Add DSSP v4 support to do_dssp

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_do_dssp.cpp

diff --git a/src/gromacs/gmxana/gmx_do_dssp.cpp b/src/gromacs/gmxana/gmx_do_dssp.cpp
index 71c8c5ddc006c179309c6c0558864532fd3a7bd1..f88a65c567f218f42a82d439a0f6dcd9c994bcc9 100644 (file)
--- a/src/gromacs/gmxana/gmx_do_dssp.cpp
+++ b/src/gromacs/gmxana/gmx_do_dssp.cpp
@@ -4,7 +4,7 @@
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
  * Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * 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.
@@ -111,13 +111,13 @@ static int strip_dssp(FILE*                   tapeout,
                       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 */
@@ -133,7 +133,7 @@ static int strip_dssp(FILE*                   tapeout,
          * 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;
@@ -481,19 +481,19 @@ int gmx_do_dssp(int argc, char* argv[])
         "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 ",
         // 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",
+        "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].",
@@ -523,7 +523,7 @@ int gmx_do_dssp(int argc, char* argv[])
           FALSE,
           etINT,
           { &dsspVersion },
-          "DSSP major version. Syntax changed with version 2" }
+          "DSSP major version. Syntax changed with version 2 and 4." }
     };
 
     t_trxstatus*      status;
@@ -643,14 +643,30 @@ int gmx_do_dssp(int argc, char* argv[])
     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
     {
@@ -713,7 +729,8 @@ int gmx_do_dssp(int argc, char* argv[])
         }
         gmx_rmpbc(gpbc, natoms, box, x);
         tapein = gmx_ffopen(pdbfile, "w");
-        write_pdbfile_indexed(tapein, nullptr, atoms, x, pbcType, 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 */