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/********************************************************************** |
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mol.h - Handle molecules. Declarations of OBMol, OBAtom, OBBond, OBResidue. |
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(the main header for Open Babel) |
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|
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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Some portions Copyright (C) 2003 by Michael Banck |
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|
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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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|
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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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|
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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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|
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#ifndef OB_MOL_H |
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#define OB_MOL_H |
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|
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#include "config.h" |
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|
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#ifndef EXTERN |
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# define EXTERN extern |
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#endif |
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|
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#include <math.h> |
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|
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#include <algorithm> |
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#include <vector> |
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#include <string> |
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#include <map> |
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|
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#if HAVE_IOSTREAM |
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#include <iostream> |
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#elif HAVE_IOSTREAM_H |
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#include <iostream.h> |
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#endif |
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|
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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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|
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#include "base.hpp" |
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#include "data.hpp" |
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#include "chains.hpp" |
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#include "vector3.hpp" |
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#include "bitvec.hpp" |
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#include "ring.hpp" |
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#include "generic.hpp" |
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#include "typer.hpp" |
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#include "oberror.hpp" |
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#include "obiter.hpp" |
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#include "reaction.hpp" //so it gets notices in DLL builds |
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|
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namespace OpenBabel |
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{ |
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|
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class OBAtom; |
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class OBBond; |
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class OBMol; |
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class OBInternalCoord; |
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|
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// Class OBResidue |
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// class introduction in residue.cpp |
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class OBAPI OBResidue |
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{ |
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public: |
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|
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//! Constructor |
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OBResidue(void); |
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//! Copy constructor |
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OBResidue(const OBResidue &); |
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//! Destructor |
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virtual ~OBResidue(void); |
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|
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OBResidue &operator=(const OBResidue &); |
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|
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void AddAtom(OBAtom *atom); |
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void InsertAtom(OBAtom *atom); |
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void RemoveAtom(OBAtom *atom); |
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void Clear(void); |
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|
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void SetName(const std::string &resname); |
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void SetNum(unsigned int resnum); |
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void SetChain(char chain); |
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void SetChainNum(unsigned int chainnum); |
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void SetIdx(unsigned int idx); |
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|
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void SetAtomID(OBAtom *atom, const std::string &id); |
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void SetHetAtom(OBAtom *atom, bool hetatm); |
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//! Set the atomic serial number for a given atom (see OBSerialNums) |
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void SetSerialNum(OBAtom *atom, unsigned int sernum); |
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|
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std::string GetName(void) const; |
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unsigned int GetNum(void) const; |
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unsigned int GetNumAtoms() const; |
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char GetChain(void) const; |
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unsigned int GetChainNum(void) const; |
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unsigned int GetIdx(void) const; |
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unsigned int GetResKey(void) const; |
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|
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std::vector<OBAtom*> GetAtoms(void) const; |
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std::vector<OBBond*> GetBonds(bool = true) const; |
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|
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std::string GetAtomID(OBAtom *atom) const; |
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//! \return the serial number of the supplied atom (uses OBSerialNums) |
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unsigned GetSerialNum(OBAtom *atom) const; |
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|
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bool GetAminoAcidProperty(int) const; |
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bool GetAtomProperty(OBAtom *, int) const; |
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bool GetResidueProperty(int) const; |
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|
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bool IsHetAtom(OBAtom *atom) const; |
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bool IsResidueType(int) const; |
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|
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//! \deprecated Use FOR_ATOMS_OF_RESIDUE and OBResidueAtomIter instead |
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OBAtom *BeginAtom(std::vector<OBAtom*>::iterator &i); |
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//! \deprecated Use FOR_ATOMS_OF_RESIDUE and OBResidueAtomIter instead |
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OBAtom *NextAtom(std::vector<OBAtom*>::iterator &i); |
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|
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//! \name Methods for handling generic data |
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//@{ |
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bool HasData(std::string &); |
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bool HasData(const char *); |
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bool HasData(unsigned int type); |
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void DeleteData(unsigned int type); |
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void DeleteData(OBGenericData*); |
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void DeleteData(std::vector<OBGenericData*>&); |
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void SetData(OBGenericData *d) |
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{ _vdata.push_back(d); } |
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//! \return the number of OBGenericData items attached to this residue |
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unsigned int DataSize() |
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{ return(_vdata.size()); } |
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OBGenericData *GetData(unsigned int type); |
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OBGenericData *GetData(std::string&); |
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OBGenericData *GetData(const char *); |
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std::vector<OBGenericData*> &GetData() |
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{ return(_vdata); } |
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std::vector<OBGenericData*>::iterator BeginData() |
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{ return(_vdata.begin()); } |
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std::vector<OBGenericData*>::iterator EndData() |
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{ return(_vdata.end()); } |
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//@} |
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|
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protected: // members |
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|
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unsigned int _idx; //!< Residue index (i.e., internal index in an OBMol) |
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char _chain; //!< Chain ID |
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unsigned int _aakey; //!< Amino Acid key ID -- see SetResidueKeys() |
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unsigned int _reskey;//!< Residue key ID -- see SetResidueKeys() |
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unsigned int _resnum;//!< Residue number (i.e., in file) |
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std::string _resname;//!< Residue text name |
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|
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std::vector<bool> _hetatm;//!< Is a given atom a HETAM |
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std::vector<std::string> _atomid;//!< Residue atom text IDs |
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std::vector<OBAtom*> _atoms; //!< List of OBAtom in this residue |
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std::vector<unsigned int> _sernum;//!< List of serial numbers |
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std::vector<OBGenericData*> _vdata; //!< Custom data |
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}; // OBResidue |
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|
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|
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//ATOM Property Macros (flags) |
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//! Atom is in a 4-membered ring |
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#define OB_4RING_ATOM (1<<1) |
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//! Atom is in a 3-membered ring |
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#define OB_3RING_ATOM (1<<2) |
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//! Atom is aromatic |
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#define OB_AROMATIC_ATOM (1<<3) |
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//! Atom is in a ring |
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#define OB_RING_ATOM (1<<4) |
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//! Atom has clockwise SMILES chiral stereochemistry (i.e., "@@") |
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#define OB_CSTEREO_ATOM (1<<5) |
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//! Atom has anticlockwise SMILES chiral stereochemistry (i.e., "@") |
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#define OB_ACSTEREO_ATOM (1<<6) |
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//! Atom is an electron donor |
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#define OB_DONOR_ATOM (1<<7) |
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//! Atom is an electron acceptor |
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#define OB_ACCEPTOR_ATOM (1<<8) |
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//! Atom is chiral |
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#define OB_CHIRAL_ATOM (1<<9) |
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//! Atom has + chiral volume |
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#define OB_POS_CHIRAL_ATOM (1<<10) |
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//! Atom has - chiral volume |
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#define OB_NEG_CHIRAL_ATOM (1<<11) |
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// 12-16 currently unused |
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|
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// Class OBAtom |
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// class introduction in atom.cpp |
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class OBAPI OBAtom : public OBNodeBase |
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{ |
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protected: |
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char _ele; //!< atomic number (type char to minimize space -- allows for 0..255 elements) |
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char _impval; //!< implicit valence |
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char _type[6]; //!< atomic type |
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short _fcharge; //!< formal charge |
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unsigned short _isotope; //!< isotope (0 = most abundant) |
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short _spinmultiplicity;//!< atomic spin, e.g., 2 for radical 1 or 3 for carbene |
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|
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//unsigned short int _idx; //!< index in parent (inherited) |
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unsigned short _cidx; //!< index into coordinate array |
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unsigned short _hyb; //!< hybridization |
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unsigned short _flags; //!< bitwise flags (e.g. aromaticity) |
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double _pcharge; //!< partial charge |
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double **_c; //!< coordinate array in double* |
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vector3 _v; //!< coordinate vector |
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OBResidue *_residue; //!< parent residue (if applicable) |
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//OBMol *_parent; //!< parent molecule (inherited) |
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//vector<OBBond*> _bond; //!< connections (inherited) |
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std::vector<OBGenericData*> _vdata; //!< custom data |
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|
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int GetFlag() const { return(_flags); } |
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void SetFlag(int flag) { _flags |= flag; } |
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bool HasFlag(int flag) { return((_flags & flag) ? true : false); } |
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|
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public: |
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|
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//! Constructor |
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OBAtom(); |
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//! Destructor |
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virtual ~OBAtom(); |
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//! Assignment |
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OBAtom &operator = (OBAtom &); |
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//! Clear all data |
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void Clear(); |
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|
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//! \name Methods to set atomic information |
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//@{ |
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//! Set atom index (i.e., in an OBMol) |
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void SetIdx(int idx) { _idx = idx; _cidx = (idx-1)*3; } |
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//! Set atom hybridization (i.e., 1 = sp, 2 = sp2, 3 = sp3 ...) |
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void SetHyb(int hyb) { _hyb = hyb; } |
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//! Set atomic number |
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void SetAtomicNum(int atomicnum) { _ele = (char)atomicnum; } |
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//! Set isotope number (actual atomic weight is tabulated automatically, 0 = most abundant) |
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void SetIsotope(unsigned int iso); |
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void SetImplicitValence(int val) { _impval = (char)val; } |
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void IncrementImplicitValence() { _impval++; } |
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void DecrementImplicitValence() { _impval--; } |
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void SetFormalCharge(int fcharge) { _fcharge = fcharge; } |
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void SetSpinMultiplicity(short spin){ _spinmultiplicity = spin; } |
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void SetType(char *type); |
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void SetType(std::string &type); |
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void SetPartialCharge(double pcharge){ _pcharge = pcharge; } |
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void SetVector(vector3 &v); |
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void SetVector(const double x,const double y,const double z); |
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//! Set the position of this atom from a pointer-driven array of coordinates |
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void SetCoordPtr(double **c) { _c = c; _cidx = (GetIdx()-1)*3; } |
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//! Set the position of this atom based on the internal pointer array (i.e. from SetCoordPtr() ) |
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void SetVector(); |
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void SetResidue(OBResidue *res) { _residue=res; } |
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// void SetParent(OBMol *ptr) { _parent=ptr; } // inherited |
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void SetAromatic() { SetFlag(OB_AROMATIC_ATOM); } |
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void UnsetAromatic() { _flags &= (~(OB_AROMATIC_ATOM)); } |
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//! Mark atom as having SMILES clockwise stereochemistry (i.e., "@@") |
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void SetClockwiseStereo() { SetFlag(OB_CSTEREO_ATOM|OB_CHIRAL_ATOM); } |
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//! Mark atom as having SMILES anticlockwise stereochemistry (i.e., "@") |
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void SetAntiClockwiseStereo() { SetFlag(OB_ACSTEREO_ATOM|OB_CHIRAL_ATOM); } |
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//! Mark an atom as having + chiral volume |
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void SetPositiveStereo() { SetFlag(OB_POS_CHIRAL_ATOM|OB_CHIRAL_ATOM); } |
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//! Mark an atom as having - chiral volume |
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void SetNegativeStereo() { SetFlag(OB_NEG_CHIRAL_ATOM|OB_CHIRAL_ATOM); } |
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//! Clear all stereochemistry information |
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void UnsetStereo() |
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{ |
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_flags &= ~(OB_ACSTEREO_ATOM); |
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_flags &= ~(OB_CSTEREO_ATOM); |
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_flags &= ~(OB_POS_CHIRAL_ATOM); |
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_flags &= ~(OB_NEG_CHIRAL_ATOM); |
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_flags &= ~(OB_CHIRAL_ATOM); |
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} |
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//! Mark an atom as belonging to at least one ring |
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void SetInRing() { SetFlag(OB_RING_ATOM); } |
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//! Mark an atom as being chiral with unknown stereochemistry |
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void SetChiral() { SetFlag(OB_CHIRAL_ATOM); } |
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//! Clear the internal coordinate pointer |
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void ClearCoordPtr() { _c = NULL; _cidx=0; } |
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//@} |
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|
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//! \name Methods to retrieve atomic information |
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//@{ |
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//int GetStereo() const { return((int)_stereo);} |
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int GetFormalCharge() const { return(_fcharge); } |
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unsigned int GetAtomicNum() const { return((unsigned int)_ele); } |
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unsigned short int GetIsotope() const { return(_isotope); } |
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int GetSpinMultiplicity() const { return(_spinmultiplicity); } |
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//! The atomic mass of this atom given by standard IUPAC average molar mass |
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double GetAtomicMass() const; |
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//! The atomic mass of given by the isotope (default of 0 s most abundant isotope) |
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double GetExactMass() const; |
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unsigned int GetIdx() const { return((int)_idx); } |
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unsigned int GetCoordinateIdx() const { return((int)_cidx); } |
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//! \deprecated Use GetCoordinateIdx() instead |
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unsigned int GetCIdx() const { return((int)_cidx); } |
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//! The current number of explicit connections |
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unsigned int GetValence() const |
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{ |
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return((_vbond.empty()) ? 0 : _vbond.size()); |
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} |
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//! The hybridization of this atom (i.e. 1 for sp, 2 for sp2, 3 for sp3) |
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unsigned int GetHyb() const; |
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//! The implicit valence of this atom type (i.e. maximum number of connections expected) |
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unsigned int GetImplicitValence() const; |
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//! The number of non-hydrogens connected to this atom |
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unsigned int GetHvyValence() const; |
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//! The number of heteroatoms connected to an atom |
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unsigned int GetHeteroValence() const; |
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char *GetType(); |
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|
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//! The x coordinate |
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double GetX() { return(x()); } |
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//! The y coordinate |
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double GetY() { return(y()); } |
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//! The z coordinate |
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double GetZ() { return(z()); } |
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double x() |
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{ |
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if (_c) |
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return((*_c)[_cidx]); |
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else |
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return _v.x(); |
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} |
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double y() |
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{ |
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if (_c) |
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return((*_c)[_cidx+1]); |
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else |
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return _v.y(); |
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} |
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double z() |
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{ |
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if (_c) |
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return((*_c)[_cidx+2]); |
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else |
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return _v.z(); |
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} |
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//! \return the coordinates as a double* |
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double *GetCoordinate() |
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{ |
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return(&(*_c)[_cidx]); |
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} |
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//! \return the coordinates as a vector3 object |
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vector3 &GetVector(); |
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//! \return the partial charge of this atom, calculating a Gasteiger charge if needed |
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double GetPartialCharge(); |
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OBResidue *GetResidue(); |
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//OBMol *GetParent() {return((OBMol*)_parent);} |
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//! Create a vector for a new bond from this atom, with length given by the supplied parameter |
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bool GetNewBondVector(vector3 &v,double length); |
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OBBond *GetBond(OBAtom *); |
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OBAtom *GetNextAtom(); |
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//@} |
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|
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//! \name Iterator methods |
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//@{ |
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//! \deprecated Use FOR_BONDS_OF_ATOM and OBAtomBondIter instead |
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std::vector<OBEdgeBase*>::iterator BeginBonds() |
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{ return(_vbond.begin()); } |
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//! \deprecated Use FOR_BONDS_OF_ATOM and OBAtomBondIter instead |
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std::vector<OBEdgeBase*>::iterator EndBonds() |
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{ return(_vbond.end()); } |
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//! \deprecated Use FOR_BONDS_OF_ATOM and OBAtomBondIter instead |
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OBBond *BeginBond(std::vector<OBEdgeBase*>::iterator &i); |
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//! \deprecated Use FOR_BONDS_OF_ATOM and OBAtomBondIter instead |
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OBBond *NextBond(std::vector<OBEdgeBase*>::iterator &i); |
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//! \deprecated Use FOR_NBORS_OF_ATOM and OBAtomAtomIter instead |
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OBAtom *BeginNbrAtom(std::vector<OBEdgeBase*>::iterator &); |
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//! \deprecated Use FOR_NBORS_OF_ATOM and OBAtomAtomIter instead |
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OBAtom *NextNbrAtom(std::vector<OBEdgeBase*>::iterator &); |
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//@} |
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|
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//! \return the distance to the atom defined by OBMol::GetAtom() |
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double GetDistance(int index); |
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//! \return the distance to the supplied OBAtom |
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double GetDistance(OBAtom*); |
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//! \return the angle defined by this atom -> b (vertex) -> c |
| 383 |
double GetAngle(int b, int c); |
| 384 |
//! \return the angle defined by this atom -> b (vertex) -> c |
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double GetAngle(OBAtom *b, OBAtom *c); |
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|
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//! \name Addition of residue/bond info. for an atom |
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//@{ |
| 389 |
void NewResidue() |
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{ |
| 391 |
if (!_residue) |
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_residue = new OBResidue; |
| 393 |
} |
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void DeleteResidue() |
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{ |
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if (_residue) |
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delete _residue; |
| 398 |
} |
| 399 |
void AddBond(OBBond *bond) |
| 400 |
{ |
| 401 |
_vbond.push_back((OBEdgeBase*)bond); |
| 402 |
} |
| 403 |
void InsertBond(std::vector<OBEdgeBase*>::iterator &i, OBBond *bond) |
| 404 |
{ |
| 405 |
_vbond.insert(i, (OBEdgeBase*)bond); |
| 406 |
} |
| 407 |
bool DeleteBond(OBBond*); |
| 408 |
void ClearBond() {_vbond.clear();} |
| 409 |
//@} |
| 410 |
|
| 411 |
//! \name Requests for atomic property information |
| 412 |
//@{ |
| 413 |
//! The number of oxygen atoms connected that only have one heavy valence |
| 414 |
unsigned int CountFreeOxygens() const; |
| 415 |
//! The number of hydrogens needed to fill the implicit valence of this atom |
| 416 |
unsigned int ImplicitHydrogenCount() const; |
| 417 |
//! The number of hydrogens explicitly bound to this atom currently |
| 418 |
unsigned int ExplicitHydrogenCount() const; |
| 419 |
//! The number of rings that contain this atom |
| 420 |
unsigned int MemberOfRingCount() const; |
| 421 |
//! The size of the smallest ring that contains this atom (0 if not in a ring) |
| 422 |
unsigned int MemberOfRingSize() const; |
| 423 |
//! The smallest angle of bonds to this atom |
| 424 |
double SmallestBondAngle(); |
| 425 |
//! The average angle of bonds to this atom |
| 426 |
double AverageBondAngle(); |
| 427 |
//! The sum of the bond orders of the bonds to the atom (i.e. double bond = 2...) |
| 428 |
unsigned int BOSum() const; |
| 429 |
//! The sum of the bond orders of bonds to the atom, considering only KDouble, KTriple bonds |
| 430 |
unsigned int KBOSum() const; |
| 431 |
//@} |
| 432 |
|
| 433 |
//! \name Builder utilities |
| 434 |
//@{ |
| 435 |
//! If this is a hydrogen atom, transform into a methyl group |
| 436 |
bool HtoMethyl(); |
| 437 |
//! Change the hybridization of this atom and modify the geometry accordingly |
| 438 |
bool SetHybAndGeom(int); |
| 439 |
//@} |
| 440 |
|
| 441 |
//! \name Property information |
| 442 |
//@{ |
| 443 |
//! Is there any residue information? |
| 444 |
bool HasResidue() { return(_residue != NULL); } |
| 445 |
bool IsHydrogen() { return(GetAtomicNum() == 1); } |
| 446 |
bool IsCarbon() { return(GetAtomicNum() == 6); } |
| 447 |
bool IsNitrogen() { return(GetAtomicNum() == 7); } |
| 448 |
bool IsOxygen() { return(GetAtomicNum() == 8); } |
| 449 |
bool IsSulfur() { return(GetAtomicNum() == 16);} |
| 450 |
bool IsPhosphorus() { return(GetAtomicNum() == 15);} |
| 451 |
bool IsAromatic() const; |
| 452 |
bool IsInRing() const; |
| 453 |
bool IsInRingSize(int) const; |
| 454 |
//! Is this atom an element in the 15th or 16th main groups (i.e., N, O, P, S ...) ? |
| 455 |
bool IsHeteroatom(); |
| 456 |
//! Is this atom any element except carbon or hydrogen? |
| 457 |
bool IsNotCorH(); |
| 458 |
//! Is this atom connected to the supplied OBAtom? |
| 459 |
bool IsConnected(OBAtom*); |
| 460 |
//! Is this atom related to the supplied OBAtom in a 1,3 bonding pattern? |
| 461 |
bool IsOneThree(OBAtom*); |
| 462 |
//! Is this atom related to the supplied OBAtom in a 1,4 bonding pattern? |
| 463 |
bool IsOneFour(OBAtom*); |
| 464 |
//! Is this atom an oxygen in a carboxyl (-CO2 or CO2H) group? |
| 465 |
bool IsCarboxylOxygen(); |
| 466 |
//! Is this atom an oxygen in a phosphate (R-PO3) group? |
| 467 |
bool IsPhosphateOxygen(); |
| 468 |
//! Is this atom an oxygen in a sulfate (-SO3) group? |
| 469 |
bool IsSulfateOxygen(); |
| 470 |
//! Is this atom an oxygen in a nitro (-NO2) group? |
| 471 |
bool IsNitroOxygen(); |
| 472 |
bool IsAmideNitrogen(); |
| 473 |
bool IsPolarHydrogen(); |
| 474 |
bool IsNonPolarHydrogen(); |
| 475 |
bool IsAromaticNOxide(); |
| 476 |
//! Is this atom chiral? |
| 477 |
bool IsChiral(); |
| 478 |
bool IsAxial(); |
| 479 |
//! Does this atom have SMILES-specified clockwise "@@" stereochemistry? |
| 480 |
bool IsClockwise() { return(HasFlag(OB_CSTEREO_ATOM)); } |
| 481 |
//! Does this atom have SMILES-specified anticlockwise "@" stereochemistry? |
| 482 |
bool IsAntiClockwise() { return(HasFlag(OB_ACSTEREO_ATOM)); } |
| 483 |
//! Does this atom have a positive chiral volume? |
| 484 |
bool IsPositiveStereo() { return(HasFlag(OB_POS_CHIRAL_ATOM)); } |
| 485 |
//! Does this atom have a negative chiral volume? |
| 486 |
bool IsNegativeStereo() { return(HasFlag(OB_NEG_CHIRAL_ATOM)); } |
| 487 |
//! Does this atom have SMILES-specified stereochemistry? |
| 488 |
bool HasChiralitySpecified() |
| 489 |
{ return(HasFlag(OB_CSTEREO_ATOM|OB_ACSTEREO_ATOM)); } |
| 490 |
//! Does this atom have a specified chiral volume? |
| 491 |
bool HasChiralVolume() |
| 492 |
{ return(HasFlag(OB_POS_CHIRAL_ATOM|OB_NEG_CHIRAL_ATOM)); } |
| 493 |
//! Is this atom a hydrogen-bond acceptor (receptor)? |
| 494 |
bool IsHbondAcceptor(); |
| 495 |
//! Is this atom a hydrogen-bond donor? |
| 496 |
bool IsHbondDonor(); |
| 497 |
//! Is this a hydrogen atom attached to a hydrogen-bond donor? |
| 498 |
bool IsHbondDonorH(); |
| 499 |
bool HasAlphaBetaUnsat(bool includePandS=true); |
| 500 |
bool HasBondOfOrder(unsigned int); |
| 501 |
int CountBondsOfOrder(unsigned int); |
| 502 |
bool HasNonSingleBond(); |
| 503 |
bool HasSingleBond() { return(HasBondOfOrder(1)); } |
| 504 |
bool HasDoubleBond() { return(HasBondOfOrder(2)); } |
| 505 |
bool HasAromaticBond() { return(HasBondOfOrder(5)); } |
| 506 |
//! Determines if this atom matches the first atom in a given SMARTS pattern |
| 507 |
bool MatchesSMARTS(const char *); |
| 508 |
//@} |
| 509 |
|
| 510 |
//! \name Methods for handling generic data |
| 511 |
//@{ |
| 512 |
bool HasData(std::string &); |
| 513 |
bool HasData(const char *); |
| 514 |
bool HasData(unsigned int type); |
| 515 |
void DeleteData(unsigned int type); |
| 516 |
void DeleteData(OBGenericData*); |
| 517 |
void DeleteData(std::vector<OBGenericData*>&); |
| 518 |
void SetData(OBGenericData *d) |
| 519 |
{ _vdata.push_back(d); } |
| 520 |
//! \return the number of OBGenericData items attached to this atom |
| 521 |
unsigned int DataSize() |
| 522 |
{ return(_vdata.size()); } |
| 523 |
OBGenericData *GetData(unsigned int type); |
| 524 |
OBGenericData *GetData(std::string&); |
| 525 |
OBGenericData *GetData(const char *); |
| 526 |
std::vector<OBGenericData*> &GetData() { return(_vdata); } |
| 527 |
std::vector<OBGenericData*>::iterator BeginData() |
| 528 |
{ return(_vdata.begin()); } |
| 529 |
std::vector<OBGenericData*>::iterator EndData() |
| 530 |
{ return(_vdata.end()); } |
| 531 |
//@} |
| 532 |
}; // class OBAtom |
| 533 |
|
| 534 |
|
| 535 |
// Class OBBond |
| 536 |
|
| 537 |
//BOND Property Macros (flags) |
| 538 |
//! An aromatic bond (regardless of bond order) |
| 539 |
#define OB_AROMATIC_BOND (1<<1) |
| 540 |
//! A solid black wedge in 2D representations -- i.e., "up" from the 2D plane |
| 541 |
#define OB_WEDGE_BOND (1<<2) |
| 542 |
//! A dashed "hash" bond in 2D representations -- i.e., "down" from the 2D plane |
| 543 |
#define OB_HASH_BOND (1<<3) |
| 544 |
//! A bond in a ring |
| 545 |
#define OB_RING_BOND (1<<4) |
| 546 |
//! The "upper" bond in a double bond cis/trans isomer (i.e., "/" in SMILES) |
| 547 |
#define OB_TORUP_BOND (1<<5) |
| 548 |
//! The "down" bond in a double bond cis/trans isomer (i.e., "\" in SMILES) |
| 549 |
#define OB_TORDOWN_BOND (1<<6) |
| 550 |
//! A Kekule single bond |
| 551 |
#define OB_KSINGLE_BOND (1<<7) |
| 552 |
//! A Kekule double bond |
| 553 |
#define OB_KDOUBLE_BOND (1<<8) |
| 554 |
//! A Kekule triple bond |
| 555 |
#define OB_KTRIPLE_BOND (1<<9) |
| 556 |
#define OB_CLOSURE_BOND (1<<10) |
| 557 |
// 11-16 currently unused |
| 558 |
|
| 559 |
// class introduction in bond.cpp |
| 560 |
class OBAPI OBBond : public OBEdgeBase |
| 561 |
{ |
| 562 |
protected: |
| 563 |
char _order; //!< Bond order (1, 2, 3, 5=aromatic) |
| 564 |
unsigned short int _flags; //!< Any flags for this bond |
| 565 |
//OBAtom *_bgn; //!< Not needed, inherited from OBEdgeBase |
| 566 |
//OBAtom *_end; //!< Not needed, inherited from OBEdgeBase |
| 567 |
//OBMol *_parent;//!< Not needed, inherited from OBEdgeBase |
| 568 |
//unsigned short int _idx; //!< Not needed, inherited from OBEdgeBase |
| 569 |
std::vector<OBGenericData*> _vdata; //!< Generic data for custom information |
| 570 |
|
| 571 |
bool HasFlag(int flag) { return((_flags & flag) != 0); } |
| 572 |
void SetFlag(int flag) { _flags |= flag; } |
| 573 |
|
| 574 |
public: |
| 575 |
//! Constructor |
| 576 |
OBBond(); |
| 577 |
//! Destructor |
| 578 |
virtual ~OBBond(); |
| 579 |
|
| 580 |
//! \name Bond modification methods |
| 581 |
//@{ |
| 582 |
void SetIdx(int idx) |
| 583 |
{ |
| 584 |
_idx = idx; |
| 585 |
} |
| 586 |
void SetBO(int order); |
| 587 |
void SetBegin(OBAtom *begin) |
| 588 |
{ |
| 589 |
_bgn = begin; |
| 590 |
} |
| 591 |
void SetEnd(OBAtom *end) |
| 592 |
{ |
| 593 |
_end = end; |
| 594 |
} |
| 595 |
// void SetParent(OBMol *ptr) {_parent=ptr;} // (inherited) |
| 596 |
void SetLength(OBAtom*,double); |
| 597 |
void Set(int,OBAtom*,OBAtom*,int,int); |
| 598 |
void SetKSingle(); |
| 599 |
void SetKDouble(); |
| 600 |
void SetKTriple(); |
| 601 |
void SetAromatic() { SetFlag(OB_AROMATIC_BOND); } |
| 602 |
void SetHash() { SetFlag(OB_HASH_BOND); } |
| 603 |
void SetWedge() { SetFlag(OB_WEDGE_BOND); } |
| 604 |
void SetUp() { SetFlag(OB_TORUP_BOND); } |
| 605 |
void SetDown() { SetFlag(OB_TORDOWN_BOND); } |
| 606 |
void SetInRing() { SetFlag(OB_RING_BOND); } |
| 607 |
void SetClosure() { SetFlag(OB_CLOSURE_BOND); } |
| 608 |
|
| 609 |
void UnsetAromatic() { _flags &= (~(OB_AROMATIC_BOND)); } |
| 610 |
void UnsetKekule() |
| 611 |
{ |
| 612 |
_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND)); |
| 613 |
} |
| 614 |
//@} |
| 615 |
|
| 616 |
//! \name bond data request methods |
| 617 |
//@{ |
| 618 |
unsigned int GetBO() const { return((int)_order); } |
| 619 |
unsigned int GetBondOrder() const { return((int)_order); } |
| 620 |
unsigned int GetFlags() const { return(_flags); } |
| 621 |
unsigned int GetBeginAtomIdx() const { return(_bgn->GetIdx()); } |
| 622 |
unsigned int GetEndAtomIdx() const { return(_end->GetIdx()); } |
| 623 |
OBAtom *GetBeginAtom() { return((OBAtom*)_bgn); } |
| 624 |
OBAtom *GetEndAtom() { return((OBAtom*)_end); } |
| 625 |
OBAtom *GetNbrAtom(OBAtom *ptr) |
| 626 |
{ |
| 627 |
return((ptr != _bgn)? (OBAtom*)_bgn : (OBAtom*)_end); |
| 628 |
} |
| 629 |
// OBMol *GetParent() {return(_parent);} // (inherited) |
| 630 |
double GetEquibLength(); |
| 631 |
double GetLength(); |
| 632 |
int GetNbrAtomIdx(OBAtom *ptr) |
| 633 |
{ |
| 634 |
return((ptr!=_bgn)?_bgn->GetIdx():_end->GetIdx()); |
| 635 |
} |
| 636 |
//@} |
| 637 |
|
| 638 |
//! \name property request methods |
| 639 |
//@{ |
| 640 |
bool IsAromatic() const; |
| 641 |
bool IsInRing() const; |
| 642 |
bool IsRotor(); |
| 643 |
bool IsAmide(); |
| 644 |
bool IsPrimaryAmide(); |
| 645 |
bool IsSecondaryAmide(); |
| 646 |
bool IsEster(); |
| 647 |
bool IsCarbonyl(); |
| 648 |
bool IsSingle(); |
| 649 |
bool IsDouble(); |
| 650 |
bool IsTriple(); |
| 651 |
bool IsKSingle(); |
| 652 |
bool IsKDouble(); |
| 653 |
bool IsKTriple(); |
| 654 |
bool IsClosure(); |
| 655 |
//! \return whether this is the "upper" bond in a double bond cis/trans |
| 656 |
//! isomer (i.e., "/" in SMILES) |
| 657 |
bool IsUp() { return(HasFlag(OB_TORUP_BOND)); } |
| 658 |
//! \return whether this is the "lower" bond in a double bond cis/trans |
| 659 |
//! isomer (i.e., "\" in SMILES) |
| 660 |
bool IsDown() { return(HasFlag(OB_TORDOWN_BOND)); } |
| 661 |
bool IsWedge() { return(HasFlag(OB_WEDGE_BOND)); } |
| 662 |
bool IsHash() { return(HasFlag(OB_HASH_BOND)); } |
| 663 |
//! \return whether the geometry around this bond looks unsaturated |
| 664 |
bool IsDoubleBondGeometry(); |
| 665 |
//@} |
| 666 |
|
| 667 |
//! \name Methods for handling generic data |
| 668 |
//@{ |
| 669 |
bool HasData(std::string &); |
| 670 |
bool HasData(const char *); |
| 671 |
bool HasData(unsigned int type); |
| 672 |
void DeleteData(unsigned int type); |
| 673 |
void DeleteData(OBGenericData*); |
| 674 |
void DeleteData(std::vector<OBGenericData*>&); |
| 675 |
void SetData(OBGenericData *d) |
| 676 |
{ |
| 677 |
_vdata.push_back(d); |
| 678 |
} |
| 679 |
//! \return the number of OBGenericData items attached to this bond |
| 680 |
unsigned int DataSize() |
| 681 |
{ |
| 682 |
return(_vdata.size()); |
| 683 |
} |
| 684 |
OBGenericData *GetData(unsigned int type); |
| 685 |
OBGenericData *GetData(std::string&); |
| 686 |
OBGenericData *GetData(const char *); |
| 687 |
std::vector<OBGenericData*> &GetData() |
| 688 |
{ |
| 689 |
return(_vdata); |
| 690 |
} |
| 691 |
std::vector<OBGenericData*>::iterator BeginData() |
| 692 |
{ |
| 693 |
return(_vdata.begin()); |
| 694 |
} |
| 695 |
std::vector<OBGenericData*>::iterator EndData() |
| 696 |
{ |
| 697 |
return(_vdata.end()); |
| 698 |
} |
| 699 |
//@} |
| 700 |
} |
| 701 |
; // class OBBond |
| 702 |
|
| 703 |
|
| 704 |
// Class OBMol |
| 705 |
|
| 706 |
//MOL Property Macros (flags) -- 32+ bits |
| 707 |
#define OB_SSSR_MOL (1<<1) |
| 708 |
#define OB_RINGFLAGS_MOL (1<<2) |
| 709 |
#define OB_AROMATIC_MOL (1<<3) |
| 710 |
#define OB_ATOMTYPES_MOL (1<<4) |
| 711 |
#define OB_CHIRALITY_MOL (1<<5) |
| 712 |
#define OB_PCHARGE_MOL (1<<6) |
| 713 |
#define OB_HYBRID_MOL (1<<8) |
| 714 |
#define OB_IMPVAL_MOL (1<<9) |
| 715 |
#define OB_KEKULE_MOL (1<<10) |
| 716 |
#define OB_CLOSURE_MOL (1<<11) |
| 717 |
#define OB_H_ADDED_MOL (1<<12) |
| 718 |
#define OB_PH_CORRECTED_MOL (1<<13) |
| 719 |
#define OB_AROM_CORRECTED_MOL (1<<14) |
| 720 |
#define OB_CHAINS_MOL (1<<15) |
| 721 |
#define OB_TCHARGE_MOL (1<<16) |
| 722 |
#define OB_TSPIN_MOL (1<<17) |
| 723 |
// flags 18-32 unspecified |
| 724 |
#define OB_CURRENT_CONFORMER -1 |
| 725 |
|
| 726 |
// class introduction in mol.cpp |
| 727 |
class OBAPI OBMol : public OBGraphBase |
| 728 |
{ |
| 729 |
protected: |
| 730 |
int _flags; //!< bitfield of flags |
| 731 |
bool _autoPartialCharge; //!< Assign partial charges automatically |
| 732 |
bool _autoFormalCharge; //!< Assign formal charges automatically |
| 733 |
std::string _title; //!< Molecule title |
| 734 |
//vector<OBAtom*> _atom; //!< not needed (inherited) |
| 735 |
//vector<OBBond*> _bond; //!< not needed (inherited) |
| 736 |
unsigned short int _dimension; //!< Dimensionality of coordinates |
| 737 |
double _energy; //!< Molecular heat of formation (if applicable) |
| 738 |
int _totalCharge; //!< Total charge on the molecule |
| 739 |
unsigned int _totalSpin; //!< Total spin on the molecule (if not specified, assumes lowest possible spin) |
| 740 |
double *_c; //!< coordinate array |
| 741 |
std::vector<double*> _vconf; //!< vector of conformers |
| 742 |
unsigned short int _natoms; //!< Number of atoms |
| 743 |
unsigned short int _nbonds; //!< Number of bonds |
| 744 |
std::vector<OBResidue*> _residue; //!< Residue information (if applicable) |
| 745 |
std::vector<OBInternalCoord*> _internals; //!< Internal Coordinates (if applicable) |
| 746 |
std::vector<OBGenericData*> _vdata; //!< Custom data -- see OBGenericData class for more |
| 747 |
unsigned short int _mod; //!< Number of nested calls to BeginModify() |
| 748 |
|
| 749 |
bool HasFlag(int flag) { return((_flags & flag) ? true : false); } |
| 750 |
void SetFlag(int flag) { _flags |= flag; } |
| 751 |
|
| 752 |
//! \name Internal Kekulization routines -- see kekulize.cpp and NewPerceiveKekuleBonds() |
| 753 |
//@{ |
| 754 |
void start_kekulize(std::vector <OBAtom*> &cycle, std::vector<int> &electron); |
| 755 |
int expand_kekulize(OBAtom *atom1, OBAtom *atom2, std::vector<int> ¤tState, std::vector<int> &initState, std::vector<int> &bcurrentState, std::vector<int> &binitState, std::vector<bool> &mark); |
| 756 |
int getorden(OBAtom *atom); |
| 757 |
void expandcycle(OBAtom *atom, OBBitVec &avisit); |
| 758 |
//@} |
| 759 |
|
| 760 |
public: |
| 761 |
|
| 762 |
//! \name Initialization and data (re)size methods |
| 763 |
//@{ |
| 764 |
//! Constructor |
| 765 |
OBMol(); |
| 766 |
//! Copy constructor |
| 767 |
OBMol(const OBMol &); |
| 768 |
//! Destructor |
| 769 |
virtual ~OBMol(); |
| 770 |
//! Assignment |
| 771 |
OBMol &operator=(const OBMol &mol); |
| 772 |
OBMol &operator+=(const OBMol &mol); |
| 773 |
void ReserveAtoms(int natoms) |
| 774 |
{ |
| 775 |
if (natoms && _mod) |
| 776 |
_vatom.reserve(natoms); |
| 777 |
} |
| 778 |
virtual OBAtom *CreateAtom(void); |
| 779 |
virtual OBBond *CreateBond(void); |
| 780 |
virtual void DestroyAtom(OBNodeBase*); |
| 781 |
virtual void DestroyBond(OBEdgeBase*); |
| 782 |
bool AddAtom(OBAtom&); |
| 783 |
bool AddBond(int,int,int,int flags=0,int insertpos=-1); |
| 784 |
bool AddBond(OBBond&); |
| 785 |
bool AddResidue(OBResidue&); |
| 786 |
bool InsertAtom(OBAtom &); |
| 787 |
bool DeleteAtom(OBAtom*); |
| 788 |
bool DeleteBond(OBBond*); |
| 789 |
bool DeleteResidue(OBResidue*); |
| 790 |
OBAtom *NewAtom(); |
| 791 |
OBResidue *NewResidue(); |
| 792 |
//@} |
| 793 |
|
| 794 |
//! \name Molecule modification methods |
| 795 |
//@{ |
| 796 |
//! Call when making many modifications -- clears conformer/rotomer data. |
| 797 |
virtual void BeginModify(void); |
| 798 |
//! Call when done with modificaions -- re-perceive data as needed. |
| 799 |
virtual void EndModify(bool nukePerceivedData=true); |
| 800 |
int GetMod() |
| 801 |
{ |
| 802 |
return(_mod); |
| 803 |
} |
| 804 |
void IncrementMod() |
| 805 |
{ |
| 806 |
_mod++; |
| 807 |
} |
| 808 |
void DecrementMod() |
| 809 |
{ |
| 810 |
_mod--; |
| 811 |
} |
| 812 |
//@} |
| 813 |
|
| 814 |
//! \name Generic data handling methods (via OBGenericData) |
| 815 |
//@{ |
| 816 |
//! \returns whether the generic attribute/value pair exists |
| 817 |
bool HasData(std::string &); |
| 818 |
//! \returns whether the generic attribute/value pair exists |
| 819 |
bool HasData(const char *); |
| 820 |
//! \returns whether the generic attribute/value pair exists |
| 821 |
bool HasData(unsigned int type); |
| 822 |
void DeleteData(unsigned int type); |
| 823 |
void DeleteData(OBGenericData*); |
| 824 |
void DeleteData(std::vector<OBGenericData*>&); |
| 825 |
void SetData(OBGenericData *d) |
| 826 |
{ |
| 827 |
_vdata.push_back(d); |
| 828 |
} |
| 829 |
//! \return the number of OBGenericData items attached to this molecule. |
| 830 |
unsigned int DataSize(){ return(_vdata.size()); } |
| 831 |
OBGenericData *GetData(unsigned int type); |
| 832 |
OBGenericData *GetData(std::string&); |
| 833 |
OBGenericData *GetData(const char *); |
| 834 |
std::vector<OBGenericData*> &GetData() { return(_vdata); } |
| 835 |
std::vector<OBGenericData*>::iterator BeginData() |
| 836 |
{ |
| 837 |
return(_vdata.begin()); |
| 838 |
} |
| 839 |
std::vector<OBGenericData*>::iterator EndData() |
| 840 |
{ |
| 841 |
return(_vdata.end()); |
| 842 |
} |
| 843 |
//@} |
| 844 |
|
| 845 |
//! \name Data retrieval methods |
| 846 |
//@{ |
| 847 |
int GetFlags() { return(_flags); } |
| 848 |
//! \return the title of this molecule (often the filename) |
| 849 |
const char *GetTitle() const { return(_title.c_str()); } |
| 850 |
//! \return the number of atoms (i.e. OBAtom children) |
| 851 |
unsigned int NumAtoms() const { return(_natoms); } |
| 852 |
//! \return the number of bonds (i.e. OBBond children) |
| 853 |
unsigned int NumBonds() const { return(_nbonds); } |
| 854 |
//! \return the number of non-hydrogen atoms |
| 855 |
unsigned int NumHvyAtoms(); |
| 856 |
//! \return the number of residues (i.e. OBResidue substituents) |
| 857 |
unsigned int NumResidues() const { return(_residue.size()); } |
| 858 |
//! \return the number of rotatble bonds |
| 859 |
unsigned int NumRotors(); |
| 860 |
|
| 861 |
OBAtom *GetAtom(int); |
| 862 |
OBAtom *GetFirstAtom(); |
| 863 |
OBBond *GetBond(int); |
| 864 |
OBBond *GetBond(int, int); |
| 865 |
OBBond *GetBond(OBAtom*,OBAtom*); |
| 866 |
OBResidue *GetResidue(int); |
| 867 |
std::vector<OBInternalCoord*> GetInternalCoord(); |
| 868 |
//! \return the dihedral angle between the four atoms supplied a1-a2-a3-a4) |
| 869 |
double GetTorsion(int,int,int,int); |
| 870 |
//! \return the dihedral angle between the four atoms supplied a1-a2-a3-a4) |
| 871 |
double GetTorsion(OBAtom*,OBAtom*,OBAtom*,OBAtom*); |
| 872 |
//! \return the stochoimetric formula (e.g., C4H6O) |
| 873 |
std::string GetFormula(); |
| 874 |
//! \return the heat of formation for this molecule (in kcal/mol) |
| 875 |
double GetEnergy() const { return(_energy); } |
| 876 |
//! \return the standard molar mass given by IUPAC atomic masses (amu) |
| 877 |
double GetMolWt(); |
| 878 |
//! \return the mass given by isotopes (or most abundant isotope, if not specified) |
| 879 |
double GetExactMass(); |
| 880 |
//! \return the total charge on this molecule (i.e., 0 = neutral, +1, -1...) |
| 881 |
int GetTotalCharge(); |
| 882 |
//! \return the total spin on this molecule (i.e., 1 = singlet, 2 = doublet...) |
| 883 |
unsigned int GetTotalSpinMultiplicity(); |
| 884 |
//! \return the dimensionality of coordinates (i.e., 0 = unknown or no coord, 2=2D, 3=3D) |
| 885 |
unsigned short int GetDimension() const { return _dimension; } |
| 886 |
double *GetCoordinates() { return(_c); } |
| 887 |
//! \return the Smallest Set of Smallest Rings has been run (see OBRing class |
| 888 |
std::vector<OBRing*> &GetSSSR(); |
| 889 |
//! Get the current flag for whether formal charges are set with pH correction |
| 890 |
bool AutomaticFormalCharge() { return(_autoFormalCharge); } |
| 891 |
//! Get the current flag for whether partial charges are auto-determined |
| 892 |
bool AutomaticPartialCharge() { return(_autoPartialCharge); } |
| 893 |
//@} |
| 894 |
|
| 895 |
|
| 896 |
//! \name Data modification methods |
| 897 |
//@{ |
| 898 |
void SetTitle(const char *title); |
| 899 |
void SetTitle(std::string &title); |
| 900 |
//! Set the stochiometric formula for this molecule |
| 901 |
void SetFormula(std::string molFormula); |
| 902 |
//! Set the heat of formation for this molecule (in kcal/mol) |
| 903 |
void SetEnergy(double energy) { _energy = energy; } |
| 904 |
//! Set the dimension of this molecule (i.e., 0, 1 , 2, 3) |
| 905 |
void SetDimension(unsigned short int d) { _dimension = d; } |
| 906 |
void SetTotalCharge(int charge); |
| 907 |
void SetTotalSpinMultiplicity(unsigned int spin); |
| 908 |
void SetInternalCoord(std::vector<OBInternalCoord*> int_coord) |
| 909 |
{ _internals = int_coord; } |
| 910 |
//! Set the flag for determining automatic formal charges with pH (default=true) |
| 911 |
void SetAutomaticFormalCharge(bool val) |
| 912 |
{ _autoFormalCharge=val; } |
| 913 |
//! Set the flag for determining partial charges automatically (default=true) |
| 914 |
void SetAutomaticPartialCharge(bool val) |
| 915 |
{ _autoPartialCharge=val; } |
| 916 |
|
| 917 |
//! Mark that aromaticity has been perceived for this molecule (see OBAromaticTyper) |
| 918 |
void SetAromaticPerceived() { SetFlag(OB_AROMATIC_MOL); } |
| 919 |
//! Mark that Smallest Set of Smallest Rings has been run (see OBRing class) |
| 920 |
void SetSSSRPerceived() { SetFlag(OB_SSSR_MOL); } |
| 921 |
//! Mark that rings have been perceived (see OBRing class for details) |
| 922 |
void SetRingAtomsAndBondsPerceived(){SetFlag(OB_RINGFLAGS_MOL);} |
| 923 |
//! Mark that atom types have been perceived (see OBAtomTyper for details) |
| 924 |
void SetAtomTypesPerceived() { SetFlag(OB_ATOMTYPES_MOL); } |
| 925 |
//! Mark that chains and residues have been perceived (see OBChainsParser) |
| 926 |
void SetChainsPerceived() { SetFlag(OB_CHAINS_MOL); } |
| 927 |
//! Mark that chirality has been perceived |
| 928 |
void SetChiralityPerceived() { SetFlag(OB_CHIRALITY_MOL); } |
| 929 |
//! Mark that partial charges have been assigned |
| 930 |
void SetPartialChargesPerceived(){ SetFlag(OB_PCHARGE_MOL); } |
| 931 |
void SetHybridizationPerceived() { SetFlag(OB_HYBRID_MOL); } |
| 932 |
void SetImplicitValencePerceived(){ SetFlag(OB_IMPVAL_MOL); } |
| 933 |
void SetKekulePerceived() { SetFlag(OB_KEKULE_MOL); } |
| 934 |
void SetClosureBondsPerceived(){ SetFlag(OB_CLOSURE_MOL); } |
| 935 |
void SetHydrogensAdded() { SetFlag(OB_H_ADDED_MOL); } |
| 936 |
void SetCorrectedForPH() { SetFlag(OB_PH_CORRECTED_MOL);} |
| 937 |
void SetAromaticCorrected() { SetFlag(OB_AROM_CORRECTED_MOL);} |
| 938 |
void SetSpinMultiplicityAssigned(){ SetFlag(OB_TSPIN_MOL); } |
| 939 |
void SetFlags(int flags) { _flags = flags; } |
| 940 |
|
| 941 |
void UnsetAromaticPerceived() { _flags &= (~(OB_AROMATIC_MOL)); } |
| 942 |
void UnsetPartialChargesPerceived(){ _flags &= (~(OB_PCHARGE_MOL));} |
| 943 |
void UnsetImplicitValencePerceived(){_flags &= (~(OB_IMPVAL_MOL)); } |
| 944 |
void UnsetFlag(int flag) { _flags &= (~(flag)); } |
| 945 |
|
| 946 |
//! \name Molecule modification methods |
| 947 |
//@{ |
| 948 |
// Description in transform.cpp |
| 949 |
virtual OBBase* DoTransformations(const std::map<std::string,std::string>* pOptions); |
| 950 |
static const char* ClassDescription(); |
| 951 |
//! Clear all information from a molecule |
| 952 |
bool Clear(); |
| 953 |
//! Renumber the atoms of this molecule according to the order in the supplied vector |
| 954 |
void RenumberAtoms(std::vector<OBNodeBase*>&); |
| 955 |
//! Translate one conformer and rotate by a rotation matrix (which is returned) to the inertial frame-of-reference |
| 956 |
void ToInertialFrame(int conf, double *rmat); |
| 957 |
//! Translate all conformers to the inertial frame-of-reference |
| 958 |
void ToInertialFrame(); |
| 959 |
//! Translates all conformers in the molecule by the supplied vector |
| 960 |
void Translate(const vector3 &v); |
| 961 |
//! Translates one conformer in the molecule by the supplied vector |
| 962 |
void Translate(const vector3 &v, int conf); |
| 963 |
void Rotate(const double u[3][3]); |
| 964 |
void Rotate(const double m[9]); |
| 965 |
void Rotate(const double m[9],int nconf); |
| 966 |
//! Translate to the center of all coordinates (for this conformer) |
| 967 |
void Center(); |
| 968 |
//! Transform to standard Kekule bond structure (presumably from an aromatic form) |
| 969 |
bool Kekulize(); |
| 970 |
bool PerceiveKekuleBonds(); |
| 971 |
|
| 972 |
void NewPerceiveKekuleBonds(); |
| 973 |
|
| 974 |
bool DeleteHydrogen(OBAtom*); |
| 975 |
bool DeleteHydrogens(); |
| 976 |
bool DeleteHydrogens(OBAtom*); |
| 977 |
bool DeleteNonPolarHydrogens(); |
| 978 |
bool AddHydrogens(bool polaronly=false,bool correctForPH=true); |
| 979 |
bool AddHydrogens(OBAtom*); |
| 980 |
bool AddPolarHydrogens(); |
| 981 |
|
| 982 |
//! Deletes all atoms except for the largest contiguous fragment |
| 983 |
bool StripSalts(); |
| 984 |
//! Converts the charged form of coordinate bonds, e.g.[N+]([O-])=O to N(=O)=O |
| 985 |
bool ConvertDativeBonds(); |
| 986 |
|
| 987 |
bool CorrectForPH(); |
| 988 |
bool AssignSpinMultiplicity(); |
| 989 |
vector3 Center(int nconf); |
| 990 |
//! Set the torsion defined by these atoms, rotating bonded neighbors |
| 991 |
void SetTorsion(OBAtom*,OBAtom*,OBAtom*,OBAtom*,double); |
| 992 |
//@} |
| 993 |
|
| 994 |
//! \name Molecule utilities and perception methods |
| 995 |
//@{ |
| 996 |
//! Find Smallest Set of Smallest Rings (see OBRing class for more details) |
| 997 |
void FindSSSR(); |
| 998 |
void FindRingAtomsAndBonds(); |
| 999 |
void FindChiralCenters(); |
| 1000 |
void FindChildren(std::vector<int> &,int,int); |
| 1001 |
void FindChildren(std::vector<OBAtom*>&,OBAtom*,OBAtom*); |
| 1002 |
void FindLargestFragment(OBBitVec &); |
| 1003 |
//! Sort a list of contig fragments by size from largest to smallest |
| 1004 |
//! Each vector<int> contains the atom numbers of a contig fragment |
| 1005 |
void ContigFragList(std::vector<std::vector<int> >&); |
| 1006 |
//! Aligns atom a on p1 and atom b along p1->p2 vector |
| 1007 |
void Align(OBAtom*,OBAtom*,vector3&,vector3&); |
| 1008 |
//! Adds single bonds based on atom proximity |
| 1009 |
void ConnectTheDots(); |
| 1010 |
//! Attempts to perceive multiple bonds based on geometries |
| 1011 |
void PerceiveBondOrders(); |
| 1012 |
void FindTorsions(); |
| 1013 |
// documented in mol.cpp: graph-theoretical distance for each atom |
| 1014 |
bool GetGTDVector(std::vector<int> &); |
| 1015 |
// documented in mol.cpp: graph-invariant index for each atom |
| 1016 |
void GetGIVector(std::vector<unsigned int> &); |
| 1017 |
// documented in mol.cpp: calculate symmetry-unique identifiers |
| 1018 |
void GetGIDVector(std::vector<unsigned int> &); |
| 1019 |
//@} |
| 1020 |
|
| 1021 |
//! \name Methods to check for existence of properties |
| 1022 |
//@{ |
| 1023 |
//! Are there non-zero coordinates in two dimensions (i.e. X and Y)? |
| 1024 |
bool Has2D(); |
| 1025 |
//! Are there non-zero coordinates in all three dimensions (i.e. X, Y, Z)? |
| 1026 |
bool Has3D(); |
| 1027 |
//! Are there any non-zero coordinates? |
| 1028 |
bool HasNonZeroCoords(); |
| 1029 |
bool HasAromaticPerceived() { return(HasFlag(OB_AROMATIC_MOL)); } |
| 1030 |
bool HasSSSRPerceived() { return(HasFlag(OB_SSSR_MOL)); } |
| 1031 |
bool HasRingAtomsAndBondsPerceived(){return(HasFlag(OB_RINGFLAGS_MOL));} |
| 1032 |
bool HasAtomTypesPerceived() { return(HasFlag(OB_ATOMTYPES_MOL));} |
| 1033 |
bool HasChiralityPerceived() { return(HasFlag(OB_CHIRALITY_MOL));} |
| 1034 |
bool HasPartialChargesPerceived() { return(HasFlag(OB_PCHARGE_MOL));} |
| 1035 |
bool HasHybridizationPerceived() { return(HasFlag(OB_HYBRID_MOL)); } |
| 1036 |
bool HasImplicitValencePerceived() { return(HasFlag(OB_IMPVAL_MOL));} |
| 1037 |
bool HasKekulePerceived() { return(HasFlag(OB_KEKULE_MOL)); } |
| 1038 |
bool HasClosureBondsPerceived() { return(HasFlag(OB_CLOSURE_MOL)); } |
| 1039 |
bool HasChainsPerceived() { return(HasFlag(OB_CHAINS_MOL)); } |
| 1040 |
bool HasHydrogensAdded() { return(HasFlag(OB_H_ADDED_MOL)); } |
| 1041 |
bool HasAromaticCorrected() { return(HasFlag(OB_AROM_CORRECTED_MOL));} |
| 1042 |
bool IsCorrectedForPH() { return(HasFlag(OB_PH_CORRECTED_MOL)); } |
| 1043 |
bool HasSpinMultiplicityAssigned() { return(HasFlag(OB_TSPIN_MOL)); } |
| 1044 |
//! Is this molecule chiral? |
| 1045 |
bool IsChiral(); |
| 1046 |
//! Are there any atoms in this molecule? |
| 1047 |
bool Empty() { return(_natoms == 0); } |
| 1048 |
//@} |
| 1049 |
|
| 1050 |
//! \name Multiple conformer member functions |
| 1051 |
//@{ |
| 1052 |
int NumConformers() { return((_vconf.empty())?0:_vconf.size()); } |
| 1053 |
void SetConformers(std::vector<double*> &v); |
| 1054 |
void AddConformer(double *f) { _vconf.push_back(f); } |
| 1055 |
void SetConformer(int i) { _c = _vconf[i]; } |
| 1056 |
void CopyConformer(double*,int); |
| 1057 |
void DeleteConformer(int); |
| 1058 |
double *GetConformer(int i) { return(_vconf[i]); } |
| 1059 |
double *BeginConformer(std::vector<double*>::iterator&i) |
| 1060 |
{ i = _vconf.begin(); |
| 1061 |
return((i == _vconf.end()) ? NULL:*i); } |
| 1062 |
double *NextConformer(std::vector<double*>::iterator&i) |
| 1063 |
{ i++; |
| 1064 |
return((i == _vconf.end()) ? NULL:*i); } |
| 1065 |
std::vector<double*> &GetConformers() { return(_vconf); } |
| 1066 |
//@} |
| 1067 |
|
| 1068 |
//! \name Iterator methods |
| 1069 |
//@{ |
| 1070 |
//! \deprecated Use FOR_ATOMS_OF_MOL and OBMolAtomIter instead |
| 1071 |
OBAtom *BeginAtom(std::vector<OBNodeBase*>::iterator &i); |
| 1072 |
//! \deprecated Use FOR_ATOMS_OF_MOL and OBMolAtomIter instead |
| 1073 |
OBAtom *NextAtom(std::vector<OBNodeBase*>::iterator &i); |
| 1074 |
//! \deprecated Use FOR_BONDS_OF_MOL and OBMolBondIter instead |
| 1075 |
OBBond *BeginBond(std::vector<OBEdgeBase*>::iterator &i); |
| 1076 |
//! \deprecated Use FOR_BONDS_OF_MOL and OBMolBondIter instead |
| 1077 |
OBBond *NextBond(std::vector<OBEdgeBase*>::iterator &i); |
| 1078 |
//! \deprecated Use FOR_RESIDUES_OF_MOL and OBResidueIter instead |
| 1079 |
OBResidue *BeginResidue(std::vector<OBResidue*>::iterator &i) |
| 1080 |
{ |
| 1081 |
i = _residue.begin(); |
| 1082 |
return((i == _residue.end()) ? NULL:*i); |
| 1083 |
} |
| 1084 |
//! \deprecated Use FOR_RESIDUES_OF_MOL and OBResidueIter instead |
| 1085 |
OBResidue *NextResidue(std::vector<OBResidue*>::iterator &i) |
| 1086 |
{ |
| 1087 |
i++; |
| 1088 |
return((i == _residue.end()) ? NULL:*i); |
| 1089 |
} |
| 1090 |
OBInternalCoord *BeginInternalCoord(std::vector<OBInternalCoord*>::iterator &i) |
| 1091 |
{ |
| 1092 |
i = _internals.begin(); |
| 1093 |
return((i == _internals.end()) ? NULL:*i); |
| 1094 |
} |
| 1095 |
OBInternalCoord *NextInternalCoord(std::vector<OBInternalCoord*>::iterator &i) |
| 1096 |
{ |
| 1097 |
i++; |
| 1098 |
return((i == _internals.end()) ? NULL:*i); |
| 1099 |
} |
| 1100 |
//@} |
| 1101 |
|
| 1102 |
// Removed with OBConversion framework -- see OBConversion class instead |
| 1103 |
//! \name Convenience functions for I/O |
| 1104 |
//@{ |
| 1105 |
// friend std::ostream& operator<< ( std::ostream&, OBMol& ) ; |
| 1106 |
// friend std::istream& operator>> ( std::istream&, OBMol& ) ; |
| 1107 |
//@} |
| 1108 |
}; |
| 1109 |
|
| 1110 |
//! \brief Used to transform from z-matrix to cartesian coordinates. |
| 1111 |
class OBAPI OBInternalCoord |
| 1112 |
{ |
| 1113 |
public: |
| 1114 |
//class members |
| 1115 |
OBAtom *_a,*_b,*_c; |
| 1116 |
double _dst,_ang,_tor; |
| 1117 |
//! Constructor |
| 1118 |
OBInternalCoord(OBAtom *a=(OBAtom*)NULL, |
| 1119 |
OBAtom *b=(OBAtom*)NULL, |
| 1120 |
OBAtom *c=(OBAtom*)NULL) |
| 1121 |
{ |
| 1122 |
_a = a; |
| 1123 |
_b = b; |
| 1124 |
_c = c; |
| 1125 |
_dst = _ang = _tor = 0.0; |
| 1126 |
} |
| 1127 |
}; |
| 1128 |
|
| 1129 |
//function prototypes |
| 1130 |
|
| 1131 |
OBAPI bool tokenize(std::vector<std::string>&, const char *buf, const char *delimstr=" \t\n"); |
| 1132 |
OBAPI bool tokenize(std::vector<std::string>&, std::string&, const char *delimstr=" \t\n", int limit=-1); |
| 1133 |
//! remove leading and trailing whitespace from a string |
| 1134 |
OBAPI void Trim(std::string& txt); |
| 1135 |
//! \deprecated -- use OBMessageHandler class instead |
| 1136 |
OBAPI void ThrowError(char *str); |
| 1137 |
//! \deprecated -- use OBMessageHandler class instead |
| 1138 |
OBAPI void ThrowError(std::string &str); |
| 1139 |
OBAPI void CartesianToInternal(std::vector<OBInternalCoord*>&,OBMol&); |
| 1140 |
OBAPI void InternalToCartesian(std::vector<OBInternalCoord*>&,OBMol&); |
| 1141 |
OBAPI std::string NewExtension(std::string&,char*); |
| 1142 |
// Now handled by OBConversion class |
| 1143 |
// OBAPI bool SetInputType(OBMol&,std::string&); |
| 1144 |
// OBAPI bool SetOutputType(OBMol&,std::string&); |
| 1145 |
|
| 1146 |
//global definitions |
| 1147 |
//! Global OBElementTable for element properties |
| 1148 |
EXTERN OBElementTable etab; |
| 1149 |
//! Global OBTypeTable for translating between different atom types |
| 1150 |
//! (e.g., Sybyl <-> MM2) |
| 1151 |
EXTERN OBTypeTable ttab; |
| 1152 |
//! Global OBIsotopeTable for isotope properties |
| 1153 |
EXTERN OBIsotopeTable isotab; |
| 1154 |
//! Global OBAromaticTyper for detecting aromatic atoms and bonds |
| 1155 |
EXTERN OBAromaticTyper aromtyper; |
| 1156 |
//! Global OBAtomTyper for marking internal valence, hybridization, |
| 1157 |
//! and atom types (for internal and external use) |
| 1158 |
EXTERN OBAtomTyper atomtyper; |
| 1159 |
//! Global OBChainsParser for detecting macromolecular chains and residues |
| 1160 |
EXTERN OBChainsParser chainsparser; |
| 1161 |
//! Global OBMessageHandler error handler |
| 1162 |
EXTERN OBMessageHandler obErrorLog; |
| 1163 |
//! Global OBResidueData biomolecule residue database |
| 1164 |
EXTERN OBResidueData resdat; |
| 1165 |
|
| 1166 |
//Utility Macros |
| 1167 |
|
| 1168 |
#ifndef BUFF_SIZE |
| 1169 |
#define BUFF_SIZE 32768 |
| 1170 |
#endif |
| 1171 |
|
| 1172 |
#ifndef EQ |
| 1173 |
#define EQ(a,b) (!strcmp((a), (b))) |
| 1174 |
#endif |
| 1175 |
|
| 1176 |
#ifndef EQn |
| 1177 |
#define EQn(a,b,n) (!strncmp((a), (b), (n))) |
| 1178 |
#endif |
| 1179 |
|
| 1180 |
#ifndef SQUARE |
| 1181 |
#define SQUARE(x) ((x)*(x)) |
| 1182 |
#endif |
| 1183 |
|
| 1184 |
#ifndef IsUnsatType |
| 1185 |
#define IsUnsatType(x) (EQ(x,"Car") || EQ(x,"C2") || EQ(x,"Sox") || EQ(x,"Sac") || EQ(x,"Pac") || EQ(x,"So2")) |
| 1186 |
#endif |
| 1187 |
|
| 1188 |
#ifndef __KCC |
| 1189 |
extern "C" |
| 1190 |
{ |
| 1191 |
OBAPI void get_rmat(double*,double*,double*,int); |
| 1192 |
OBAPI void ob_make_rmat(double mat[3][3],double rmat[9]); |
| 1193 |
OBAPI void qtrfit (double *r,double *f,int size,double u[3][3]); |
| 1194 |
OBAPI double superimpose(double*,double*,int); |
| 1195 |
} |
| 1196 |
#else |
| 1197 |
OBAPI void get_rmat(double*,double*,double*,int); |
| 1198 |
OBAPI void ob_make_rmat(double mat[3][3],double rmat[9]); |
| 1199 |
OBAPI void qtrfit (double *r,double *f,int size,double u[3][3]); |
| 1200 |
OBAPI double superimpose(double*,double*,int); |
| 1201 |
#endif // __KCC |
| 1202 |
|
| 1203 |
} // end namespace OpenBabel |
| 1204 |
|
| 1205 |
#endif // OB_MOL_H |
| 1206 |
|
| 1207 |
//! \file |
| 1208 |
//! \brief Handle molecules. Declarations of OBMol, OBAtom, OBBond, OBResidue. |
| 1209 |
//! (the main header for Open Babel) |
