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/********************************************************************** |
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rotamer.h - Handle rotamer list data. |
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Copyright (C) 1998-2000 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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#ifndef OB_ROTAMER_H |
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#define OB_ROTAMER_H |
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#include <vector> |
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#include <map> |
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#if HAVE_FSTREAM |
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#include <fstream> |
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#elif HAVE_FSTREAM_H |
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#include <fstream.h> |
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#endif |
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#include "mol.hpp" |
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#include "rotor.hpp" |
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#include "generic.hpp" |
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namespace OpenBabel |
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{ |
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//! Supports a set of rotomer coordinate sets for some number of potentially rotatable bonds |
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class OBAPI OBRotamerList : public OBGenericData |
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{ |
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unsigned int _NBaseCoords; |
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std::vector<double*> _c; |
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std::vector<std::vector<double> > _vres; |
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std::vector<unsigned char*> _vrotamer; |
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std::vector<std::pair<OBAtom**,std::vector<int> > > _vrotor; |
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OBRotamerList(const OBRotamerList &cpy) : OBGenericData(cpy) |
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{} |
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OBRotamerList& operator =(const OBRotamerList &) |
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{ |
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return *this; |
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} |
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public: |
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OBRotamerList() |
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{ |
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_NBaseCoords=0; |
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_type= OBGenericDataType::RotamerList; |
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_attr="RotamerList"; |
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} |
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~OBRotamerList(); |
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void Setup(OBMol&,OBRotorList&); |
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void Setup(OBMol&,unsigned char*,int); |
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//! \return the number of rotatable bonds considered |
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unsigned int NumRotors() const |
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{ |
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return (unsigned int)_vrotor.size(); |
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} |
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//! \return the number of rotamer (conformation) coordinate sets |
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unsigned int NumRotamers() const |
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{ |
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return (unsigned int)_vrotamer.size(); |
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} |
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void AddRotamer(double*); |
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void AddRotamer(int *arr); |
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void AddRotamer(unsigned char *arr); |
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void AddRotamers(unsigned char*,int); |
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void GetReferenceArray(unsigned char*); |
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void ExpandConformerList(OBMol&,std::vector<double*>&); |
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std::vector<unsigned char*>::iterator BeginRotamer() |
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{ |
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return _vrotamer.begin(); |
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} |
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std::vector<unsigned char*>::iterator EndRotamer() |
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{ |
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return _vrotamer.end(); |
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} |
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// Support for internal storage of base coordinate sets that |
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// rotamers operate on |
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//! Create a conformer list using the internal base set of coordinates |
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std::vector<double*> CreateConformerList(OBMol& mol); |
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//! Copies the mol's conformers (the coordinates, NOT the pointers) |
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//! into the object as base coordinates |
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void SetBaseCoordinateSets(OBMol& mol) |
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{ |
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SetBaseCoordinateSets(mol.GetConformers(),mol.NumAtoms()); |
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} |
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//! Copies the coordinates in bc, NOT the pointers, into the object |
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void SetBaseCoordinateSets(std::vector<double*> bc, unsigned int N); |
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unsigned int NumBaseCoordinateSets() const |
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{ |
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return (unsigned int)_c.size(); |
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} |
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//! Get a pointer to a specific base pointer |
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double *GetBaseCoordinateSet(unsigned int i) |
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{ |
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return (i<_c.size()) ? _c[i] : NULL; |
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} |
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unsigned int NumAtoms() const |
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{ |
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return _NBaseCoords; |
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} |
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}; |
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int Swab(int); |
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} |
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#endif // OB_ROTAMER_H |
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//! \file rotamer.h |
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//! \brief Handle rotamer list data. |
