source: src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp@ 2fe4a5

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Last change on this file since 2fe4a5 was 270bdf, checked in by Frederik Heber <heber@…>, 10 years ago

atom::getMolecule() now returns ptr to const molecule.

  • changed some places where getMolecule() was used. Most of them required only const access anyway. World is allowed to const'cast the constness away as it commands over molecules anyway.
  • Property mode set to 100644
File size: 4.5 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2012 University of Bonn. All rights reserved.
5 * Copyright (C) 2013 Frederik Heber. All rights reserved.
6 *
7 *
8 * This file is part of MoleCuilder.
9 *
10 * MoleCuilder is free software: you can redistribute it and/or modify
11 * it under the terms of the GNU General Public License as published by
12 * the Free Software Foundation, either version 2 of the License, or
13 * (at your option) any later version.
14 *
15 * MoleCuilder is distributed in the hope that it will be useful,
16 * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18 * GNU General Public License for more details.
19 *
20 * You should have received a copy of the GNU General Public License
21 * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
22 */
23
24/*
25 * CopyAtoms_withBonds.cpp
26 *
27 * Created on: Mar 17, 2012
28 * Author: heber
29 */
30
31
32// include config.h
33#ifdef HAVE_CONFIG_H
34#include <config.h>
35#endif
36
37#include "CodePatterns/MemDebug.hpp"
38
39#include "CopyAtoms_withBonds.hpp"
40
41#include "Bond/bond.hpp"
42#include "CodePatterns/Assert.hpp"
43#include "CodePatterns/Log.hpp"
44#include "Descriptors/MoleculeIdDescriptor.hpp"
45#include "molecule.hpp"
46#include "WorldTime.hpp"
47
48void CopyAtoms_withBonds::operator()(const AtomVector &_atoms)
49{
50 CopyAtoms_Simple::operator()(_atoms);
51
52 // create LookupMap
53 LookupMap_t LookupMap = createLookup(_atoms);
54 ASSERT( LookupMap.size() == _atoms.size(),
55 "CopyAtoms_withBonds::operator() - Lookupmap and original AtomVectors differ in size: "
56 +toString(LookupMap.size())+" != "+toString(_atoms.size())+".");
57 ASSERT( LookupMap.size() == CopiedAtoms.size(),
58 "CopyAtoms_withBonds::operator() - Lookupmap and copied AtomVectors differ in size.: "
59 +toString(LookupMap.size())+" != "+toString(CopiedAtoms.size())+".");
60
61 // then go through the bonds of each original atom
62 for (AtomVector::const_iterator original_iter = _atoms.begin();
63 original_iter != _atoms.end(); ++original_iter) {
64 const BondList ListOfBonds = (*original_iter)->getListOfBonds();
65 for(BondList::const_iterator iter = ListOfBonds.begin(); iter != ListOfBonds.end(); ++iter) {
66 // check both bond partners have been copied
67 const bond::ptr Binder = *iter;
68 if (*original_iter == Binder->leftatom) {
69 LookupMap_t::const_iterator leftiter = LookupMap.find(Binder->leftatom);
70 LookupMap_t::const_iterator rightiter = LookupMap.find(Binder->rightatom);
71 if ((leftiter != LookupMap.end()) && (rightiter != LookupMap.end())) {
72 // create new bond, copy its properties, and register with both copies
73 atom * const LeftAtom = leftiter->second;
74 atom * const RightAtom = rightiter->second;
75 bond::ptr const NewBond = LeftAtom->addBond(WorldTime::getTime(), RightAtom);
76 LOG(3, "DEBUG: Creating copy bond between original " << Binder->leftatom->getId()
77 << " and " << Binder->rightatom->getId() << ": " << *NewBond << ".");
78 NewBond->setDegree(Binder->getDegree());
79 NewBond->Cyclic = Binder->Cyclic;
80 NewBond->Type = Binder->Type;
81 } else {
82 LOG(4, "DEBUG: Skipping bond between original atoms " << Binder->leftatom->getId()
83 << " and " << Binder->rightatom->getId() << " as one of them is not present in copied atoms.");
84 }
85 } else {
86 LOG(4, "DEBUG: Skipping bond between original atoms " << Binder->leftatom->getId()
87 << " and " << Binder->rightatom->getId() << " due to wrong order.");
88 }
89 }
90 }
91
92 // associate cloned atoms with molecule from original atom
93 for (AtomVector::const_iterator original_iter = _atoms.begin();
94 original_iter != _atoms.end(); ++original_iter) {
95 const atom * const _atom = *original_iter;
96 const molecule * const mol = _atom->getMolecule();
97 if (mol != NULL) {
98 ASSERT( LookupMap.count(_atom),
99 "CopyAtoms_withBonds::operator() - atom "+toString(_atom)+" not found in LookupMap.");
100 molecule * non_const_mol = World::getInstance().getMolecule(MoleculeById(mol->getId()));
101 non_const_mol->AddAtom(LookupMap[_atom]);
102 }
103 }
104
105 // print copied atoms
106 if (DoLog(3))
107 for (AtomVector::const_iterator copy_iter = CopiedAtoms.begin();
108 copy_iter != CopiedAtoms.end(); ++copy_iter) {
109 const BondList ListOfBonds = (*copy_iter)->getListOfBonds();
110 LOG(3, "DEBUG: List of bonds for " << **copy_iter << ": " << ListOfBonds << ".");
111 }
112}
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