*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, 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.
#if HAVE_PIPES || GMX_NATIVE_WINDOWS
sprintf(dssp, "%s -i %s %s", strings.dptr.c_str(), strings.pdbfile.c_str(), redirectionString.c_str());
#else
- sprintf(dssp, "%s -i %s -o %s > %s %s", strings.dptr.c_str(), strings.pdbfile.c_str(),
- strings.tmpfile.c_str(), NULL_DEVICE, redirectionString.c_str());
+ sprintf(dssp,
+ "%s -i %s -o %s > %s %s",
+ strings.dptr.c_str(),
+ strings.pdbfile.c_str(),
+ strings.tmpfile.c_str(),
+ NULL_DEVICE,
+ redirectionString.c_str());
#endif
}
int average_area[],
const gmx_output_env_t* oenv)
{
- static gmx_bool bFirst = TRUE;
- static char* ssbuf;
- char buf[STRLEN + 1];
- char SSTP;
- int nr, iacc, nresidues;
- int naccf, naccb; /* Count hydrophobic and hydrophilic residues */
- real iaccf, iaccb;
+ static gmx_bool bFirst = TRUE;
+ static std::string ssbuf;
+ char buf[STRLEN + 1];
+ char SSTP;
+ int nr, iacc, nresidues;
+ int naccf, naccb; /* Count hydrophobic and hydrophilic residues */
+ real iaccf, iaccb;
/* Skip header */
* we allocate 2*nres-1, since for each chain there is a
* separating line in the temp file. (At most each residue
* could have been defined as a separate chain.) */
- snew(ssbuf, 2 * nres - 1);
+ ssbuf.resize(2 * nres - 1);
}
iaccb = iaccf = 0;
{
if (nullptr != acc)
{
- fprintf(stderr, "%d residues were classified as hydrophobic and %d as hydrophilic.\n",
- naccb, naccf);
+ fprintf(stderr, "%d residues were classified as hydrophobic and %d as hydrophilic.\n", naccb, naccf);
}
mat->title = "Secondary structure";
mat->axis_y.resize(nr);
std::iota(mat->axis_y.begin(), mat->axis_y.end(), 1);
mat->axis_x.resize(0);
- mat->matrix.resize(0, 0);
+ mat->matrix.resize(1, 1);
bFirst = false;
}
mat->axis_x.push_back(t);
- mat->matrix.resize(mat->matrix.extent(0), nr);
- mat->nx = mat->matrix.extent(0);
+ mat->matrix.resize(++(mat->nx), nr);
auto columnIndex = mat->nx - 1;
for (int i = 0; i < nr; i++)
{
if (i != j)
{
fprintf(stderr,
- "Not all residues were recognized (%d from %d), the result may be inaccurate!\n", j, i);
+ "Not all residues were recognized (%d from %d), the result may be inaccurate!\n",
+ j,
+ i);
}
for (i = 0; (i < n_surf); i++)
static void check_oo(t_atoms* atoms)
{
- char* OOO;
+ char* OOO = gmx_strdup("O");
- int i;
-
- OOO = gmx_strdup("O");
-
- for (i = 0; (i < atoms->nr); i++)
+ for (int i = 0; (i < atoms->nr); i++)
{
- if (std::strcmp(*(atoms->atomname[i]), "OXT") == 0)
- {
- *atoms->atomname[i] = OOO;
- }
- else if (std::strcmp(*(atoms->atomname[i]), "O1") == 0)
- {
- *atoms->atomname[i] = OOO;
- }
- else if (std::strcmp(*(atoms->atomname[i]), "OC1") == 0)
+ if ((std::strcmp(*(atoms->atomname[i]), "OXT") == 0)
+ || (std::strcmp(*(atoms->atomname[i]), "O1") == 0)
+ || (std::strcmp(*(atoms->atomname[i]), "OC1") == 0)
+ || (std::strcmp(*(atoms->atomname[i]), "OT1") == 0))
{
*atoms->atomname[i] = OOO;
}
}
else
{
- fprintf(stderr, "Residue %s not found in surface database (%s)\n",
- *atoms->resinfo[i].name, surffn);
+ fprintf(stderr, "Residue %s not found in surface database (%s)\n", *atoms->resinfo[i].name, surffn);
}
}
}
}
fp = gmx_ffopen(fn, "w");
nlev = static_cast<int>(hi - lo + 1);
- write_xpm(fp, 0, "Solvent Accessible Surface", "Surface (A^2)", "Time", "Residue Index",
- nframe, nres, mat->axis_x.data(), mat->axis_y.data(), accr, lo, hi, rlo, rhi, &nlev);
+ write_xpm(fp,
+ 0,
+ "Solvent Accessible Surface",
+ "Surface (A^2)",
+ "Time",
+ "Residue Index",
+ nframe,
+ nres,
+ mat->axis_x.data(),
+ mat->axis_y.data(),
+ accr,
+ lo,
+ hi,
+ rlo,
+ rhi,
+ &nlev);
gmx_ffclose(fp);
}
}
leg.emplace_back(m.desc);
}
- fp = xvgropen(outfile, "Secondary Structure", output_env_get_xvgr_tlabel(oenv),
- "Number of Residues", oenv);
+ fp = xvgropen(
+ outfile, "Secondary Structure", output_env_get_xvgr_tlabel(oenv), "Number of Residues", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"Structure = ");
"reads a trajectory file and computes the secondary structure for",
"each time frame ",
"calling the dssp program. If you do not have the dssp program,",
- "get it from http://swift.cmbi.ru.nl/gv/dssp. [THISMODULE] assumes ",
+ "get it from https://swift.cmbi.umcn.nl/gv/dssp. [THISMODULE] assumes ",
"that the dssp executable is located in ",
- "[TT]/usr/local/bin/dssp[tt]. If this is not the case, then you should",
- "set an environment variable [TT]DSSP[tt] pointing to the dssp",
+ // NOLINTNEXTLINE(bugprone-suspicious-missing-comma)
+ "[TT]" GMX_DSSP_PROGRAM_PATH "[tt]. If this is not the case, then you should",
+ "set an environment variable [TT]DSSP[tt] pointing to the dssp ",
"executable, e.g.: [PAR]",
"[TT]setenv DSSP /opt/dssp/bin/dssp[tt][PAR]",
- "Since version 2.0.0, dssp is invoked with a syntax that differs",
- "from earlier versions. If you have an older version of dssp,",
- "use the [TT]-ver[tt] option to direct do_dssp to use the older syntax.",
+ "The dssp program is invoked with a syntax that differs",
+ "depending on version. Version 1, 2 and 4 are supported, and the correct",
+ "invocation format can be selected using the [TT]-ver[tt] option.",
"By default, do_dssp uses the syntax introduced with version 2.0.0.",
- "Even newer versions (which at the time of writing are not yet released)",
- "are assumed to have the same syntax as 2.0.0.[PAR]",
+ "Newer versions might also have executable name [TT]mkdssp[tt] instead",
+ "of [TT]dssp[tt].[PAR]",
"The structure assignment for each residue and time is written to an",
"[REF].xpm[ref] matrix file. This file can be visualized with for instance",
"[TT]xv[tt] and can be converted to postscript with [TT]xpm2ps[tt].",
FALSE,
etINT,
{ &dsspVersion },
- "DSSP major version. Syntax changed with version 2" }
+ "DSSP major version. Syntax changed with version 2 and 4." }
};
t_trxstatus* status;
const char * fnSCount, *fnArea, *fnTArea, *fnAArea;
const char* leg[] = { "Phobic", "Phylic" };
t_topology top;
- int ePBC;
+ PbcType pbcType;
t_atoms* atoms;
t_matrix mat;
int nres, nr0, naccr, nres_plus_separators;
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
+ NFILE,
+ fnm,
+ asize(pa),
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
fnAArea = opt2fn_null("-aa", NFILE, fnm);
bDoAccSurf = ((fnArea != nullptr) || (fnTArea != nullptr) || (fnAArea != nullptr));
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xp, nullptr, box, FALSE);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &pbcType, &xp, nullptr, box, FALSE);
atoms = &(top.atoms);
check_oo(atoms);
bPhbres = bPhobics(atoms);
}
fclose(tmpf);
+ const std::string defpathenv = GMX_DSSP_PROGRAM_PATH;
if ((dptr = getenv("DSSP")) == nullptr)
{
- dptr = "/usr/local/bin/dssp";
+ dptr = defpathenv.c_str();
}
if (!gmx_fexist(dptr))
{
dsspStrings.tmpfile = tmpfile;
if (dsspVersion >= 2)
{
- if (dsspVersion > 2)
+ if (dsspVersion == 4)
+ {
+ std::string mkdsspCommandLine = dsspStrings.dptr;
+ mkdsspCommandLine += " --output-format dssp ";
+ mkdsspCommandLine += dsspStrings.pdbfile;
+
+#if not HAVE_PIPES && not GMX_NATIVE_WINDOWS
+ // Without pipe/popen, rely on temporary file for output
+ mkdsspCommandLine += " " + dsspStrings.tmpfile;
+#endif
+
+ GMX_RELEASE_ASSERT(mkdsspCommandLine.size() < 255, "DSSP v4 command line too long");
+ strcpy(dssp, mkdsspCommandLine.c_str());
+ }
+ else if (dsspVersion == 2)
+ {
+ printDsspResult(dssp, dsspStrings, redirectionString);
+ }
+ else
{
printf("\nWARNING: You use DSSP version %d, which is not explicitly\nsupported by "
"do_dssp. Assuming version 2 syntax.\n\n",
dsspVersion);
}
-
- printDsspResult(dssp, dsspStrings, redirectionString);
}
else
{
if (fnTArea)
{
- fTArea = xvgropen(fnTArea, "Solvent Accessible Surface Area",
- output_env_get_xvgr_tlabel(oenv), "Area (nm\\S2\\N)", oenv);
+ fTArea = xvgropen(fnTArea,
+ "Solvent Accessible Surface Area",
+ output_env_get_xvgr_tlabel(oenv),
+ "Area (nm\\S2\\N)",
+ oenv);
xvgr_legend(fTArea, 2, leg, oenv);
}
else
accr = nullptr;
naccr = 0;
- gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
+ gpbc = gmx_rmpbc_init(&top.idef, pbcType, natoms);
do
{
t = output_env_conv_time(oenv, t);
}
gmx_rmpbc(gpbc, natoms, box, x);
tapein = gmx_ffopen(pdbfile, "w");
- write_pdbfile_indexed(tapein, nullptr, atoms, x, ePBC, box, ' ', -1, gnx, index, nullptr, FALSE);
+ write_pdbfile_indexed(
+ tapein, nullptr, atoms, x, pbcType, box, 'A', -1, gnx, index, nullptr, FALSE, true);
gmx_ffclose(tapein);
/* strip_dssp returns the number of lines found in the dssp file, i.e.
* the number of residues plus the separator lines */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff