Chemical Data Processing Library C++ API - Version 1.1.1
Reaction.hpp
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1 /*
2  * Reaction.hpp
3  *
4  * This file is part of the Chemical Data Processing Toolkit
5  *
6  * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>
7  *
8  * This library is free software; you can redistribute it and/or
9  * modify it under the terms of the GNU Lesser General Public
10  * License as published by the Free Software Foundation; either
11  * version 2 of the License, or (at your option) any later version.
12  *
13  * This library is distributed in the hope that it will be useful,
14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16  * Lesser General Public License for more details.
17  *
18  * You should have received a copy of the GNU Lesser General Public License
19  * along with this library; see the file COPYING. If not, write to
20  * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
21  * Boston, MA 02111-1307, USA.
22  */
23 
29 #ifndef CDPL_CHEM_REACTION_HPP
30 #define CDPL_CHEM_REACTION_HPP
31 
32 #include <memory>
33 #include <functional>
34 
35 #include "CDPL/Chem/APIPrefix.hpp"
38 
39 
40 namespace CDPL
41 {
42 
43  namespace Chem
44  {
45 
46  class Molecule;
47 
52  {
53 
54  class ConstComponentAccessor;
55  class ComponentAccessor;
56 
57  public:
61  typedef std::shared_ptr<Reaction> SharedPointer;
62 
67 
72 
73  typedef std::function<void(Reaction&, const Reaction&)> CopyPostprocessingFunction;
74 
78  virtual ~Reaction() {}
79 
83  virtual void clear() = 0;
84 
89  virtual std::size_t getNumComponents() const = 0;
90 
98  virtual std::size_t getNumComponents(unsigned int role) const = 0;
99 
108  virtual unsigned int getComponentRole(const Molecule& mol) const = 0;
109 
116  virtual std::size_t getComponentIndex(const Molecule& mol) const = 0;
117 
123  virtual bool containsComponent(const Molecule& mol) const = 0;
124 
130 
136 
142 
148 
154 
160 
166 
172 
182  ConstComponentIterator getComponentsBegin(unsigned int role) const;
183 
194 
204  ConstComponentIterator getComponentsEnd(unsigned int role) const;
205 
216 
223  virtual const Molecule& getComponent(std::size_t idx) const = 0;
224 
231  virtual Molecule& getComponent(std::size_t idx) = 0;
232 
244  virtual const Molecule& getComponent(std::size_t idx, unsigned int role) const = 0;
245 
257  virtual Molecule& getComponent(std::size_t idx, unsigned int role) = 0;
258 
266  virtual Molecule& addComponent(unsigned int role) = 0;
267 
278  virtual void swapComponentRoles(unsigned int role1, unsigned int role2) = 0;
279 
285  virtual void removeComponent(std::size_t idx) = 0;
286 
296  virtual void removeComponent(std::size_t idx, unsigned int role) = 0;
297 
306 
313  virtual void removeComponents(unsigned int role) = 0;
314 
319  virtual SharedPointer clone() const = 0;
320 
326  virtual void copy(const Reaction& rxn) = 0;
327 
337  Reaction& operator=(const Reaction& rxn);
338 
340 
341  protected:
343 
344  private:
345  class CDPL_CHEM_API ConstComponentAccessor
346  {
347 
348  friend class Reaction;
349 
350  public:
351  ConstComponentAccessor(const ComponentAccessor& accessor):
352  reaction(accessor.reaction), compRole(accessor.compRole) {}
353  ConstComponentAccessor(const Reaction* rxn, unsigned int role):
354  reaction(rxn), compRole(role) {}
355 
356  const Molecule& operator()(std::size_t idx) const;
357 
358  bool operator==(const ConstComponentAccessor& accessor) const;
359 
360  private:
361  const Reaction* reaction;
362  unsigned int compRole;
363  };
364 
365  class CDPL_CHEM_API ComponentAccessor
366  {
367 
368  friend class Reaction;
369  friend class ConstComponentAccessor;
370 
371  public:
372  ComponentAccessor(Reaction* rxn, unsigned int role):
373  reaction(rxn), compRole(role) {}
374 
375  Molecule& operator()(std::size_t idx) const;
376 
377  bool operator==(const ComponentAccessor& accessor) const;
378 
379  private:
380  Reaction* reaction;
381  unsigned int compRole;
382  };
383  };
384  } // namespace Chem
385 } // namespace CDPL
386 
387 #endif // CDPL_CHEM_REACTION_HPP
CDPL::Chem::Reaction::begin
ComponentIterator begin()
Returns a mutable iterator pointing to the beginning of the reaction components.
CDPL::Chem::Reaction::removeComponent
ComponentIterator removeComponent(const ComponentIterator &it)
Removes the reaction component specified by the iterator it.
APIPrefix.hpp
Definition of the preprocessor macro CDPL_CHEM_API.
CDPL::Chem::Reaction::addComponent
virtual Molecule & addComponent(unsigned int role)=0
Creates a new reaction component with the specified role.
IndexedElementIterator.hpp
Definition of the class CDPL::Util::IndexedElementIterator.
CDPL_CHEM_API
#define CDPL_CHEM_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::Math::operator==
GridEquality< E1, E2 >::ResultType operator==(const GridExpression< E1 > &e1, const GridExpression< E2 > &e2)
Definition: GridExpression.hpp:339
CDPL::Chem::Reaction::containsComponent
virtual bool containsComponent(const Molecule &mol) const =0
Tells whether the specified molecule is a component of this reaction.
CDPL::Util::IndexedElementIterator
A STL compatible random access iterator for container elements accessible by index.
Definition: IndexedElementIterator.hpp:125
CDPL::Chem::Reaction::registerCopyPostprocessingFunction
static void registerCopyPostprocessingFunction(const CopyPostprocessingFunction &func)
CDPL::Chem::Reaction::getNumComponents
virtual std::size_t getNumComponents() const =0
Returns the number of reaction components.
CDPL::Chem::Reaction::copy
virtual void copy(const Reaction &rxn)=0
Replaces the current set of reaction components and properties by a copy of the components and proper...
CDPL::Chem::Molecule
Molecule.
Definition: Molecule.hpp:49
CDPL::Chem::Reaction::removeComponent
virtual void removeComponent(std::size_t idx)=0
Removes the reaction component at the specified index.
CDPL::Chem::Reaction::getComponent
virtual Molecule & getComponent(std::size_t idx)=0
Returns a non-const reference to the reaction component at index idx.
CDPL::Chem::Reaction::getComponentsEnd
ConstComponentIterator getComponentsEnd(unsigned int role) const
Returns a constant iterator pointing to the end of the reaction components with the specified role.
CDPL::Chem::Reaction::begin
ConstComponentIterator begin() const
Returns a constant iterator pointing to the beginning of the reaction components.
CDPL::Chem::Reaction::getComponent
virtual const Molecule & getComponent(std::size_t idx, unsigned int role) const =0
Returns a const reference to the reaction component at index idx in the list of components with the s...
CDPL::Chem::Reaction::getComponentsBegin
ConstComponentIterator getComponentsBegin() const
Returns a constant iterator pointing to the beginning of the reaction components.
CDPL::Chem::Reaction::SharedPointer
std::shared_ptr< Reaction > SharedPointer
A reference-counted smart pointer [SHPTR] for dynamically allocated Reaction instances.
Definition: Reaction.hpp:55
CDPL::Chem::Reaction::getComponent
virtual const Molecule & getComponent(std::size_t idx) const =0
Returns a const reference to the reaction component at index idx.
CDPL::Chem::Reaction::invokeCopyPostprocessingFunctions
void invokeCopyPostprocessingFunctions(const Reaction &src_rxn)
CDPL::Chem::Reaction::getNumComponents
virtual std::size_t getNumComponents(unsigned int role) const =0
Returns the number of reaction components with the specified role.
CDPL::Chem::Reaction::getComponentsEnd
ConstComponentIterator getComponentsEnd() const
Returns a constant iterator pointing to the end of the reaction components.
CDPL::Chem::Reaction::ComponentIterator
Util::IndexedElementIterator< Molecule, ComponentAccessor > ComponentIterator
A mutable random access iterator used to iterate over the components of the reaction.
Definition: Reaction.hpp:71
CDPL::Chem::Reaction::getComponentRole
virtual unsigned int getComponentRole(const Molecule &mol) const =0
Returns the reaction role of the specified component.
CDPL::Base::PropertyContainer
A class providing methods for the storage and lookup of object properties.
Definition: PropertyContainer.hpp:75
CDPL::Chem::Reaction::getComponentsBegin
ComponentIterator getComponentsBegin(unsigned int role)
Returns a mutable iterator pointing to the beginning of the reaction components with the specified ro...
CDPL::Chem::Reaction::clone
virtual SharedPointer clone() const =0
Creates a copy of the current reaction state.
CDPL
The namespace of the Chemical Data Processing Library.
CDPL::Chem::Reaction::getComponentsBegin
ConstComponentIterator getComponentsBegin(unsigned int role) const
Returns a constant iterator pointing to the beginning of the reaction components with the specified r...
CDPL::Chem::Reaction
Reaction.
Definition: Reaction.hpp:52
CDPL::Chem::Reaction::getComponentsBegin
ComponentIterator getComponentsBegin()
Returns a mutable iterator pointing to the beginning of the reaction components.
CDPL::Chem::Reaction::removeComponent
virtual void removeComponent(std::size_t idx, unsigned int role)=0
Removes the reaction component at index idx in the list of components with the specified role.
CDPL::Chem::Reaction::end
ConstComponentIterator end() const
Returns a constant iterator pointing to the end of the reaction components.
CDPL::Chem::Reaction::~Reaction
virtual ~Reaction()
Virtual destructor.
Definition: Reaction.hpp:78
CDPL::Chem::Reaction::getComponentsEnd
ComponentIterator getComponentsEnd(unsigned int role)
Returns a mutable iterator pointing to the end of the reaction components with the specified role.
CDPL::Chem::Reaction::ConstComponentIterator
Util::IndexedElementIterator< const Molecule, ConstComponentAccessor > ConstComponentIterator
A constant random access iterator used to iterate over the components of the reaction.
Definition: Reaction.hpp:66
CDPL::Chem::Reaction::getComponentIndex
virtual std::size_t getComponentIndex(const Molecule &mol) const =0
Returns the index of the specified reaction component.
CDPL::Chem::Reaction::clear
virtual void clear()=0
Removes all components and clears all properties of the reaction.
PropertyContainer.hpp
Definition of the class CDPL::Base::PropertyContainer.
CDPL::Chem::Reaction::getComponent
virtual Molecule & getComponent(std::size_t idx, unsigned int role)=0
Returns a non-const reference to the reaction component at index idx in the list of components with t...
CDPL::Chem::Reaction::getComponentsEnd
ComponentIterator getComponentsEnd()
Returns a mutable iterator pointing to the end of the reaction components.
CDPL::Chem::Reaction::swapComponentRoles
virtual void swapComponentRoles(unsigned int role1, unsigned int role2)=0
Swaps the reaction roles of the component sets specified by role1 and role2.
CDPL::Chem::Reaction::removeComponents
virtual void removeComponents(unsigned int role)=0
Removes all components with the specified role.
CDPL::Chem::Reaction::CopyPostprocessingFunction
std::function< void(Reaction &, const Reaction &)> CopyPostprocessingFunction
Definition: Reaction.hpp:73
CDPL::Chem::Reaction::end
ComponentIterator end()
Returns a mutable iterator pointing to the end of the reaction components.