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/********************************************************************** |
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atom.cpp - Handle OBAtom class. |
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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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#include "mol.hpp" |
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#include "typer.hpp" |
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#include "molchrg.hpp" |
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#include "phmodel.hpp" |
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|
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#include "matrix3x3.hpp" |
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|
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#if !HAVE_STRNCASECMP |
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extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); |
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#endif |
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|
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using namespace std; |
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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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\brief Atom class |
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|
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To understand the OBAtom class it is important to state a key |
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decision on which the design was based. In OBabel the atom class |
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existed, but it was only a data container. All data access and |
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modification of atoms was done through the molecule. The result |
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was a molecule class that was very large an unwieldy. So the OBAtom |
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class was made smarter, and many of the atom-specific routines |
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were separated into the OBAtom thereby decentralizing and |
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shrinking the OBMol class. As a result the OBAtom class not only |
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holds data, but facilitates extraction of data perceived from both |
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the atom and the molecule. |
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|
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A number of data extraction methods perform what is called |
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<a href="http://en.wikipedia.org/wiki/Lazy_evaluation">`Lazy Evaluation,'</a> which is essentially on-the-fly evaluation. |
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For example, when an atom is queried as to whether it is cyclic |
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or what it's hybridization state is the information is perceived |
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automatically. The perception of a particular trait is actually |
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performed on the entire molecule the first time it is requested of |
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an atom or bond, and stored for subsequent requests for the same |
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trait of additional atoms or bonds.The OBAtom class is similar to |
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OBMol and the whole of Open Babel in that data access and modification |
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is done through Get and Set methods. |
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|
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The following code demonstrates how to print out the atom numbers, |
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element numbers, and coordinates of a molecule: |
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\code |
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OBMol mol; |
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|
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FOR_ATOMS_IN_MOL(atom, mol) |
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{ |
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cout << atom->GetIdx() << ` `; |
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cout << atom->GetAtomicNum() << ` `; |
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cout << atom->GetVector() << endl; |
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} |
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\endcode |
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A number of the property member functions indicate that atoms |
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have some knowlege of their covalently attached neighbor atoms. |
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Bonding information is partly redundant within a molecule in |
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that an OBMol has a complete list of bonds in a molecule, and |
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an OBAtom has a list bonds of which it is a member. The following |
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code demonstrates how an OBAtom uses its bond information to loop |
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over atoms attached to itself: |
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\code |
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OBMol mol; |
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OBAtom *atom; |
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|
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atom = mol.GetAtom(1); |
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FOR_NBORS_OF_ATOM(nbr, atom) |
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{ |
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cout << "atom #" << atom->GetIdx() << " is attached to atom #" << nbr->GetIdx() << endl; |
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} |
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\endcode |
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|
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should produce an output like |
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\code |
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atom #1 is attached to atom #2 |
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\endcode |
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*/ |
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|
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extern OBAromaticTyper aromtyper; |
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extern OBAtomTyper atomtyper; |
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extern OBPhModel phmodel; |
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|
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// |
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// OBAtom member functions |
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// |
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|
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OBAtom::OBAtom() |
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{ |
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_parent = (OBMol*)NULL; |
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Clear(); |
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} |
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|
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OBAtom::~OBAtom() |
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{ |
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if (_residue != NULL) |
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_residue->RemoveAtom(this); |
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if (!_vdata.empty()) |
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{ |
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vector<OBGenericData*>::iterator m; |
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for (m = _vdata.begin();m != _vdata.end();m++) |
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delete *m; |
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_vdata.clear(); |
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} |
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} |
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|
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void OBAtom::Clear() |
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{ |
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_c = (double**)NULL; |
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_cidx = 0; |
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_flags=0; |
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_idx = 0; |
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_hyb = 0; |
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_ele = (char)0; |
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_isotope = 0; |
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_spinmultiplicity=0; // CM 18 Sept 2003 |
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_impval = 0; |
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_fcharge = 0; |
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_type[0] = '\0'; |
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_pcharge = 0.0; |
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_vbond.clear(); |
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_vbond.reserve(4); |
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_residue = (OBResidue*)NULL; |
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_vdata.clear(); |
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} |
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|
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OBAtom &OBAtom::operator=(OBAtom &src) |
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//copy atom information |
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//bond info is not copied here as ptrs may be invalid |
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//vdata is also not copied yet (again it's unclear what can work) |
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{ |
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_idx = src.GetIdx(); |
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_hyb = src.GetHyb(); |
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_ele = src.GetAtomicNum(); |
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_isotope = src.GetIsotope(); |
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_fcharge = src.GetFormalCharge(); |
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_spinmultiplicity = src.GetSpinMultiplicity(); |
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strcpy(_type,src.GetType()); |
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_pcharge = src.GetPartialCharge(); |
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_v = src.GetVector(); |
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_flags = src.GetFlag(); |
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_residue = (OBResidue*)NULL; |
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return(*this); |
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} |
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|
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bool OBAtom::IsConnected(OBAtom *a1) |
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{ |
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vector<OBEdgeBase*>::iterator i; |
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OBBond *bond; |
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|
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for (bond = BeginBond(i);bond;bond = NextBond(i)) |
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if (bond->GetBeginAtom() == a1 || bond->GetEndAtom() == a1) |
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return(true); |
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|
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return(false); |
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} |
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|
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bool OBAtom::IsOneThree(OBAtom *a1) |
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{ |
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OBAtom *atom1,*atom2; |
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OBBond *bond1,*bond2; |
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vector<OBEdgeBase*>::iterator i,j; |
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atom1 = this; |
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atom2 = a1; |
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|
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for (bond1 = atom1->BeginBond(i);bond1;bond1 = atom1->NextBond(i)) |
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for (bond2 = atom2->BeginBond(j);bond2;bond2 = atom2->NextBond(j)) |
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if (bond1->GetNbrAtom(atom1) == bond2->GetNbrAtom(atom2)) |
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return(true); |
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|
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return(false); |
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} |
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|
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bool OBAtom::IsOneFour(OBAtom *a1) |
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{ |
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OBAtom *atom1,*atom2; |
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OBBond *bond1,*bond2; |
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vector<OBEdgeBase*>::iterator i,j; |
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atom1 = this; |
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atom2 = a1; |
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|
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for (bond1 = atom1->BeginBond(i);bond1;bond1 = atom1->NextBond(i)) |
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for (bond2 = atom2->BeginBond(j);bond2;bond2 = atom2->NextBond(j)) |
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if ((bond1->GetNbrAtom(atom1))->IsConnected(bond2->GetNbrAtom(atom2))) |
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return(true); |
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|
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return(false); |
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} |
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|
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bool OBAtom::IsAxial() |
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{ |
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double tor; |
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OBAtom *a,*b,*c; |
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vector<OBEdgeBase*>::iterator i,j,k; |
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|
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for (a = BeginNbrAtom(i);a;a = NextNbrAtom(i)) |
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if (a->GetHyb() == 3 && a->IsInRing() && !(*i)->IsInRing()) |
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for (b = a->BeginNbrAtom(j);b;b = a->NextNbrAtom(j)) |
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if (b != this && b->IsInRing() && b->GetHyb() == 3) |
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for (c = b->BeginNbrAtom(k);c;c = b->NextNbrAtom(k)) |
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if (c != a && c->IsInRing()) |
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{ |
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tor = fabs(((OBMol*)GetParent())->GetTorsion(this,a,b,c)); |
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return(tor > 55.0 && tor < 75.0); |
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} |
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|
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return(false); |
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} |
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|
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|
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bool OBAtom::HasAlphaBetaUnsat(bool includePandS) |
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{ |
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OBAtom *a1,*a2; |
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vector<OBEdgeBase*>::iterator i,j; |
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|
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for (a1 = BeginNbrAtom(i);a1;a1 = NextNbrAtom(i)) |
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if (includePandS || (!a1->IsPhosphorus() && !a1->IsSulfur())) |
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for (a2 = a1->BeginNbrAtom(j);a2;a2 = a1->NextNbrAtom(j)) |
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if (a2 != this && ((*j)->GetBO() == 2 || (*j)->GetBO() == 3 || (*j)->GetBO() == 5)) |
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return(true); |
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|
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return(false); |
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} |
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|
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bool OBAtom::HasBondOfOrder(unsigned int order) |
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{ |
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator i; |
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for (bond = BeginBond(i);bond;bond = NextBond(i)) |
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if (bond->GetBO() == order) |
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return(true); |
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|
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return(false); |
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} |
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|
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int OBAtom::CountBondsOfOrder(unsigned int order) |
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{ |
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int count = 0; |
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator i; |
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for (bond = BeginBond(i);bond;bond = NextBond(i)) |
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if (bond->GetBO() == order) |
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count++; |
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|
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return(count); |
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} |
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|
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bool OBAtom::HasNonSingleBond() |
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{ |
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator i; |
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for (bond = BeginBond(i);bond;bond = NextBond(i)) |
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if (bond->GetBO() != 1) |
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return(true); |
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|
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return(false); |
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} |
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|
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bool OBAtom::IsPolarHydrogen() |
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{ |
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if (!IsHydrogen()) |
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return(false); |
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|
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OBAtom *atom; |
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator i; |
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for (bond = BeginBond(i);bond;bond = NextBond(i)) |
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{ |
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atom = bond->GetNbrAtom(this); |
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if (atom->GetAtomicNum() == 7) |
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return(true); |
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if (atom->GetAtomicNum() == 8) |
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return(true); |
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if (atom->GetAtomicNum() == 15) |
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return(true); |
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if (atom->GetAtomicNum() == 16) |
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return(true); |
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} |
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|
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return(false); |
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} |
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|
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bool OBAtom::IsNonPolarHydrogen() |
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{ |
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if (!IsHydrogen()) |
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return(false); |
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|
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OBAtom *atom; |
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator i; |
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for (bond = BeginBond(i);bond;bond = NextBond(i)) |
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{ |
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atom = bond->GetNbrAtom(this); |
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if (atom->GetAtomicNum() == 6) |
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return(true); |
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} |
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|
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return(false); |
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} |
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|
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vector3 &OBAtom::GetVector() |
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{ |
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if (!_c) |
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return(_v); |
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|
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_v.Set((*_c)[_cidx],(*_c)[_cidx+1],(*_c)[_cidx+2]); |
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return(_v); |
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} |
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|
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void OBAtom::SetVector() |
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{ |
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// obAssert(_c); |
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if (_c) |
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_v.Set((*_c)[_cidx],(*_c)[_cidx+1],(*_c)[_cidx+2]); |
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} |
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|
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void OBAtom::SetVector(vector3 &v) |
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{ |
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if (!_c) |
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_v = v; |
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else |
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{ |
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(*_c)[_cidx ] = v.x(); |
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(*_c)[_cidx+1] = v.y(); |
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(*_c)[_cidx+2] = v.z(); |
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} |
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} |
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|
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void OBAtom::SetVector(const double x,const double y,const double z) |
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{ |
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if (!_c) |
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_v.Set(x,y,z); |
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else |
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{ |
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(*_c)[_cidx ] = x; |
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(*_c)[_cidx+1] = y; |
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(*_c)[_cidx+2] = z; |
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} |
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} |
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|
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void OBAtom::SetType(char *type) |
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{ |
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strcpy(_type,type); |
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if (_ele == 1 && type[0] == 'D') |
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_isotope = 2; |
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} |
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|
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void OBAtom::SetType(string &type) |
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{ |
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strcpy(_type,type.c_str()); |
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if (_ele == 1 && type[0] == 'D') |
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_isotope = 2; |
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} |
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|
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void OBAtom::SetIsotope(unsigned int iso) |
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{ |
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if (_ele == 1 && iso == 2) |
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SetType("D"); |
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else if (_ele == 1 && (iso == 1 || iso == 0)) |
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SetType("H"); |
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|
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_isotope = iso; |
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} |
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|
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OBAtom *OBAtom::GetNextAtom() |
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{ |
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OBMol *mol = (OBMol*)GetParent(); |
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return(((unsigned)GetIdx() == mol->NumAtoms())? NULL : mol->GetAtom(GetIdx()+1)); |
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} |
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|
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OBResidue *OBAtom::GetResidue() |
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{ |
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if (_residue != NULL) |
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return _residue; |
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else if (!((OBMol*)GetParent())->HasChainsPerceived()) |
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{ |
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chainsparser.PerceiveChains(*((OBMol*)GetParent())); |
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((OBMol*)GetParent())->SetChainsPerceived(); |
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return _residue; |
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} |
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else |
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return NULL; |
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} |
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|
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double OBAtom::GetAtomicMass() const |
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{ |
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if (_isotope == 0) |
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return etab.GetMass(_ele); |
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else |
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return isotab.GetExactMass(_ele, _isotope); |
| 409 |
} |
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|
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double OBAtom::GetExactMass() const |
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{ |
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return isotab.GetExactMass(_ele, _isotope); |
| 414 |
} |
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|
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char *OBAtom::GetType() |
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{ |
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OBMol *mol = (OBMol*)GetParent(); |
| 419 |
if (mol && !mol->HasAtomTypesPerceived()) |
| 420 |
atomtyper.AssignTypes(*((OBMol*)GetParent())); |
| 421 |
|
| 422 |
if (strlen(_type) == 0) // Somehow we still don't have a type! |
| 423 |
{ |
| 424 |
char num[6]; |
| 425 |
string fromType = ttab.GetFromType(); // save previous types |
| 426 |
string toType = ttab.GetToType(); |
| 427 |
|
| 428 |
ttab.SetFromType("ATN"); |
| 429 |
ttab.SetToType("INT"); |
| 430 |
snprintf(num, 6, "%d", GetAtomicNum()); |
| 431 |
ttab.Translate(_type, num); |
| 432 |
|
| 433 |
ttab.SetFromType(fromType.c_str()); |
| 434 |
ttab.SetToType(toType.c_str()); |
| 435 |
} |
| 436 |
if (_ele == 1 && _isotope == 2) |
| 437 |
snprintf(_type, 6, "%s", "D"); |
| 438 |
|
| 439 |
return(_type); |
| 440 |
} |
| 441 |
|
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unsigned int OBAtom::GetImplicitValence() const |
| 443 |
{ |
| 444 |
OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent(); |
| 445 |
if (mol && !mol->HasImplicitValencePerceived()) |
| 446 |
atomtyper.AssignImplicitValence(*((OBMol*)((OBAtom*)this)->GetParent())); |
| 447 |
|
| 448 |
return((unsigned int)_impval); |
| 449 |
} |
| 450 |
|
| 451 |
unsigned int OBAtom::GetHyb() const |
| 452 |
{ |
| 453 |
//hybridization is assigned when atoms are typed |
| 454 |
OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent(); |
| 455 |
if (mol && !mol->HasHybridizationPerceived()) |
| 456 |
atomtyper.AssignHyb(*mol); |
| 457 |
|
| 458 |
return(_hyb); |
| 459 |
} |
| 460 |
|
| 461 |
|
| 462 |
unsigned int OBAtom::GetHvyValence() const |
| 463 |
{ |
| 464 |
unsigned int count=0; |
| 465 |
|
| 466 |
OBBond *bond; |
| 467 |
vector<OBEdgeBase*>::iterator i; |
| 468 |
for (bond = ((OBAtom*)this)->BeginBond(i); bond; bond = ((OBAtom*)this)->NextBond(i)) |
| 469 |
if (!(bond->GetNbrAtom((OBAtom*)this)->IsHydrogen())) |
| 470 |
count++; |
| 471 |
|
| 472 |
return(count); |
| 473 |
} |
| 474 |
|
| 475 |
unsigned int OBAtom::GetHeteroValence() const |
| 476 |
{ |
| 477 |
unsigned int count=0; |
| 478 |
OBBond *bond; |
| 479 |
vector<OBEdgeBase*>::iterator i; |
| 480 |
for (bond = ((OBAtom*)this)->BeginBond(i);bond;bond = ((OBAtom*)this)->NextBond(i)) |
| 481 |
if (bond->GetNbrAtom((OBAtom*)this)->IsHeteroatom()) |
| 482 |
count++; |
| 483 |
|
| 484 |
return((unsigned int)count); |
| 485 |
} |
| 486 |
|
| 487 |
double OBAtom::GetPartialCharge() |
| 488 |
{ |
| 489 |
if (!GetParent()) |
| 490 |
return(_pcharge); |
| 491 |
if (!((OBMol*)GetParent())->AutomaticPartialCharge()) |
| 492 |
return(_pcharge); |
| 493 |
|
| 494 |
if (!((OBMol*)GetParent())->HasPartialChargesPerceived()) |
| 495 |
{ |
| 496 |
//seed partial charges are set in the atom typing procedure |
| 497 |
OBAtom *atom; |
| 498 |
OBMol *mol = (OBMol*)GetParent(); |
| 499 |
vector<OBNodeBase*>::iterator i; |
| 500 |
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i)) |
| 501 |
atom->SetPartialCharge(0.0); |
| 502 |
|
| 503 |
phmodel.AssignSeedPartialCharge(*((OBMol*)GetParent())); |
| 504 |
OBGastChrg gc; |
| 505 |
gc.AssignPartialCharges(*((OBMol*)GetParent())); |
| 506 |
} |
| 507 |
|
| 508 |
return(_pcharge); |
| 509 |
} |
| 510 |
|
| 511 |
//! Returns true if nitrogen is part of an amide |
| 512 |
bool OBAtom::IsAmideNitrogen() |
| 513 |
{ |
| 514 |
if (!IsNitrogen()) |
| 515 |
return(false); |
| 516 |
|
| 517 |
OBAtom *nbratom,*atom; |
| 518 |
OBBond *abbond,*bond; |
| 519 |
|
| 520 |
vector<OBEdgeBase*>::iterator i,j; |
| 521 |
atom = this; |
| 522 |
for (bond = BeginBond(i);bond;bond = NextBond(i)) |
| 523 |
{ |
| 524 |
nbratom = bond->GetNbrAtom(atom); |
| 525 |
for (abbond = nbratom->BeginBond(j);abbond;abbond = nbratom->NextBond(j)) |
| 526 |
if (abbond->GetBO() == 2 && |
| 527 |
(((abbond->GetNbrAtom(nbratom))->GetAtomicNum() == 8) || |
| 528 |
((abbond->GetNbrAtom(nbratom))->GetAtomicNum() == 16))) |
| 529 |
return(true); |
| 530 |
} |
| 531 |
|
| 532 |
return(false); |
| 533 |
} |
| 534 |
|
| 535 |
bool OBAtom::IsAromaticNOxide() |
| 536 |
{ |
| 537 |
if (!IsNitrogen() || !IsAromatic()) |
| 538 |
return(false); |
| 539 |
|
| 540 |
OBAtom *atom; |
| 541 |
vector<OBEdgeBase*>::iterator i; |
| 542 |
|
| 543 |
for (atom = BeginNbrAtom(i);atom;atom = NextNbrAtom(i)) |
| 544 |
if (atom->IsOxygen() && !(*i)->IsInRing() && (*i)->GetBO() == 2) |
| 545 |
return(true); |
| 546 |
|
| 547 |
return(false); |
| 548 |
} |
| 549 |
|
| 550 |
bool OBAtom::IsCarboxylOxygen() |
| 551 |
{ |
| 552 |
if (!IsOxygen()) |
| 553 |
return(false); |
| 554 |
if (GetHvyValence() != 1) |
| 555 |
return(false); |
| 556 |
|
| 557 |
OBAtom *atom; |
| 558 |
OBBond *bond; |
| 559 |
vector<OBEdgeBase*>::iterator i; |
| 560 |
|
| 561 |
atom = NULL; |
| 562 |
for (bond = BeginBond(i);bond;bond = NextBond(i)) |
| 563 |
if ((bond->GetNbrAtom(this))->IsCarbon()) |
| 564 |
{ |
| 565 |
atom = bond->GetNbrAtom(this); |
| 566 |
break; |
| 567 |
} |
| 568 |
if (!atom) |
| 569 |
return(false); |
| 570 |
if (atom->CountFreeOxygens() != 2) |
| 571 |
return(false); |
| 572 |
|
| 573 |
//atom is connected to a carbon that has a total |
| 574 |
//of 2 attached free oxygens |
| 575 |
return(true); |
| 576 |
} |
| 577 |
|
| 578 |
bool OBAtom::IsPhosphateOxygen() |
| 579 |
{ |
| 580 |
if (!IsOxygen()) |
| 581 |
return(false); |
| 582 |
if (GetHvyValence() != 1) |
| 583 |
return(false); |
| 584 |
|
| 585 |
OBAtom *atom; |
| 586 |
OBBond *bond; |
| 587 |
vector<OBEdgeBase*>::iterator i; |
| 588 |
|
| 589 |
atom = NULL; |
| 590 |
for (bond = BeginBond(i);bond;bond = NextBond(i)) |
| 591 |
if ((bond->GetNbrAtom(this))->IsPhosphorus()) |
| 592 |
{ |
| 593 |
atom = bond->GetNbrAtom(this); |
| 594 |
break; |
| 595 |
} |
| 596 |
if (!atom) |
| 597 |
return(false); |
| 598 |
if (atom->CountFreeOxygens() > 2) |
| 599 |
return(true); |
| 600 |
|
| 601 |
//atom is connected to a carbon that has a total |
| 602 |
//of 2 attached free oxygens |
| 603 |
return(false); |
| 604 |
} |
| 605 |
|
| 606 |
bool OBAtom::IsSulfateOxygen() |
| 607 |
{ |
| 608 |
if (!IsOxygen()) |
| 609 |
return(false); |
| 610 |
if (GetHvyValence() != 1) |
| 611 |
return(false); |
| 612 |
|
| 613 |
OBAtom *atom; |
| 614 |
OBBond *bond; |
| 615 |
vector<OBEdgeBase*>::iterator i; |
| 616 |
|
| 617 |
atom = NULL; |
| 618 |
for (bond = BeginBond(i);bond;bond = NextBond(i)) |
| 619 |
if ((bond->GetNbrAtom(this))->IsSulfur()) |
| 620 |
{ |
| 621 |
atom = bond->GetNbrAtom(this); |
| 622 |
break; |
| 623 |
} |
| 624 |
if (!atom) |
| 625 |
return(false); |
| 626 |
if (atom->CountFreeOxygens() < 3) |
| 627 |
return(false); |
| 628 |
|
| 629 |
//atom is connected to a carbon that has a total |
| 630 |
//of 2 attached free oxygens |
| 631 |
return(true); |
| 632 |
} |
| 633 |
|
| 634 |
bool OBAtom::IsNitroOxygen() |
| 635 |
{ |
| 636 |
if (!IsOxygen()) |
| 637 |
return(false); |
| 638 |
if (GetHvyValence() != 1) |
| 639 |
return(false); |
| 640 |
|
| 641 |
OBAtom *atom; |
| 642 |
OBBond *bond; |
| 643 |
vector<OBEdgeBase*>::iterator i; |
| 644 |
|
| 645 |
atom = NULL; |
| 646 |
for (bond = BeginBond(i);bond;bond = NextBond(i)) |
| 647 |
if ((bond->GetNbrAtom(this))->IsNitrogen()) |
| 648 |
{ |
| 649 |
atom = bond->GetNbrAtom(this); |
| 650 |
break; |
| 651 |
} |
| 652 |
if (!atom) |
| 653 |
return(false); |
| 654 |
if (atom->CountFreeOxygens() != 2) |
| 655 |
return(false); |
| 656 |
|
| 657 |
//atom is connected to a nitrogen that has a total |
| 658 |
//of 2 attached free oxygens |
| 659 |
return(true); |
| 660 |
} |
| 661 |
|
| 662 |
bool OBAtom::IsHeteroatom() |
| 663 |
{ |
| 664 |
switch(GetAtomicNum()) |
| 665 |
{ |
| 666 |
case 7: |
| 667 |
case 8: |
| 668 |
case 15: |
| 669 |
case 16: |
| 670 |
case 33: |
| 671 |
case 34: |
| 672 |
case 51: |
| 673 |
case 52: |
| 674 |
case 83: |
| 675 |
case 84: |
| 676 |
return(true); |
| 677 |
} |
| 678 |
return(false); |
| 679 |
} |
| 680 |
|
| 681 |
bool OBAtom::IsNotCorH() |
| 682 |
{ |
| 683 |
switch(GetAtomicNum()) |
| 684 |
{ |
| 685 |
case 1: |
| 686 |
case 6: |
| 687 |
return(false); |
| 688 |
} |
| 689 |
return(true); |
| 690 |
} |
| 691 |
|
| 692 |
bool OBAtom::IsAromatic() const |
| 693 |
{ |
| 694 |
if (((OBAtom*)this)->HasFlag(OB_AROMATIC_ATOM)) |
| 695 |
return(true); |
| 696 |
|
| 697 |
OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent(); |
| 698 |
|
| 699 |
if (!mol->HasAromaticPerceived()) |
| 700 |
{ |
| 701 |
aromtyper.AssignAromaticFlags(*mol); |
| 702 |
if (((OBAtom*)this)->HasFlag(OB_AROMATIC_ATOM)) |
| 703 |
return(true); |
| 704 |
} |
| 705 |
|
| 706 |
return(false); |
| 707 |
} |
| 708 |
|
| 709 |
bool OBAtom::IsInRing() const |
| 710 |
{ |
| 711 |
if (((OBAtom*)this)->HasFlag(OB_RING_ATOM)) |
| 712 |
return(true); |
| 713 |
|
| 714 |
OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent(); |
| 715 |
if (!mol->HasRingAtomsAndBondsPerceived()) |
| 716 |
{ |
| 717 |
mol->FindRingAtomsAndBonds(); |
| 718 |
if (((OBAtom*)this)->HasFlag(OB_RING_ATOM)) |
| 719 |
return(true); |
| 720 |
} |
| 721 |
|
| 722 |
return(false); |
| 723 |
} |
| 724 |
|
| 725 |
bool OBAtom::IsChiral() |
| 726 |
{ |
| 727 |
if (HasFlag(OB_CHIRAL_ATOM)) |
| 728 |
return(true); |
| 729 |
|
| 730 |
if (!((OBMol*)GetParent())->HasChiralityPerceived()) |
| 731 |
{ |
| 732 |
((OBMol*)GetParent())->FindChiralCenters(); |
| 733 |
if (HasFlag(OB_CHIRAL_ATOM)) |
| 734 |
return(true); |
| 735 |
} |
| 736 |
|
| 737 |
return(false); |
| 738 |
} |
| 739 |
|
| 740 |
bool OBAtom::IsInRingSize(int size) const |
| 741 |
{ |
| 742 |
vector<OBRing*> rlist; |
| 743 |
vector<OBRing*>::iterator i; |
| 744 |
|
| 745 |
OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent(); |
| 746 |
if (!mol->HasSSSRPerceived()) |
| 747 |
mol->FindSSSR(); |
| 748 |
|
| 749 |
if (!((OBAtom*)this)->HasFlag(OB_RING_ATOM)) |
| 750 |
return(false); |
| 751 |
|
| 752 |
rlist = mol->GetSSSR(); |
| 753 |
for (i = rlist.begin();i != rlist.end();i++) |
| 754 |
if ((*i)->IsInRing(GetIdx()) && (*i)->PathSize() == size) |
| 755 |
return(true); |
| 756 |
|
| 757 |
return(false); |
| 758 |
} |
| 759 |
|
| 760 |
unsigned int OBAtom::MemberOfRingCount() const |
| 761 |
{ |
| 762 |
vector<OBRing*> rlist; |
| 763 |
vector<OBRing*>::iterator i; |
| 764 |
unsigned int count=0; |
| 765 |
|
| 766 |
OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent(); |
| 767 |
|
| 768 |
if (!mol->HasSSSRPerceived()) |
| 769 |
mol->FindSSSR(); |
| 770 |
|
| 771 |
if (!((OBAtom*)this)->IsInRing()) |
| 772 |
return(0); |
| 773 |
|
| 774 |
rlist = mol->GetSSSR(); |
| 775 |
|
| 776 |
for (i = rlist.begin();i != rlist.end();i++) |
| 777 |
if ((*i)->IsInRing(GetIdx())) |
| 778 |
count++; |
| 779 |
|
| 780 |
return((unsigned int)count); |
| 781 |
} |
| 782 |
|
| 783 |
unsigned int OBAtom::MemberOfRingSize() const |
| 784 |
{ |
| 785 |
vector<OBRing*> rlist; |
| 786 |
vector<OBRing*>::iterator i; |
| 787 |
|
| 788 |
OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent(); |
| 789 |
|
| 790 |
if (!mol->HasSSSRPerceived()) |
| 791 |
mol->FindSSSR(); |
| 792 |
|
| 793 |
if (!((OBAtom*)this)->IsInRing()) |
| 794 |
return(0); |
| 795 |
|
| 796 |
rlist = mol->GetSSSR(); |
| 797 |
|
| 798 |
for (i = rlist.begin();i != rlist.end();i++) |
| 799 |
if ((*i)->IsInRing(GetIdx())) |
| 800 |
return((*i)->Size()); |
| 801 |
|
| 802 |
return(0); |
| 803 |
} |
| 804 |
|
| 805 |
double OBAtom::SmallestBondAngle() |
| 806 |
{ |
| 807 |
OBAtom *b, *c; |
| 808 |
vector3 v1, v2; |
| 809 |
double degrees, minDegrees; |
| 810 |
// vector<OBNodeBase*>::iterator i; |
| 811 |
vector<OBEdgeBase*>::iterator j,k; |
| 812 |
|
| 813 |
minDegrees = 360.0; |
| 814 |
|
| 815 |
for (b = BeginNbrAtom(j); b; b = NextNbrAtom(j)) |
| 816 |
{ |
| 817 |
k = j; |
| 818 |
for (c = NextNbrAtom(k); c; c = NextNbrAtom(k)) |
| 819 |
{ |
| 820 |
v1 = b->GetVector() - GetVector(); |
| 821 |
v2 = c->GetVector() - GetVector(); |
| 822 |
degrees = vectorAngle(v1, v2); |
| 823 |
if (degrees < minDegrees) |
| 824 |
minDegrees = degrees; |
| 825 |
} |
| 826 |
} |
| 827 |
return minDegrees; |
| 828 |
} |
| 829 |
|
| 830 |
double OBAtom::AverageBondAngle() |
| 831 |
{ |
| 832 |
OBAtom *b, *c; |
| 833 |
vector3 v1, v2; |
| 834 |
double degrees, avgDegrees; |
| 835 |
// vector<OBNodeBase*>::iterator i; |
| 836 |
vector<OBEdgeBase*>::iterator j,k; |
| 837 |
int n=0; |
| 838 |
|
| 839 |
avgDegrees = 0.0; |
| 840 |
|
| 841 |
for (b = BeginNbrAtom(j); b; b = NextNbrAtom(j)) |
| 842 |
{ |
| 843 |
k = j; |
| 844 |
for (c = NextNbrAtom(k); c; c = NextNbrAtom(k)) |
| 845 |
{ |
| 846 |
v1 = b->GetVector() - GetVector(); |
| 847 |
v2 = c->GetVector() - GetVector(); |
| 848 |
degrees = vectorAngle(v1, v2); |
| 849 |
avgDegrees += degrees; |
| 850 |
n++; |
| 851 |
} |
| 852 |
} |
| 853 |
|
| 854 |
if (n >=1) |
| 855 |
avgDegrees /= n; |
| 856 |
|
| 857 |
return avgDegrees; |
| 858 |
} |
| 859 |
|
| 860 |
unsigned int OBAtom::CountFreeOxygens() const |
| 861 |
{ |
| 862 |
unsigned int count = 0; |
| 863 |
OBAtom *atom; |
| 864 |
OBBond *bond; |
| 865 |
vector<OBEdgeBase*>::iterator i; |
| 866 |
|
| 867 |
for (bond = ((OBAtom*)this)->BeginBond(i);bond;bond = ((OBAtom*)this)->NextBond(i)) |
| 868 |
{ |
| 869 |
atom = bond->GetNbrAtom((OBAtom*)this); |
| 870 |
if (atom->IsOxygen() && atom->GetHvyValence() == 1) |
| 871 |
count++; |
| 872 |
} |
| 873 |
|
| 874 |
return(count); |
| 875 |
} |
| 876 |
|
| 877 |
unsigned int OBAtom::BOSum() const |
| 878 |
{ |
| 879 |
unsigned int bo; |
| 880 |
unsigned int bosum=0; |
| 881 |
OBBond *bond; |
| 882 |
vector<OBEdgeBase*>::iterator i; |
| 883 |
|
| 884 |
for (bond = ((OBAtom*)this)->BeginBond(i);bond;bond = ((OBAtom*)this)->NextBond(i)) |
| 885 |
{ |
| 886 |
bo = bond->GetBO(); |
| 887 |
bosum += (bo < 4) ? 2*bo : 3; |
| 888 |
} |
| 889 |
|
| 890 |
bosum /= 2; |
| 891 |
return(bosum); |
| 892 |
} |
| 893 |
|
| 894 |
unsigned int OBAtom::KBOSum() const |
| 895 |
{ |
| 896 |
OBBond *bond; |
| 897 |
unsigned int bosum; |
| 898 |
vector<OBEdgeBase*>::iterator i; |
| 899 |
|
| 900 |
bosum = GetImplicitValence(); |
| 901 |
|
| 902 |
for (bond = ((OBAtom*)this)->BeginBond(i);bond;bond = ((OBAtom*)this)->NextBond(i)) |
| 903 |
{ |
| 904 |
if (bond->IsKDouble()) |
| 905 |
bosum++; |
| 906 |
else if (bond->IsKTriple()) |
| 907 |
bosum += 2; |
| 908 |
} |
| 909 |
|
| 910 |
return(bosum); |
| 911 |
} |
| 912 |
|
| 913 |
unsigned int OBAtom::ImplicitHydrogenCount() const |
| 914 |
{ |
| 915 |
//handles H,C,N,S,O,X |
| 916 |
OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent(); |
| 917 |
if (mol && !mol->HasImplicitValencePerceived()) |
| 918 |
atomtyper.AssignImplicitValence(*((OBMol*)((OBAtom*)this)->GetParent())); |
| 919 |
|
| 920 |
int impval = _impval - GetHvyValence(); |
| 921 |
//Jan 05 Implicit valency now left alone; use spin multiplicity for implicit Hs |
| 922 |
int mult = GetSpinMultiplicity(); |
| 923 |
if(mult==2) //radical |
| 924 |
impval-=1; |
| 925 |
else if(mult==1 || mult==3) //carbene |
| 926 |
impval-=2; |
| 927 |
return((impval>0)?impval:0); |
| 928 |
} |
| 929 |
|
| 930 |
unsigned int OBAtom::ExplicitHydrogenCount() const |
| 931 |
{ |
| 932 |
int numH=0; |
| 933 |
OBAtom *atom; |
| 934 |
vector<OBEdgeBase*>::iterator i; |
| 935 |
for (atom = ((OBAtom*)this)->BeginNbrAtom(i);atom;atom = ((OBAtom*)this)->NextNbrAtom(i)) |
| 936 |
if (atom->IsHydrogen()) |
| 937 |
numH++; |
| 938 |
|
| 939 |
return(numH); |
| 940 |
} |
| 941 |
|
| 942 |
bool OBAtom::DeleteBond(OBBond *bond) |
| 943 |
{ |
| 944 |
vector<OBEdgeBase*>::iterator i; |
| 945 |
for (i = _vbond.begin();i != _vbond.end();i++) |
| 946 |
if ((OBBond*)bond == *i) |
| 947 |
{ |
| 948 |
_vbond.erase(i); |
| 949 |
return(true); |
| 950 |
} |
| 951 |
return(false); |
| 952 |
} |
| 953 |
|
| 954 |
bool OBAtom::MatchesSMARTS(const char *pattern) |
| 955 |
{ |
| 956 |
OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent(); |
| 957 |
vector<vector<int> > mlist; |
| 958 |
vector<vector<int> >::iterator l; |
| 959 |
|
| 960 |
OBSmartsPattern test; |
| 961 |
test.Init(pattern); |
| 962 |
if (test.Match(*mol)) |
| 963 |
{ |
| 964 |
mlist = test.GetUMapList(); |
| 965 |
for (l = mlist.begin(); l != mlist.end(); l++) |
| 966 |
if (GetIdx() == mol->GetAtom((*l)[0])->GetIdx()) |
| 967 |
return true; |
| 968 |
} |
| 969 |
return false; |
| 970 |
} |
| 971 |
|
| 972 |
OBBond *OBAtom::BeginBond(vector<OBEdgeBase*>::iterator &i) |
| 973 |
{ |
| 974 |
i = _vbond.begin(); |
| 975 |
return((i == _vbond.end()) ? (OBBond*)NULL : (OBBond*)*i); |
| 976 |
} |
| 977 |
|
| 978 |
OBBond *OBAtom::NextBond(vector<OBEdgeBase*>::iterator &i) |
| 979 |
{ |
| 980 |
i++; |
| 981 |
return((i == _vbond.end()) ? (OBBond*)NULL : (OBBond*)*i); |
| 982 |
} |
| 983 |
|
| 984 |
OBAtom *OBAtom::BeginNbrAtom(vector<OBEdgeBase*>::iterator &i) |
| 985 |
{ |
| 986 |
i = _vbond.begin(); |
| 987 |
return((i != _vbond.end()) ? ((OBBond*) *i)->GetNbrAtom(this):NULL); |
| 988 |
} |
| 989 |
|
| 990 |
OBAtom *OBAtom::NextNbrAtom(vector<OBEdgeBase*>::iterator &i) |
| 991 |
{ |
| 992 |
i++; |
| 993 |
return((i != _vbond.end()) ? ((OBBond*) *i)->GetNbrAtom(this):NULL); |
| 994 |
} |
| 995 |
|
| 996 |
double OBAtom::GetDistance(OBAtom *b) |
| 997 |
{ |
| 998 |
return(( this->GetVector() - b->GetVector() ).length()); |
| 999 |
} |
| 1000 |
|
| 1001 |
double OBAtom::GetDistance(int b) |
| 1002 |
{ |
| 1003 |
OBMol *mol = (OBMol*)GetParent(); |
| 1004 |
return(( this->GetVector() - mol->GetAtom(b)->GetVector() ).length()); |
| 1005 |
} |
| 1006 |
|
| 1007 |
double OBAtom::GetAngle(OBAtom *b, OBAtom *c) |
| 1008 |
{ |
| 1009 |
vector3 v1,v2; |
| 1010 |
|
| 1011 |
v1 = this->GetVector() - b->GetVector(); |
| 1012 |
v2 = c->GetVector() - b->GetVector(); |
| 1013 |
|
| 1014 |
return(vectorAngle(v1, v2)); |
| 1015 |
} |
| 1016 |
|
| 1017 |
double OBAtom::GetAngle(int b, int c) |
| 1018 |
{ |
| 1019 |
OBMol *mol = (OBMol*)GetParent(); |
| 1020 |
vector3 v1,v2; |
| 1021 |
|
| 1022 |
v1 = this->GetVector() - mol->GetAtom(b)->GetVector(); |
| 1023 |
v2 = mol->GetAtom(c)->GetVector() - mol->GetAtom(b)->GetVector(); |
| 1024 |
|
| 1025 |
return(vectorAngle(v1, v2)); |
| 1026 |
} |
| 1027 |
|
| 1028 |
bool OBAtom::GetNewBondVector(vector3 &v,double length) |
| 1029 |
{ |
| 1030 |
// ***experimental code*** |
| 1031 |
|
| 1032 |
OBAtom *atom; |
| 1033 |
vector<OBEdgeBase*>::iterator i,j; |
| 1034 |
v = VZero; |
| 1035 |
|
| 1036 |
if (GetValence() == 0) |
| 1037 |
{ |
| 1038 |
v = VX; |
| 1039 |
v *= length; |
| 1040 |
v += GetVector(); |
| 1041 |
return(true); |
| 1042 |
} |
| 1043 |
|
| 1044 |
if (GetValence() == 1) |
| 1045 |
{ |
| 1046 |
vector3 vtmp,v1,v2; |
| 1047 |
atom = BeginNbrAtom(i); |
| 1048 |
if (atom) |
| 1049 |
vtmp = GetVector() - atom->GetVector(); |
| 1050 |
|
| 1051 |
if (GetHyb() == 2 || (IsOxygen() && HasAlphaBetaUnsat())) |
| 1052 |
{ |
| 1053 |
bool quit = false; |
| 1054 |
OBAtom *a1,*a2; |
| 1055 |
v2 = VZero; |
| 1056 |
for (a1 = BeginNbrAtom(i);a1 && !quit;a1 = NextNbrAtom(i)) |
| 1057 |
for (a2 = a1->BeginNbrAtom(j);a2 && !quit;a2 = a1->NextNbrAtom(j)) |
| 1058 |
if (a1 && a2 && a2 != this) |
| 1059 |
{ |
| 1060 |
v2 = a1->GetVector() - a2->GetVector(); |
| 1061 |
quit = true; |
| 1062 |
} |
| 1063 |
|
| 1064 |
if (v2 == VZero) |
| 1065 |
{ |
| 1066 |
v1 = cross(vtmp,VX); |
| 1067 |
v2 = cross(vtmp,VY); |
| 1068 |
if (v1.length() < v2.length()) |
| 1069 |
v1 = v2; |
| 1070 |
} |
| 1071 |
else |
| 1072 |
v1 = cross(vtmp,v2); |
| 1073 |
|
| 1074 |
matrix3x3 m; |
| 1075 |
m.RotAboutAxisByAngle(v1,60.0); |
| 1076 |
v = m*vtmp; |
| 1077 |
v.normalize(); |
| 1078 |
} |
| 1079 |
else if (GetHyb() == 3) |
| 1080 |
{ |
| 1081 |
v1 = cross(vtmp,VX); |
| 1082 |
v2 = cross(vtmp,VY); |
| 1083 |
if (v1.length() < v2.length()) |
| 1084 |
v1 = v2; |
| 1085 |
matrix3x3 m; |
| 1086 |
m.RotAboutAxisByAngle(v1,70.5); |
| 1087 |
v = m*vtmp; |
| 1088 |
v.normalize(); |
| 1089 |
} |
| 1090 |
if (GetHyb() == 1) |
| 1091 |
v = vtmp; |
| 1092 |
|
| 1093 |
v *= length; |
| 1094 |
v += GetVector(); |
| 1095 |
return(true); |
| 1096 |
} |
| 1097 |
|
| 1098 |
if (GetValence() == 2) |
| 1099 |
{ |
| 1100 |
vector3 v1,v2,vtmp,vsum,vnorm; |
| 1101 |
atom = BeginNbrAtom(i); |
| 1102 |
if (!atom) |
| 1103 |
return(false); |
| 1104 |
v1 = GetVector() - atom->GetVector(); |
| 1105 |
atom = NextNbrAtom(i); |
| 1106 |
if (!atom) |
| 1107 |
return(false); |
| 1108 |
v2 = GetVector() - atom->GetVector(); |
| 1109 |
v1.normalize(); |
| 1110 |
v2.normalize(); |
| 1111 |
vsum = v1+v2; |
| 1112 |
vsum.normalize(); |
| 1113 |
|
| 1114 |
if (GetHyb() == 2) |
| 1115 |
v = vsum; |
| 1116 |
else if (GetHyb() == 3) |
| 1117 |
{ |
| 1118 |
vnorm = cross(v2,v1); |
| 1119 |
vnorm.normalize(); |
| 1120 |
|
| 1121 |
#ifndef ONE_OVER_SQRT3 |
| 1122 |
#define ONE_OVER_SQRT3 0.57735026918962576451 |
| 1123 |
#endif //SQRT_TWO_THIRDS |
| 1124 |
#ifndef SQRT_TWO_THIRDS |
| 1125 |
#define SQRT_TWO_THIRDS 0.81649658092772603272 |
| 1126 |
#endif //ONE_OVER_SQRT3 |
| 1127 |
|
| 1128 |
vsum *= ONE_OVER_SQRT3; |
| 1129 |
vnorm *= SQRT_TWO_THIRDS; |
| 1130 |
|
| 1131 |
v = vsum + vnorm; |
| 1132 |
} |
| 1133 |
|
| 1134 |
v *= length; |
| 1135 |
|
| 1136 |
v += GetVector(); |
| 1137 |
return(true); |
| 1138 |
} |
| 1139 |
|
| 1140 |
if (GetValence() == 3) |
| 1141 |
{ |
| 1142 |
vector3 vtmp,vsum; |
| 1143 |
OBAtom *atom; |
| 1144 |
vector<OBEdgeBase*>::iterator i; |
| 1145 |
for (atom = BeginNbrAtom(i);atom;atom = NextNbrAtom(i)) |
| 1146 |
{ |
| 1147 |
vtmp = GetVector() - atom->GetVector(); |
| 1148 |
vtmp.normalize(); |
| 1149 |
vtmp /= 3.0; |
| 1150 |
vsum += vtmp; |
| 1151 |
} |
| 1152 |
vsum.normalize(); |
| 1153 |
v = vsum; |
| 1154 |
v *= length; |
| 1155 |
v += GetVector(); |
| 1156 |
return(true); |
| 1157 |
} |
| 1158 |
|
| 1159 |
return(true); |
| 1160 |
} |
| 1161 |
|
| 1162 |
bool OBAtom::HtoMethyl() |
| 1163 |
{ |
| 1164 |
if (!IsHydrogen()) |
| 1165 |
return(false); |
| 1166 |
|
| 1167 |
obErrorLog.ThrowError(__FUNCTION__, |
| 1168 |
"Ran OpenBabel::HtoMethyl", obAuditMsg); |
| 1169 |
|
| 1170 |
OBMol *mol = (OBMol*)GetParent(); |
| 1171 |
|
| 1172 |
mol->BeginModify(); |
| 1173 |
|
| 1174 |
SetAtomicNum(6); |
| 1175 |
SetType("C3"); |
| 1176 |
SetHyb(3); |
| 1177 |
|
| 1178 |
OBAtom *atom; |
| 1179 |
OBBond *bond; |
| 1180 |
vector<OBEdgeBase*>::iterator i; |
| 1181 |
atom = BeginNbrAtom(i); |
| 1182 |
bond = (OBBond *)*i; |
| 1183 |
if (!atom) |
| 1184 |
{ |
| 1185 |
mol->EndModify(); |
| 1186 |
return(false); |
| 1187 |
} |
| 1188 |
|
| 1189 |
double br1,br2; |
| 1190 |
br1 = etab.CorrectedBondRad(6,3); |
| 1191 |
br2 = etab.CorrectedBondRad(atom->GetAtomicNum(),atom->GetHyb()); |
| 1192 |
bond->SetLength(atom,br1+br2); |
| 1193 |
|
| 1194 |
OBAtom *hatom; |
| 1195 |
br2 = etab.CorrectedBondRad(1,0); |
| 1196 |
vector3 v; |
| 1197 |
|
| 1198 |
for (int j = 0;j < 3;j++) |
| 1199 |
{ |
| 1200 |
hatom = mol->NewAtom(); |
| 1201 |
hatom->SetAtomicNum(1); |
| 1202 |
hatom->SetType("H"); |
| 1203 |
|
| 1204 |
GetNewBondVector(v,br1+br2); |
| 1205 |
hatom->SetVector(v); |
| 1206 |
mol->AddBond(GetIdx(),mol->NumAtoms(),1); |
| 1207 |
} |
| 1208 |
|
| 1209 |
mol->EndModify(); |
| 1210 |
return(true); |
| 1211 |
} |
| 1212 |
|
| 1213 |
static void ApplyRotMatToBond(OBMol &mol,matrix3x3 &m,OBAtom *a1,OBAtom *a2) |
| 1214 |
{ |
| 1215 |
vector<int> children; |
| 1216 |
mol.FindChildren(children,a1->GetIdx(),a2->GetIdx()); |
| 1217 |
children.push_back(a2->GetIdx()); |
| 1218 |
|
| 1219 |
vector3 v; |
| 1220 |
vector<int>::iterator i; |
| 1221 |
for (i = children.begin();i != children.end();i++) |
| 1222 |
{ |
| 1223 |
v = mol.GetAtom(*i)->GetVector(); |
| 1224 |
v -= a1->GetVector(); |
| 1225 |
v *= m; |
| 1226 |
v += a1->GetVector(); |
| 1227 |
mol.GetAtom(*i)->SetVector(v); |
| 1228 |
} |
| 1229 |
|
| 1230 |
} |
| 1231 |
|
| 1232 |
bool OBAtom::SetHybAndGeom(int hyb) |
| 1233 |
{ |
| 1234 |
obErrorLog.ThrowError(__FUNCTION__, |
| 1235 |
"Ran OpenBabel::SetHybridizationAndGeometry", |
| 1236 |
obAuditMsg); |
| 1237 |
|
| 1238 |
//if (hyb == GetHyb()) return(true); |
| 1239 |
if (GetAtomicNum() == 1) |
| 1240 |
return(false); |
| 1241 |
if (hyb == 0 && GetHvyValence() > 1) |
| 1242 |
return(false); |
| 1243 |
if (hyb == 1 && GetHvyValence() > 2) |
| 1244 |
return(false); |
| 1245 |
if (hyb == 2 && GetHvyValence() > 3) |
| 1246 |
return(false); |
| 1247 |
if (hyb == 3 && GetHvyValence() > 4) |
| 1248 |
return(false); |
| 1249 |
|
| 1250 |
OBMol *mol = (OBMol*)GetParent(); |
| 1251 |
|
| 1252 |
OBAtom *nbr; |
| 1253 |
vector<OBAtom*> delatm; |
| 1254 |
vector<OBEdgeBase*>::iterator i; |
| 1255 |
|
| 1256 |
for (nbr = BeginNbrAtom(i);nbr;nbr = NextNbrAtom(i)) |
| 1257 |
if (nbr->IsHydrogen()) |
| 1258 |
delatm.push_back(nbr); |
| 1259 |
|
| 1260 |
//delete attached hydrogens |
| 1261 |
mol->IncrementMod(); |
| 1262 |
vector<OBAtom*>::iterator j; |
| 1263 |
for (j = delatm.begin();j != delatm.end();j++) |
| 1264 |
mol->DeleteAtom(*j); |
| 1265 |
mol->DecrementMod(); |
| 1266 |
|
| 1267 |
double targetAngle; |
| 1268 |
if (hyb == 3) |
| 1269 |
targetAngle = 109.5; |
| 1270 |
else if (hyb == 2) |
| 1271 |
targetAngle = 120.0; |
| 1272 |
else if (hyb == 1) |
| 1273 |
targetAngle = 180.0; |
| 1274 |
else |
| 1275 |
targetAngle = 0.0; |
| 1276 |
|
| 1277 |
if (IsInRing()) |
| 1278 |
targetAngle = 180.0 - (360.0 / MemberOfRingSize()); |
| 1279 |
|
| 1280 |
//adjust attached acyclic bond lengths |
| 1281 |
double br1,br2, length; |
| 1282 |
br1 = etab.CorrectedBondRad(GetAtomicNum(),hyb); |
| 1283 |
for (nbr = BeginNbrAtom(i);nbr;nbr = NextNbrAtom(i)) |
| 1284 |
if (!(*i)->IsInRing()) |
| 1285 |
{ |
| 1286 |
br2 = etab.CorrectedBondRad(nbr->GetAtomicNum(),nbr->GetHyb()); |
| 1287 |
length = br1 + br2; |
| 1288 |
if ((*i)->IsAromatic()) |
| 1289 |
length *= 0.93; |
| 1290 |
else if ((*i)->GetBO() == 2) |
| 1291 |
length *= 0.91; |
| 1292 |
else if ((*i)->GetBO() == 3) |
| 1293 |
length *= 0.87; |
| 1294 |
((OBBond*) *i)->SetLength(this, length); |
| 1295 |
} |
| 1296 |
|
| 1297 |
if (GetValence() > 1) |
| 1298 |
{ |
| 1299 |
double angle; |
| 1300 |
matrix3x3 m; |
| 1301 |
vector3 v1,v2,v3,v4,n,s; |
| 1302 |
OBAtom *r1,*r2,*r3,*a1,*a2,*a3,*a4; |
| 1303 |
r1 = r2 = r3 = a1 = a2 = a3 = a4 = NULL; |
| 1304 |
|
| 1305 |
//find ring atoms first |
| 1306 |
for (nbr = BeginNbrAtom(i);nbr;nbr = NextNbrAtom(i)) |
| 1307 |
if ((*i)->IsInRing()) |
| 1308 |
if (!r1) |
| 1309 |
r1 = nbr; |
| 1310 |
else if (!r2) |
| 1311 |
r2 = nbr; |
| 1312 |
else if (!r3) |
| 1313 |
r3 = nbr; |
| 1314 |
|
| 1315 |
//find non-ring atoms |
| 1316 |
for (nbr = BeginNbrAtom(i);nbr;nbr = NextNbrAtom(i)) |
| 1317 |
if (!(*i)->IsInRing()) |
| 1318 |
if (!a1) |
| 1319 |
a1 = nbr; |
| 1320 |
else if (!a2) |
| 1321 |
a2 = nbr; |
| 1322 |
else if (!a3) |
| 1323 |
a3 = nbr; |
| 1324 |
else if (!a4) |
| 1325 |
a4 = nbr; |
| 1326 |
|
| 1327 |
//adjust geometries of heavy atoms according to hybridization |
| 1328 |
if (hyb == 1) |
| 1329 |
{ |
| 1330 |
if (a2) |
| 1331 |
{ |
| 1332 |
v1 = a1->GetVector()-GetVector(); |
| 1333 |
v1.normalize(); |
| 1334 |
v2 = a2->GetVector()-GetVector(); |
| 1335 |
v2.normalize(); |
| 1336 |
n = cross(v1,v2); |
| 1337 |
angle = vectorAngle(v1,v2)-targetAngle; |
| 1338 |
m.RotAboutAxisByAngle(n,-angle); |
| 1339 |
ApplyRotMatToBond(*mol,m,this,a1); |
| 1340 |
} |
| 1341 |
} |
| 1342 |
else if (hyb == 2) |
| 1343 |
{ |
| 1344 |
if (r1 && r2 && a1) |
| 1345 |
{ |
| 1346 |
v1 = r1->GetVector()-GetVector(); |
| 1347 |
v1.normalize(); |
| 1348 |
v2 = r2->GetVector()-GetVector(); |
| 1349 |
v2.normalize(); |
| 1350 |
v3 = a1->GetVector()-GetVector(); |
| 1351 |
s = v1+v2; |
| 1352 |
s.normalize(); |
| 1353 |
s *= -1.0; |
| 1354 |
n = cross(s,v3); |
| 1355 |
angle = vectorAngle(s,v3); |
| 1356 |
m.RotAboutAxisByAngle(n,angle); |
| 1357 |
ApplyRotMatToBond(*mol,m,this,a1); |
| 1358 |
} |
| 1359 |
else |
| 1360 |
{ |
| 1361 |
if (a2) |
| 1362 |
{ |
| 1363 |
v1 = a1->GetVector()-GetVector(); |
| 1364 |
v1.normalize(); |
| 1365 |
v2 = a2->GetVector()-GetVector(); |
| 1366 |
v2.normalize(); |
| 1367 |
n = cross(v1,v2); |
| 1368 |
angle = vectorAngle(v1,v2)-targetAngle; |
| 1369 |
m.RotAboutAxisByAngle(n,-angle); |
| 1370 |
ApplyRotMatToBond(*mol,m,this,a1); |
| 1371 |
} |
| 1372 |
if (a3) |
| 1373 |
{ |
| 1374 |
v1 = a1->GetVector()-GetVector(); |
| 1375 |
v1.normalize(); |
| 1376 |
v2 = a2->GetVector()-GetVector(); |
| 1377 |
v2.normalize(); |
| 1378 |
v3 = a3->GetVector()-GetVector(); |
| 1379 |
s = v1+v2; |
| 1380 |
s.normalize(); |
| 1381 |
s *= -1.0; |
| 1382 |
n = cross(s,v3); |
| 1383 |
angle = vectorAngle(s,v3); |
| 1384 |
m.RotAboutAxisByAngle(n,angle); |
| 1385 |
ApplyRotMatToBond(*mol,m,this,a3); |
| 1386 |
} |
| 1387 |
} |
| 1388 |
} |
| 1389 |
else if (hyb == 3) |
| 1390 |
{ |
| 1391 |
if (r1 && r2 && r3 && a1) |
| 1392 |
{ |
| 1393 |
v1 = r1->GetVector()-GetVector(); |
| 1394 |
v1.normalize(); |
| 1395 |
v2 = r2->GetVector()-GetVector(); |
| 1396 |
v2.normalize(); |
| 1397 |
v3 = r3->GetVector()-GetVector(); |
| 1398 |
v3.normalize(); |
| 1399 |
v4 = a1->GetVector()-GetVector(); |
| 1400 |
s = v1 + v2 + v3; |
| 1401 |
s *= -1.0; |
| 1402 |
s.normalize(); |
| 1403 |
n = cross(s,v4); |
| 1404 |
angle = vectorAngle(s,v4); |
| 1405 |
m.RotAboutAxisByAngle(n,angle); |
| 1406 |
ApplyRotMatToBond(*mol,m,this,a1); |
| 1407 |
} |
| 1408 |
else if (r1 && r2 && !r3 && a1) |
| 1409 |
{ |
| 1410 |
v1 = r1->GetVector()-GetVector(); |
| 1411 |
v1.normalize(); |
| 1412 |
v2 = r2->GetVector()-GetVector(); |
| 1413 |
v2.normalize(); |
| 1414 |
v3 = a1->GetVector()-GetVector(); |
| 1415 |
s = v1+v2; |
| 1416 |
s *= -1.0; |
| 1417 |
s.normalize(); |
| 1418 |
n = cross(v1,v2); |
| 1419 |
n.normalize(); |
| 1420 |
s *= ONE_OVER_SQRT3; //1/sqrt(3) |
| 1421 |
n *= SQRT_TWO_THIRDS; //sqrt(2/3) |
| 1422 |
s += n; |
| 1423 |
s.normalize(); |
| 1424 |
n = cross(s,v3); |
| 1425 |
angle = vectorAngle(s,v3); |
| 1426 |
m.RotAboutAxisByAngle(n,angle); |
| 1427 |
ApplyRotMatToBond(*mol,m,this,a1); |
| 1428 |
|
| 1429 |
if (a2) |
| 1430 |
{ |
| 1431 |
v1 = r1->GetVector()-GetVector(); |
| 1432 |
v1.normalize(); |
| 1433 |
v2 = r2->GetVector()-GetVector(); |
| 1434 |
v2.normalize(); |
| 1435 |
v3 = a1->GetVector()-GetVector(); |
| 1436 |
v3.normalize(); |
| 1437 |
v4 = a2->GetVector()-GetVector(); |
| 1438 |
s = v1 + v2 + v3; |
| 1439 |
s *= -1.0; |
| 1440 |
s.normalize(); |
| 1441 |
n = cross(s,v4); |
| 1442 |
angle = vectorAngle(s,v4); |
| 1443 |
m.RotAboutAxisByAngle(n,angle); |
| 1444 |
ApplyRotMatToBond(*mol,m,this,a2); |
| 1445 |
} |
| 1446 |
} |
| 1447 |
else |
| 1448 |
{ |
| 1449 |
if (a2) |
| 1450 |
{ |
| 1451 |
v1 = a1->GetVector()-GetVector(); |
| 1452 |
v1.normalize(); |
| 1453 |
v2 = a2->GetVector()-GetVector(); |
| 1454 |
v2.normalize(); |
| 1455 |
n = cross(v1,v2); |
| 1456 |
angle = vectorAngle(v1,v2)-targetAngle; |
| 1457 |
m.RotAboutAxisByAngle(n,-angle); |
| 1458 |
ApplyRotMatToBond(*mol,m,this,a1); |
| 1459 |
} |
| 1460 |
if (a3) |
| 1461 |
{ |
| 1462 |
v1 = a1->GetVector()-GetVector(); |
| 1463 |
v1.normalize(); |
| 1464 |
v2 = a2->GetVector()-GetVector(); |
| 1465 |
v2.normalize(); |
| 1466 |
v3 = a3->GetVector()-GetVector(); |
| 1467 |
s = v1+v2; |
| 1468 |
s *= -1.0; |
| 1469 |
s.normalize(); |
| 1470 |
n = cross(v1,v2); |
| 1471 |
n.normalize(); |
| 1472 |
s *= ONE_OVER_SQRT3; //1/sqrt(3) |
| 1473 |
n *= SQRT_TWO_THIRDS; //sqrt(2/3) |
| 1474 |
s += n; |
| 1475 |
s.normalize(); |
| 1476 |
n = cross(s,v3); |
| 1477 |
angle = vectorAngle(s,v3); |
| 1478 |
m.RotAboutAxisByAngle(n,angle); |
| 1479 |
ApplyRotMatToBond(*mol,m,this,a3); |
| 1480 |
} |
| 1481 |
} |
| 1482 |
} |
| 1483 |
} |
| 1484 |
|
| 1485 |
//add hydrogens back to atom |
| 1486 |
int impval=1; |
| 1487 |
switch (GetAtomicNum()) |
| 1488 |
{ |
| 1489 |
case 6: |
| 1490 |
if (hyb == 3) |
| 1491 |
impval = 4; |
| 1492 |
if (hyb == 2) |
| 1493 |
impval = 3; |
| 1494 |
if (hyb == 1) |
| 1495 |
impval = 2; |
| 1496 |
break; |
| 1497 |
case 7: |
| 1498 |
if (hyb == 3) |
| 1499 |
impval = 3; |
| 1500 |
if (hyb == 2) |
| 1501 |
impval = 2; |
| 1502 |
if (hyb == 1) |
| 1503 |
impval = 1; |
| 1504 |
break; |
| 1505 |
case 8: |
| 1506 |
if (hyb == 3) |
| 1507 |
impval = 2; |
| 1508 |
if (hyb == 2) |
| 1509 |
impval = 2; |
| 1510 |
if (hyb == 1) |
| 1511 |
impval = 2; |
| 1512 |
case 16: |
| 1513 |
if (hyb == 3) |
| 1514 |
impval = 2; |
| 1515 |
if (hyb == 2) |
| 1516 |
impval = 2; |
| 1517 |
if (hyb == 1) |
| 1518 |
impval = 0; |
| 1519 |
break; |
| 1520 |
case 15: |
| 1521 |
if (hyb == 3) |
| 1522 |
impval = 4; |
| 1523 |
if (hyb == 2) |
| 1524 |
impval = 3; |
| 1525 |
if (hyb == 1) |
| 1526 |
impval = 2; |
| 1527 |
break; |
| 1528 |
default: |
| 1529 |
impval = 1; |
| 1530 |
} |
| 1531 |
|
| 1532 |
int hcount = impval-GetHvyValence(); |
| 1533 |
if (hcount) |
| 1534 |
{ |
| 1535 |
int k; |
| 1536 |
vector3 v; |
| 1537 |
OBAtom *atom; |
| 1538 |
double brsum = etab.CorrectedBondRad(1,0)+ |
| 1539 |
etab.CorrectedBondRad(GetAtomicNum(),GetHyb()); |
| 1540 |
SetHyb(hyb); |
| 1541 |
|
| 1542 |
mol->BeginModify(); |
| 1543 |
for (k = 0;k < hcount;k++) |
| 1544 |
{ |
| 1545 |
GetNewBondVector(v,brsum); |
| 1546 |
atom = mol->NewAtom(); |
| 1547 |
atom->SetAtomicNum(1); |
| 1548 |
atom->SetType("H"); |
| 1549 |
atom->SetVector(v); |
| 1550 |
mol->AddBond(atom->GetIdx(),GetIdx(),1); |
| 1551 |
} |
| 1552 |
mol->EndModify(); |
| 1553 |
} |
| 1554 |
|
| 1555 |
|
| 1556 |
return(true); |
| 1557 |
} |
| 1558 |
|
| 1559 |
OBBond *OBAtom::GetBond(OBAtom *nbr) |
| 1560 |
{ |
| 1561 |
OBBond *bond; |
| 1562 |
vector<OBEdgeBase *>::iterator i; |
| 1563 |
for (bond = BeginBond(i) ; bond ; bond = NextBond(i)) |
| 1564 |
if (bond->GetNbrAtom(this) == nbr) |
| 1565 |
return bond; |
| 1566 |
return NULL; |
| 1567 |
} |
| 1568 |
|
| 1569 |
// OBGenericData methods |
| 1570 |
bool OBAtom::HasData(string &s) |
| 1571 |
//returns true if the generic attribute/value pair exists |
| 1572 |
{ |
| 1573 |
if (_vdata.empty()) |
| 1574 |
return(false); |
| 1575 |
|
| 1576 |
vector<OBGenericData*>::iterator i; |
| 1577 |
|
| 1578 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1579 |
if ((*i)->GetAttribute() == s) |
| 1580 |
return(true); |
| 1581 |
|
| 1582 |
return(false); |
| 1583 |
} |
| 1584 |
|
| 1585 |
bool OBAtom::HasData(const char *s) |
| 1586 |
//returns true if the generic attribute/value pair exists |
| 1587 |
{ |
| 1588 |
if (_vdata.empty()) |
| 1589 |
return(false); |
| 1590 |
|
| 1591 |
vector<OBGenericData*>::iterator i; |
| 1592 |
|
| 1593 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1594 |
if ((*i)->GetAttribute() == s) |
| 1595 |
return(true); |
| 1596 |
|
| 1597 |
return(false); |
| 1598 |
} |
| 1599 |
|
| 1600 |
bool OBAtom::HasData(unsigned int dt) |
| 1601 |
//returns true if the generic attribute/value pair exists |
| 1602 |
{ |
| 1603 |
if (_vdata.empty()) |
| 1604 |
return(false); |
| 1605 |
|
| 1606 |
vector<OBGenericData*>::iterator i; |
| 1607 |
|
| 1608 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1609 |
if ((*i)->GetDataType() == dt) |
| 1610 |
return(true); |
| 1611 |
|
| 1612 |
return(false); |
| 1613 |
} |
| 1614 |
|
| 1615 |
OBGenericData *OBAtom::GetData(string &s) |
| 1616 |
//returns the value given an attribute |
| 1617 |
{ |
| 1618 |
vector<OBGenericData*>::iterator i; |
| 1619 |
|
| 1620 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1621 |
if ((*i)->GetAttribute() == s) |
| 1622 |
return(*i); |
| 1623 |
|
| 1624 |
return(NULL); |
| 1625 |
} |
| 1626 |
|
| 1627 |
OBGenericData *OBAtom::GetData(const char *s) |
| 1628 |
//returns the value given an attribute |
| 1629 |
{ |
| 1630 |
vector<OBGenericData*>::iterator i; |
| 1631 |
|
| 1632 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1633 |
if ((*i)->GetAttribute() == s) |
| 1634 |
return(*i); |
| 1635 |
|
| 1636 |
return(NULL); |
| 1637 |
} |
| 1638 |
|
| 1639 |
OBGenericData *OBAtom::GetData(unsigned int dt) |
| 1640 |
{ |
| 1641 |
vector<OBGenericData*>::iterator i; |
| 1642 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1643 |
if ((*i)->GetDataType() == dt) |
| 1644 |
return(*i); |
| 1645 |
return(NULL); |
| 1646 |
} |
| 1647 |
|
| 1648 |
void OBAtom::DeleteData(unsigned int dt) |
| 1649 |
{ |
| 1650 |
vector<OBGenericData*> vdata; |
| 1651 |
vector<OBGenericData*>::iterator i; |
| 1652 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1653 |
if ((*i)->GetDataType() == dt) |
| 1654 |
delete *i; |
| 1655 |
else |
| 1656 |
vdata.push_back(*i); |
| 1657 |
_vdata = vdata; |
| 1658 |
} |
| 1659 |
|
| 1660 |
void OBAtom::DeleteData(vector<OBGenericData*> &vg) |
| 1661 |
{ |
| 1662 |
vector<OBGenericData*> vdata; |
| 1663 |
vector<OBGenericData*>::iterator i,j; |
| 1664 |
|
| 1665 |
bool del; |
| 1666 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1667 |
{ |
| 1668 |
del = false; |
| 1669 |
for (j = vg.begin();j != vg.end();j++) |
| 1670 |
if (*i == *j) |
| 1671 |
{ |
| 1672 |
del = true; |
| 1673 |
break; |
| 1674 |
} |
| 1675 |
if (del) |
| 1676 |
delete *i; |
| 1677 |
else |
| 1678 |
vdata.push_back(*i); |
| 1679 |
} |
| 1680 |
_vdata = vdata; |
| 1681 |
} |
| 1682 |
|
| 1683 |
void OBAtom::DeleteData(OBGenericData *gd) |
| 1684 |
{ |
| 1685 |
vector<OBGenericData*>::iterator i; |
| 1686 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1687 |
if (*i == gd) |
| 1688 |
{ |
| 1689 |
delete *i; |
| 1690 |
_vdata.erase(i); |
| 1691 |
} |
| 1692 |
|
| 1693 |
} |
| 1694 |
|
| 1695 |
bool OBAtom::IsHbondAcceptor() |
| 1696 |
{ |
| 1697 |
return _ele == 7 || _ele == 8 || _ele == 9 ; |
| 1698 |
} |
| 1699 |
|
| 1700 |
bool OBAtom::IsHbondDonor() |
| 1701 |
{ |
| 1702 |
return MatchesSMARTS("[$([#8,#7H,#9;!H0])]"); |
| 1703 |
} |
| 1704 |
|
| 1705 |
bool OBAtom::IsHbondDonorH() |
| 1706 |
{ |
| 1707 |
if (!IsHydrogen()) return(false); |
| 1708 |
|
| 1709 |
OBAtom *atom; |
| 1710 |
OBBond *bond; |
| 1711 |
vector<OBEdgeBase*>::iterator i; |
| 1712 |
for (bond = BeginBond(i);bond;bond = NextBond(i)) |
| 1713 |
{ |
| 1714 |
atom = bond->GetNbrAtom(this); |
| 1715 |
if (atom->GetAtomicNum() == 7) return(true); |
| 1716 |
if (atom->GetAtomicNum() == 8) return(true); |
| 1717 |
if (atom->GetAtomicNum() == 9) return(true); |
| 1718 |
} |
| 1719 |
|
| 1720 |
return(false); |
| 1721 |
} |
| 1722 |
|
| 1723 |
} // end namespace OpenBabel |
| 1724 |
|
| 1725 |
//! \file atom.cpp |
| 1726 |
//! \brief Handle OBAtom class |
