#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TOOLS_SOURCES} PARENT_SCOPE)
if (BUILD_TESTING)
-# add_subdirectory(tests)
+ add_subdirectory(tests)
endif()
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * 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
+ * http://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 http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "report-methods.h"
+
+#include "gromacs/commandline/cmdlineoptionsmodule.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/filetypes.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/state.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/ioptionscontainer.h"
+#include "gromacs/selection/selectionoptionbehavior.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/fileredirector.h"
+#include "gromacs/utility/filestream.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+void writeHeader(TextWriter *writer, const std::string &text, const std::string §ion, bool writeFormattedText)
+{
+ std::string formattedText;
+ if (writeFormattedText)
+ {
+ formattedText = "\\" + section + "{" + text + "}\n";
+ }
+ else
+ {
+ formattedText = section + ": " + text + "\n";
+ }
+ writer->writeString(formattedText);
+}
+
+void writeSystemInformation(TextWriter *writer, const gmx_mtop_t &top, bool writeFormattedText)
+{
+ int nmol, nvsite = 0;
+ gmx_mtop_atomloop_block_t aloop;
+ const t_atom *atom;
+
+ writeHeader(writer, "Simulation system", "subsection", writeFormattedText);
+ aloop = gmx_mtop_atomloop_block_init(&top);
+ while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
+ {
+ if (atom->ptype == eptVSite)
+ {
+ nvsite += nmol;
+ }
+ }
+ {
+ writer->writeLine(formatString("A system of %d molecules (%d atoms) was simulated.",
+ gmx_mtop_num_molecules(top), top.natoms-nvsite));
+ }
+ if (nvsite)
+ {
+ writer->writeLine(formatString("Virtual sites were used in some of the molecules."));
+ }
+ writer->ensureEmptyLine();
+}
+
+void writeParameterInformation(TextWriter *writer, const t_inputrec &ir, bool writeFormattedText)
+{
+ writeHeader(writer, "Simulation settings", "subsection", writeFormattedText);
+ writer->writeLine(formatString("A total of %g ns were simulated with a time step of %g fs.",
+ ir.nsteps*ir.delta_t*0.001, 1000*ir.delta_t));
+ writer->writeLine(formatString("Neighbor searching was performed every %d steps.", ir.nstlist));
+ writer->writeLine(formatString("The %s algorithm was used for electrostatic interactions.",
+ EELTYPE(ir.coulombtype)));
+ writer->writeLine(formatString("with a cut-off of %g nm.", ir.rcoulomb));
+ if (ir.coulombtype == eelPME)
+ {
+ writer->writeLine(formatString("A reciprocal grid of %d x %d x %d cells was used with %dth order B-spline interpolation.", ir.nkx, ir.nky, ir.nkz, ir.pme_order));
+ }
+ writer->writeLine(formatString("A single cut-off of %g nm was used for Van der Waals interactions.", ir.rlist));
+ if (ir.etc != 0)
+ {
+ writer->writeLine(formatString("Temperature coupling was done with the %s algorithm.",
+ etcoupl_names[ir.etc]));
+ }
+ if (ir.epc != 0)
+ {
+ writer->writeLine(formatString("Pressure coupling was done with the %s algorithm.",
+ epcoupl_names[ir.epc]));
+ }
+ writer->ensureEmptyLine();
+}
+
+void writeInformation(TextOutputFile *outputStream, const t_inputrec &ir,
+ const gmx_mtop_t &top, bool writeFormattedText, bool notStdout)
+{
+ TextWriter writer(outputStream);
+ writer.ensureEmptyLine();
+ writeHeader(&writer, "Methods", "section", writeFormattedText);
+ writeSystemInformation(&writer, top, writeFormattedText);
+ writeParameterInformation(&writer, ir, writeFormattedText);
+ writer.ensureEmptyLine();
+
+ if (notStdout)
+ {
+ writer.close();
+ }
+}
+
+namespace
+{
+
+class ReportMethods : public ICommandLineOptionsModule
+{
+ public:
+ ReportMethods()
+ : writeLatex_(false), writePlainText_(false)
+ {
+ }
+
+ // From ICommandLineOptionsModule
+ void init(CommandLineModuleSettings * /*settings*/) override
+ {
+ }
+ void initOptions(IOptionsContainer *options,
+ ICommandLineOptionsModuleSettings *settings) override;
+ void optionsFinished() override;
+ int run() override;
+
+ private:
+
+ //! File name for the output LaTeX file or empty.
+ std::string outputFileLatex_;
+ //! File name for the unformatted output file or empty.
+ std::string outputFileUnformatted_;
+ //! File name of the run input file with full topology.
+ std::string inputTopology_;
+ //! Boolean reporting if writing to the LaTeX output file is requested.
+ bool writeLatex_;
+ //! Boolean reporting if writing to unformatted output is requested.
+ bool writePlainText_;
+};
+
+void ReportMethods::initOptions(IOptionsContainer *options,
+ ICommandLineOptionsModuleSettings *settings)
+{
+ const char *const desc[] = {
+ "[THISMODULE] reports basic system information for the run input",
+ "file specfied with [TT]-s[tt] either to the",
+ "terminal, to a LaTeX formatted output file if run with",
+ "the [TT]-m[tt] option or to an unformatted file with",
+ "the [TT]-o[tt] option.",
+ "The functionality has been moved here from its previous",
+ "place in [gmx-check]."
+ };
+
+ settings->setHelpText(desc);
+
+ options->addOption(FileNameOption("s")
+ .filetype(eftTopology).inputFile().required()
+ .store(&inputTopology_)
+ .defaultBasename("topol")
+ .description("Run input file for report"));
+
+ // TODO: Replace use of legacyType.
+ options->addOption(FileNameOption("m")
+ .legacyType(efTEX).outputFile()
+ .store(&outputFileLatex_).storeIsSet(&writeLatex_)
+ .defaultBasename("report")
+ .description("LaTeX formatted report output"));
+ options->addOption(FileNameOption("o")
+ .legacyType(efOUT).outputFile()
+ .store(&outputFileUnformatted_).storeIsSet(&writePlainText_)
+ .defaultBasename("report")
+ .description("Unformatted report output to file"));
+
+}
+
+void ReportMethods::optionsFinished()
+{
+}
+
+int ReportMethods::run()
+{
+ t_state state;
+ t_inputrec ir;
+ gmx_mtop_t top;
+ read_tpx_state(inputTopology_.c_str(), &ir, &state, &top);
+ if (writeLatex_)
+ {
+ TextOutputFile file(outputFileLatex_);
+ writeInformation(&file, ir, top, true, true);
+ }
+ if (writePlainText_)
+ {
+ TextOutputFile file(outputFileUnformatted_);
+ writeInformation(&file, ir, top, false, true);
+ }
+ TextOutputFile &stdoutFile = TextOutputFile::standardOutput();
+ writeInformation(&stdoutFile, ir, top, false, false);
+
+ return 0;
+}
+
+} // namespace
+
+const char ReportMethodsInfo::name[] = "report";
+const char ReportMethodsInfo::shortDescription[] =
+ "Write short summary about the simulation setup to a text file "
+ "and/or to the standard output.";
+ICommandLineOptionsModulePointer ReportMethodsInfo::create()
+{
+ return ICommandLineOptionsModulePointer(compat::make_unique<ReportMethods>());
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * 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
+ * http://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 http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_TOOLS_REPORT_METHODS_H
+#define GMX_TOOLS_REPORT_METHODS_H
+
+#include "gromacs/commandline/cmdlineoptionsmodule.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/filestream.h"
+#include "gromacs/utility/textwriter.h"
+
+namespace gmx
+{
+
+class ReportMethodsInfo
+{
+ public:
+ static const char name[];
+ static const char shortDescription[];
+ static ICommandLineOptionsModulePointer create();
+};
+
+// Helper functions of the class
+
+/*! \brief
+ * Write appropiate Header to output stream.
+ *
+ * \param[in] writer TextWriter object for writing information.
+ * \param[in] text String with the header before writing.
+ * \param[in] section String with section text for header.
+ * \param[in] writeFormattedText If we need to format the text for LaTeX output or not
+ */
+void writeHeader(TextWriter *writer, const std::string &text, const std::string §ion, bool writeFormattedText);
+
+/*! \brief
+ * Write information about the molecules in the system.
+ *
+ * This method should write all possible information about
+ * the molecular composition of the system.
+ *
+ * \param[in] writer TextWriter object for writing information.
+ * \param[in] top Local topology used to derive the information to write out.
+ * \param[in] writeFormattedText Decide if we want formatted text output or not.
+ *
+ */
+void writeSystemInformation(TextWriter *writer, const gmx_mtop_t &top, bool writeFormattedText);
+
+/*! \brief
+ * Write information about system parameters.
+ *
+ * This method writes the basic information for the system parameters
+ * and simulation settings as reported in the \p ir.
+ *
+ * \param[in] writer TextWriter object for writing information.
+ * \param[in] ir Reference to inputrec of the run input.
+ * \param[in] writeFormattedText Decide if we want formatted text output or not.
+ */
+void writeParameterInformation(TextWriter *writer, const t_inputrec &ir, bool writeFormattedText);
+
+/*! \brief
+ * Wrapper for writing out information.
+ *
+ * This function is actual called from within the run method
+ * to write the information to the terminal or to file.
+ * New write out methods should be added to it instead of adding them in run.
+ *
+ * \param[in] outputStream The filestream used to write the information to.
+ * \param[in] ir Reference to inputrec of the run input.
+ * \param[in] top Local topology used to derive the information to write out.
+ * \param[in] writeFormattedText Decide if we want formatted text output or not.
+ * \param[in] notStdout Bool to see if we can close the file after writing or not in case of stdout.
+ */
+void writeInformation(TextOutputFile *outputStream, const t_inputrec &ir,
+ const gmx_mtop_t &top, bool writeFormattedText, bool notStdout);
+
+} // namespace gmx
+
+#endif
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2018, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# 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
+# http://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 http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test(ToolUnitTests tool-test
+ report-methods.cpp)
+
--- /dev/null
+TITLE First 10 residues from 1AKI
+REMARK THIS IS A SIMULATION BOX
+CRYST1 59.062 68.451 30.517 90.00 90.00 90.00 P 1 1
+MODEL 1
+ATOM 1 N LYS B 1 35.360 22.340 -11.980 1.00 0.00 N
+ATOM 2 H1 LYS B 1 36.120 22.880 -12.360 1.00 0.00 H
+ATOM 3 H2 LYS B 1 34.700 22.140 -12.700 1.00 0.00 H
+ATOM 4 H3 LYS B 1 34.920 22.860 -11.250 1.00 0.00 H
+ATOM 5 CA LYS B 1 35.890 21.070 -11.430 1.00 0.00 C
+ATOM 6 HA LYS B 1 36.330 20.550 -12.160 1.00 0.00 H
+ATOM 7 CB LYS B 1 36.870 21.440 -10.310 1.00 0.00 C
+ATOM 8 HB1 LYS B 1 37.630 21.950 -10.700 1.00 0.00 H
+ATOM 9 HB2 LYS B 1 36.390 22.010 -9.640 1.00 0.00 H
+ATOM 10 CG LYS B 1 37.450 20.250 -9.560 1.00 0.00 C
+ATOM 11 HG1 LYS B 1 36.760 19.890 -8.940 1.00 0.00 H
+ATOM 12 HG2 LYS B 1 37.700 19.540 -10.230 1.00 0.00 H
+ATOM 13 CD LYS B 1 38.690 20.650 -8.770 1.00 0.00 C
+ATOM 14 HD1 LYS B 1 39.450 20.830 -9.400 1.00 0.00 H
+ATOM 15 HD2 LYS B 1 38.490 21.470 -8.240 1.00 0.00 H
+ATOM 16 CE LYS B 1 39.060 19.510 -7.840 1.00 0.00 C
+ATOM 17 HE1 LYS B 1 38.410 19.460 -7.080 1.00 0.00 H
+ATOM 18 HE2 LYS B 1 39.060 18.640 -8.330 1.00 0.00 H
+ATOM 19 NZ LYS B 1 40.420 19.770 -7.300 1.00 0.00 N
+ATOM 20 HZ1 LYS B 1 40.690 19.030 -6.680 1.00 0.00 H
+ATOM 21 HZ2 LYS B 1 41.080 19.820 -8.060 1.00 0.00 H
+ATOM 22 HZ3 LYS B 1 40.420 20.640 -6.800 1.00 0.00 H
+ATOM 23 C LYS B 1 34.740 20.260 -10.840 1.00 0.00 C
+ATOM 24 O LYS B 1 33.950 20.810 -10.080 1.00 0.00 O
+ATOM 25 N VAL B 2 34.740 18.960 -11.040 1.00 0.00 N
+ATOM 26 H VAL B 2 35.360 18.600 -11.740 1.00 0.00 H
+ATOM 27 CA VAL B 2 33.900 18.000 -10.330 1.00 0.00 C
+ATOM 28 HA VAL B 2 33.170 18.520 -9.900 1.00 0.00 H
+ATOM 29 CB VAL B 2 33.140 17.030 -11.230 1.00 0.00 C
+ATOM 30 HB VAL B 2 33.860 16.520 -11.700 1.00 0.00 H
+ATOM 31 CG1 VAL B 2 32.250 16.080 -10.430 1.00 0.00 C
+ATOM 32 1HG1 VAL B 2 31.770 15.470 -11.060 1.00 0.00 H
+ATOM 33 2HG1 VAL B 2 32.820 15.550 -9.810 1.00 0.00 H
+ATOM 34 3HG1 VAL B 2 31.580 16.610 -9.910 1.00 0.00 H
+ATOM 35 CG2 VAL B 2 32.290 17.710 -12.290 1.00 0.00 C
+ATOM 36 1HG2 VAL B 2 31.830 17.020 -12.840 1.00 0.00 H
+ATOM 37 2HG2 VAL B 2 31.620 18.300 -11.850 1.00 0.00 H
+ATOM 38 3HG2 VAL B 2 32.880 18.270 -12.880 1.00 0.00 H
+ATOM 39 C VAL B 2 34.800 17.310 -9.290 1.00 0.00 C
+ATOM 40 O VAL B 2 35.760 16.610 -9.660 1.00 0.00 O
+ATOM 41 N PHE B 3 34.490 17.550 -8.040 1.00 0.00 N
+ATOM 42 H PHE B 3 33.750 18.190 -7.840 1.00 0.00 H
+ATOM 43 CA PHE B 3 35.190 16.900 -6.920 1.00 0.00 C
+ATOM 44 HA PHE B 3 36.150 16.970 -7.170 1.00 0.00 H
+ATOM 45 CB PHE B 3 34.970 17.630 -5.590 1.00 0.00 C
+ATOM 46 HB1 PHE B 3 34.050 18.020 -5.580 1.00 0.00 H
+ATOM 47 HB2 PHE B 3 35.060 16.980 -4.840 1.00 0.00 H
+ATOM 48 CG PHE B 3 35.940 18.740 -5.380 1.00 0.00 C
+ATOM 49 CD1 PHE B 3 35.670 20.050 -5.800 1.00 0.00 C
+ATOM 50 HD1 PHE B 3 34.810 20.250 -6.270 1.00 0.00 H
+ATOM 51 CD2 PHE B 3 37.000 18.560 -4.470 1.00 0.00 C
+ATOM 52 HD2 PHE B 3 37.130 17.660 -4.050 1.00 0.00 H
+ATOM 53 CE1 PHE B 3 36.580 21.080 -5.570 1.00 0.00 C
+ATOM 54 HE1 PHE B 3 36.480 21.950 -6.040 1.00 0.00 H
+ATOM 55 CE2 PHE B 3 37.870 19.590 -4.160 1.00 0.00 C
+ATOM 56 HE2 PHE B 3 38.660 19.420 -3.570 1.00 0.00 H
+ATOM 57 CZ PHE B 3 37.640 20.870 -4.670 1.00 0.00 C
+ATOM 58 HZ PHE B 3 38.220 21.640 -4.390 1.00 0.00 H
+ATOM 59 C PHE B 3 34.740 15.440 -6.770 1.00 0.00 C
+ATOM 60 O PHE B 3 33.520 15.160 -6.860 1.00 0.00 O
+ATOM 61 N GLY B 4 35.720 14.640 -6.330 1.00 0.00 N
+ATOM 62 H GLY B 4 36.670 14.950 -6.320 1.00 0.00 H
+ATOM 63 CA GLY B 4 35.370 13.280 -5.870 1.00 0.00 C
+ATOM 64 HA1 GLY B 4 34.620 12.920 -6.430 1.00 0.00 H
+ATOM 65 HA2 GLY B 4 36.160 12.680 -5.940 1.00 0.00 H
+ATOM 66 C GLY B 4 34.920 13.420 -4.420 1.00 0.00 C
+ATOM 67 O GLY B 4 35.300 14.400 -3.780 1.00 0.00 O
+ATOM 68 N ARG B 5 34.050 12.540 -3.970 1.00 0.00 N
+ATOM 69 H ARG B 5 33.710 11.840 -4.600 1.00 0.00 H
+ATOM 70 CA ARG B 5 33.560 12.540 -2.590 1.00 0.00 C
+ATOM 71 HA ARG B 5 32.980 13.340 -2.520 1.00 0.00 H
+ATOM 72 CB ARG B 5 32.760 11.260 -2.330 1.00 0.00 C
+ATOM 73 HB1 ARG B 5 32.000 11.220 -2.970 1.00 0.00 H
+ATOM 74 HB2 ARG B 5 33.360 10.470 -2.470 1.00 0.00 H
+ATOM 75 CG ARG B 5 32.210 11.200 -0.920 1.00 0.00 C
+ATOM 76 HG1 ARG B 5 32.970 11.170 -0.270 1.00 0.00 H
+ATOM 77 HG2 ARG B 5 31.650 12.010 -0.750 1.00 0.00 H
+ATOM 78 CD ARG B 5 31.380 10.000 -0.720 1.00 0.00 C
+ATOM 79 HD1 ARG B 5 31.040 9.990 0.220 1.00 0.00 H
+ATOM 80 HD2 ARG B 5 30.600 10.050 -1.350 1.00 0.00 H
+ATOM 81 NE ARG B 5 32.060 8.750 -0.960 1.00 0.00 N
+ATOM 82 HE ARG B 5 32.020 8.400 -1.890 1.00 0.00 H
+ATOM 83 CZ ARG B 5 32.730 8.010 -0.100 1.00 0.00 C
+ATOM 84 NH1 ARG B 5 32.840 8.330 1.190 1.00 0.00 N
+ATOM 85 1HH1 ARG B 5 32.390 9.160 1.530 1.00 0.00 H
+ATOM 86 2HH1 ARG B 5 33.360 7.750 1.810 1.00 0.00 H
+ATOM 87 NH2 ARG B 5 33.250 6.840 -0.530 1.00 0.00 N
+ATOM 88 1HH2 ARG B 5 33.110 6.550 -1.470 1.00 0.00 H
+ATOM 89 2HH2 ARG B 5 33.760 6.260 0.100 1.00 0.00 H
+ATOM 90 C ARG B 5 34.670 12.730 -1.560 1.00 0.00 C
+ATOM 91 O ARG B 5 34.670 13.650 -0.700 1.00 0.00 O
+ATOM 92 N CYS B 6 35.670 11.850 -1.610 1.00 0.00 N
+ATOM 93 H CYS B 6 35.670 11.160 -2.330 1.00 0.00 H
+ATOM 94 CA CYS B 6 36.780 11.870 -0.650 1.00 0.00 C
+ATOM 95 HA CYS B 6 36.310 12.020 0.220 1.00 0.00 H
+ATOM 96 CB CYS B 6 37.490 10.530 -0.620 1.00 0.00 C
+ATOM 97 HB1 CYS B 6 37.700 10.340 -1.580 1.00 0.00 H
+ATOM 98 HB2 CYS B 6 38.340 10.720 -0.130 1.00 0.00 H
+ATOM 99 SG CYS B 6 36.540 9.200 0.140 1.00 0.00 S
+ATOM 100 HG CYS B 6 37.075 8.355 0.120 1.00 0.00 H
+ATOM 101 C CYS B 6 37.750 13.050 -0.780 1.00 0.00 C
+ATOM 102 O CYS B 6 38.150 13.610 0.260 1.00 0.00 O
+ATOM 103 N GLU B 7 37.860 13.480 -2.020 1.00 0.00 N
+ATOM 104 H GLU B 7 37.400 13.000 -2.760 1.00 0.00 H
+ATOM 105 CA GLU B 7 38.680 14.690 -2.310 1.00 0.00 C
+ATOM 106 HA GLU B 7 39.600 14.550 -1.930 1.00 0.00 H
+ATOM 107 CB GLU B 7 38.780 14.850 -3.820 1.00 0.00 C
+ATOM 108 HB1 GLU B 7 39.230 14.020 -4.170 1.00 0.00 H
+ATOM 109 HB2 GLU B 7 37.850 14.890 -4.170 1.00 0.00 H
+ATOM 110 CG GLU B 7 39.540 16.050 -4.380 1.00 0.00 C
+ATOM 111 HG1 GLU B 7 39.130 16.870 -3.990 1.00 0.00 H
+ATOM 112 HG2 GLU B 7 40.490 15.980 -4.070 1.00 0.00 H
+ATOM 113 CD GLU B 7 39.580 16.240 -5.870 1.00 0.00 C
+ATOM 114 OE1 GLU B 7 38.670 15.640 -6.490 1.00 0.00 O
+ATOM 115 OE2 GLU B 7 40.420 16.950 -6.380 1.00 0.00 O
+ATOM 116 C GLU B 7 38.050 15.930 -1.660 1.00 0.00 C
+ATOM 117 O GLU B 7 38.740 16.730 -1.010 1.00 0.00 O
+ATOM 118 N LEU B 8 36.740 16.050 -1.820 1.00 0.00 N
+ATOM 119 H LEU B 8 36.260 15.350 -2.350 1.00 0.00 H
+ATOM 120 CA LEU B 8 35.960 17.160 -1.250 1.00 0.00 C
+ATOM 121 HA LEU B 8 36.400 18.010 -1.560 1.00 0.00 H
+ATOM 122 CB LEU B 8 34.530 17.170 -1.810 1.00 0.00 C
+ATOM 123 HB1 LEU B 8 34.570 17.220 -2.810 1.00 0.00 H
+ATOM 124 HB2 LEU B 8 34.060 16.330 -1.530 1.00 0.00 H
+ATOM 125 CG LEU B 8 33.720 18.350 -1.310 1.00 0.00 C
+ATOM 126 HG LEU B 8 33.780 18.420 -0.310 1.00 0.00 H
+ATOM 127 CD1 LEU B 8 34.300 19.660 -1.840 1.00 0.00 C
+ATOM 128 1HD1 LEU B 8 33.760 20.430 -1.500 1.00 0.00 H
+ATOM 129 2HD1 LEU B 8 35.240 19.750 -1.530 1.00 0.00 H
+ATOM 130 3HD1 LEU B 8 34.270 19.650 -2.840 1.00 0.00 H
+ATOM 131 CD2 LEU B 8 32.250 18.140 -1.600 1.00 0.00 C
+ATOM 132 1HD2 LEU B 8 31.720 18.930 -1.260 1.00 0.00 H
+ATOM 133 2HD2 LEU B 8 32.110 18.050 -2.580 1.00 0.00 H
+ATOM 134 3HD2 LEU B 8 31.930 17.310 -1.140 1.00 0.00 H
+ATOM 135 C LEU B 8 36.050 17.130 0.270 1.00 0.00 C
+ATOM 136 O LEU B 8 36.160 18.170 0.920 1.00 0.00 O
+ATOM 137 N ALA B 9 35.750 15.980 0.830 1.00 0.00 N
+ATOM 138 H ALA B 9 35.460 15.220 0.240 1.00 0.00 H
+ATOM 139 CA ALA B 9 35.840 15.760 2.280 1.00 0.00 C
+ATOM 140 HA ALA B 9 35.080 16.260 2.690 1.00 0.00 H
+ATOM 141 CB ALA B 9 35.660 14.290 2.620 1.00 0.00 C
+ATOM 142 HB1 ALA B 9 35.720 14.160 3.610 1.00 0.00 H
+ATOM 143 HB2 ALA B 9 34.760 13.980 2.300 1.00 0.00 H
+ATOM 144 HB3 ALA B 9 36.370 13.750 2.180 1.00 0.00 H
+ATOM 145 C ALA B 9 37.140 16.310 2.840 1.00 0.00 C
+ATOM 146 O ALA B 9 37.150 16.980 3.900 1.00 0.00 O
+ATOM 147 N ALA B 10 38.270 15.980 2.200 1.00 0.00 N
+ATOM 148 H ALA B 10 38.200 15.390 1.400 1.00 0.00 H
+ATOM 149 CA ALA B 10 39.610 16.430 2.620 1.00 0.00 C
+ATOM 150 HA ALA B 10 39.690 16.190 3.580 1.00 0.00 H
+ATOM 151 CB ALA B 10 40.710 15.710 1.840 1.00 0.00 C
+ATOM 152 HB1 ALA B 10 41.600 16.030 2.150 1.00 0.00 H
+ATOM 153 HB2 ALA B 10 40.640 14.720 2.010 1.00 0.00 H
+ATOM 154 HB3 ALA B 10 40.600 15.890 0.860 1.00 0.00 H
+ATOM 155 C ALA B 10 39.740 17.940 2.460 1.00 0.00 C
+ATOM 156 O ALA B 10 40.190 18.500 3.470 1.00 0.00 O
+TER
+ENDMDL
--- /dev/null
+; Include forcefield parameters
+#include "oplsaa.ff/forcefield.itp"
+
+[ moleculetype ]
+; Name nrexcl
+Protein_chain_B 3
+
+[ atoms ]
+; nr type resnr residue atom cgnr charge mass typeB chargeB massB
+; residue 1 LYS rtp LYSH q +2.0
+ 1 opls_287 1 LYS N 1 -0.3 14.0027 ; qtot -0.3
+ 2 opls_290 1 LYS H1 1 0.33 1.008 ; qtot 0.03
+ 3 opls_290 1 LYS H2 1 0.33 1.008 ; qtot 0.36
+ 4 opls_290 1 LYS H3 1 0.33 1.008 ; qtot 0.69
+ 5 opls_293B 1 LYS CA 1 0.25 12.011 ; qtot 0.94
+ 6 opls_140 1 LYS HA 1 0.06 1.008 ; qtot 1
+ 7 opls_136 1 LYS CB 2 -0.12 12.011 ; qtot 0.88
+ 8 opls_140 1 LYS HB1 2 0.06 1.008 ; qtot 0.94
+ 9 opls_140 1 LYS HB2 2 0.06 1.008 ; qtot 1
+ 10 opls_136 1 LYS CG 3 -0.12 12.011 ; qtot 0.88
+ 11 opls_140 1 LYS HG1 3 0.06 1.008 ; qtot 0.94
+ 12 opls_140 1 LYS HG2 3 0.06 1.008 ; qtot 1
+ 13 opls_136 1 LYS CD 4 -0.12 12.011 ; qtot 0.88
+ 14 opls_140 1 LYS HD1 4 0.06 1.008 ; qtot 0.94
+ 15 opls_140 1 LYS HD2 4 0.06 1.008 ; qtot 1
+ 16 opls_292 1 LYS CE 5 0.19 12.011 ; qtot 1.19
+ 17 opls_140 1 LYS HE1 5 0.06 1.008 ; qtot 1.25
+ 18 opls_140 1 LYS HE2 5 0.06 1.008 ; qtot 1.31
+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067 ; qtot 1.01
+ 20 opls_290 1 LYS HZ1 6 0.33 1.008 ; qtot 1.34
+ 21 opls_290 1 LYS HZ2 6 0.33 1.008 ; qtot 1.67
+ 22 opls_290 1 LYS HZ3 6 0.33 1.008 ; qtot 2
+ 23 opls_235 1 LYS C 7 0.5 12.011 ; qtot 2.5
+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2
+; residue 2 VAL rtp VAL q 0.0
+ 25 opls_238 2 VAL N 8 -0.5 14.0067 ; qtot 1.5
+ 26 opls_241 2 VAL H 8 0.3 1.008 ; qtot 1.8
+ 27 opls_224B 2 VAL CA 8 0.14 12.011 ; qtot 1.94
+ 28 opls_140 2 VAL HA 8 0.06 1.008 ; qtot 2
+ 29 opls_137 2 VAL CB 9 -0.06 12.011 ; qtot 1.94
+ 30 opls_140 2 VAL HB 9 0.06 1.008 ; qtot 2
+ 31 opls_135 2 VAL CG1 10 -0.18 12.011 ; qtot 1.82
+ 32 opls_140 2 VAL HG11 10 0.06 1.008 ; qtot 1.88
+ 33 opls_140 2 VAL HG12 10 0.06 1.008 ; qtot 1.94
+ 34 opls_140 2 VAL HG13 10 0.06 1.008 ; qtot 2
+ 35 opls_135 2 VAL CG2 11 -0.18 12.011 ; qtot 1.82
+ 36 opls_140 2 VAL HG21 11 0.06 1.008 ; qtot 1.88
+ 37 opls_140 2 VAL HG22 11 0.06 1.008 ; qtot 1.94
+ 38 opls_140 2 VAL HG23 11 0.06 1.008 ; qtot 2
+ 39 opls_235 2 VAL C 12 0.5 12.011 ; qtot 2.5
+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2
+; residue 3 PHE rtp PHE q 0.0
+ 41 opls_238 3 PHE N 13 -0.5 14.0067 ; qtot 1.5
+ 42 opls_241 3 PHE H 13 0.3 1.008 ; qtot 1.8
+ 43 opls_224B 3 PHE CA 13 0.14 12.011 ; qtot 1.94
+ 44 opls_140 3 PHE HA 13 0.06 1.008 ; qtot 2
+ 45 opls_149 3 PHE CB 14 -0.005 12.011 ; qtot 1.995
+ 46 opls_140 3 PHE HB1 14 0.06 1.008 ; qtot 2.055
+ 47 opls_140 3 PHE HB2 14 0.06 1.008 ; qtot 2.115
+ 48 opls_145 3 PHE CG 14 -0.115 12.011 ; qtot 2
+ 49 opls_145 3 PHE CD1 15 -0.115 12.011 ; qtot 1.885
+ 50 opls_146 3 PHE HD1 15 0.115 1.008 ; qtot 2
+ 51 opls_145 3 PHE CD2 16 -0.115 12.011 ; qtot 1.885
+ 52 opls_146 3 PHE HD2 16 0.115 1.008 ; qtot 2
+ 53 opls_145 3 PHE CE1 17 -0.115 12.011 ; qtot 1.885
+ 54 opls_146 3 PHE HE1 17 0.115 1.008 ; qtot 2
+ 55 opls_145 3 PHE CE2 18 -0.115 12.011 ; qtot 1.885
+ 56 opls_146 3 PHE HE2 18 0.115 1.008 ; qtot 2
+ 57 opls_145 3 PHE CZ 19 -0.115 12.011 ; qtot 1.885
+ 58 opls_146 3 PHE HZ 19 0.115 1.008 ; qtot 2
+ 59 opls_235 3 PHE C 20 0.5 12.011 ; qtot 2.5
+ 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2
+; residue 4 GLY rtp GLY q 0.0
+ 61 opls_238 4 GLY N 21 -0.5 14.0067 ; qtot 1.5
+ 62 opls_241 4 GLY H 21 0.3 1.008 ; qtot 1.8
+ 63 opls_223B 4 GLY CA 21 0.08 12.011 ; qtot 1.88
+ 64 opls_140 4 GLY HA1 21 0.06 1.008 ; qtot 1.94
+ 65 opls_140 4 GLY HA2 21 0.06 1.008 ; qtot 2
+ 66 opls_235 4 GLY C 22 0.5 12.011 ; qtot 2.5
+ 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2
+; residue 5 ARG rtp ARG q +1.0
+ 68 opls_238 5 ARG N 23 -0.5 14.0067 ; qtot 1.5
+ 69 opls_241 5 ARG H 23 0.3 1.008 ; qtot 1.8
+ 70 opls_224B 5 ARG CA 23 0.14 12.011 ; qtot 1.94
+ 71 opls_140 5 ARG HA 23 0.06 1.008 ; qtot 2
+ 72 opls_136 5 ARG CB 24 -0.12 12.011 ; qtot 1.88
+ 73 opls_140 5 ARG HB1 24 0.06 1.008 ; qtot 1.94
+ 74 opls_140 5 ARG HB2 24 0.06 1.008 ; qtot 2
+ 75 opls_308 5 ARG CG 25 -0.05 12.011 ; qtot 1.95
+ 76 opls_140 5 ARG HG1 25 0.06 1.008 ; qtot 2.01
+ 77 opls_140 5 ARG HG2 25 0.06 1.008 ; qtot 2.07
+ 78 opls_307 5 ARG CD 26 0.19 12.011 ; qtot 2.26
+ 79 opls_140 5 ARG HD1 26 0.06 1.008 ; qtot 2.32
+ 80 opls_140 5 ARG HD2 26 0.06 1.008 ; qtot 2.38
+ 81 opls_303 5 ARG NE 27 -0.7 14.0067 ; qtot 1.68
+ 82 opls_304 5 ARG HE 27 0.44 1.008 ; qtot 2.12
+ 83 opls_302 5 ARG CZ 27 0.64 12.011 ; qtot 2.76
+ 84 opls_300 5 ARG NH1 28 -0.8 14.0067 ; qtot 1.96
+ 85 opls_301 5 ARG HH11 28 0.46 1.008 ; qtot 2.42
+ 86 opls_301 5 ARG HH12 28 0.46 1.008 ; qtot 2.88
+ 87 opls_300 5 ARG NH2 29 -0.8 14.0067 ; qtot 2.08
+ 88 opls_301 5 ARG HH21 29 0.46 1.008 ; qtot 2.54
+ 89 opls_301 5 ARG HH22 29 0.46 1.008 ; qtot 3
+ 90 opls_235 5 ARG C 30 0.5 12.011 ; qtot 3.5
+ 91 opls_236 5 ARG O 30 -0.5 15.9994 ; qtot 3
+; residue 6 CYS rtp CYSH q 0.0
+ 92 opls_238 6 CYS N 31 -0.5 14.0067 ; qtot 2.5
+ 93 opls_241 6 CYS H 31 0.3 1.008 ; qtot 2.8
+ 94 opls_224B 6 CYS CA 31 0.14 12.011 ; qtot 2.94
+ 95 opls_140 6 CYS HA 31 0.06 1.008 ; qtot 3
+ 96 opls_206 6 CYS CB 32 0.06 12.011 ; qtot 3.06
+ 97 opls_140 6 CYS HB1 32 0.06 1.008 ; qtot 3.12
+ 98 opls_140 6 CYS HB2 32 0.06 1.008 ; qtot 3.18
+ 99 opls_200 6 CYS SG 33 -0.335 32.06 ; qtot 2.845
+ 100 opls_204 6 CYS HG 33 0.155 1.008 ; qtot 3
+ 101 opls_235 6 CYS C 34 0.5 12.011 ; qtot 3.5
+ 102 opls_236 6 CYS O 34 -0.5 15.9994 ; qtot 3
+; residue 7 GLU rtp GLU q -1.0
+ 103 opls_238 7 GLU N 35 -0.5 14.0067 ; qtot 2.5
+ 104 opls_241 7 GLU H 35 0.3 1.008 ; qtot 2.8
+ 105 opls_224B 7 GLU CA 35 0.14 12.011 ; qtot 2.94
+ 106 opls_140 7 GLU HA 35 0.06 1.008 ; qtot 3
+ 107 opls_136 7 GLU CB 36 -0.12 12.011 ; qtot 2.88
+ 108 opls_140 7 GLU HB1 36 0.06 1.008 ; qtot 2.94
+ 109 opls_140 7 GLU HB2 36 0.06 1.008 ; qtot 3
+ 110 opls_274 7 GLU CG 37 -0.22 12.011 ; qtot 2.78
+ 111 opls_140 7 GLU HG1 37 0.06 1.008 ; qtot 2.84
+ 112 opls_140 7 GLU HG2 37 0.06 1.008 ; qtot 2.9
+ 113 opls_271 7 GLU CD 38 0.7 12.011 ; qtot 3.6
+ 114 opls_272 7 GLU OE1 38 -0.8 15.9994 ; qtot 2.8
+ 115 opls_272 7 GLU OE2 38 -0.8 15.9994 ; qtot 2
+ 116 opls_235 7 GLU C 39 0.5 12.011 ; qtot 2.5
+ 117 opls_236 7 GLU O 39 -0.5 15.9994 ; qtot 2
+; residue 8 LEU rtp LEU q 0.0
+ 118 opls_238 8 LEU N 40 -0.5 14.0067 ; qtot 1.5
+ 119 opls_241 8 LEU H 40 0.3 1.008 ; qtot 1.8
+ 120 opls_224B 8 LEU CA 40 0.14 12.011 ; qtot 1.94
+ 121 opls_140 8 LEU HA 40 0.06 1.008 ; qtot 2
+ 122 opls_136 8 LEU CB 41 -0.12 12.011 ; qtot 1.88
+ 123 opls_140 8 LEU HB1 41 0.06 1.008 ; qtot 1.94
+ 124 opls_140 8 LEU HB2 41 0.06 1.008 ; qtot 2
+ 125 opls_137 8 LEU CG 42 -0.06 12.011 ; qtot 1.94
+ 126 opls_140 8 LEU HG 42 0.06 1.008 ; qtot 2
+ 127 opls_135 8 LEU CD1 43 -0.18 12.011 ; qtot 1.82
+ 128 opls_140 8 LEU HD11 43 0.06 1.008 ; qtot 1.88
+ 129 opls_140 8 LEU HD12 43 0.06 1.008 ; qtot 1.94
+ 130 opls_140 8 LEU HD13 43 0.06 1.008 ; qtot 2
+ 131 opls_135 8 LEU CD2 44 -0.18 12.011 ; qtot 1.82
+ 132 opls_140 8 LEU HD21 44 0.06 1.008 ; qtot 1.88
+ 133 opls_140 8 LEU HD22 44 0.06 1.008 ; qtot 1.94
+ 134 opls_140 8 LEU HD23 44 0.06 1.008 ; qtot 2
+ 135 opls_235 8 LEU C 45 0.5 12.011 ; qtot 2.5
+ 136 opls_236 8 LEU O 45 -0.5 15.9994 ; qtot 2
+; residue 9 ALA rtp ALA q 0.0
+ 137 opls_238 9 ALA N 46 -0.5 14.0067 ; qtot 1.5
+ 138 opls_241 9 ALA H 46 0.3 1.008 ; qtot 1.8
+ 139 opls_224B 9 ALA CA 46 0.14 12.011 ; qtot 1.94
+ 140 opls_140 9 ALA HA 46 0.06 1.008 ; qtot 2
+ 141 opls_135 9 ALA CB 47 -0.18 12.011 ; qtot 1.82
+ 142 opls_140 9 ALA HB1 47 0.06 1.008 ; qtot 1.88
+ 143 opls_140 9 ALA HB2 47 0.06 1.008 ; qtot 1.94
+ 144 opls_140 9 ALA HB3 47 0.06 1.008 ; qtot 2
+ 145 opls_235 9 ALA C 48 0.5 12.011 ; qtot 2.5
+ 146 opls_236 9 ALA O 48 -0.5 15.9994 ; qtot 2
+; residue 10 ALA rtp ALA q 0.0
+ 147 opls_238 10 ALA N 49 -0.5 14.0067 ; qtot 1.5
+ 148 opls_241 10 ALA H 49 0.3 1.008 ; qtot 1.8
+ 149 opls_224B 10 ALA CA 49 0.14 12.011 ; qtot 1.94
+ 150 opls_140 10 ALA HA 49 0.06 1.008 ; qtot 2
+ 151 opls_135 10 ALA CB 50 -0.18 12.011 ; qtot 1.82
+ 152 opls_140 10 ALA HB1 50 0.06 1.008 ; qtot 1.88
+ 153 opls_140 10 ALA HB2 50 0.06 1.008 ; qtot 1.94
+ 154 opls_140 10 ALA HB3 50 0.06 1.008 ; qtot 2
+ 155 opls_235 10 ALA C 51 0.5 12.011 ; qtot 2.5
+ 156 opls_236 10 ALA O 51 -0.5 15.9994 ; qtot 2
+
+[ bonds ]
+; ai aj funct c0 c1 c2 c3
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 23 1
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+
+[ pairs ]
+; ai aj funct c0 c1 c2 c3
+ 1 8 1
+ 1 9 1
+ 1 10 1
+ 1 24 1
+ 1 25 1
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+
+[ angles ]
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+
+[ dihedrals ]
+; ai aj ak al funct c0 c1 c2 c3 c4 c5
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+ 2 1 5 7 3
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+ 13 16 19 21 3 dih_LYS_chi5_C_C_N_H
+ 13 16 19 22 3 dih_LYS_chi5_C_C_N_H
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+
+[ dihedrals ]
+; ai aj ak al funct c0 c1 c2 c3
+ 5 25 23 24 1 improper_O_C_X_Y
+ 23 27 25 26 1 improper_Z_N_X_Y
+ 27 41 39 40 1 improper_O_C_X_Y
+ 39 43 41 42 1 improper_Z_N_X_Y
+ 43 61 59 60 1 improper_O_C_X_Y
+ 45 48 51 49 1 improper_Z_CA_X_Y
+ 48 53 49 50 1 improper_Z_CA_X_Y
+ 48 55 51 52 1 improper_Z_CA_X_Y
+ 49 57 53 54 1 improper_Z_CA_X_Y
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+ 53 55 57 58 1 improper_Z_CA_X_Y
+ 59 63 61 62 1 improper_Z_N_X_Y
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+ 78 83 81 82 1 improper_Z_N_X_Y
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+ 83 85 84 86 1 improper_Z_N_X_Y
+ 83 88 87 89 1 improper_Z_N_X_Y
+ 90 94 92 93 1 improper_Z_N_X_Y
+ 94 103 101 102 1 improper_O_C_X_Y
+ 101 105 103 104 1 improper_Z_N_X_Y
+ 105 118 116 117 1 improper_O_C_X_Y
+ 110 114 113 115 1 improper_O_C_X_Y
+ 116 120 118 119 1 improper_Z_N_X_Y
+ 120 137 135 136 1 improper_O_C_X_Y
+ 135 139 137 138 1 improper_Z_N_X_Y
+ 139 147 145 146 1 improper_O_C_X_Y
+ 145 149 147 148 1 improper_Z_N_X_Y
+
+[ system ]
+; Name
+First 10 residues from 1AKI
+
+[ molecules ]
+; Compound #mols
+Protein_chain_B 1
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * 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
+ * http://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 http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for functionality of the "report" tool to write system information.
+ *
+ * \author
+ */
+#include "gmxpre.h"
+
+#include "gromacs/tools/report-methods.h"
+
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxpreprocess/grompp.h"
+#include "gromacs/mdtypes/state.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/stringstream.h"
+#include "gromacs/utility/textwriter.h"
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/refdata.h"
+#include "testutils/testfilemanager.h"
+#include "testutils/textblockmatchers.h"
+
+namespace gmx
+{
+
+namespace test
+{
+
+namespace
+{
+
+/*! \brief
+ * Generates a tpr for the test.
+ *
+ * Generates the tpr from a sample pdb file using grompp,and returns the path
+ * to the file as std::string for reading it in later.
+ *
+ * \param[in] fileManager Filemanager to keep track of the input file.
+ * \param[in] filename Basename of the input and output files.
+ */
+std::string generateTprInput(TestFileManager *fileManager, const std::string &filename)
+{
+// generate temporary tpr file from test system
+ const std::string mdpInputFileName = fileManager->getTemporaryFilePath(filename + ".mdp");
+ TextWriter::writeFileFromString(mdpInputFileName, "");
+ std::string tprName = fileManager->getTemporaryFilePath(filename + ".tpr");
+ {
+ CommandLine caller;
+ caller.append("grompp");
+ caller.addOption("-f", mdpInputFileName);
+ caller.addOption("-p", TestFileManager::getInputFilePath(filename));
+ caller.addOption("-c", TestFileManager::getInputFilePath(filename + ".pdb"));
+ caller.addOption("-o", tprName);
+ EXPECT_EQ(0, gmx_grompp(caller.argc(), caller.argv()));
+ }
+ return tprName;
+}
+
+/*! \brief
+ * Generates and reads a tpr for the test.
+ *
+ * Generates a tpr from a sample pdb file using grompp, and reads it in to
+ * have access to the system information for print out.
+ *
+ * \param[in] filename Basename of the input and output files.
+ * \param[in] mtop Pointer to topology datastructure to populate.
+ * \param[in] ir Pointer to inputrec to populate.
+ */
+void generateAndReadTprInput(const std::string &filename, gmx_mtop_t *mtop, t_inputrec *ir)
+{
+ TestFileManager fileManager;
+ std::string tprName = generateTprInput(&fileManager, filename);
+// read tpr into variables needed for output
+ {
+ t_state state;
+ read_tpx_state(tprName.c_str(), ir, &state, mtop);
+ }
+}
+
+TEST(ReportMethodsTest, WritesCorrectHeadersFormated)
+{
+ gmx::StringOutputStream stream;
+ gmx::TextWriter test(&stream);
+ writeHeader(&test, "Test", "Test", true);
+
+ std::string referenceString = "\\Test{Test}\n";
+
+ EXPECT_EQ(stream.toString(), referenceString);
+}
+TEST(ReportMethodsTest, WritesCorrectHeadersUnformatted)
+{
+ gmx::StringOutputStream stream;
+ gmx::TextWriter test(&stream);
+ writeHeader(&test, "Test", "Test", false);
+
+ std::string referenceString = "Test: Test\n";
+
+ EXPECT_EQ(stream.toString(), referenceString);
+}
+
+TEST(ReportMethodsTest, WritesCorrectInformation)
+{
+ gmx_mtop_t top;
+ t_inputrec ir;
+ EXPECT_NO_THROW(generateAndReadTprInput("lysozyme", &top, &ir));
+
+ // Test both formatted and unformatted output in the same test
+ {
+ gmx::StringOutputStream stream;
+ gmx::TextWriter test(&stream);
+
+ writeSystemInformation(&test, top, true);
+
+ std::string referenceString = "\\subsection{Simulation system}\n"
+ "A system of 1 molecules (156 atoms) was simulated.\n";
+
+ EXPECT_EQ(stream.toString(), referenceString);
+ }
+
+ {
+ gmx::StringOutputStream stream;
+ gmx::TextWriter test(&stream);
+
+ writeSystemInformation(&test, top, false);
+
+ std::string referenceString = "subsection: Simulation system\n"
+ "A system of 1 molecules (156 atoms) was simulated.\n";
+
+ EXPECT_EQ(stream.toString(), referenceString);
+ }
+
+ // Test for correct parameter information as well
+ {
+ gmx::StringOutputStream stream;
+ gmx::TextWriter test(&stream);
+
+ writeParameterInformation(&test, ir, true);
+
+ std::string referenceString = "\\subsection{Simulation settings}\n"
+ "A total of 0 ns were simulated with a time step of 1 fs.\n"
+ "Neighbor searching was performed every 10 steps.\n"
+ "The Cut-off algorithm was used for electrostatic interactions.\n"
+ "with a cut-off of 1 nm.\nA single cut-off of 1.1 nm was used "
+ "for Van der Waals interactions.\n";
+
+ EXPECT_EQ(stream.toString(), referenceString);
+ }
+}
+
+TEST(ReportMethodsTest, ToolEndToEndTest)
+{
+ TestFileManager fileManager;
+ std::string tprName = generateTprInput(&fileManager, "lysozyme");
+ const char *const command[] = {
+ "report", "-s", tprName.c_str()
+ };
+ CommandLine cmdline(command);
+ EXPECT_EQ(0, gmx::test::CommandLineTestHelper::runModuleFactory(
+ &gmx::ReportMethodsInfo::create, &cmdline));
+
+}
+
+} // namespace
+
+} // namespace test
+
+} // namespace gmx
#include "gromacs/tools/check.h"
#include "gromacs/tools/convert_tpr.h"
#include "gromacs/tools/dump.h"
+#include "gromacs/tools/report-methods.h"
#include "mdrun/mdrun_main.h"
#include "view/view.h"
gmx::InsertMoleculesInfo::shortDescription(),
&gmx::InsertMoleculesInfo::create);
+ gmx::ICommandLineOptionsModule::registerModuleFactory(
+ manager, gmx::ReportMethodsInfo::name,
+ gmx::ReportMethodsInfo::shortDescription,
+ &gmx::ReportMethodsInfo::create);
+
+
// Modules from gmx_ana.h.
registerModule(manager, &gmx_do_dssp, "do_dssp",
"Assign secondary structure and calculate solvent accessible surface area");
group.addModule("mk_angndx");
group.addModule("trjorder");
group.addModule("xpm2ps");
+ group.addModule("report");
}
{
gmx::CommandLineModuleGroup group =
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff