tells if there are any data records left to read.

Returns
true if there are data records left to read, and false otherwise.
Exceptions
Base::IOErrorif an I/O error occurred.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ getRecordIndex()

std::size_t CDPL::Pharm::PSDMoleculeReader::getRecordIndex ( ) const

◆ setRecordIndex()

void CDPL::Pharm::PSDMoleculeReader::setRecordIndex ( std::size_t  idx)
virtual

Sets the index of the current data record to idx.

Parameters
idxThe zero-based index of the data record.
Exceptions
Base::IndexErrorif idx is greater or equal to the number of available data records. Base::IOError if an I/O error occurred.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ getNumRecords()

std::size_t CDPL::Pharm::PSDMoleculeReader::getNumRecords ( )
virtual

Returns the total number of available data records.

Returns
The total number of available data records.
Exceptions
Base::IOErrorif an I/O error occurred.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ operator const void *()

CDPL::Pharm::PSDMoleculeReader::operator const void * ( ) const

◆ operator!()

bool CDPL::Pharm::PSDMoleculeReader::operator! ( ) const

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