Add DSSP v4 support to do_dssp

diff --git a/api/legacy/include/gromacs/fileio/pdbio.h b/api/legacy/include/gromacs/fileio/pdbio.h
index c34562e095dd86d4fb0b72a812bd668e0cabf6fd..87da7ead73d50d90fee4952680eb131f5ee33bec 100644 (file)
--- a/api/legacy/include/gromacs/fileio/pdbio.h
+++ b/api/legacy/include/gromacs/fileio/pdbio.h
@@ -107,7 +107,8 @@ void write_pdbfile_indexed(FILE*          out,
                            int            nindex,
                            const int      index[],
                            gmx_conect     conect,
-                           bool           usePqrFormat);
+                           bool           usePqrFormat,
+                           bool           standardCompliantMode = false);
 /* REALLY low level */
 
 void write_pdbfile(FILE*          out,

diff --git a/docs/linkcheckerrc b/docs/linkcheckerrc
index 5d9755753a024a6b5d8db50f59c0b7575d5738df..dd6d9a04460034d31f4695d8503c0bf145826b7f 100644 (file)
--- a/docs/linkcheckerrc
+++ b/docs/linkcheckerrc
@@ -6,5 +6,3 @@
 ignore=
 # This site gives warnings about URLs if you try to refer to page.html\#heading
  cmake.org
-# This site gives warnings because it redirects to itself
- http://swift.cmbi.ru.nl/gv/dssp

diff --git a/docs/release-notes/2022/major/tools.rst b/docs/release-notes/2022/major/tools.rst
index b1612a9822530766d66fb7e3187793e0f504f3e2..882df1162f16e4729c62c5eb75974ff70db3d575 100644 (file)
--- a/docs/release-notes/2022/major/tools.rst
+++ b/docs/release-notes/2022/major/tools.rst
@@ -44,3 +44,12 @@ removed, because it served no purpose. This makes ``gmx chi`` easier to use.
 
 Reporting about file handling and input-file column contents are easier to
 follow.
+
+``gmx do_dssp`` supports DSSP version 4
+"""""""""""""""""""""""""""""""""""""""
+
+The newer DSSP version 4 program can be used by ``do_dssp`` by specifying 
+option ``-ver 4`` and setting the DSSP environement variable to the ``mkdssp``
+executable path (e.g. ``setenv DSSP /opt/dssp/mkdssp``)
+
+:issue:`4129`

diff --git a/src/gromacs/fileio/pdbio.cpp b/src/gromacs/fileio/pdbio.cpp
index 07de14f92c63b6bab2e895be6d0cf2a44ee11d7c..c3c3995039774070b923690aa6330de820617a77 100644 (file)
--- a/src/gromacs/fileio/pdbio.cpp
+++ b/src/gromacs/fileio/pdbio.cpp
@@ -296,7 +296,8 @@ void write_pdbfile_indexed(FILE*          out,
                            int            nindex,
                            const int      index[],
                            gmx_conect     conect,
-                           bool           usePqrFormat)
+                           bool           usePqrFormat,
+                           bool           standardCompliantMode)
 {
     gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
     PdbRecordType type;
@@ -304,8 +305,27 @@ void write_pdbfile_indexed(FILE*          out,
     real          occup, bfac;
     gmx_bool      bOccup;
 
+    if (standardCompliantMode)
+    {
+        fprintf(out, "HEADER    GROMACS SIMULATION BOX                  01-JAN-00   0000\n");
+        fprintf(out,
+                "TITLE     Gromacs simulation box\n"
+                "COMPND    MOL_ID:  1;                                                           \n"
+                "COMPND   2 MOLECULE:  GROMACS SIMULATION BOX;                                   \n"
+                "COMPND   3 CHAIN: A;  \n"
+                "SOURCE    MOL_ID: 1;\n"
+                "SOURCE   2 SYNTHETIC\n"
+                "KEYWDS    GROMACS\n"
+                "EXPDTA    PURE PRODUCT OF COMPUTER SIMULATION\n"
+                "AUTHOR    GROMACS\n"
+                "REVDAT   1   01-JAN-00 0000    0\n");
+    }
+    else
+    {
+        fprintf(out, "TITLE     %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
+    }
+
 
-    fprintf(out, "TITLE     %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
     if (box && ((norm2(box[XX]) != 0.0F) || (norm2(box[YY]) != 0.0F) || (norm2(box[ZZ]) != 0.0F)))
     {
         gmx_write_pdb_box(out, pbcType, box);
@@ -329,6 +349,11 @@ void write_pdbfile_indexed(FILE*          out,
 
     fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
 
+    // Collect last printed values for TER record
+    int         lastAtomNumber = 0;
+    std::string lastResName;
+    int         lastResNr = 0;
+
     for (int ii = 0; ii < nindex; ii++)
     {
         int         i      = index[ii];
@@ -391,6 +416,10 @@ void write_pdbfile_indexed(FILE*          out,
                                      bfac,
                                      atoms->atom[i].elem);
 
+            lastAtomNumber = i + 1;
+            lastResName    = resnm;
+            lastResNr      = resnr;
+
             if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
             {
                 fprintf(out,
@@ -426,7 +455,15 @@ void write_pdbfile_indexed(FILE*          out,
         }
     }
 
-    fprintf(out, "TER\n");
+    if (standardCompliantMode)
+    {
+        fprintf(out, "TER   %5d      %4.4s%c%4d\n", lastAtomNumber, lastResName.c_str(), chainid, lastResNr);
+    }
+    else
+    {
+        fprintf(out, "TER\n");
+    }
+
     fprintf(out, "ENDMDL\n");
 
     if (nullptr != gc)

diff --git a/src/gromacs/gmxana/gmx_do_dssp.cpp b/src/gromacs/gmxana/gmx_do_dssp.cpp
index 36fb601e93df2e5dde55686f2c0ae6abf661f9f4..f88a65c567f218f42a82d439a0f6dcd9c994bcc9 100644 (file)
--- a/src/gromacs/gmxana/gmx_do_dssp.cpp
+++ b/src/gromacs/gmxana/gmx_do_dssp.cpp
@@ -485,15 +485,15 @@ int gmx_do_dssp(int argc, char* argv[])
         "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 */