Chemical Data Processing Library C++ API - Version 1.1.1
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#include <BasicPharmacophore.hpp>
Public Types | |
typedef std::shared_ptr< BasicPharmacophore > | SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated BasicPharmacophore instances. More... | |
typedef boost::indirect_iterator< FeatureList::iterator, BasicFeature > | FeatureIterator |
typedef boost::indirect_iterator< FeatureList::const_iterator, const BasicFeature > | ConstFeatureIterator |
Public Types inherited from CDPL::Pharm::Pharmacophore | |
typedef std::shared_ptr< Pharmacophore > | SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated Pharmacophore instances. More... | |
typedef FeatureContainer::ConstFeatureIterator | ConstFeatureIterator |
A constant random access iterator used to iterate over the stored const Pharm::Feature objects. More... | |
typedef FeatureContainer::FeatureIterator | FeatureIterator |
A mutable random access iterator used to iterate over the stored Pharm::Feature objects. More... | |
Public Types inherited from CDPL::Pharm::FeatureContainer | |
typedef std::shared_ptr< FeatureContainer > | SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated FeatureContainer instances. More... | |
typedef Util::IndexedElementIterator< const Feature, ConstFeatureAccessor > | ConstFeatureIterator |
A constant random access iterator used to iterate over the stored const Pharm::Feature objects. More... | |
typedef Util::IndexedElementIterator< Feature, FeatureAccessor > | FeatureIterator |
A mutable random access iterator used to iterate over the stored Pharm::Feature objects. More... | |
Public Types inherited from CDPL::Chem::Entity3DContainer | |
typedef Util::IndexedElementIterator< const Entity3D, ConstEntityAccessor > | ConstEntityIterator |
A constant random access iterator used to iterate over the stored const Chem::Entity3D objects. More... | |
typedef Util::IndexedElementIterator< Entity3D, EntityAccessor > | EntityIterator |
A mutable random access iterator used to iterate over the stored Chem::Entity3D objects. More... | |
Public Types inherited from CDPL::Base::PropertyContainer | |
typedef PropertyMap::value_type | PropertyEntry |
A Base::LookupKey / Base::Any pair that stores the property value for a given property key. More... | |
typedef PropertyMap::const_iterator | ConstPropertyIterator |
A constant iterator used to iterate over the property entries. More... | |
Public Member Functions | |
BasicPharmacophore () | |
Constructs an empty BasicPharmacophore instance. More... | |
BasicPharmacophore (const BasicPharmacophore &pharm) | |
Constructs a copy of the BasicPharmacophore instance pharm. More... | |
BasicPharmacophore (const Pharmacophore &pharm) | |
Constructs a copy of the Pharm::Pharmacophore instance pharm. More... | |
BasicPharmacophore (const FeatureContainer &cntnr) | |
Constructs a BasicPharmacophore instance with copies of the features in the Pharm::FeatureContainer instance cntnr. More... | |
~BasicPharmacophore () | |
Destructor. More... | |
void | clear () |
Removes all features and clears all properties of the pharmacophore. More... | |
std::size_t | getNumFeatures () const |
Returns the number of pharmacophore features. More... | |
ConstFeatureIterator | getFeaturesBegin () const |
Returns a constant iterator pointing to the beginning of the features. More... | |
FeatureIterator | getFeaturesBegin () |
Returns a mutable iterator pointing to the beginning of the features. More... | |
ConstFeatureIterator | getFeaturesEnd () const |
Returns a constant iterator pointing to the end of the features. More... | |
FeatureIterator | getFeaturesEnd () |
Returns a mutable iterator pointing to the end of the features. More... | |
const BasicFeature & | getFeature (std::size_t idx) const |
Returns a const reference to the pharmacophore feature at index idx. More... | |
BasicFeature & | getFeature (std::size_t idx) |
Returns a non-const reference to the pharmacophore feature at index idx. More... | |
BasicFeature & | addFeature () |
Creates a new pharmacophore feature and adds it to the pharmacophore. More... | |
void | removeFeature (std::size_t idx) |
Removes the pharmacophore feature at the specified index. More... | |
FeatureIterator | removeFeature (const FeatureIterator &it) |
Removes the feature specified by the iterator it. More... | |
bool | containsFeature (const Feature &feature) const |
Tells whether the specified feature instance is stored in this pharmacophore. More... | |
std::size_t | getFeatureIndex (const Feature &feature) const |
Returns the index of the specified feature in this pharmacophore. More... | |
BasicPharmacophore & | operator= (const BasicPharmacophore &pharm) |
Replaces the current set of features by a copy of the features and properties of the pharmacophore pharm. More... | |
BasicPharmacophore & | operator+= (const BasicPharmacophore &pharm) |
Extends the current set of features by a copy of the features in the pharmacophore pharm. More... | |
Pharmacophore::SharedPointer | clone () const |
Creates a copy of the current pharmacophore state. More... | |
void | copy (const BasicPharmacophore &pharm) |
Replaces the current set of features and properties by a copy of the features and properties of the pharmacophore pharm. More... | |
void | copy (const Pharmacophore &pharm) |
Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the pharmacophore pharm. More... | |
void | copy (const FeatureContainer &cntnr) |
Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the feature container cntnr. More... | |
void | append (const BasicPharmacophore &pharm) |
Extends the current set of features by a copy of the features in the pharmacophore pharm. More... | |
void | append (const Pharmacophore &pharm) |
Extends the current set of pharmacophore features by a copy of the features in the pharmacophore pharm. More... | |
void | append (const FeatureContainer &cntnr) |
Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr. More... | |
void | remove (const FeatureContainer &cntnr) |
Removes the pharmacophore features referenced by the feature container cntnr from this Pharmacophore instance. More... | |
Pharmacophore & | operator= (const Pharmacophore &pharm) |
Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the pharmacophore pharm. More... | |
Pharmacophore & | operator= (const FeatureContainer &cntnr) |
Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the feature container cntnr. More... | |
Pharmacophore & | operator+= (const Pharmacophore &pharm) |
Extends the current set of pharmacophore features by a copy of the features in the pharmacophore pharm. More... | |
Pharmacophore & | operator+= (const FeatureContainer &cntnr) |
Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr. More... | |
Public Member Functions inherited from CDPL::Pharm::Pharmacophore | |
virtual | ~Pharmacophore () |
Virtual destructor. More... | |
FeatureIterator | removeFeature (const FeatureIterator &it) |
Removes the pharmacophore feature specified by the iterator it. More... | |
Pharmacophore & | operator= (const Pharmacophore &pharm) |
Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the pharmacophore pharm. More... | |
Pharmacophore & | operator= (const FeatureContainer &cntnr) |
Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the feature container cntnr. More... | |
Pharmacophore & | operator+= (const Pharmacophore &pharm) |
Extends the current set of pharmacophore features by a copy of the features in the pharmacophore pharm. More... | |
Pharmacophore & | operator+= (const FeatureContainer &cntnr) |
Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr. More... | |
Pharmacophore & | operator-= (const FeatureContainer &cntnr) |
Removes the pharmacophore features referenced by the feature container cntnr from this Pharmacophore instance. More... | |
ConstFeatureIterator | getFeaturesBegin () const |
Returns a constant iterator pointing to the beginning of the stored const Pharm::Feature objects. More... | |
FeatureIterator | getFeaturesBegin () |
Returns a mutable iterator pointing to the beginning of the stored Pharm::Feature objects. More... | |
ConstFeatureIterator | getFeaturesEnd () const |
Returns a constant iterator pointing to the end of the stored const Pharm::Feature objects. More... | |
FeatureIterator | getFeaturesEnd () |
Returns a mutable iterator pointing to the end of the stored Pharm::Feature objects. More... | |
Public Member Functions inherited from CDPL::Pharm::FeatureContainer | |
virtual | ~FeatureContainer () |
Virtual destructor. More... | |
ConstFeatureIterator | getFeaturesBegin () const |
Returns a constant iterator pointing to the beginning of the stored const Pharm::Feature objects. More... | |
ConstFeatureIterator | getFeaturesEnd () const |
Returns a constant iterator pointing to the end of the stored const Pharm::Feature objects. More... | |
FeatureIterator | getFeaturesBegin () |
Returns a mutable iterator pointing to the beginning of the stored Pharm::Feature objects. More... | |
FeatureIterator | getFeaturesEnd () |
Returns a mutable iterator pointing to the end of the stored Pharm::Feature objects. More... | |
ConstFeatureIterator | begin () const |
Returns a constant iterator pointing to the beginning of the stored const Pharm::Feature objects. More... | |
ConstFeatureIterator | end () const |
Returns a constant iterator pointing to the end of the stored const Pharm::Feature objects. More... | |
FeatureIterator | begin () |
Returns a mutable iterator pointing to the beginning of the stored Pharm::Feature objects. More... | |
FeatureIterator | end () |
Returns a mutable iterator pointing to the end of the stored Pharm::Feature objects. More... | |
virtual std::size_t | getNumEntities () const |
Returns the number of stored Chem::Entity3D objects. More... | |
virtual const Chem::Entity3D & | getEntity (std::size_t idx) const |
Returns a const reference to the Chem::Entity3D instance at index idx. More... | |
virtual Chem::Entity3D & | getEntity (std::size_t idx) |
Returns a non-const reference to the entity at index idx. More... | |
Public Member Functions inherited from CDPL::Chem::Entity3DContainer | |
ConstEntityIterator | getEntitiesBegin () const |
Returns a constant iterator pointing to the beginning of the stored const Chem::Entity3D objects. More... | |
ConstEntityIterator | getEntitiesEnd () const |
Returns a constant iterator pointing to the end of the stored const Chem::Entity3D objects. More... | |
EntityIterator | getEntitiesBegin () |
Returns a mutable iterator pointing to the beginning of the stored Chem::Entity3D objects. More... | |
EntityIterator | getEntitiesEnd () |
Returns a mutable iterator pointing to the end of the stored Chem::Entity3D objects. More... | |
ConstEntityIterator | begin () const |
Returns a constant iterator pointing to the beginning of the stored const Chem::Entity3D objects. More... | |
ConstEntityIterator | end () const |
Returns a constant iterator pointing to the end of the stored const Chem::Entity3D objects. More... | |
EntityIterator | begin () |
Returns a mutable iterator pointing to the beginning of the stored Chem::Entity3D objects. More... | |
EntityIterator | end () |
Returns a mutable iterator pointing to the end of the stored Chem::Entity3D objects. More... | |
const Entity3DContainer & | getEntities () const |
Returns a const reference to itself. More... | |
Entity3DContainer & | getEntities () |
Returns a reference to itself. More... | |
Public Member Functions inherited from CDPL::Base::PropertyContainer | |
std::size_t | getNumProperties () const |
Returns the number of property entries. More... | |
template<typename T > | |
void | setProperty (const LookupKey &key, T &&val) |
Sets the value of the property specified by key to val. More... | |
template<typename T > | |
const T & | getProperty (const LookupKey &key) const |
Returns the value of the property specified by key as a const reference to an object of type T. More... | |
template<typename T > | |
const T & | getPropertyOrDefault (const LookupKey &key, const T &def_val) const |
Returns the value of the property 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... | |
const Any & | getProperty (const LookupKey &key, bool throw_=false) const |
Returns the value of the property specified by key. More... | |
bool | isPropertySet (const LookupKey &key) const |
Tells whether or not a value has been assigned to the property specified by key. More... | |
ConstPropertyIterator | getPropertiesBegin () const |
Returns a constant iterator pointing to the beginning of the property entries. More... | |
ConstPropertyIterator | getPropertiesEnd () const |
Returns a constant iterator pointing to the end of the property entries. More... | |
ConstPropertyIterator | begin () const |
Returns a constant iterator pointing to the beginning of the property entries. More... | |
ConstPropertyIterator | end () const |
Returns a constant iterator pointing to the end of the property entries. More... | |
bool | removeProperty (const LookupKey &key) |
Clears the value of the property specified by key. More... | |
void | clearProperties () |
Clears all property values. More... | |
void | addProperties (const PropertyContainer &cntnr) |
Adds the property value entries in the PropertyContainer instance cntnr. More... | |
void | copyProperties (const PropertyContainer &cntnr) |
Replaces the current set of properties by a copy of the entries in cntnr. More... | |
void | swap (PropertyContainer &cntnr) |
Exchanges the properties of this container with the properties of the container cntnr. More... | |
const PropertyContainer & | getProperties () const |
Returns a const reference to itself. More... | |
Additional Inherited Members | |
Protected Member Functions inherited from CDPL::Pharm::FeatureContainer | |
FeatureContainer & | operator= (const FeatureContainer &cntnr) |
Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the container cntnr. More... | |
Protected Member Functions inherited from CDPL::Chem::Entity3DContainer | |
virtual | ~Entity3DContainer () |
Virtual destructor. More... | |
Entity3DContainer & | operator= (const Entity3DContainer &cntnr) |
Assignment operator. More... | |
Protected Member Functions inherited from CDPL::Base::PropertyContainer | |
PropertyContainer () | |
Constructs an empty PropertyContainer instance. More... | |
PropertyContainer (const PropertyContainer &cntnr) | |
Constructs a copy of the PropertyContainer instance cntnr. More... | |
virtual | ~PropertyContainer () |
Virtual destructor. More... | |
PropertyContainer & | operator= (const PropertyContainer &cntnr) |
Assignment operator. More... | |
typedef std::shared_ptr<BasicPharmacophore> CDPL::Pharm::BasicPharmacophore::SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated BasicPharmacophore
instances.
typedef boost::indirect_iterator<FeatureList::iterator, BasicFeature> CDPL::Pharm::BasicPharmacophore::FeatureIterator |
typedef boost::indirect_iterator<FeatureList::const_iterator, const BasicFeature> CDPL::Pharm::BasicPharmacophore::ConstFeatureIterator |
CDPL::Pharm::BasicPharmacophore::BasicPharmacophore | ( | ) |
Constructs an empty BasicPharmacophore
instance.
CDPL::Pharm::BasicPharmacophore::BasicPharmacophore | ( | const BasicPharmacophore & | pharm | ) |
Constructs a copy of the BasicPharmacophore
instance pharm.
pharm | The other BasicPharmacophore instance to copy. |
CDPL::Pharm::BasicPharmacophore::BasicPharmacophore | ( | const Pharmacophore & | pharm | ) |
Constructs a copy of the Pharm::Pharmacophore instance pharm.
pharm | The other Pharm::Pharmacophore instance to copy. |
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explicit |
Constructs a BasicPharmacophore instance with copies of the features in the Pharm::FeatureContainer instance cntnr.
cntnr | The Pharm::FeatureContainer instance with the features to copy. |
CDPL::Pharm::BasicPharmacophore::~BasicPharmacophore | ( | ) |
Destructor.
Destroys the BasicPharmacophore
instance and frees all allocated resources.
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virtual |
Removes all features and clears all properties of the pharmacophore.
Implements CDPL::Pharm::Pharmacophore.
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virtual |
Returns the number of pharmacophore features.
Implements CDPL::Pharm::Pharmacophore.
ConstFeatureIterator CDPL::Pharm::BasicPharmacophore::getFeaturesBegin | ( | ) | const |
Returns a constant iterator pointing to the beginning of the features.
FeatureIterator CDPL::Pharm::BasicPharmacophore::getFeaturesBegin | ( | ) |
Returns a mutable iterator pointing to the beginning of the features.
ConstFeatureIterator CDPL::Pharm::BasicPharmacophore::getFeaturesEnd | ( | ) | const |
Returns a constant iterator pointing to the end of the features.
FeatureIterator CDPL::Pharm::BasicPharmacophore::getFeaturesEnd | ( | ) |
Returns a mutable iterator pointing to the end of the features.
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virtual |
Returns a const
reference to the pharmacophore feature at index idx.
idx | The zero-based index of the feature to return. |
const
reference to the feature at the specified index. Base::IndexError | if the number of pharmacophore features is zero or idx is not in the range [0, getNumFeatures() - 1]. |
Implements CDPL::Pharm::Pharmacophore.
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virtual |
Returns a non-const
reference to the pharmacophore feature at index idx.
idx | The zero-based index of the feature to return. |
const
reference to the feature at the specified index. Base::IndexError | if the number of featuress is zero or idx is not in the range [0, getNumFeatures() - 1]. |
Implements CDPL::Pharm::Pharmacophore.
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virtual |
Creates a new pharmacophore feature and adds it to the pharmacophore.
Implements CDPL::Pharm::Pharmacophore.
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virtual |
Removes the pharmacophore feature at the specified index.
idx | The index of the feature to remove. |
Base::IndexError | if the number of features is zero or idx is not in the range [0, getNumFeatures() - 1]. |
Implements CDPL::Pharm::Pharmacophore.
FeatureIterator CDPL::Pharm::BasicPharmacophore::removeFeature | ( | const FeatureIterator & | it | ) |
Removes the feature specified by the iterator it.
it | An iterator that specifies the feature to remove. |
Base::RangeError | if the number of features is zero or it is not in the range [getFeaturesBegin(), getFeaturesEnd() - 1]. |
Tells whether the specified feature instance is stored in this pharmacophore.
feature | The feature to look for. |
true
if feature is stored in the pharmacophore, and false
otherwise. Implements CDPL::Pharm::Pharmacophore.
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virtual |
Returns the index of the specified feature in this pharmacophore.
feature | The feature instance for which to return the index. |
Base::ItemNotFound | if the specified feature instance could not be found. |
Implements CDPL::Pharm::Pharmacophore.
BasicPharmacophore& CDPL::Pharm::BasicPharmacophore::operator= | ( | const BasicPharmacophore & | pharm | ) |
Replaces the current set of features by a copy of the features and properties of the pharmacophore pharm.
Internally calls copy() to perform the actual work.
pharm | The pharmacophore to copy. |
BasicPharmacophore& CDPL::Pharm::BasicPharmacophore::operator+= | ( | const BasicPharmacophore & | pharm | ) |
Extends the current set of features by a copy of the features in the pharmacophore pharm.
Internally calls append() to perform the actual work.
pharm | The pharmacophore providing the features to append. |
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virtual |
Creates a copy of the current pharmacophore state.
Implements CDPL::Pharm::Pharmacophore.
void CDPL::Pharm::BasicPharmacophore::copy | ( | const BasicPharmacophore & | pharm | ) |
Replaces the current set of features and properties by a copy of the features and properties of the pharmacophore pharm.
pharm | The pharmacophore to copy. |
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virtual |
Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the pharmacophore pharm.
pharm | The pharmacophore to copy. |
Implements CDPL::Pharm::Pharmacophore.
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virtual |
Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the feature container cntnr.
cntnr | The Pharm::FeatureContainer instance providing the features and properties to copy. |
Implements CDPL::Pharm::Pharmacophore.
void CDPL::Pharm::BasicPharmacophore::append | ( | const BasicPharmacophore & | pharm | ) |
Extends the current set of features by a copy of the features in the pharmacophore pharm.
pharm | The pharmacophore providing the features to append. |
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virtual |
Extends the current set of pharmacophore features by a copy of the features in the pharmacophore pharm.
pharm | The pharmacophore providing the features to append. |
Implements CDPL::Pharm::Pharmacophore.
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virtual |
Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr.
cntnr | The Pharm::FeatureContainer instance providing the features to append. |
Implements CDPL::Pharm::Pharmacophore.
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virtual |
Removes the pharmacophore features referenced by the feature container cntnr from this Pharmacophore
instance.
cntnr | The Pharm::FeatureContainer instance providing the features to remove. |
this != &cntr
. Implements CDPL::Pharm::Pharmacophore.
Pharmacophore& CDPL::Pharm::Pharmacophore::operator= |
Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the pharmacophore pharm.
Internally calls copy() to perform the actual work.
pharm | The pharmacophore to copy. |
Pharmacophore& CDPL::Pharm::Pharmacophore::operator= |
Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the feature container cntnr.
Internally calls copy() to perform the actual work.
cntnr | The Pharm::FeatureContainer instance providing the features and properties to copy. |
Pharmacophore& CDPL::Pharm::Pharmacophore::operator+= |
Extends the current set of pharmacophore features by a copy of the features in the pharmacophore pharm.
Internally calls append() to perform the actual work.
pharm | The pharmacophore providing the features to append. |
Pharmacophore& CDPL::Pharm::Pharmacophore::operator+= |
Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr.
Internally calls append() to perform the actual work.
cntnr | The Pharm::FeatureContainer instance providing the features to append. |