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/********************************************************************** |
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obiter.cpp - STL-style iterators 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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|
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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 <vector> |
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|
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#include "mol.hpp" |
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#include "obiter.hpp" |
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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 OBMolAtomIter |
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|
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To facilitate iteration through all atoms in a molecule, without resorting |
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to atom indexes (which may change in the future) or the OBMol::BeginAtom() |
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and OBMol::NextAtom() methods which may only be safely used by one method |
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at once (e.g., if a method above your code or underneath your code uses these |
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methods, errors will occur). |
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|
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Therefore, it is <strong>highly recommended</strong> to use the separate |
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STL-style iterator classes. |
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|
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This has been made significantly easier by a series of macros in the |
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obiter.h header file: |
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|
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\code |
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\#define FOR_ATOMS_OF_MOL(a,m) for( OBMolAtomIter a(m); a; a++ ) |
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\endcode |
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|
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Here is an example: |
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\code |
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#include "obiter.hpp" |
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#include "mol.hpp" |
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|
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OBMol mol; |
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double exactMass = 0.0f; |
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FOR_ATOMS_OF_MOL(a, mol) |
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{ |
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exactMass += a->GetExactMass(); |
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} |
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\endcode |
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**/ |
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|
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OBMolAtomIter::OBMolAtomIter(OBMol *mol) |
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{ |
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_parent = mol; |
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_ptr = _parent->BeginAtom(_i); |
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} |
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|
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OBMolAtomIter::OBMolAtomIter(OBMol &mol) |
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{ |
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_parent = &mol; |
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_ptr = _parent->BeginAtom(_i); |
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} |
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|
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OBMolAtomIter::OBMolAtomIter(const OBMolAtomIter &ai) |
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{ |
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_parent = ai._parent; |
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_ptr = ai._ptr; |
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_i = ai._i; |
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} |
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|
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OBMolAtomIter& OBMolAtomIter::operator=(const OBMolAtomIter &ai) |
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{ |
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if (this != &ai) |
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{ |
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_parent = ai._parent; |
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_ptr = ai._ptr; |
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_i = ai._i; |
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} |
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return *this; |
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} |
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|
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OBMolAtomIter OBMolAtomIter::operator++(int) |
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{ |
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_ptr = _parent->NextAtom(_i); |
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return *this; |
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} |
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|
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|
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/** \class OBMolBondIter |
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|
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To facilitate iteration through all bonds in a molecule, without resorting |
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to bond indexes (which may change in the future) or the OBMol::BeginBond() |
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and OBMol::NextBond() methods which may only be safely used by one method |
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at once (e.g., if a method above your code or underneath your code uses these |
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methods, errors will occur). |
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|
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Therefore, it is <strong>highly recommended</strong> to use the separate |
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STL-style iterator classes. |
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|
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This has been made significantly easier by a series of macros in the |
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obiter.h header file: |
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|
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\code |
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\#define FOR_BONDS_OF_MOL(b,m) for( OBMolBondIter b(m); b; b++ ) |
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\endcode |
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|
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Here is an example: |
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\code |
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#include "obiter.hpp" |
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#include "mol.hpp" |
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|
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OBMol mol; |
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unsigned int bondOrderSum = 0; |
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FOR_BONDS_OF_MOL(b, mol) |
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{ |
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bondOrderSum += b->GetBO(); |
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} |
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\endcode |
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**/ |
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|
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OBMolBondIter::OBMolBondIter(OBMol *mol) |
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{ |
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_parent = mol; |
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_ptr = _parent->BeginBond(_i); |
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} |
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|
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OBMolBondIter::OBMolBondIter(OBMol &mol) |
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{ |
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_parent = &mol; |
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_ptr = _parent->BeginBond(_i); |
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} |
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|
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OBMolBondIter::OBMolBondIter(const OBMolBondIter &bi) |
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{ |
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_parent = bi._parent; |
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_ptr = bi._ptr; |
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_i = bi._i; |
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} |
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|
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OBMolBondIter& OBMolBondIter::operator=(const OBMolBondIter &bi) |
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{ |
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if (this != &bi) |
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{ |
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_parent = bi._parent; |
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_ptr = bi._ptr; |
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_i = bi._i; |
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} |
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return *this; |
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} |
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|
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OBMolBondIter OBMolBondIter::operator++(int) |
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{ |
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_ptr = _parent->NextBond(_i); |
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return *this; |
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} |
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|
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/** \class OBAtomAtomIter |
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|
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To facilitate iteration through all neighbors of an atom, without resorting |
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to bond indexes (which may change in the future) or the OBAtom::BeginNbr() |
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and OBAtom::NextNbr() methods which may only be safely used by one method |
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at once (e.g., if a method above your code or underneath your code uses these |
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methods, errors will occur). |
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|
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Therefore, it is <strong>highly recommended</strong> to use the separate |
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STL-style iterator classes. |
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|
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This has been made significantly easier by a series of macros in the |
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obiter.h header file: |
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|
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\code |
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\#define FOR_NBORS_OF_ATOM(a,p) for( OBAtomAtomIter a(p); a; a++ ) |
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\endcode |
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|
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Here is an example: |
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\code |
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#include "obiter.hpp" |
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#include "mol.hpp" |
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|
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OBMol mol; |
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FOR_ATOMS_OF_MOL(a, mol) |
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{ |
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FOR_NBORS_OF_ATOM(b, a) |
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{ |
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... |
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} |
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} |
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\endcode |
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**/ |
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|
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OBAtomAtomIter::OBAtomAtomIter(OBAtom *atm) |
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{ |
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_parent = atm; |
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_ptr = _parent->BeginNbrAtom(_i); |
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} |
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|
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OBAtomAtomIter::OBAtomAtomIter(OBAtom &atm) |
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{ |
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_parent = &atm; |
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_ptr = _ptr->BeginNbrAtom(_i); |
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} |
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|
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OBAtomAtomIter::OBAtomAtomIter(const OBAtomAtomIter &ai) |
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{ |
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_parent = ai._parent; |
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_ptr = ai._ptr; |
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_i = ai._i; |
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} |
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|
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OBAtomAtomIter& OBAtomAtomIter::operator=(const OBAtomAtomIter &ai) |
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{ |
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if (this != &ai) |
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{ |
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_parent = ai._parent; |
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_ptr = ai._ptr; |
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_i = ai._i; |
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} |
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return *this; |
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} |
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|
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OBAtomAtomIter OBAtomAtomIter::operator++(int) |
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{ |
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_ptr = _parent->NextNbrAtom(_i); |
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return *this; |
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} |
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|
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/** \class OBAtomBondIter |
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|
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To facilitate iteration through all bonds on an atom, without resorting |
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to bond indexes (which may change in the future) or the OBAtom::BeginBond() |
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and OBAtom::NextBond() methods which may only be safely used by one method |
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at once (e.g., if a method above your code or underneath your code uses these |
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methods, errors will occur). |
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|
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Therefore, it is <strong>highly recommended</strong> to use the separate |
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STL-style iterator classes. |
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|
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This has been made significantly easier by a series of macros in the |
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obiter.h header file: |
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|
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\code |
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\#define FOR_BONDS_OF_ATOM(b,p) for( OBAtomBondIter b(p); b; b++ ) |
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\endcode |
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|
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Here is an example: |
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\code |
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#include "obiter.hpp" |
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#include "mol.hpp" |
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|
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OBAtom atom; |
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unsigned int tripleBondCount; |
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FOR_BONDS_OF_ATOM(b, atom) |
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{ |
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if (b->GetBO() == 3) |
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tripleBondCount++; |
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} |
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\endcode |
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**/ |
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|
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OBAtomBondIter::OBAtomBondIter(OBAtom *atm) |
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{ |
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_parent = atm; |
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_ptr = _parent->BeginBond(_i); |
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} |
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|
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OBAtomBondIter::OBAtomBondIter(OBAtom &atm) |
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{ |
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_parent = &atm; |
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_ptr = _parent->BeginBond(_i); |
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} |
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|
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OBAtomBondIter::OBAtomBondIter(const OBAtomBondIter &bi) |
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{ |
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_parent = bi._parent; |
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_ptr = bi._ptr; |
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_i = bi._i; |
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} |
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|
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OBAtomBondIter& OBAtomBondIter::operator=(const OBAtomBondIter &bi) |
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{ |
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if (this != &bi) |
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{ |
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_parent = bi._parent; |
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_ptr = bi._ptr; |
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_i = bi._i; |
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} |
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return *this; |
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} |
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|
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OBAtomBondIter OBAtomBondIter::operator++(int) |
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{ |
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_ptr = _parent->NextBond(_i); |
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return *this; |
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} |
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|
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/** \class OBResidueIter |
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|
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To facilitate iteration through all residues in a molecule, without resorting |
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to residue indexes (which may change in the future) or the OBMol::BeginResidue() |
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and OBMol::NextResidue() methods which may only be safely used by one method |
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at once (e.g., if a method above your code or underneath your code uses these |
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methods, errors will occur). |
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|
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Therefore, it is <strong>highly recommended</strong> to use the separate |
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STL-style iterator classes. |
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|
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This has been made significantly easier by a series of macros in the |
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obiter.h header file: |
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|
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\code |
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\#define FOR_RESIDUES_OF_MOL(a,m) for( OBResidueIter a(m); a; a++ ) |
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\endcode |
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|
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Here is an example: |
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\code |
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#include "obiter.hpp" |
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#include "mol.hpp" |
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|
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OBMol mol; |
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FOR_RESIDUES_OF_MOL(r, mol) |
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{ |
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if (r->GetName() == resname && r->GetNum() == rnum) |
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{ |
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// got a match, let's go to work |
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... |
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} |
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} |
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\endcode |
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**/ |
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|
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OBResidueIter::OBResidueIter(OBMol *mol) |
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{ |
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_parent = mol; |
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_ptr = _parent->BeginResidue(_i); |
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} |
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|
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OBResidueIter::OBResidueIter(OBMol &mol) |
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{ |
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_parent = &mol; |
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_ptr = _parent->BeginResidue(_i); |
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} |
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|
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OBResidueIter::OBResidueIter(const OBResidueIter &ri) |
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{ |
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_parent = ri._parent; |
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_ptr = ri._ptr; |
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_i = ri._i; |
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} |
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|
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OBResidueIter& OBResidueIter::operator=(const OBResidueIter &ri) |
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{ |
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if (this != &ri) |
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{ |
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_parent = ri._parent; |
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_ptr = ri._ptr; |
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_i = ri._i; |
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} |
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return *this; |
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} |
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|
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OBResidueIter OBResidueIter::operator++(int) |
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{ |
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_ptr = _parent->NextResidue(_i); |
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return *this; |
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} |
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|
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/** \class OBResidueAtomIter |
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|
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To facilitate iteration through all atoms in a residue, without resorting |
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to atom indexes (which may change in the future) or the OBResidue::BeginAtom() |
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and OBResidue::NextAtom() methods which may only be safely used by one method |
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at once (e.g., if a method above your code or underneath your code uses these |
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methods, errors will occur). |
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|
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Therefore, it is <strong>highly recommended</strong> to use the separate |
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STL-style iterator classes. |
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|
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This has been made significantly easier by a series of macros in the |
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obiter.h header file: |
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|
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\code |
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\#define FOR_ATOMS_OF_RESIDUE(a,r) for( OBResidueAtomIter a(r); a; a++ ) |
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\endcode |
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|
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Here is an example: |
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\code |
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#include "obiter.hpp" |
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#include "mol.hpp" |
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|
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OBMol mol; |
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double residueMass = 0.0; |
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FOR_RESIDUES_OF_MOL(r, mol) |
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{ |
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if (r->GetName() == resname && r->GetNum() == rnum) |
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{ |
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FOR_ATOMS_OF_RESIDUE(a, r) |
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{ |
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residueMass += a->GetMass(); |
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} |
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} |
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} |
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\endcode |
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**/ |
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|
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OBResidueAtomIter::OBResidueAtomIter(OBResidue *res) |
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{ |
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_parent = res; |
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_ptr = _parent->BeginAtom(_i); |
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} |
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|
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OBResidueAtomIter::OBResidueAtomIter(OBResidue &res) |
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{ |
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_parent = &res; |
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_ptr = _parent->BeginAtom(_i); |
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} |
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|
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OBResidueAtomIter::OBResidueAtomIter(const OBResidueAtomIter &ri) |
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{ |
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_parent = ri._parent; |
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_ptr = ri._ptr; |
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_i = ri._i; |
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} |
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|
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OBResidueAtomIter & OBResidueAtomIter::operator = (const OBResidueAtomIter &ri) |
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{ |
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if (this != &ri) |
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{ |
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_parent = ri._parent; |
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_ptr = ri._ptr; |
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_i = ri._i; |
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} |
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|
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return (*this); |
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} |
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|
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OBResidueAtomIter OBResidueAtomIter::operator++ (int) |
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{ |
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_ptr = _parent->NextAtom(_i); |
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return (*this); |
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} |
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|
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} // namespace OpenBabel |
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|
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//! \file obiter.cpp |
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//! \brief STL-style iterators for Open Babel. |
