source: src/Parser/PdbAtomInfoContainer.cpp@ 48eab8

Action_Thermostats Add_AtomRandomPerturbation Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 ChangeBugEmailaddress ChemicalSpaceEvaluator EmpiricalPotential_contain_HomologyGraph_documentation Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_oldresults ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion GeometryObjects Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps stable
Last change on this file since 48eab8 was 9eb71b3, checked in by Frederik Heber <frederik.heber@…>, 9 years ago

Commented out MemDebug include and Memory::ignore.

  • MemDebug clashes with various allocation operators that use a specific placement in memory. It is so far not possible to wrap new/delete fully. Hence, we stop this effort which so far has forced us to put ever more includes (with clashes) into MemDebug and thereby bloat compilation time.
  • MemDebug does not add that much usefulness which is not also provided by valgrind.
  • Property mode set to 100644
File size: 7.3 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 * PdbAtomInfoContainer.cpp
25 *
26 * Created on: Dec 4, 2010
27 * Author: heber
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 "CodePatterns/Assert.hpp"
38//#include "CodePatterns/Log.hpp"
39#include "CodePatterns/toString.hpp"
40//#include "CodePatterns/Verbose.hpp"
41#include "LinearAlgebra/Vector.hpp"
42#include "PdbAtomInfoContainer.hpp"
43
44PdbAtomInfoContainer::knownDataKeysMap PdbAtomInfoContainer::knownDataKeys;
45bool PdbAtomInfoContainer::knownDataKeys_Filled = false;
46
47PdbAtomInfoContainer::PdbAtomInfoContainer() :
48 token("ATOM"),
49 serial(0),
50 name("-"),
51 altLoc('0'),
52 resName("-"),
53 chainID('0'),
54 resSeq(0),
55 iCode(' '),
56 occupancy(0.),
57 tempFactor(0.),
58 element(""),
59 charge(0)
60{
61 if (!knownDataKeys_Filled)
62 fillknownDataKeys();
63}
64
65PdbAtomInfoContainer::~PdbAtomInfoContainer()
66{}
67
68void PdbAtomInfoContainer::fillknownDataKeys()
69{
70 knownDataKeys[PdbKey::token] = "token";
71 knownDataKeys[PdbKey::serial] = "serial";
72 knownDataKeys[PdbKey::name] = "name";
73 knownDataKeys[PdbKey::altLoc] = "altLoc";
74 knownDataKeys[PdbKey::resName] = "resName";
75 knownDataKeys[PdbKey::chainID] = "chainID";
76 knownDataKeys[PdbKey::resSeq] = "resSeq";
77 knownDataKeys[PdbKey::iCode] = "iCode";
78 knownDataKeys[PdbKey::X] = "X";
79 knownDataKeys[PdbKey::Y] = "Y";
80 knownDataKeys[PdbKey::Z] = "Z";
81 knownDataKeys[PdbKey::occupancy] = "occupancy";
82 knownDataKeys[PdbKey::tempFactor] = "tempFactor";
83 knownDataKeys[PdbKey::element] = "element";
84 knownDataKeys[PdbKey::charge] = "charge";
85 knownDataKeys_Filled = true;
86}
87
88void PdbAtomInfoContainer::clearknownDataKeys()
89{
90 knownDataKeys.clear();
91 knownDataKeys_Filled = false;
92}
93
94void PdbAtomInfoContainer::set(const PdbKey::PdbDataKey key, std::string value)
95{
96 switch (key) {
97 case PdbKey::token :
98 ScanKey(token, value);
99 break;
100 case PdbKey::serial :
101 ScanKey(serial, value);
102 break;
103 case PdbKey::name :
104 ScanKey(name, value);
105 break;
106 case PdbKey::altLoc :
107 ScanKey(altLoc, value);
108 break;
109 case PdbKey::resName :
110 ScanKey(resName, value);
111 break;
112 case PdbKey::chainID :
113 ScanKey(chainID, value);
114 break;
115 case PdbKey::resSeq :
116 ScanKey(resSeq, value);
117 break;
118 case PdbKey::iCode :
119 ScanKey(iCode, value);
120 break;
121 case PdbKey::X :
122 ScanKey(XYZ[0], value);
123 break;
124 case PdbKey::Y :
125 ScanKey(XYZ[1], value);
126 break;
127 case PdbKey::Z :
128 ScanKey(XYZ[2], value);
129 break;
130 case PdbKey::occupancy :
131 ScanKey(occupancy, value);
132 break;
133 case PdbKey::tempFactor :
134 ScanKey(tempFactor, value);
135 break;
136 case PdbKey::element :
137 ScanKey(element, value);
138 break;
139 case PdbKey::charge :
140 ScanKey(charge, value);
141 break;
142 default :
143 std::cout << "Unknown key: " << key << ", value: " << value << std::endl;
144 break;
145 }
146}
147
148template <>
149std::string PdbAtomInfoContainer::get<std::string>(const PdbKey::PdbDataKey key) const
150{
151 switch (key) {
152 case PdbKey::token :
153 return toString(token);
154 case PdbKey::serial :
155 return toString(serial);
156 case PdbKey::name :
157 return toString(name);
158 case PdbKey::altLoc :
159 return toString(altLoc);
160 case PdbKey::resName :
161 return toString(resName);
162 case PdbKey::chainID :
163 return toString(chainID);
164 case PdbKey::resSeq :
165 return toString(resSeq);
166 case PdbKey::iCode :
167 return toString(iCode);
168 case PdbKey::X :
169 return toString(XYZ[0]);
170 case PdbKey::Y :
171 return toString(XYZ[1]);
172 case PdbKey::Z :
173 return toString(XYZ[2]);
174 case PdbKey::occupancy :
175 return toString(occupancy);
176 case PdbKey::tempFactor :
177 return toString(tempFactor);
178 case PdbKey::element :
179 return toString(element);
180 case PdbKey::charge :
181 return toString(charge);
182 default :
183 std::cout << "Unknown key: " << key << std::endl;
184 return "";
185 }
186}
187
188template <>
189int PdbAtomInfoContainer::get<int>(const PdbKey::PdbDataKey key) const
190{
191 switch (key) {
192 case PdbKey::serial :
193 return serial;
194 case PdbKey::resSeq :
195 return resSeq;
196 case PdbKey::charge :
197 return charge;
198 default :
199 std::cout << "Unknown key or not presentable as int: " << key << std::endl;
200 return 0;
201 }
202}
203
204template <>
205double PdbAtomInfoContainer::get<double>(const PdbKey::PdbDataKey key) const
206{
207 switch (key) {
208 case PdbKey::X :
209 return XYZ[0];
210 case PdbKey::Y :
211 return XYZ[1];
212 case PdbKey::Z :
213 return XYZ[2];
214 case PdbKey::occupancy :
215 return occupancy;
216 case PdbKey::tempFactor :
217 return tempFactor;
218 default :
219 std::cout << "Unknown key or not presentable as double: " << key << std::endl;
220 return 0.;
221 }
222}
223
224const std::string& PdbAtomInfoContainer::getDataKey(PdbKey::PdbDataKey key) const
225{
226 knownDataKeysMap::const_iterator iter;
227 iter = knownDataKeys.find(key);
228 ASSERT(iter != knownDataKeys.end(),
229 "PdbAtomInfoContainer::getDataKey() - unknown key "
230 +toString(key)+" request, did someone add a key to PdbKey?");
231 return iter->second;
232}
233
234std::ostream& operator<<(std::ostream &ost, const PdbAtomInfoContainer& m)
235{
236 ost << m.getDataKey(PdbKey::token) << "(" << m.get<std::string>(PdbKey::token) <<") ";
237 ost << m.getDataKey(PdbKey::serial) << "(" << m.get<std::string>(PdbKey::serial) <<") ";
238 ost << m.getDataKey(PdbKey::name) << "(" << m.get<std::string>(PdbKey::name) <<") ";
239 ost << m.getDataKey(PdbKey::altLoc) << "(" << m.get<std::string>(PdbKey::altLoc) <<") ";
240 ost << m.getDataKey(PdbKey::resName) << "(" << m.get<std::string>(PdbKey::resName) <<") ";
241 ost << m.getDataKey(PdbKey::chainID) << "(" << m.get<std::string>(PdbKey::chainID) <<") ";
242 ost << m.getDataKey(PdbKey::resSeq) << "(" << m.get<std::string>(PdbKey::resSeq) <<") ";
243 ost << m.getDataKey(PdbKey::iCode) << "(" << m.get<std::string>(PdbKey::iCode) <<") ";
244 ost << m.getDataKey(PdbKey::X) << "(" << m.get<std::string>(PdbKey::X) <<") ";
245 ost << m.getDataKey(PdbKey::Y) << "(" << m.get<std::string>(PdbKey::Y) <<") ";
246 ost << m.getDataKey(PdbKey::Z) << "(" << m.get<std::string>(PdbKey::Z) <<") ";
247 ost << m.getDataKey(PdbKey::occupancy) << "(" << m.get<std::string>(PdbKey::occupancy) <<") ";
248 ost << m.getDataKey(PdbKey::tempFactor) << "(" << m.get<std::string>(PdbKey::tempFactor) <<") ";
249 ost << m.getDataKey(PdbKey::element) << "(" << m.get<std::string>(PdbKey::element) <<") ";
250 ost << m.getDataKey(PdbKey::charge) << "(" << m.get<std::string>(PdbKey::charge) <<") ";
251 return ost;
252}
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