source: src/Descriptors/AtomDescriptor.cpp@ 97445f

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since 97445f was 94d5ac6, checked in by Frederik Heber <heber@…>, 12 years ago

FIX: As we use GSL internally, we are as of now required to use GPL v2 license.

  • GNU Scientific Library is used at every place in the code, especially the sub-package LinearAlgebra is based on it which in turn is used really everywhere in the remainder of MoleCuilder. Hence, we have to use the GPL license for the whole of MoleCuilder. In effect, GPL's COPYING was present all along and stated the terms of the GPL v2 license.
  • Hence, I added the default GPL v2 disclaimer to every source file and removed the note about a (actually missing) LICENSE file.
  • also, I added a help-redistribute action which again gives the disclaimer of the GPL v2.
  • also, I changed in the disclaimer that is printed at every program start in builder_init.cpp.
  • TEST: Added check on GPL statement present in every module to test CodeChecks project-disclaimer.
  • Property mode set to 100644
File size: 5.2 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
5 *
6 *
7 * This file is part of MoleCuilder.
8 *
9 * MoleCuilder is free software: you can redistribute it and/or modify
10 * it under the terms of the GNU General Public License as published by
11 * the Free Software Foundation, either version 2 of the License, or
12 * (at your option) any later version.
13 *
14 * MoleCuilder is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 * GNU General Public License for more details.
18 *
19 * You should have received a copy of the GNU General Public License
20 * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
21 */
22
23/*
24 * AtomDescriptor.cpp
25 *
26 * Created on: Feb 5, 2010
27 * Author: crueger
28 */
29
30// include config.h
31#ifdef HAVE_CONFIG_H
32#include <config.h>
33#endif
34
35#include "CodePatterns/MemDebug.hpp"
36
37#include "Descriptors/AtomDescriptor.hpp"
38#include "Descriptors/AtomDescriptor_impl.hpp"
39
40#include "World.hpp"
41#include "Atom/atom.hpp"
42#include "CodePatterns/Observer/ObservedContainer_impl.hpp"
43
44#include <boost/bind.hpp>
45
46#include <iostream>
47
48using namespace std;
49
50typedef World::AtomSet::internal_iterator atoms_iter_t;
51
52/************************ Forwarding object **************************************/
53
54
55AtomDescriptor::AtomDescriptor(impl_ptr _impl) :
56 impl(_impl)
57{}
58
59AtomDescriptor::AtomDescriptor(const AtomDescriptor& src) :
60 impl(src.get_impl())
61{}
62
63AtomDescriptor::~AtomDescriptor()
64{}
65
66AtomDescriptor& AtomDescriptor::operator=(AtomDescriptor &src){
67 if(&src!=this) {
68 impl=src.get_impl();
69 }
70 return *this;
71}
72
73atom* AtomDescriptor::find(){
74 return impl->find();
75}
76
77std::vector<atom*> AtomDescriptor::findAll(){
78 return impl->findAll();
79}
80
81AtomDescriptor::impl_ptr AtomDescriptor::get_impl() const{
82 return impl;
83}
84
85
86
87
88/**************************** implementation ********************/
89
90AtomDescriptor_impl::AtomDescriptor_impl()
91{
92}
93
94AtomDescriptor_impl::~AtomDescriptor_impl()
95{
96}
97
98World::AtomSet& AtomDescriptor_impl::getAtoms(){
99 return World::getInstance().atoms;
100}
101
102atom* AtomDescriptor_impl::find() {
103 World::AtomSet &atoms = getAtoms();
104 atoms_iter_t res = find_if(atoms.begin_internal(),atoms.end_internal(),boost::bind(&AtomDescriptor_impl::predicate,this,_1));
105 return (res!=atoms.end_internal())?((*res).second):0;
106}
107
108vector<atom*> AtomDescriptor_impl::findAll() {
109 vector<atom*> res;
110 World::AtomSet atoms = getAtoms();
111 for_each(atoms.begin_internal(),
112 atoms.end_internal(),
113 boost::bind(&AtomDescriptor_impl::checkAndAdd,
114 this,&res,_1));
115 return res;
116}
117
118void AtomDescriptor_impl::checkAndAdd(std::vector<atom*> *v,std::pair<atomId_t,atom*> p){
119 if(predicate(p)){
120 v->push_back(p.second);
121 }
122}
123
124/************************** Universe and Emptyset *****************/
125
126AtomAllDescriptor_impl::AtomAllDescriptor_impl()
127{}
128
129AtomAllDescriptor_impl::~AtomAllDescriptor_impl()
130{}
131
132bool AtomAllDescriptor_impl::predicate(std::pair<atomId_t,atom*>){
133 return true;
134}
135
136AtomDescriptor AllAtoms(){
137 return AtomDescriptor(AtomDescriptor::impl_ptr(new AtomAllDescriptor_impl));
138}
139
140AtomNoneDescriptor_impl::AtomNoneDescriptor_impl()
141{}
142
143AtomNoneDescriptor_impl::~AtomNoneDescriptor_impl()
144{}
145
146bool AtomNoneDescriptor_impl::predicate(std::pair<atomId_t,atom*>){
147 return false;
148}
149
150AtomDescriptor NoAtoms(){
151 return AtomDescriptor(AtomDescriptor::impl_ptr(new AtomNoneDescriptor_impl));
152}
153
154/************************** Operator stuff ************************/
155
156// AND
157AtomAndDescriptor_impl::AtomAndDescriptor_impl(AtomDescriptor::impl_ptr _lhs, AtomDescriptor::impl_ptr _rhs) :
158 lhs(_lhs), rhs(_rhs)
159{}
160
161AtomAndDescriptor_impl::~AtomAndDescriptor_impl()
162{}
163
164bool AtomAndDescriptor_impl::predicate(std::pair<atomId_t,atom*> atom){
165 return lhs->predicate(atom) && rhs->predicate(atom);
166}
167AtomDescriptor operator&&(const AtomDescriptor &lhs, const AtomDescriptor &rhs){
168 AtomDescriptor::impl_ptr newImpl = AtomDescriptor::impl_ptr(new AtomAndDescriptor_impl(lhs.get_impl(),rhs.get_impl()));
169 return AtomDescriptor(newImpl);
170}
171
172// OR
173AtomOrDescriptor_impl::AtomOrDescriptor_impl(AtomDescriptor::impl_ptr _lhs ,AtomDescriptor::impl_ptr _rhs) :
174 lhs(_lhs), rhs(_rhs)
175{}
176
177AtomOrDescriptor_impl::~AtomOrDescriptor_impl(){
178}
179
180bool AtomOrDescriptor_impl::predicate(std::pair<atomId_t,atom*> atom){
181 return lhs->predicate(atom) || rhs->predicate(atom);
182}
183
184AtomDescriptor operator||(const AtomDescriptor &lhs, const AtomDescriptor &rhs){
185 AtomDescriptor::impl_ptr newImpl = AtomDescriptor::impl_ptr(new AtomOrDescriptor_impl(lhs.get_impl(),rhs.get_impl()));
186 return AtomDescriptor(newImpl);
187}
188
189// NOT
190
191AtomNotDescriptor_impl::AtomNotDescriptor_impl(AtomDescriptor::impl_ptr _arg) :
192 arg(_arg)
193{}
194
195
196AtomNotDescriptor_impl::~AtomNotDescriptor_impl()
197{
198}
199
200bool AtomNotDescriptor_impl::predicate(std::pair<atomId_t,atom*> atom){
201 return !(arg->predicate(atom));
202}
203
204AtomDescriptor operator!(const AtomDescriptor &arg){
205 AtomDescriptor::impl_ptr newImpl = AtomDescriptor::impl_ptr(new AtomNotDescriptor_impl(arg.get_impl()));
206 return AtomDescriptor(newImpl);
207}
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