1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
|
/*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright 2011- The GROMACS Authors
* and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
* Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
* GROMACS is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with GROMACS; if not, see
* https://www.gnu.org/licenses, or write to the Free Software Foundation,
* Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
* If you want to redistribute modifications to GROMACS, please
* consider that scientific software is very special. Version
* control is crucial - bugs must be traceable. We will be happy to
* consider code for inclusion in the official distribution, but
* derived work must not be called official GROMACS. Details are found
* in the README & COPYING files - if they are missing, get the
* official version at https://www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out https://www.gromacs.org.
*/
#include <string>
#include <vector>
#include "gromacs/analysisdata/analysisdata.h"
#include "gromacs/analysisdata/modules/average.h"
#include "gromacs/analysisdata/modules/plot.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/options.h"
#include "gromacs/selection/nbsearch.h"
#include "gromacs/selection/selectionoption.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/trajectoryanalysis/analysismodule.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
#include "gromacs/trajectoryanalysis/cmdlinerunner.h"
using namespace gmx;
/*! \brief
* Template class to serve as a basis for user analysis tools.
*/
class AnalysisTemplate : public TrajectoryAnalysisModule
{
public:
AnalysisTemplate();
virtual void initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings);
virtual void initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& top);
virtual void analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata);
virtual void finishAnalysis(int nframes);
virtual void writeOutput();
private:
class ModuleData;
std::string fnDist_;
double cutoff_;
Selection refsel_;
SelectionList sel_;
AnalysisNeighborhood nb_;
AnalysisData data_;
AnalysisDataAverageModulePointer avem_;
};
AnalysisTemplate::AnalysisTemplate() : cutoff_(0.0)
{
registerAnalysisDataset(&data_, "avedist");
}
void AnalysisTemplate::initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings)
{
static const char* const desc[] = {
"This is a template for writing your own analysis tools for",
"GROMACS. The advantage of using GROMACS for this is that you",
"have access to all information in the topology, and your",
"program will be able to handle all types of coordinates and",
"trajectory files supported by GROMACS. In addition,",
"you get a lot of functionality for free from the trajectory",
"analysis library, including support for flexible dynamic",
"selections. Go ahead an try it![PAR]",
"To get started with implementing your own analysis program,",
"follow the instructions in the README file provided.",
"This template implements a simple analysis programs that calculates",
"average distances from a reference group to one or more",
"analysis groups."
};
settings->setHelpText(desc);
options->addOption(FileNameOption("o")
.filetype(OptionFileType::Plot)
.outputFile()
.store(&fnDist_)
.defaultBasename("avedist")
.description("Average distances from reference group"));
options->addOption(
SelectionOption("reference").store(&refsel_).required().description("Reference group to calculate distances from"));
options->addOption(SelectionOption("select").storeVector(&sel_).required().multiValue().description(
"Groups to calculate distances to"));
options->addOption(DoubleOption("cutoff").store(&cutoff_).description(
"Cutoff for distance calculation (0 = no cutoff)"));
settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
}
void AnalysisTemplate::initAnalysis(const TrajectoryAnalysisSettings& settings,
const TopologyInformation& /*top*/)
{
nb_.setCutoff(static_cast<real>(cutoff_));
data_.setColumnCount(0, sel_.size());
avem_.reset(new AnalysisDataAverageModule());
data_.addModule(avem_);
if (!fnDist_.empty())
{
AnalysisDataPlotModulePointer plotm(new AnalysisDataPlotModule(settings.plotSettings()));
plotm->setFileName(fnDist_);
plotm->setTitle("Average distance");
plotm->setXAxisIsTime();
plotm->setYLabel("Distance (nm)");
data_.addModule(plotm);
}
}
void AnalysisTemplate::analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata)
{
AnalysisDataHandle dh = pdata->dataHandle(data_);
const Selection& refsel = pdata->parallelSelection(refsel_);
AnalysisNeighborhoodSearch nbsearch = nb_.initSearch(pbc, refsel);
dh.startFrame(frnr, fr.time);
for (size_t g = 0; g < sel_.size(); ++g)
{
const Selection& sel = pdata->parallelSelection(sel_[g]);
int nr = sel.posCount();
real frave = 0.0;
for (int i = 0; i < nr; ++i)
{
SelectionPosition p = sel.position(i);
frave += nbsearch.minimumDistance(p.x());
}
frave /= nr;
dh.setPoint(g, frave);
}
dh.finishFrame();
}
void AnalysisTemplate::finishAnalysis(int /*nframes*/) {}
void AnalysisTemplate::writeOutput()
{
// We print out the average of the mean distances for each group.
for (size_t g = 0; g < sel_.size(); ++g)
{
fprintf(stderr, "Average mean distance for '%s': %.3f nm\n", sel_[g].name(), avem_->average(0, g));
}
}
/*! \brief
* The main function for the analysis template.
*/
int main(int argc, char* argv[])
{
return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<AnalysisTemplate>(argc, argv);
}
|
