Chemical Data Processing Library C++ API - Version 1.1.1
Biomol/MolecularGraphFunctions.hpp
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1 /*
2  * MolecularGraphFunctions.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_BIOMOL_MOLECULARGRAPHFUNCTIONS_HPP
30 #define CDPL_BIOMOL_MOLECULARGRAPHFUNCTIONS_HPP
31 
32 #include <string>
33 #include <cstddef>
34 
36 #include "CDPL/Biomol/PDBData.hpp"
40 
41 
42 namespace CDPL
43 {
44 
45  namespace Chem
46  {
47 
48  class MolecularGraph;
49  class Fragment;
50  } // namespace Chem
51 
52  namespace Biomol
53  {
54 
55  CDPL_BIOMOL_API const std::string& getResidueCode(const Chem::MolecularGraph& molgraph);
56 
57  CDPL_BIOMOL_API void setResidueCode(Chem::MolecularGraph& molgraph, const std::string& code);
58 
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82  CDPL_BIOMOL_API const std::string& getChainID(const Chem::MolecularGraph& molgraph);
83 
84  CDPL_BIOMOL_API void setChainID(Chem::MolecularGraph& molgraph, const std::string& id);
85 
87 
89 
90 
91  CDPL_BIOMOL_API std::size_t getModelNumber(const Chem::MolecularGraph& molgraph);
92 
93  CDPL_BIOMOL_API void setModelNumber(Chem::MolecularGraph& molgraph, std::size_t model_no);
94 
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111  CDPL_BIOMOL_API void extractResidueSubstructures(const Chem::MolecularGraph& molgraph, const Chem::MolecularGraph& parent_molgraph, Chem::Fragment& res_substructs,
112  bool cnctd_only = false, unsigned int flags = AtomPropertyFlag::DEFAULT, bool append = false);
113 
115  double max_dist, bool inc_core_atoms = false, bool append = false);
116 
118  const Chem::Atom3DCoordinatesFunction& coords_func, double max_dist, bool inc_core_atoms = false, bool append = false);
119 
121  double max_dist, bool append = false);
122 
124  const Chem::Atom3DCoordinatesFunction& coords_func, double max_dist, bool append = false);
125 
127 
128  CDPL_BIOMOL_API bool matchesResidueInfo(const Chem::MolecularGraph& molgraph, const char* res_code = 0, const char* chain_id = 0, long res_seq_no = IGNORE_SEQUENCE_NO,
129  char ins_code = 0, std::size_t model_no = 0);
130  } // namespace Biomol
131 } // namespace CDPL
132 
133 #endif // CDPL_BIOMOL_MOLECULARGRAPHFUNCTIONS_HPP
CDPL::Biomol::setResidueCode
CDPL_BIOMOL_API void setResidueCode(Chem::Atom &atom, const std::string &code)
CDPL::Biomol::clearResidueSequenceNumber
CDPL_BIOMOL_API void clearResidueSequenceNumber(Chem::Atom &atom)
CDPL::Biomol::AtomPropertyFlag::DEFAULT
const unsigned int DEFAULT
Represents the default set of atom properties.
Definition: Biomol/AtomPropertyFlag.hpp:53
CDPL::Biomol::matchesResidueInfo
CDPL_BIOMOL_API bool matchesResidueInfo(const Chem::Atom &atom, const char *res_code=0, const char *chain_id=0, long res_seq_no=IGNORE_SEQUENCE_NO, char ins_code=0, std::size_t model_no=0, const char *atom_name=0, long serial_no=IGNORE_SERIAL_NO)
CDPL::Biomol::clearChainID
CDPL_BIOMOL_API void clearChainID(Chem::Atom &atom)
CDPL::Biomol::getResidueSequenceNumber
CDPL_BIOMOL_API long getResidueSequenceNumber(const Chem::Atom &atom)
CDPL::Biomol::extractProximalAtoms
CDPL_BIOMOL_API void extractProximalAtoms(const Chem::MolecularGraph &core, const Chem::MolecularGraph &macromol, Chem::Fragment &env_atoms, double max_dist, bool inc_core_atoms=false, bool append=false)
CDPL::Biomol::clearModelNumber
CDPL_BIOMOL_API void clearModelNumber(Chem::Atom &atom)
CDPL::Biomol::setHydrogenResidueSequenceInfo
CDPL_BIOMOL_API void setHydrogenResidueSequenceInfo(Chem::MolecularGraph &molgraph, bool overwrite, unsigned int flags=AtomPropertyFlag::DEFAULT)
CDPL::Biomol::clearResidueInsertionCode
CDPL_BIOMOL_API void clearResidueInsertionCode(Chem::Atom &atom)
PDBData.hpp
Definition of the class CDPL::Biomol::PDBData.
CDPL::Biomol::setResidueSequenceNumber
CDPL_BIOMOL_API void setResidueSequenceNumber(Chem::Atom &atom, long seq_no)
CDPL::Biomol::hasChainID
CDPL_BIOMOL_API bool hasChainID(const Chem::Atom &atom)
CDPL::Chem::Fragment
Fragment.
Definition: Fragment.hpp:52
CDPL::Biomol::hasResidueCode
CDPL_BIOMOL_API bool hasResidueCode(const Chem::Atom &atom)
CDPL::Biomol::hasModelNumber
CDPL_BIOMOL_API bool hasModelNumber(const Chem::Atom &atom)
CDPL::Biomol::convertMOL2ToPDBResidueInfo
CDPL_BIOMOL_API void convertMOL2ToPDBResidueInfo(Chem::MolecularGraph &molgraph, bool overwrite)
ProcessingFlags.hpp
Definition of flags for serial and residue sequence number processing.
AtomPropertyFlag.hpp
Definition of constants in namespace CDPL::Biomol::AtomPropertyFlag.
CDPL::Biomol::setModelNumber
CDPL_BIOMOL_API void setModelNumber(Chem::Atom &atom, std::size_t model_no)
CDPL::Biomol::hasResidueInsertionCode
CDPL_BIOMOL_API bool hasResidueInsertionCode(const Chem::Atom &atom)
CDPL::Biomol::hasPDBData
CDPL_BIOMOL_API bool hasPDBData(const Chem::MolecularGraph &molgraph)
CDPL::Biomol::hasResidueSequenceNumber
CDPL_BIOMOL_API bool hasResidueSequenceNumber(const Chem::Atom &atom)
CDPL::Chem::MolecularGraph
MolecularGraph.
Definition: MolecularGraph.hpp:52
Atom3DCoordinatesFunction.hpp
Type definition of a generic wrapper class for storing user-defined Chem::Atom 3D-coordinates functio...
CDPL::Biomol::extractResidueSubstructures
CDPL_BIOMOL_API void extractResidueSubstructures(const Chem::MolecularGraph &molgraph, const Chem::MolecularGraph &parent_molgraph, Chem::Fragment &res_substructs, bool cnctd_only=false, unsigned int flags=AtomPropertyFlag::DEFAULT, bool append=false)
CDPL::Biomol::IGNORE_SEQUENCE_NO
const long IGNORE_SEQUENCE_NO
Definition: ProcessingFlags.hpp:41
CDPL::Biomol::getResidueCode
CDPL_BIOMOL_API const std::string & getResidueCode(const Chem::Atom &atom)
CDPL::Biomol::getResidueInsertionCode
CDPL_BIOMOL_API char getResidueInsertionCode(const Chem::Atom &atom)
CDPL::Biomol::getChainID
CDPL_BIOMOL_API const std::string & getChainID(const Chem::Atom &atom)
CDPL::Biomol::getModelNumber
CDPL_BIOMOL_API std::size_t getModelNumber(const Chem::Atom &atom)
CDPL::Biomol::setPDBData
CDPL_BIOMOL_API void setPDBData(Chem::MolecularGraph &molgraph, const PDBData::SharedPointer &data)
CDPL::Biomol::clearPDBData
CDPL_BIOMOL_API void clearPDBData(Chem::MolecularGraph &molgraph)
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
APIPrefix.hpp
Definition of the preprocessor macro CDPL_BIOMOL_API.
CDPL
The namespace of the Chemical Data Processing Library.
CDPL::Biomol::getPDBData
CDPL_BIOMOL_API const PDBData::SharedPointer & getPDBData(const Chem::MolecularGraph &molgraph)
CDPL::Biomol::extractEnvironmentResidues
CDPL_BIOMOL_API void extractEnvironmentResidues(const Chem::MolecularGraph &core, const Chem::MolecularGraph &macromol, Chem::Fragment &env_residues, double max_dist, bool append=false)
CDPL::Biomol::setChainID
CDPL_BIOMOL_API void setChainID(Chem::Atom &atom, const std::string &id)
CDPL::Biomol::setResidueInsertionCode
CDPL_BIOMOL_API void setResidueInsertionCode(Chem::Atom &atom, char code)
CDPL_BIOMOL_API
#define CDPL_BIOMOL_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::Biomol::PDBData::SharedPointer
std::shared_ptr< PDBData > SharedPointer
Definition: PDBData.hpp:53
CDPL::Biomol::clearResidueCode
CDPL_BIOMOL_API void clearResidueCode(Chem::Atom &atom)