Chemical Data Processing Library C++ API - Version 1.1.1
Chem/MoleculeFunctions.hpp
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1 /*
2  * MoleculeFunctions.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_MOLECULEFUNCTIONS_HPP
30 #define CDPL_CHEM_MOLECULEFUNCTIONS_HPP
31 
32 #include <cstddef>
33 
34 #include "CDPL/Chem/APIPrefix.hpp"
37 
38 
39 namespace CDPL
40 {
41 
42  namespace Chem
43  {
44 
45  class Molecule;
46  class MolecularGraph;
47 
55  CDPL_CHEM_API bool makeHydrogenDeplete(Molecule& mol, bool corr_impl_h_count = true);
56 
66  CDPL_CHEM_API bool makeOrdinaryHydrogenDeplete(Molecule& mol, unsigned int flags, bool corr_impl_h_count = true);
67 
75  CDPL_CHEM_API bool makeHydrogenComplete(Molecule& mol, bool corr_impl_h_count = true);
76 
77  CDPL_CHEM_API void connectAtoms(Molecule& mol, double dist_tol = 0.3, std::size_t atom_idx_offs = 0);
78 
80  double dist_tol = 0.3, std::size_t atom_idx_offs = 0);
81 
83 
85  } // namespace Chem
86 } // namespace CDPL
87 
88 #endif // CDPL_CHEM_MOLECULEFUNCTIONS_HPP
CDPL::Chem::removeAtomsIf
CDPL_CHEM_API void removeAtomsIf(Fragment &frag, const AtomPredicate &pred)
APIPrefix.hpp
Definition of the preprocessor macro CDPL_CHEM_API.
CDPL_CHEM_API
#define CDPL_CHEM_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::Chem::connectAtoms
CDPL_CHEM_API void connectAtoms(Molecule &mol, double dist_tol=0.3, std::size_t atom_idx_offs=0)
Atom3DCoordinatesFunction.hpp
Type definition of a generic wrapper class for storing user-defined Chem::Atom 3D-coordinates functio...
CDPL::Chem::Molecule
Molecule.
Definition: Molecule.hpp:49
CDPL::Chem::AtomPredicate
std::function< bool(const Chem::Atom &)> AtomPredicate
A generic wrapper class used to store a user-defined atom predicate.
Definition: AtomPredicate.hpp:41
CDPL::Chem::makeHydrogenComplete
CDPL_CHEM_API bool makeHydrogenComplete(Molecule &mol, bool corr_impl_h_count=true)
Converts all implicit hydrogens of the molecule mol to explicit hydrogen atoms.
AtomPredicate.hpp
Type definition of a generic wrapper class for storing user-defined Chem::Atom predicates.
CDPL::Chem::makeHydrogenDeplete
CDPL_CHEM_API bool makeHydrogenDeplete(Fragment &frag)
Removes all explicit hydrogen atoms from the fragment frag.
CDPL::Chem::makeOrdinaryHydrogenDeplete
CDPL_CHEM_API bool makeOrdinaryHydrogenDeplete(Fragment &frag, unsigned int flags)
Removes all explicit ordinary hydrogen atoms from the fragment frag.
CDPL::Chem::Atom3DCoordinatesFunction
std::function< const Math::Vector3D &(const Chem::Atom &)> Atom3DCoordinatesFunction
A generic wrapper class used to store a user-defined Chem::Atom 3D-coordinates function.
Definition: Atom3DCoordinatesFunction.hpp:43
CDPL::Chem::removeAtomsIfNot
CDPL_CHEM_API void removeAtomsIfNot(Fragment &frag, const AtomPredicate &pred)
CDPL
The namespace of the Chemical Data Processing Library.