Remove under the hood editing of pdb files

The routines in pdbio.cpp would change atom names for hydrogens
without explicit user consent. This could lead to problems interpreting
NMR files. In addition from a software design point of view, reading
and writing data to files is not the same as interpreting it.

Fixes #3649

Change-Id: Id68c39700bfe56800e9e5dd135bc8b98ada77e8b

diff --git a/docs/release-notes/2021/major/bugs-fixed.rst b/docs/release-notes/2021/major/bugs-fixed.rst
index 0828fe124620465b0b6d4ebde45570fb43fa2b19..5d1551ae540096dcfb8b20aace3f20c7cdcf177d 100644 (file)
--- a/docs/release-notes/2021/major/bugs-fixed.rst
+++ b/docs/release-notes/2021/major/bugs-fixed.rst
@@ -15,3 +15,12 @@ existing include paths and add GMX_DOUBLE define to interface
 definitions. The target now gets exported into the Gromacs namespace.
 
 :issue:`3468`
+
+Fixed unsolicited changing of atom names in pdb file
+""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Remove functions to change atoms names when reading 
+and writing pdb files. This affected naming of
+H atoms in particular.
+
+:issue:`3469`

diff --git a/src/gromacs/fileio/pdbio.cpp b/src/gromacs/fileio/pdbio.cpp
index 8e170a04df91d7337abe1d07ed88790959beb7a9..f551dde39129a3e06e80fd3f854f0325377f421b 100644 (file)
--- a/src/gromacs/fileio/pdbio.cpp
+++ b/src/gromacs/fileio/pdbio.cpp
@@ -79,40 +79,6 @@ static const char* pdbtp[epdbNR] = { "ATOM  ", "HETATM", "ANISOU", "CRYST1", "CO
 
 #define REMARK_SIM_BOX "REMARK    THIS IS A SIMULATION BOX"
 
-static void xlate_atomname_pdb2gmx(char* name)
-{
-    int  i, length;
-    char temp;
-
-    length = std::strlen(name);
-    if (length > 3 && std::isdigit(name[0]))
-    {
-        temp = name[0];
-        for (i = 1; i < length; i++)
-        {
-            name[i - 1] = name[i];
-        }
-        name[length - 1] = temp;
-    }
-}
-
-// Deliberately taking a copy of name to return it later
-static std::string xlate_atomname_gmx2pdb(std::string name)
-{
-    size_t length = name.size();
-    if (length > 3 && std::isdigit(name[length - 1]))
-    {
-        char temp = name[length - 1];
-        for (size_t i = length - 1; i > 0; --i)
-        {
-            name[i] = name[i - 1];
-        }
-        name[0] = temp;
-    }
-    return name;
-}
-
-
 void gmx_write_pdb_box(FILE* out, PbcType pbcType, const matrix box)
 {
     real alpha, beta, gamma;
@@ -338,8 +304,6 @@ void write_pdbfile_indexed(FILE*          out,
         std::string resnm  = *atoms->resinfo[resind].name;
         std::string nm     = *atoms->atomname[i];
 
-        /* rename HG12 to 2HG1, etc. */
-        nm                  = xlate_atomname_gmx2pdb(nm);
         int           resnr = atoms->resinfo[resind].nr;
         unsigned char resic = atoms->resinfo[resind].ic;
         unsigned char ch;
@@ -575,8 +539,7 @@ void get_pdb_atomnumber(const t_atoms* atoms, AtomProperties* aps)
     }
 }
 
-static int
-read_atom(t_symtab* symtab, const char line[], int type, int natom, t_atoms* atoms, rvec x[], int chainnum, gmx_bool bChange)
+static int read_atom(t_symtab* symtab, const char line[], int type, int natom, t_atoms* atoms, rvec x[], int chainnum)
 {
     t_atom*       atomn;
     int           j, k;
@@ -696,10 +659,6 @@ read_atom(t_symtab* symtab, const char line[], int type, int natom, t_atoms* ato
         {
             atomn->resind = atoms->atom[natom - 1].resind;
         }
-        if (bChange)
-        {
-            xlate_atomname_pdb2gmx(anm);
-        }
         atoms->atomname[natom] = put_symtab(symtab, anm);
         atomn->m               = 0.0;
         atomn->q               = 0.0;
@@ -833,7 +792,6 @@ int read_pdbfile(FILE*      in,
                  rvec       x[],
                  PbcType*   pbcType,
                  matrix     box,
-                 gmx_bool   bChange,
                  gmx_conect conect)
 {
     gmx_conect_t* gc = conect;
@@ -873,7 +831,7 @@ int read_pdbfile(FILE*      in,
         {
             case epdbATOM:
             case epdbHETATM:
-                natom = read_atom(symtab, line, line_type, natom, atoms, x, chainnum, bChange);
+                natom = read_atom(symtab, line, line_type, natom, atoms, x, chainnum);
                 break;
 
             case epdbANISOU:
@@ -1005,7 +963,7 @@ void gmx_pdb_read_conf(const char* infile, t_symtab* symtab, char** name, t_atom
 {
     FILE* in = gmx_fio_fopen(infile, "r");
     char  title[STRLEN];
-    read_pdbfile(in, title, nullptr, atoms, symtab, x, pbcType, box, TRUE, nullptr);
+    read_pdbfile(in, title, nullptr, atoms, symtab, x, pbcType, box, nullptr);
     if (name != nullptr)
     {
         *name = gmx_strdup(title);

diff --git a/src/gromacs/fileio/pdbio.h b/src/gromacs/fileio/pdbio.h
index d9e918c27590854c3ef0086c73e44cf8a3059c60..fee2ab1373b2d457b2d915120449164257b8a3af 100644 (file)
--- a/src/gromacs/fileio/pdbio.h
+++ b/src/gromacs/fileio/pdbio.h
@@ -142,7 +142,6 @@ int read_pdbfile(FILE*            in,
                  rvec             x[],
                  PbcType*         pbcType,
                  matrix           box,
-                 gmx_bool         bChange,
                  gmx_conect       conect);
 /* Function returns number of atoms found.
  * pbcType and gmx_conect structure may be NULL.

diff --git a/src/gromacs/fileio/trxio.cpp b/src/gromacs/fileio/trxio.cpp
index 06ff8bcf12af59313c64b003711044a002f27726..b1f3a82014f34fe862d64fd769e5beba5d337688 100644 (file)
--- a/src/gromacs/fileio/trxio.cpp
+++ b/src/gromacs/fileio/trxio.cpp
@@ -708,7 +708,7 @@ static gmx_bool pdb_next_x(t_trxstatus* status, FILE* fp, t_trxframe* fr)
     /* the other pointers in atoms should not be accessed if these are NULL */
     snew(symtab, 1);
     open_symtab(symtab);
-    na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &pbcType, boxpdb, TRUE, nullptr);
+    na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &pbcType, boxpdb, nullptr);
     free_symtab(symtab);
     sfree(symtab);
     setTrxFramePbcType(fr, pbcType);

diff --git a/src/gromacs/gmxpreprocess/tests/chainTer.pdb b/src/gromacs/gmxpreprocess/tests/chainTer.pdb
index 87bfebbd79922fbbcc3710490e30eb1d97f3253f..a0f01d9e30fc91d5d093590cedf8d440330349b8 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/chainTer.pdb
+++ b/src/gromacs/gmxpreprocess/tests/chainTer.pdb
@@ -216,8 +216,8 @@ ATOM    211  HG2 GLN C  15      41.126  12.817   5.312  1.00  0.00
 ATOM    212  CD  GLN C  15      42.940  12.640   4.310  1.00  0.00            
 ATOM    213  OE1 GLN C  15      44.150  12.890   4.440  1.00  0.00            
 ATOM    214  NE2 GLN C  15      42.340  12.800   3.080  1.00  0.00            
-ATOM    215 1HE2 GLN C  15      41.345  12.742   2.998  1.00  0.00            
-ATOM    216 2HE2 GLN C  15      42.899  12.974   2.270  1.00  0.00            
+ATOM    215 HE21 GLN C  15      41.345  12.742   2.998  1.00  0.00            
+ATOM    216 HE22 GLN C  15      42.899  12.974   2.270  1.00  0.00            
 ATOM    217  C   GLN C  15      42.420  15.300   5.880  1.00  0.00            
 ATOM    218  O   GLN C  15      41.590  15.410   4.980  1.00  0.00            
 ATOM    219  N   ARG C  16      43.500  16.140   5.860  1.00  0.00            

diff --git a/src/gromacs/gmxpreprocess/tests/fragment1.pdb b/src/gromacs/gmxpreprocess/tests/fragment1.pdb
index 68cdcea74eea9e06d474050d4c678fafd7494dc2..b00bb9f76054eafc12cc027c6e79d725e2149f35 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/fragment1.pdb
+++ b/src/gromacs/gmxpreprocess/tests/fragment1.pdb
@@ -103,12 +103,12 @@ ATOM     98  HA  ILE     9      35.483  18.676   3.409  1.00  0.00
 ATOM     99  CB  ILE     9      36.190  20.570   2.570  1.00  0.00            
 ATOM    100  HB  ILE     9      35.791  21.231   3.205  1.00  0.00            
 ATOM    101  CG1 ILE     9      36.100  21.260   1.150  1.00  0.00            
-ATOM    102 1HG1 ILE     9      36.833  20.910   0.566  1.00  0.00            
-ATOM    103 2HG1 ILE     9      35.215  21.048   0.736  1.00  0.00            
+ATOM    102 HG11 ILE     9      36.833  20.910   0.566  1.00  0.00            
+ATOM    103 HG12 ILE     9      35.215  21.048   0.736  1.00  0.00            
 ATOM    104  CG2 ILE     9      37.660  20.240   3.030  1.00  0.00            
-ATOM    105 1HG2 ILE     9      38.199  21.082   3.054  1.00  0.00            
-ATOM    106 2HG2 ILE     9      37.640  19.831   3.942  1.00  0.00            
-ATOM    107 3HG2 ILE     9      38.075  19.598   2.385  1.00  0.00            
+ATOM    105 HG21 ILE     9      38.199  21.082   3.054  1.00  0.00            
+ATOM    106 HG22 ILE     9      37.640  19.831   3.942  1.00  0.00            
+ATOM    107 HG23 ILE     9      38.075  19.598   2.385  1.00  0.00            
 ATOM    108  CD  ILE     9      36.230  22.760   1.170  1.00  0.00            
 ATOM    109  HD1 ILE     9      36.162  23.113   0.237  1.00  0.00            
 ATOM    110  HD2 ILE     9      35.498  23.151   1.728  1.00  0.00            
@@ -147,13 +147,13 @@ ATOM    142  HB2 LEU    11      30.687  14.049   3.034  1.00  0.00
 ATOM    143  CG  LEU    11      29.790  14.450   1.200  1.00  0.00            
 ATOM    144  HG  LEU    11      29.964  15.033   0.407  1.00  0.00            
 ATOM    145  CD1 LEU    11      29.680  12.940   0.840  1.00  0.00            
-ATOM    146 1HD1 LEU    11      28.953  12.810   0.166  1.00  0.00            
-ATOM    147 2HD1 LEU    11      30.549  12.624   0.458  1.00  0.00            
-ATOM    148 3HD1 LEU    11      29.468  12.415   1.665  1.00  0.00            
+ATOM    146 HD11 LEU    11      28.953  12.810   0.166  1.00  0.00            
+ATOM    147 HD12 LEU    11      30.549  12.624   0.458  1.00  0.00            
+ATOM    148 HD13 LEU    11      29.468  12.415   1.665  1.00  0.00            
 ATOM    149  CD2 LEU    11      28.470  14.820   1.830  1.00  0.00            
-ATOM    150 1HD2 LEU    11      27.738  14.711   1.158  1.00  0.00            
-ATOM    151 2HD2 LEU    11      28.295  14.223   2.613  1.00  0.00            
-ATOM    152 3HD2 LEU    11      28.502  15.771   2.137  1.00  0.00            
+ATOM    150 HD21 LEU    11      27.738  14.711   1.158  1.00  0.00            
+ATOM    151 HD22 LEU    11      28.295  14.223   2.613  1.00  0.00            
+ATOM    152 HD23 LEU    11      28.502  15.771   2.137  1.00  0.00            
 ATOM    153  C   LEU    11      32.460  16.000   3.760  1.00  0.00            
 ATOM    154  O   LEU    11      33.540  15.530   3.410  1.00  0.00            
 ATOM    155  N   MET    12      32.300  16.580   4.990  1.00  0.00            
@@ -183,8 +183,8 @@ ATOM    178  HB2 ASN    13      37.409  14.369   4.252  1.00  0.00
 ATOM    179  CG  ASN    13      37.870  12.490   4.990  1.00  0.00            
 ATOM    180  OD1 ASN    13      38.400  12.240   6.060  1.00  0.00            
 ATOM    181  ND2 ASN    13      38.300  11.790   3.910  1.00  0.00            
-ATOM    182 1HD2 ASN    13      38.001  12.052   2.993  1.00  0.00            
-ATOM    183 2HD2 ASN    13      38.916  11.012   4.032  1.00  0.00            
+ATOM    182 HD21 ASN    13      38.001  12.052   2.993  1.00  0.00            
+ATOM    183 HD22 ASN    13      38.916  11.012   4.032  1.00  0.00            
 ATOM    184  C   ASN    13      37.490  15.100   6.860  1.00  0.00            
 ATOM    185  O   ASN    13      38.120  16.010   6.270  1.00  0.00            
 ATOM    186  N   PRO    14      37.890  14.820   8.060  1.00  0.00            
@@ -214,8 +214,8 @@ ATOM    209  HG2 GLN    15      41.126  12.817   5.312  1.00  0.00
 ATOM    210  CD  GLN    15      42.940  12.640   4.310  1.00  0.00            
 ATOM    211  OE1 GLN    15      44.150  12.890   4.440  1.00  0.00            
 ATOM    212  NE2 GLN    15      42.340  12.800   3.080  1.00  0.00            
-ATOM    213 1HE2 GLN    15      41.345  12.742   2.998  1.00  0.00            
-ATOM    214 2HE2 GLN    15      42.899  12.974   2.270  1.00  0.00            
+ATOM    213 HE21 GLN    15      41.345  12.742   2.998  1.00  0.00            
+ATOM    214 HE22 GLN    15      42.899  12.974   2.270  1.00  0.00            
 ATOM    215  C   GLN    15      42.420  15.300   5.880  1.00  0.00            
 ATOM    216  O   GLN    15      41.590  15.410   4.980  1.00  0.00            
 ATOM    217  N   ARG    16      43.500  16.140   5.860  1.00  0.00            
@@ -235,11 +235,11 @@ ATOM    230  NE  ARG    16      41.150  19.050   4.860  1.00  0.00
 ATOM    231  HE  ARG    16      41.483  18.997   3.919  1.00  0.00            
 ATOM    232  CZ  ARG    16      40.090  18.340   5.200  1.00  0.00            
 ATOM    233  NH1 ARG    16      39.790  18.070   6.490  1.00  0.00            
-ATOM    234 1HH1 ARG    16      40.379  18.411   7.222  1.00  0.00            
-ATOM    235 2HH1 ARG    16      38.979  17.529   6.712  1.00  0.00            
+ATOM    234 HH11 ARG    16      40.379  18.411   7.222  1.00  0.00            
+ATOM    235 HH12 ARG    16      38.979  17.529   6.712  1.00  0.00            
 ATOM    236  NH2 ARG    16      39.300  17.710   4.260  1.00  0.00            
-ATOM    237 1HH2 ARG    16      39.524  17.784   3.288  1.00  0.00            
-ATOM    238 2HH2 ARG    16      38.504  17.180   4.551  1.00  0.00            
+ATOM    237 HH21 ARG    16      39.524  17.784   3.288  1.00  0.00            
+ATOM    238 HH22 ARG    16      38.504  17.180   4.551  1.00  0.00            
 ATOM    239  C   ARG    16      44.990  16.800   3.910  1.00  0.00            
 ATOM    240  O   ARG    16      45.630  17.680   3.340  1.00  0.00            
 ATOM    241  N   SER    17      45.280  15.500   3.760  1.00  0.00            

diff --git a/src/gromacs/gmxpreprocess/tests/fragment2.pdb b/src/gromacs/gmxpreprocess/tests/fragment2.pdb
index f0e10fd7928624c29113a5cb21dc7fd95b73fbc8..7c4909a487596e8c9a87a5ff4a95be468f665c1e 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/fragment2.pdb
+++ b/src/gromacs/gmxpreprocess/tests/fragment2.pdb
@@ -13,9 +13,9 @@ ATOM      8  HB  THR    18      48.898  17.421  -1.916  1.00  0.00
 ATOM      9  OG1 THR    18      50.020  16.940  -0.390  1.00  0.00            
 ATOM     10  HG1 THR    18      50.725  17.599  -0.652  1.00  0.00            
 ATOM     11  CG2 THR    18      48.330  18.640  -0.210  1.00  0.00            
-ATOM     12 1HG2 THR    18      49.012  19.351  -0.380  1.00  0.00            
-ATOM     13 2HG2 THR    18      47.440  18.944  -0.551  1.00  0.00            
-ATOM     14 3HG2 THR    18      48.269  18.465   0.773  1.00  0.00            
+ATOM     12 HG21 THR    18      49.012  19.351  -0.380  1.00  0.00            
+ATOM     13 HG22 THR    18      47.440  18.944  -0.551  1.00  0.00            
+ATOM     14 HG23 THR    18      48.269  18.465   0.773  1.00  0.00            
 ATOM     15  C   THR    18      47.650  15.380  -1.660  1.00  0.00            
 ATOM     16  O   THR    18      48.350  14.370  -1.570  1.00  0.00            
 ATOM     17  N   VAL    19      46.990  15.650  -2.800  1.00  0.00            
@@ -25,13 +25,13 @@ ATOM     20  HA  VAL    19      46.794  13.844  -3.206  1.00  0.00
 ATOM     21  CB  VAL    19      45.590  14.650  -4.650  1.00  0.00            
 ATOM     22  HB  VAL    19      45.844  14.046  -5.405  1.00  0.00            
 ATOM     23  CG1 VAL    19      44.330  14.240  -3.760  1.00  0.00            
-ATOM     24 1HG1 VAL    19      43.504  14.259  -4.323  1.00  0.00            
-ATOM     25 2HG1 VAL    19      44.465  13.318  -3.396  1.00  0.00            
-ATOM     26 3HG1 VAL    19      44.232  14.886  -3.003  1.00  0.00            
+ATOM     24 HG11 VAL    19      43.504  14.259  -4.323  1.00  0.00            
+ATOM     25 HG12 VAL    19      44.465  13.318  -3.396  1.00  0.00            
+ATOM     26 HG13 VAL    19      44.232  14.886  -3.003  1.00  0.00            
 ATOM     27  CG2 VAL    19      45.210  15.960  -5.270  1.00  0.00            
-ATOM     28 1HG2 VAL    19      44.362  15.850  -5.789  1.00  0.00            
-ATOM     29 2HG2 VAL    19      45.075  16.642  -4.551  1.00  0.00            
-ATOM     30 3HG2 VAL    19      45.939  16.262  -5.884  1.00  0.00            
+ATOM     28 HG21 VAL    19      44.362  15.850  -5.789  1.00  0.00            
+ATOM     29 HG22 VAL    19      45.075  16.642  -4.551  1.00  0.00            
+ATOM     30 HG23 VAL    19      45.939  16.262  -5.884  1.00  0.00            
 ATOM     31  C   VAL    19      48.080  14.550  -4.760  1.00  0.00            
 ATOM     32  O   VAL    19      48.100  13.660  -5.600  1.00  0.00            
 ATOM     33  N   TRP    20      49.000  15.510  -4.590  1.00  0.00            
@@ -196,11 +196,11 @@ ATOM    191  NE  ARG    28      62.210  29.280 -15.420  1.00  0.00
 ATOM    192  HE  ARG    28      62.741  29.924 -14.869  1.00  0.00            
 ATOM    193  CZ  ARG    28      61.810  29.760 -16.590  1.00  0.00            
 ATOM    194  NH1 ARG    28      61.030  29.000 -17.390  1.00  0.00            
-ATOM    195 1HH1 ARG    28      60.758  28.083 -17.098  1.00  0.00            
-ATOM    196 2HH1 ARG    28      60.724  29.355 -18.274  1.00  0.00            
+ATOM    195 HH11 ARG    28      60.758  28.083 -17.098  1.00  0.00            
+ATOM    196 HH12 ARG    28      60.724  29.355 -18.274  1.00  0.00            
 ATOM    197  NH2 ARG    28      62.130  30.990 -17.080  1.00  0.00            
-ATOM    198 1HH2 ARG    28      62.709  31.606 -16.546  1.00  0.00            
-ATOM    199 2HH2 ARG    28      61.786  31.277 -17.974  1.00  0.00            
+ATOM    198 HH21 ARG    28      62.709  31.606 -16.546  1.00  0.00            
+ATOM    199 HH22 ARG    28      61.786  31.277 -17.974  1.00  0.00            
 ATOM    200  C   ARG    28      57.740  29.400 -14.290  1.00  0.00            
 ATOM    201  O   ARG    28      57.550  28.330 -14.890  1.00  0.00            
 ATOM    202  N   HIS    29      56.790  30.240 -13.940  1.00  0.00            
@@ -230,8 +230,8 @@ ATOM    225  HB2 ASN    30      57.037  33.265 -17.890  1.00  0.00
 ATOM    226  CG  ASN    30      59.070  32.840 -17.680  1.00  0.00            
 ATOM    227  OD1 ASN    30      60.030  32.530 -18.400  1.00  0.00            
 ATOM    228  ND2 ASN    30      59.200  33.370 -16.470  1.00  0.00            
-ATOM    229 1HD2 ASN    30      58.388  33.575 -15.924  1.00  0.00            
-ATOM    230 2HD2 ASN    30      60.110  33.565 -16.105  1.00  0.00            
+ATOM    229 HD21 ASN    30      58.388  33.575 -15.924  1.00  0.00            
+ATOM    230 HD22 ASN    30      60.110  33.565 -16.105  1.00  0.00            
 ATOM    231  C   ASN    30      57.820  29.900 -18.290  1.00  0.00            
 ATOM    232  O   ASN    30      58.880  30.000 -18.930  1.00  0.00            
 ATOM    233  N   SER    31      57.320  28.640 -18.020  1.00  0.00            

diff --git a/src/gromacs/gmxpreprocess/tests/fragment3.pdb b/src/gromacs/gmxpreprocess/tests/fragment3.pdb
index 2823736e2d9626e1d800b93a60a4c15515c2dd67..30616e54de366091707db6d14a6bbfa9e0af426f 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/fragment3.pdb
+++ b/src/gromacs/gmxpreprocess/tests/fragment3.pdb
@@ -21,13 +21,13 @@ ATOM     16  HA  VAL    35      52.801  36.284 -19.936  1.00  0.00
 ATOM     17  CB  VAL    35      51.200  37.010 -18.850  1.00  0.00            
 ATOM     18  HB  VAL    35      50.916  36.997 -17.891  1.00  0.00            
 ATOM     19  CG1 VAL    35      51.550  38.400 -19.240  1.00  0.00            
-ATOM     20 1HG1 VAL    35      50.749  38.988 -19.132  1.00  0.00            
-ATOM     21 2HG1 VAL    35      52.290  38.734 -18.656  1.00  0.00            
-ATOM     22 3HG1 VAL    35      51.847  38.414 -20.195  1.00  0.00            
+ATOM     20 HG11 VAL    35      50.749  38.988 -19.132  1.00  0.00            
+ATOM     21 HG12 VAL    35      52.290  38.734 -18.656  1.00  0.00            
+ATOM     22 HG13 VAL    35      51.847  38.414 -20.195  1.00  0.00            
 ATOM     23  CG2 VAL    35      50.040  36.540 -19.740  1.00  0.00            
-ATOM     24 1HG2 VAL    35      49.253  37.142 -19.607  1.00  0.00            
-ATOM     25 2HG2 VAL    35      50.323  36.568 -20.699  1.00  0.00            
-ATOM     26 3HG2 VAL    35      49.789  35.604 -19.493  1.00  0.00            
+ATOM     24 HG21 VAL    35      49.253  37.142 -19.607  1.00  0.00            
+ATOM     25 HG22 VAL    35      50.323  36.568 -20.699  1.00  0.00            
+ATOM     26 HG23 VAL    35      49.789  35.604 -19.493  1.00  0.00            
 ATOM     27  C   VAL    35      53.390  36.340 -17.860  1.00  0.00            
 ATOM     28  O   VAL    35      53.190  35.870 -16.790  1.00  0.00            
 ATOM     29  N   PRO    36      54.530  37.070 -17.950  1.00  0.00            
@@ -113,12 +113,12 @@ ATOM    108  HA  ILE    41      59.243  36.711  -7.295  1.00  0.00
 ATOM    109  CB  ILE    41      58.100  37.370  -5.670  1.00  0.00            
 ATOM    110  HB  ILE    41      58.783  37.862  -5.130  1.00  0.00            
 ATOM    111  CG1 ILE    41      57.090  36.810  -4.650  1.00  0.00            
-ATOM    112 1HG1 ILE    41      56.255  36.569  -5.146  1.00  0.00            
-ATOM    113 2HG1 ILE    41      57.487  35.986  -4.246  1.00  0.00            
+ATOM    112 HG11 ILE    41      56.255  36.569  -5.146  1.00  0.00            
+ATOM    113 HG12 ILE    41      57.487  35.986  -4.246  1.00  0.00            
 ATOM    114  CG2 ILE    41      57.410  38.320  -6.630  1.00  0.00            
-ATOM    115 1HG2 ILE    41      56.952  39.043  -6.112  1.00  0.00            
-ATOM    116 2HG2 ILE    41      58.088  38.727  -7.242  1.00  0.00            
-ATOM    117 3HG2 ILE    41      56.734  37.817  -7.169  1.00  0.00            
+ATOM    115 HG21 ILE    41      56.952  39.043  -6.112  1.00  0.00            
+ATOM    116 HG22 ILE    41      58.088  38.727  -7.242  1.00  0.00            
+ATOM    117 HG23 ILE    41      56.734  37.817  -7.169  1.00  0.00            
 ATOM    118  CD  ILE    41      56.700  37.760  -3.500  1.00  0.00            
 ATOM    119  HD1 ILE    41      56.045  37.304  -2.898  1.00  0.00            
 ATOM    120  HD2 ILE    41      57.517  38.005  -2.978  1.00  0.00            
@@ -237,13 +237,13 @@ ATOM    232  HA  VAL    48      68.349  26.031  -2.627  1.00  0.00
 ATOM    233  CB  VAL    48      68.960  27.990  -1.940  1.00  0.00            
 ATOM    234  HB  VAL    48      69.948  27.843  -1.993  1.00  0.00            
 ATOM    235  CG1 VAL    48      68.450  28.750  -3.250  1.00  0.00            
-ATOM    236 1HG1 VAL    48      68.900  29.641  -3.315  1.00  0.00            
-ATOM    237 2HG1 VAL    48      68.671  28.205  -4.059  1.00  0.00            
-ATOM    238 3HG1 VAL    48      67.460  28.880  -3.196  1.00  0.00            
+ATOM    236 HG11 VAL    48      68.900  29.641  -3.315  1.00  0.00            
+ATOM    237 HG12 VAL    48      68.671  28.205  -4.059  1.00  0.00            
+ATOM    238 HG13 VAL    48      67.460  28.880  -3.196  1.00  0.00            
 ATOM    239  CG2 VAL    48      68.670  28.850  -0.690  1.00  0.00            
-ATOM    240 1HG2 VAL    48      69.109  29.743  -0.790  1.00  0.00            
-ATOM    241 2HG2 VAL    48      67.683  28.974  -0.592  1.00  0.00            
-ATOM    242 3HG2 VAL    48      69.030  28.390   0.122  1.00  0.00            
+ATOM    240 HG21 VAL    48      69.109  29.743  -0.790  1.00  0.00            
+ATOM    241 HG22 VAL    48      67.683  28.974  -0.592  1.00  0.00            
+ATOM    242 HG23 VAL    48      69.030  28.390   0.122  1.00  0.00            
 ATOM    243  C   VAL    48      68.960  25.720  -0.780  1.00  0.00            
 ATOM    244  O   VAL    48      70.180  25.520  -0.780  1.00  0.00            
 ATOM    245  N   ALA    49      68.070  25.160   0.090  1.00  0.00            

diff --git a/src/gromacs/gmxpreprocess/tests/fragment4.pdb b/src/gromacs/gmxpreprocess/tests/fragment4.pdb
index 088f80d8911ff7e13f93afeaf7ab88da48373f41..060d753faa92fbd0f252e72a1c23c604d76360fb 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/fragment4.pdb
+++ b/src/gromacs/gmxpreprocess/tests/fragment4.pdb
@@ -142,12 +142,12 @@ ATOM    137  HA  ILE    59      47.980  25.943  -0.029  1.00  0.00
 ATOM    138  CB  ILE    59      46.730  27.790   0.410  1.00  0.00            
 ATOM    139  HB  ILE    59      46.375  28.063  -0.484  1.00  0.00            
 ATOM    140  CG1 ILE    59      46.990  29.180   1.200  1.00  0.00            
-ATOM    141 1HG1 ILE    59      47.168  29.006   2.169  1.00  0.00            
-ATOM    142 2HG1 ILE    59      47.765  29.671   0.802  1.00  0.00            
+ATOM    141 HG11 ILE    59      47.168  29.006   2.169  1.00  0.00            
+ATOM    142 HG12 ILE    59      47.765  29.671   0.802  1.00  0.00            
 ATOM    143  CG2 ILE    59      45.660  26.890   1.090  1.00  0.00            
-ATOM    144 1HG2 ILE    59      44.814  27.409   1.208  1.00  0.00            
-ATOM    145 2HG2 ILE    59      45.483  26.091   0.516  1.00  0.00            
-ATOM    146 3HG2 ILE    59      45.995  26.591   1.984  1.00  0.00            
+ATOM    144 HG21 ILE    59      44.814  27.409   1.208  1.00  0.00            
+ATOM    145 HG22 ILE    59      45.483  26.091   0.516  1.00  0.00            
+ATOM    146 HG23 ILE    59      45.995  26.591   1.984  1.00  0.00            
 ATOM    147  CD  ILE    59      45.780  30.080   1.110  1.00  0.00            
 ATOM    148  HD1 ILE    59      45.960  30.931   1.603  1.00  0.00            
 ATOM    149  HD2 ILE    59      45.588  30.285   0.150  1.00  0.00            
@@ -178,13 +178,13 @@ ATOM    173  HA  VAL    61      48.023  25.578  -6.472  1.00  0.00
 ATOM    174  CB  VAL    61      49.640  24.320  -7.100  1.00  0.00            
 ATOM    175  HB  VAL    61      50.273  23.776  -6.549  1.00  0.00            
 ATOM    176  CG1 VAL    61      48.930  23.320  -8.080  1.00  0.00            
-ATOM    177 1HG1 VAL    61      49.603  22.942  -8.716  1.00  0.00            
-ATOM    178 2HG1 VAL    61      48.513  22.578  -7.555  1.00  0.00            
-ATOM    179 3HG1 VAL    61      48.221  23.803  -8.594  1.00  0.00            
+ATOM    177 HG11 VAL    61      49.603  22.942  -8.716  1.00  0.00            
+ATOM    178 HG12 VAL    61      48.513  22.578  -7.555  1.00  0.00            
+ATOM    179 HG13 VAL    61      48.221  23.803  -8.594  1.00  0.00            
 ATOM    180  CG2 VAL    61      50.430  25.390  -7.900  1.00  0.00            
-ATOM    181 1HG2 VAL    61      51.024  24.938  -8.565  1.00  0.00            
-ATOM    182 2HG2 VAL    61      49.788  25.989  -8.379  1.00  0.00            
-ATOM    183 3HG2 VAL    61      50.987  25.933  -7.271  1.00  0.00            
+ATOM    181 HG21 VAL    61      51.024  24.938  -8.565  1.00  0.00            
+ATOM    182 HG22 VAL    61      49.788  25.989  -8.379  1.00  0.00            
+ATOM    183 HG23 VAL    61      50.987  25.933  -7.271  1.00  0.00            
 ATOM    184  C   VAL    61      47.910  23.930  -5.330  1.00  0.00            
 ATOM    185  O   VAL    61      46.710  23.730  -5.500  1.00  0.00            
 ATOM    186  N   CYS    62      48.580  23.410  -4.270  1.00  0.00            

diff --git a/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_0.xml b/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_0.xml
index bc8544ad4c21add675610e328fa5e1a40397197e..5489194072dc8a30a4af83a87b5db5cdebe6a0a5 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_0.xml
+++ b/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_0.xml
@@ -55,9 +55,9 @@ ATOM     44  HB  THR B  18      48.898  17.421  -1.916  1.00  0.00
 ATOM     45  OG1 THR B  18      50.020  16.940  -0.390  1.00  0.00           O
 ATOM     46  HG1 THR B  18      50.725  17.599  -0.652  1.00  0.00            
 ATOM     47  CG2 THR B  18      48.330  18.640  -0.210  1.00  0.00           C
-ATOM     48 1HG2 THR B  18      49.012  19.351  -0.380  1.00  0.00            
-ATOM     49 2HG2 THR B  18      47.440  18.944  -0.551  1.00  0.00            
-ATOM     50 3HG2 THR B  18      48.269  18.465   0.773  1.00  0.00            
+ATOM     48 HG21 THR B  18      49.012  19.351  -0.380  1.00  0.00            
+ATOM     49 HG22 THR B  18      47.440  18.944  -0.551  1.00  0.00            
+ATOM     50 HG23 THR B  18      48.269  18.465   0.773  1.00  0.00            
 ATOM     51  C   THR B  18      47.650  15.380  -1.660  1.00  0.00           C
 ATOM     52  O   THR B  18      48.350  14.370  -1.570  1.00  0.00           O
 ATOM     53  N   VAL B  19      46.990  15.650  -2.800  1.00  0.00           N
@@ -67,13 +67,13 @@ ATOM     56  HA  VAL B  19      46.794  13.844  -3.206  1.00  0.00
 ATOM     57  CB  VAL B  19      45.590  14.650  -4.650  1.00  0.00           C
 ATOM     58  HB  VAL B  19      45.844  14.046  -5.405  1.00  0.00            
 ATOM     59  CG1 VAL B  19      44.330  14.240  -3.760  1.00  0.00           C
-ATOM     60 1HG1 VAL B  19      43.504  14.259  -4.323  1.00  0.00            
-ATOM     61 2HG1 VAL B  19      44.465  13.318  -3.396  1.00  0.00            
-ATOM     62 3HG1 VAL B  19      44.232  14.886  -3.003  1.00  0.00            
+ATOM     60 HG11 VAL B  19      43.504  14.259  -4.323  1.00  0.00            
+ATOM     61 HG12 VAL B  19      44.465  13.318  -3.396  1.00  0.00            
+ATOM     62 HG13 VAL B  19      44.232  14.886  -3.003  1.00  0.00            
 ATOM     63  CG2 VAL B  19      45.210  15.960  -5.270  1.00  0.00           C
-ATOM     64 1HG2 VAL B  19      44.362  15.850  -5.789  1.00  0.00            
-ATOM     65 2HG2 VAL B  19      45.075  16.642  -4.551  1.00  0.00            
-ATOM     66 3HG2 VAL B  19      45.939  16.262  -5.884  1.00  0.00            
+ATOM     64 HG21 VAL B  19      44.362  15.850  -5.789  1.00  0.00            
+ATOM     65 HG22 VAL B  19      45.075  16.642  -4.551  1.00  0.00            
+ATOM     66 HG23 VAL B  19      45.939  16.262  -5.884  1.00  0.00            
 ATOM     67  C   VAL B  19      48.080  14.550  -4.760  1.00  0.00           C
 ATOM     68  O   VAL B  19      48.100  13.660  -5.600  1.00  0.00           O
 ATOM     69  N   TRP B  20      49.000  15.510  -4.590  1.00  0.00           N

diff --git a/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_1.xml b/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_1.xml
index 4542bab1f0c7d3928d56071488fa13086482bef1..5b7e09a5d97ab91d54d1e165f8758ec4c1260b20 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_1.xml
+++ b/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_1.xml
@@ -55,9 +55,9 @@ ATOM     44  HB  THR B  18      48.898  17.421  -1.916  1.00  0.00
 ATOM     45  OG1 THR B  18      50.020  16.940  -0.390  1.00  0.00           O
 ATOM     46  HG1 THR B  18      50.725  17.599  -0.652  1.00  0.00            
 ATOM     47  CG2 THR B  18      48.330  18.640  -0.210  1.00  0.00           C
-ATOM     48 1HG2 THR B  18      49.012  19.351  -0.380  1.00  0.00            
-ATOM     49 2HG2 THR B  18      47.440  18.944  -0.551  1.00  0.00            
-ATOM     50 3HG2 THR B  18      48.269  18.465   0.773  1.00  0.00            
+ATOM     48 HG21 THR B  18      49.012  19.351  -0.380  1.00  0.00            
+ATOM     49 HG22 THR B  18      47.440  18.944  -0.551  1.00  0.00            
+ATOM     50 HG23 THR B  18      48.269  18.465   0.773  1.00  0.00            
 ATOM     51  C   THR B  18      47.650  15.380  -1.660  1.00  0.00           C
 ATOM     52  O   THR B  18      48.350  14.370  -1.570  1.00  0.00           O
 ATOM     53  N   VAL B  19      46.990  15.650  -2.800  1.00  0.00           N
@@ -67,13 +67,13 @@ ATOM     56  HA  VAL B  19      46.794  13.844  -3.206  1.00  0.00
 ATOM     57  CB  VAL B  19      45.590  14.650  -4.650  1.00  0.00           C
 ATOM     58  HB  VAL B  19      45.844  14.046  -5.405  1.00  0.00            
 ATOM     59  CG1 VAL B  19      44.330  14.240  -3.760  1.00  0.00           C
-ATOM     60 1HG1 VAL B  19      43.504  14.259  -4.323  1.00  0.00            
-ATOM     61 2HG1 VAL B  19      44.465  13.318  -3.396  1.00  0.00            
-ATOM     62 3HG1 VAL B  19      44.232  14.886  -3.003  1.00  0.00            
+ATOM     60 HG11 VAL B  19      43.504  14.259  -4.323  1.00  0.00            
+ATOM     61 HG12 VAL B  19      44.465  13.318  -3.396  1.00  0.00            
+ATOM     62 HG13 VAL B  19      44.232  14.886  -3.003  1.00  0.00            
 ATOM     63  CG2 VAL B  19      45.210  15.960  -5.270  1.00  0.00           C
-ATOM     64 1HG2 VAL B  19      44.362  15.850  -5.789  1.00  0.00            
-ATOM     65 2HG2 VAL B  19      45.075  16.642  -4.551  1.00  0.00            
-ATOM     66 3HG2 VAL B  19      45.939  16.262  -5.884  1.00  0.00            
+ATOM     64 HG21 VAL B  19      44.362  15.850  -5.789  1.00  0.00            
+ATOM     65 HG22 VAL B  19      45.075  16.642  -4.551  1.00  0.00            
+ATOM     66 HG23 VAL B  19      45.939  16.262  -5.884  1.00  0.00            
 ATOM     67  C   VAL B  19      48.080  14.550  -4.760  1.00  0.00           C
 ATOM     68  O   VAL B  19      48.100  13.660  -5.600  1.00  0.00           O
 ATOM     69  N   TRP B  20      49.000  15.510  -4.590  1.00  0.00           N

diff --git a/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_2.xml b/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_2.xml
index 89bb763ef25603c9a0c6a872d5522b6e24f82e16..eda192fc9a8aba3f3dbd33178277cfe4b04ea679 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_2.xml
+++ b/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_2.xml
@@ -55,9 +55,9 @@ ATOM     44  HB  THR B  18      48.898  17.421  -1.916  1.00  0.00
 ATOM     45  OG1 THR B  18      50.020  16.940  -0.390  1.00  0.00           O
 ATOM     46  HG1 THR B  18      50.725  17.599  -0.652  1.00  0.00            
 ATOM     47  CG2 THR B  18      48.330  18.640  -0.210  1.00  0.00           C
-ATOM     48 1HG2 THR B  18      49.012  19.351  -0.380  1.00  0.00            
-ATOM     49 2HG2 THR B  18      47.440  18.944  -0.551  1.00  0.00            
-ATOM     50 3HG2 THR B  18      48.269  18.465   0.773  1.00  0.00            
+ATOM     48 HG21 THR B  18      49.012  19.351  -0.380  1.00  0.00            
+ATOM     49 HG22 THR B  18      47.440  18.944  -0.551  1.00  0.00            
+ATOM     50 HG23 THR B  18      48.269  18.465   0.773  1.00  0.00            
 ATOM     51  C   THR B  18      47.650  15.380  -1.660  1.00  0.00           C
 ATOM     52  O   THR B  18      48.350  14.370  -1.570  1.00  0.00           O
 ATOM     53  N   VAL B  19      46.990  15.650  -2.800  1.00  0.00           N
@@ -67,13 +67,13 @@ ATOM     56  HA  VAL B  19      46.794  13.844  -3.206  1.00  0.00
 ATOM     57  CB  VAL B  19      45.590  14.650  -4.650  1.00  0.00           C
 ATOM     58  HB  VAL B  19      45.844  14.046  -5.405  1.00  0.00            
 ATOM     59  CG1 VAL B  19      44.330  14.240  -3.760  1.00  0.00           C
-ATOM     60 1HG1 VAL B  19      43.504  14.259  -4.323  1.00  0.00            
-ATOM     61 2HG1 VAL B  19      44.465  13.318  -3.396  1.00  0.00            
-ATOM     62 3HG1 VAL B  19      44.232  14.886  -3.003  1.00  0.00            
+ATOM     60 HG11 VAL B  19      43.504  14.259  -4.323  1.00  0.00            
+ATOM     61 HG12 VAL B  19      44.465  13.318  -3.396  1.00  0.00            
+ATOM     62 HG13 VAL B  19      44.232  14.886  -3.003  1.00  0.00            
 ATOM     63  CG2 VAL B  19      45.210  15.960  -5.270  1.00  0.00           C
-ATOM     64 1HG2 VAL B  19      44.362  15.850  -5.789  1.00  0.00            
-ATOM     65 2HG2 VAL B  19      45.075  16.642  -4.551  1.00  0.00            
-ATOM     66 3HG2 VAL B  19      45.939  16.262  -5.884  1.00  0.00            
+ATOM     64 HG21 VAL B  19      44.362  15.850  -5.789  1.00  0.00            
+ATOM     65 HG22 VAL B  19      45.075  16.642  -4.551  1.00  0.00            
+ATOM     66 HG23 VAL B  19      45.939  16.262  -5.884  1.00  0.00            
 ATOM     67  C   VAL B  19      48.080  14.550  -4.760  1.00  0.00           C
 ATOM     68  O   VAL B  19      48.100  13.660  -5.600  1.00  0.00           O
 ATOM     69  N   TRP B  20      49.000  15.510  -4.590  1.00  0.00           N

diff --git a/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_3.xml b/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_3.xml
index 6981d01d7f35926b269c9a285c6d646266283d42..3eb79e64ee7eb118695733077131c0bf3cabbaff 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_3.xml
+++ b/src/gromacs/gmxpreprocess/tests/refdata/ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_3.xml
@@ -55,9 +55,9 @@ ATOM     44  HB  THR B  18      48.898  17.421  -1.916  1.00  0.00
 ATOM     45  OG1 THR B  18      50.020  16.940  -0.390  1.00  0.00           O
 ATOM     46  HG1 THR B  18      50.725  17.599  -0.652  1.00  0.00            
 ATOM     47  CG2 THR B  18      48.330  18.640  -0.210  1.00  0.00           C
-ATOM     48 1HG2 THR B  18      49.012  19.351  -0.380  1.00  0.00            
-ATOM     49 2HG2 THR B  18      47.440  18.944  -0.551  1.00  0.00            
-ATOM     50 3HG2 THR B  18      48.269  18.465   0.773  1.00  0.00            
+ATOM     48 HG21 THR B  18      49.012  19.351  -0.380  1.00  0.00            
+ATOM     49 HG22 THR B  18      47.440  18.944  -0.551  1.00  0.00            
+ATOM     50 HG23 THR B  18      48.269  18.465   0.773  1.00  0.00            
 ATOM     51  C   THR B  18      47.650  15.380  -1.660  1.00  0.00           C
 ATOM     52  O   THR B  18      48.350  14.370  -1.570  1.00  0.00           O
 ATOM     53  N   VAL B  19      46.990  15.650  -2.800  1.00  0.00           N
@@ -67,13 +67,13 @@ ATOM     56  HA  VAL B  19      46.794  13.844  -3.206  1.00  0.00
 ATOM     57  CB  VAL B  19      45.590  14.650  -4.650  1.00  0.00           C
 ATOM     58  HB  VAL B  19      45.844  14.046  -5.405  1.00  0.00            
 ATOM     59  CG1 VAL B  19      44.330  14.240  -3.760  1.00  0.00           C
-ATOM     60 1HG1 VAL B  19      43.504  14.259  -4.323  1.00  0.00            
-ATOM     61 2HG1 VAL B  19      44.465  13.318  -3.396  1.00  0.00            
-ATOM     62 3HG1 VAL B  19      44.232  14.886  -3.003  1.00  0.00            
+ATOM     60 HG11 VAL B  19      43.504  14.259  -4.323  1.00  0.00            
+ATOM     61 HG12 VAL B  19      44.465  13.318  -3.396  1.00  0.00            
+ATOM     62 HG13 VAL B  19      44.232  14.886  -3.003  1.00  0.00            
 ATOM     63  CG2 VAL B  19      45.210  15.960  -5.270  1.00  0.00           C
-ATOM     64 1HG2 VAL B  19      44.362  15.850  -5.789  1.00  0.00            
-ATOM     65 2HG2 VAL B  19      45.075  16.642  -4.551  1.00  0.00            
-ATOM     66 3HG2 VAL B  19      45.939  16.262  -5.884  1.00  0.00            
+ATOM     64 HG21 VAL B  19      44.362  15.850  -5.789  1.00  0.00            
+ATOM     65 HG22 VAL B  19      45.075  16.642  -4.551  1.00  0.00            
+ATOM     66 HG23 VAL B  19      45.939  16.262  -5.884  1.00  0.00            
 ATOM     67  C   VAL B  19      48.080  14.550  -4.760  1.00  0.00           C
 ATOM     68  O   VAL B  19      48.100  13.660  -5.600  1.00  0.00           O
 ATOM     69  N   TRP B  20      49.000  15.510  -4.590  1.00  0.00           N

diff --git a/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_0.xml b/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_0.xml
index 09f731362d18851550cd3fe00ede006429d9643a..c39afae65fedcdc7c13b47d1fe74a68f3b4453bb 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_0.xml
+++ b/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_0.xml
@@ -110,12 +110,12 @@ ATOM     98  HA  ILE     9      35.483  18.676   3.409  1.00  0.00           H
 ATOM     99  CB  ILE     9      36.190  20.570   2.570  1.00  0.00           C
 ATOM    100  HB  ILE     9      35.791  21.231   3.205  1.00  0.00           H
 ATOM    101  CG1 ILE     9      36.100  21.260   1.150  1.00  0.00           C
-ATOM    102 1HG1 ILE     9      36.833  20.910   0.566  1.00  0.00           H
-ATOM    103 2HG1 ILE     9      35.215  21.048   0.736  1.00  0.00           H
+ATOM    102 HG11 ILE     9      36.833  20.910   0.566  1.00  0.00           H
+ATOM    103 HG12 ILE     9      35.215  21.048   0.736  1.00  0.00           H
 ATOM    104  CG2 ILE     9      37.660  20.240   3.030  1.00  0.00           C
-ATOM    105 1HG2 ILE     9      38.199  21.082   3.054  1.00  0.00           H
-ATOM    106 2HG2 ILE     9      37.640  19.831   3.942  1.00  0.00           H
-ATOM    107 3HG2 ILE     9      38.075  19.598   2.385  1.00  0.00           H
+ATOM    105 HG21 ILE     9      38.199  21.082   3.054  1.00  0.00           H
+ATOM    106 HG22 ILE     9      37.640  19.831   3.942  1.00  0.00           H
+ATOM    107 HG23 ILE     9      38.075  19.598   2.385  1.00  0.00           H
 ATOM    108  CD  ILE     9      36.230  22.760   1.170  1.00  0.00           C
 ATOM    109  HD1 ILE     9      36.162  23.113   0.237  1.00  0.00           H
 ATOM    110  HD2 ILE     9      35.498  23.151   1.728  1.00  0.00           H
@@ -154,13 +154,13 @@ ATOM    142  HB2 LEU    11      30.687  14.049   3.034  1.00  0.00           H
 ATOM    143  CG  LEU    11      29.790  14.450   1.200  1.00  0.00           C
 ATOM    144  HG  LEU    11      29.964  15.033   0.407  1.00  0.00           H
 ATOM    145  CD1 LEU    11      29.680  12.940   0.840  1.00  0.00           C
-ATOM    146 1HD1 LEU    11      28.953  12.810   0.166  1.00  0.00           H
-ATOM    147 2HD1 LEU    11      30.549  12.624   0.458  1.00  0.00           H
-ATOM    148 3HD1 LEU    11      29.468  12.415   1.665  1.00  0.00           H
+ATOM    146 HD11 LEU    11      28.953  12.810   0.166  1.00  0.00           H
+ATOM    147 HD12 LEU    11      30.549  12.624   0.458  1.00  0.00           H
+ATOM    148 HD13 LEU    11      29.468  12.415   1.665  1.00  0.00           H
 ATOM    149  CD2 LEU    11      28.470  14.820   1.830  1.00  0.00           C
-ATOM    150 1HD2 LEU    11      27.738  14.711   1.158  1.00  0.00           H
-ATOM    151 2HD2 LEU    11      28.295  14.223   2.613  1.00  0.00           H
-ATOM    152 3HD2 LEU    11      28.502  15.771   2.137  1.00  0.00           H
+ATOM    150 HD21 LEU    11      27.738  14.711   1.158  1.00  0.00           H
+ATOM    151 HD22 LEU    11      28.295  14.223   2.613  1.00  0.00           H
+ATOM    152 HD23 LEU    11      28.502  15.771   2.137  1.00  0.00           H
 ATOM    153  C   LEU    11      32.460  16.000   3.760  1.00  0.00           C
 ATOM    154  O   LEU    11      33.540  15.530   3.410  1.00  0.00           O
 ATOM    155  N   MET    12      32.300  16.580   4.990  1.00  0.00           N
@@ -190,8 +190,8 @@ ATOM    178  HB2 ASN    13      37.409  14.369   4.252  1.00  0.00           H
 ATOM    179  CG  ASN    13      37.870  12.490   4.990  1.00  0.00           C
 ATOM    180  OD1 ASN    13      38.400  12.240   6.060  1.00  0.00           O
 ATOM    181  ND2 ASN    13      38.300  11.790   3.910  1.00  0.00           N
-ATOM    182 1HD2 ASN    13      38.001  12.052   2.993  1.00  0.00           H
-ATOM    183 2HD2 ASN    13      38.916  11.012   4.032  1.00  0.00           H
+ATOM    182 HD21 ASN    13      38.001  12.052   2.993  1.00  0.00           H
+ATOM    183 HD22 ASN    13      38.916  11.012   4.032  1.00  0.00           H
 ATOM    184  C   ASN    13      37.490  15.100   6.860  1.00  0.00           C
 ATOM    185  O   ASN    13      38.120  16.010   6.270  1.00  0.00           O
 ATOM    186  N   PRO    14      37.890  14.820   8.060  1.00  0.00           N
@@ -221,8 +221,8 @@ ATOM    209  HG2 GLN    15      41.126  12.817   5.312  1.00  0.00           H
 ATOM    210  CD  GLN    15      42.940  12.640   4.310  1.00  0.00           C
 ATOM    211  OE1 GLN    15      44.150  12.890   4.440  1.00  0.00           O
 ATOM    212  NE2 GLN    15      42.340  12.800   3.080  1.00  0.00           N
-ATOM    213 1HE2 GLN    15      41.345  12.742   2.998  1.00  0.00           H
-ATOM    214 2HE2 GLN    15      42.899  12.974   2.270  1.00  0.00           H
+ATOM    213 HE21 GLN    15      41.345  12.742   2.998  1.00  0.00           H
+ATOM    214 HE22 GLN    15      42.899  12.974   2.270  1.00  0.00           H
 ATOM    215  C   GLN    15      42.420  15.300   5.880  1.00  0.00           C
 ATOM    216  O   GLN    15      41.590  15.410   4.980  1.00  0.00           O
 ATOM    217  N   ARG    16      43.500  16.140   5.860  1.00  0.00           N
@@ -242,11 +242,11 @@ ATOM    230  NE  ARG    16      41.150  19.050   4.860  1.00  0.00           N
 ATOM    231  HE  ARG    16      41.483  18.997   3.919  1.00  0.00           H
 ATOM    232  CZ  ARG    16      40.090  18.340   5.200  1.00  0.00           C
 ATOM    233  NH1 ARG    16      39.790  18.070   6.490  1.00  0.00           N
-ATOM    234 1HH1 ARG    16      40.379  18.411   7.222  1.00  0.00           H
-ATOM    235 2HH1 ARG    16      38.979  17.529   6.712  1.00  0.00           H
+ATOM    234 HH11 ARG    16      40.379  18.411   7.222  1.00  0.00           H
+ATOM    235 HH12 ARG    16      38.979  17.529   6.712  1.00  0.00           H
 ATOM    236  NH2 ARG    16      39.300  17.710   4.260  1.00  0.00           N
-ATOM    237 1HH2 ARG    16      39.524  17.784   3.288  1.00  0.00           H
-ATOM    238 2HH2 ARG    16      38.504  17.180   4.551  1.00  0.00           H
+ATOM    237 HH21 ARG    16      39.524  17.784   3.288  1.00  0.00           H
+ATOM    238 HH22 ARG    16      38.504  17.180   4.551  1.00  0.00           H
 ATOM    239  C   ARG    16      44.990  16.800   3.910  1.00  0.00           C
 ATOM    240  O   ARG    16      45.630  17.680   3.340  1.00  0.00           O
 ATOM    241  N   SER    17      45.280  15.500   3.760  1.00  0.00           N

diff --git a/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_3.xml b/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_3.xml
index d6f7a6608793c753e30414c4dafc114a0c6ce442..1ff41371efa3f5edc2ae3331920213d75ad1ab85 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_3.xml
+++ b/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_3.xml
@@ -110,12 +110,12 @@ ATOM     98  HA  ILE     9      35.480  18.680   3.410  1.00  0.00
 ATOM     99  CB  ILE     9      36.190  20.570   2.570  1.00  0.00            
 ATOM    100  HB  ILE     9      35.790  21.230   3.200  1.00  0.00            
 ATOM    101  CG1 ILE     9      36.100  21.260   1.150  1.00  0.00            
-ATOM    102 1HG1 ILE     9      36.830  20.910   0.570  1.00  0.00            
-ATOM    103 2HG1 ILE     9      35.220  21.050   0.740  1.00  0.00            
+ATOM    102 HG11 ILE     9      36.830  20.910   0.570  1.00  0.00            
+ATOM    103 HG12 ILE     9      35.220  21.050   0.740  1.00  0.00            
 ATOM    104  CG2 ILE     9      37.660  20.240   3.030  1.00  0.00            
-ATOM    105 1HG2 ILE     9      38.200  21.080   3.050  1.00  0.00            
-ATOM    106 2HG2 ILE     9      37.640  19.830   3.940  1.00  0.00            
-ATOM    107 3HG2 ILE     9      38.070  19.600   2.380  1.00  0.00            
+ATOM    105 HG21 ILE     9      38.200  21.080   3.050  1.00  0.00            
+ATOM    106 HG22 ILE     9      37.640  19.830   3.940  1.00  0.00            
+ATOM    107 HG23 ILE     9      38.070  19.600   2.380  1.00  0.00            
 ATOM    108  CD  ILE     9      36.230  22.760   1.170  1.00  0.00            
 ATOM    109  HD1 ILE     9      36.160  23.110   0.240  1.00  0.00            
 ATOM    110  HD2 ILE     9      35.500  23.150   1.730  1.00  0.00            
@@ -154,13 +154,13 @@ ATOM    142  HB2 LEU    11      30.690  14.050   3.030  1.00  0.00
 ATOM    143  CG  LEU    11      29.790  14.450   1.200  1.00  0.00            
 ATOM    144  HG  LEU    11      29.960  15.030   0.410  1.00  0.00            
 ATOM    145  CD1 LEU    11      29.680  12.940   0.840  1.00  0.00            
-ATOM    146 1HD1 LEU    11      28.950  12.810   0.170  1.00  0.00            
-ATOM    147 2HD1 LEU    11      30.550  12.620   0.460  1.00  0.00            
-ATOM    148 3HD1 LEU    11      29.470  12.420   1.670  1.00  0.00            
+ATOM    146 HD11 LEU    11      28.950  12.810   0.170  1.00  0.00            
+ATOM    147 HD12 LEU    11      30.550  12.620   0.460  1.00  0.00            
+ATOM    148 HD13 LEU    11      29.470  12.420   1.670  1.00  0.00            
 ATOM    149  CD2 LEU    11      28.470  14.820   1.830  1.00  0.00            
-ATOM    150 1HD2 LEU    11      27.740  14.710   1.160  1.00  0.00            
-ATOM    151 2HD2 LEU    11      28.290  14.220   2.610  1.00  0.00            
-ATOM    152 3HD2 LEU    11      28.500  15.770   2.140  1.00  0.00            
+ATOM    150 HD21 LEU    11      27.740  14.710   1.160  1.00  0.00            
+ATOM    151 HD22 LEU    11      28.290  14.220   2.610  1.00  0.00            
+ATOM    152 HD23 LEU    11      28.500  15.770   2.140  1.00  0.00            
 ATOM    153  C   LEU    11      32.460  16.000   3.760  1.00  0.00            
 ATOM    154  O   LEU    11      33.540  15.530   3.410  1.00  0.00            
 ATOM    155  N   MET    12      32.300  16.580   4.990  1.00  0.00            
@@ -190,8 +190,8 @@ ATOM    178  HB2 ASN    13      37.410  14.370   4.250  1.00  0.00
 ATOM    179  CG  ASN    13      37.870  12.490   4.990  1.00  0.00            
 ATOM    180  OD1 ASN    13      38.400  12.240   6.060  1.00  0.00            
 ATOM    181  ND2 ASN    13      38.300  11.790   3.910  1.00  0.00            
-ATOM    182 1HD2 ASN    13      38.000  12.050   2.990  1.00  0.00            
-ATOM    183 2HD2 ASN    13      38.920  11.010   4.030  1.00  0.00            
+ATOM    182 HD21 ASN    13      38.000  12.050   2.990  1.00  0.00            
+ATOM    183 HD22 ASN    13      38.920  11.010   4.030  1.00  0.00            
 ATOM    184  C   ASN    13      37.490  15.100   6.860  1.00  0.00            
 ATOM    185  O   ASN    13      38.120  16.010   6.270  1.00  0.00            
 ATOM    186  N   PRO    14      37.890  14.820   8.060  1.00  0.00            
@@ -221,8 +221,8 @@ ATOM    209  HG2 GLN    15      41.130  12.820   5.310  1.00  0.00
 ATOM    210  CD  GLN    15      42.940  12.640   4.310  1.00  0.00            
 ATOM    211  OE1 GLN    15      44.150  12.890   4.440  1.00  0.00            
 ATOM    212  NE2 GLN    15      42.340  12.800   3.080  1.00  0.00            
-ATOM    213 1HE2 GLN    15      41.350  12.740   3.000  1.00  0.00            
-ATOM    214 2HE2 GLN    15      42.900  12.970   2.270  1.00  0.00            
+ATOM    213 HE21 GLN    15      41.350  12.740   3.000  1.00  0.00            
+ATOM    214 HE22 GLN    15      42.900  12.970   2.270  1.00  0.00            
 ATOM    215  C   GLN    15      42.420  15.300   5.880  1.00  0.00            
 ATOM    216  O   GLN    15      41.590  15.410   4.980  1.00  0.00            
 ATOM    217  N   ARG    16      43.500  16.140   5.860  1.00  0.00            
@@ -242,11 +242,11 @@ ATOM    230  NE  ARG    16      41.150  19.050   4.860  1.00  0.00
 ATOM    231  HE  ARG    16      41.480  19.000   3.920  1.00  0.00            
 ATOM    232  CZ  ARG    16      40.090  18.340   5.200  1.00  0.00            
 ATOM    233  NH1 ARG    16      39.790  18.070   6.490  1.00  0.00            
-ATOM    234 1HH1 ARG    16      40.380  18.410   7.220  1.00  0.00            
-ATOM    235 2HH1 ARG    16      38.980  17.530   6.710  1.00  0.00            
+ATOM    234 HH11 ARG    16      40.380  18.410   7.220  1.00  0.00            
+ATOM    235 HH12 ARG    16      38.980  17.530   6.710  1.00  0.00            
 ATOM    236  NH2 ARG    16      39.300  17.710   4.260  1.00  0.00            
-ATOM    237 1HH2 ARG    16      39.520  17.780   3.290  1.00  0.00            
-ATOM    238 2HH2 ARG    16      38.500  17.180   4.550  1.00  0.00            
+ATOM    237 HH21 ARG    16      39.520  17.780   3.290  1.00  0.00            
+ATOM    238 HH22 ARG    16      38.500  17.180   4.550  1.00  0.00            
 ATOM    239  C   ARG    16      44.990  16.800   3.910  1.00  0.00            
 ATOM    240  O   ARG    16      45.630  17.680   3.340  1.00  0.00            
 ATOM    241  N   SER    17      45.280  15.500   3.760  1.00  0.00            

diff --git a/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_6.xml b/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_6.xml
index d6f7a6608793c753e30414c4dafc114a0c6ce442..1ff41371efa3f5edc2ae3331920213d75ad1ab85 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_6.xml
+++ b/src/gromacs/gmxpreprocess/tests/refdata/SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_6.xml
@@ -110,12 +110,12 @@ ATOM     98  HA  ILE     9      35.480  18.680   3.410  1.00  0.00
 ATOM     99  CB  ILE     9      36.190  20.570   2.570  1.00  0.00            
 ATOM    100  HB  ILE     9      35.790  21.230   3.200  1.00  0.00            
 ATOM    101  CG1 ILE     9      36.100  21.260   1.150  1.00  0.00            
-ATOM    102 1HG1 ILE     9      36.830  20.910   0.570  1.00  0.00            
-ATOM    103 2HG1 ILE     9      35.220  21.050   0.740  1.00  0.00            
+ATOM    102 HG11 ILE     9      36.830  20.910   0.570  1.00  0.00            
+ATOM    103 HG12 ILE     9      35.220  21.050   0.740  1.00  0.00            
 ATOM    104  CG2 ILE     9      37.660  20.240   3.030  1.00  0.00            
-ATOM    105 1HG2 ILE     9      38.200  21.080   3.050  1.00  0.00            
-ATOM    106 2HG2 ILE     9      37.640  19.830   3.940  1.00  0.00            
-ATOM    107 3HG2 ILE     9      38.070  19.600   2.380  1.00  0.00            
+ATOM    105 HG21 ILE     9      38.200  21.080   3.050  1.00  0.00            
+ATOM    106 HG22 ILE     9      37.640  19.830   3.940  1.00  0.00            
+ATOM    107 HG23 ILE     9      38.070  19.600   2.380  1.00  0.00            
 ATOM    108  CD  ILE     9      36.230  22.760   1.170  1.00  0.00            
 ATOM    109  HD1 ILE     9      36.160  23.110   0.240  1.00  0.00            
 ATOM    110  HD2 ILE     9      35.500  23.150   1.730  1.00  0.00            
@@ -154,13 +154,13 @@ ATOM    142  HB2 LEU    11      30.690  14.050   3.030  1.00  0.00
 ATOM    143  CG  LEU    11      29.790  14.450   1.200  1.00  0.00            
 ATOM    144  HG  LEU    11      29.960  15.030   0.410  1.00  0.00            
 ATOM    145  CD1 LEU    11      29.680  12.940   0.840  1.00  0.00            
-ATOM    146 1HD1 LEU    11      28.950  12.810   0.170  1.00  0.00            
-ATOM    147 2HD1 LEU    11      30.550  12.620   0.460  1.00  0.00            
-ATOM    148 3HD1 LEU    11      29.470  12.420   1.670  1.00  0.00            
+ATOM    146 HD11 LEU    11      28.950  12.810   0.170  1.00  0.00            
+ATOM    147 HD12 LEU    11      30.550  12.620   0.460  1.00  0.00            
+ATOM    148 HD13 LEU    11      29.470  12.420   1.670  1.00  0.00            
 ATOM    149  CD2 LEU    11      28.470  14.820   1.830  1.00  0.00            
-ATOM    150 1HD2 LEU    11      27.740  14.710   1.160  1.00  0.00            
-ATOM    151 2HD2 LEU    11      28.290  14.220   2.610  1.00  0.00            
-ATOM    152 3HD2 LEU    11      28.500  15.770   2.140  1.00  0.00            
+ATOM    150 HD21 LEU    11      27.740  14.710   1.160  1.00  0.00            
+ATOM    151 HD22 LEU    11      28.290  14.220   2.610  1.00  0.00            
+ATOM    152 HD23 LEU    11      28.500  15.770   2.140  1.00  0.00            
 ATOM    153  C   LEU    11      32.460  16.000   3.760  1.00  0.00            
 ATOM    154  O   LEU    11      33.540  15.530   3.410  1.00  0.00            
 ATOM    155  N   MET    12      32.300  16.580   4.990  1.00  0.00            
@@ -190,8 +190,8 @@ ATOM    178  HB2 ASN    13      37.410  14.370   4.250  1.00  0.00
 ATOM    179  CG  ASN    13      37.870  12.490   4.990  1.00  0.00            
 ATOM    180  OD1 ASN    13      38.400  12.240   6.060  1.00  0.00            
 ATOM    181  ND2 ASN    13      38.300  11.790   3.910  1.00  0.00            
-ATOM    182 1HD2 ASN    13      38.000  12.050   2.990  1.00  0.00            
-ATOM    183 2HD2 ASN    13      38.920  11.010   4.030  1.00  0.00            
+ATOM    182 HD21 ASN    13      38.000  12.050   2.990  1.00  0.00            
+ATOM    183 HD22 ASN    13      38.920  11.010   4.030  1.00  0.00            
 ATOM    184  C   ASN    13      37.490  15.100   6.860  1.00  0.00            
 ATOM    185  O   ASN    13      38.120  16.010   6.270  1.00  0.00            
 ATOM    186  N   PRO    14      37.890  14.820   8.060  1.00  0.00            
@@ -221,8 +221,8 @@ ATOM    209  HG2 GLN    15      41.130  12.820   5.310  1.00  0.00
 ATOM    210  CD  GLN    15      42.940  12.640   4.310  1.00  0.00            
 ATOM    211  OE1 GLN    15      44.150  12.890   4.440  1.00  0.00            
 ATOM    212  NE2 GLN    15      42.340  12.800   3.080  1.00  0.00            
-ATOM    213 1HE2 GLN    15      41.350  12.740   3.000  1.00  0.00            
-ATOM    214 2HE2 GLN    15      42.900  12.970   2.270  1.00  0.00            
+ATOM    213 HE21 GLN    15      41.350  12.740   3.000  1.00  0.00            
+ATOM    214 HE22 GLN    15      42.900  12.970   2.270  1.00  0.00            
 ATOM    215  C   GLN    15      42.420  15.300   5.880  1.00  0.00            
 ATOM    216  O   GLN    15      41.590  15.410   4.980  1.00  0.00            
 ATOM    217  N   ARG    16      43.500  16.140   5.860  1.00  0.00            
@@ -242,11 +242,11 @@ ATOM    230  NE  ARG    16      41.150  19.050   4.860  1.00  0.00
 ATOM    231  HE  ARG    16      41.480  19.000   3.920  1.00  0.00            
 ATOM    232  CZ  ARG    16      40.090  18.340   5.200  1.00  0.00            
 ATOM    233  NH1 ARG    16      39.790  18.070   6.490  1.00  0.00            
-ATOM    234 1HH1 ARG    16      40.380  18.410   7.220  1.00  0.00            
-ATOM    235 2HH1 ARG    16      38.980  17.530   6.710  1.00  0.00            
+ATOM    234 HH11 ARG    16      40.380  18.410   7.220  1.00  0.00            
+ATOM    235 HH12 ARG    16      38.980  17.530   6.710  1.00  0.00            
 ATOM    236  NH2 ARG    16      39.300  17.710   4.260  1.00  0.00            
-ATOM    237 1HH2 ARG    16      39.520  17.780   3.290  1.00  0.00            
-ATOM    238 2HH2 ARG    16      38.500  17.180   4.550  1.00  0.00            
+ATOM    237 HH21 ARG    16      39.520  17.780   3.290  1.00  0.00            
+ATOM    238 HH22 ARG    16      38.500  17.180   4.550  1.00  0.00            
 ATOM    239  C   ARG    16      44.990  16.800   3.910  1.00  0.00            
 ATOM    240  O   ARG    16      45.630  17.680   3.340  1.00  0.00            
 ATOM    241  N   SER    17      45.280  15.500   3.760  1.00  0.00            

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPdbAtomname.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPdbAtomname.xml
index a5b49d272b0991eb6189ad1364898fe066791ce9..09c161b6abcca4fb74e45ab47d5f61ad84366819 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPdbAtomname.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPdbAtomname.xml
@@ -26,14 +26,14 @@
   <CompiledSelections Name="Compiled">
     <Selection Name="Selection1">
       <Sequence Name="Atoms">
-        <Int Name="Length">2</Int>
-        <Int>4</Int>
+        <Int Name="Length">1</Int>
         <Int>7</Int>
       </Sequence>
     </Selection>
     <Selection Name="Selection2">
       <Sequence Name="Atoms">
-        <Int Name="Length">0</Int>
+        <Int Name="Length">1</Int>
+        <Int>4</Int>
       </Sequence>
     </Selection>
     <Selection Name="Selection3">

diff --git a/src/gromacs/trajectoryanalysis/tests/lysozyme.pdb b/src/gromacs/trajectoryanalysis/tests/lysozyme.pdb
index d82163b43dc5b663248fae87346aac748ee2ddb9..ab0d63590c3f11bd67780abe55fe739bb4f2ec0d 100644 (file)
--- a/src/gromacs/trajectoryanalysis/tests/lysozyme.pdb
+++ b/src/gromacs/trajectoryanalysis/tests/lysozyme.pdb
@@ -33,13 +33,13 @@ 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     32 HG11 VAL B   2      31.770  15.470 -11.060  1.00  0.00           H
+ATOM     33 HG12 VAL B   2      32.820  15.550  -9.810  1.00  0.00           H
+ATOM     34 HG13 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     36 HG21 VAL B   2      31.830  17.020 -12.840  1.00  0.00           H
+ATOM     37 HG22 VAL B   2      31.620  18.300 -11.850  1.00  0.00           H
+ATOM     38 HG23 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
@@ -86,11 +86,11 @@ 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     85 HH11 ARG B   5      32.390   9.160   1.530  1.00  0.00           H
+ATOM     86 HH12 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     88 HH21 ARG B   5      33.110   6.550  -1.470  1.00  0.00           H
+ATOM     89 HH22 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
@@ -129,13 +129,13 @@ 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    128 HD11 LEU B   8      33.760  20.430  -1.500  1.00  0.00           H
+ATOM    129 HD12 LEU B   8      35.240  19.750  -1.530  1.00  0.00           H
+ATOM    130 HD13 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    132 HD21 LEU B   8      31.720  18.930  -1.260  1.00  0.00           H
+ATOM    133 HD22 LEU B   8      32.110  18.050  -2.580  1.00  0.00           H
+ATOM    134 HD23 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

diff --git a/src/gromacs/trajectoryanalysis/tests/refdata/SasaModuleTest_WritesConnollySurfaceWithSolute.xml b/src/gromacs/trajectoryanalysis/tests/refdata/SasaModuleTest_WritesConnollySurfaceWithSolute.xml
index 83ea1e519858579ab7dd98749ca6b3dfb715d036..5e4e89b1e72ff1b1905f89c1ed9ecffecf16e501 100644 (file)
--- a/src/gromacs/trajectoryanalysis/tests/refdata/SasaModuleTest_WritesConnollySurfaceWithSolute.xml
+++ b/src/gromacs/trajectoryanalysis/tests/refdata/SasaModuleTest_WritesConnollySurfaceWithSolute.xml
@@ -54,13 +54,13 @@ ATOM     28  HA  VAL     2      33.170  18.520  -9.900  1.00  0.00
 ATOM     29  CB  VAL     2      33.140  17.030 -11.230  1.00  0.00            
 ATOM     30  HB  VAL     2      33.860  16.520 -11.700  1.00  0.00            
 ATOM     31  CG1 VAL     2      32.250  16.080 -10.430  1.00  0.00            
-ATOM     32 1HG1 VAL     2      31.770  15.470 -11.060  1.00  0.00            
-ATOM     33 2HG1 VAL     2      32.820  15.550  -9.810  1.00  0.00            
-ATOM     34 3HG1 VAL     2      31.580  16.610  -9.910  1.00  0.00            
+ATOM     32 HG11 VAL     2      31.770  15.470 -11.060  1.00  0.00            
+ATOM     33 HG12 VAL     2      32.820  15.550  -9.810  1.00  0.00            
+ATOM     34 HG13 VAL     2      31.580  16.610  -9.910  1.00  0.00            
 ATOM     35  CG2 VAL     2      32.290  17.710 -12.290  1.00  0.00            
-ATOM     36 1HG2 VAL     2      31.830  17.020 -12.840  1.00  0.00            
-ATOM     37 2HG2 VAL     2      31.620  18.300 -11.850  1.00  0.00            
-ATOM     38 3HG2 VAL     2      32.880  18.270 -12.880  1.00  0.00            
+ATOM     36 HG21 VAL     2      31.830  17.020 -12.840  1.00  0.00            
+ATOM     37 HG22 VAL     2      31.620  18.300 -11.850  1.00  0.00            
+ATOM     38 HG23 VAL     2      32.880  18.270 -12.880  1.00  0.00            
 ATOM     39  C   VAL     2      34.800  17.310  -9.290  1.00  0.00            
 ATOM     40  O   VAL     2      35.760  16.610  -9.660  1.00  0.00            
 ATOM     41  N   PHE     3      34.490  17.550  -8.040  1.00  0.00            
@@ -107,11 +107,11 @@ ATOM     81  NE  ARG     5      32.060   8.750  -0.960  1.00  0.00
 ATOM     82  HE  ARG     5      32.020   8.400  -1.890  1.00  0.00            
 ATOM     83  CZ  ARG     5      32.730   8.010  -0.100  1.00  0.00            
 ATOM     84  NH1 ARG     5      32.840   8.330   1.190  1.00  0.00            
-ATOM     85 1HH1 ARG     5      32.390   9.160   1.530  1.00  0.00            
-ATOM     86 2HH1 ARG     5      33.360   7.750   1.810  1.00  0.00            
+ATOM     85 HH11 ARG     5      32.390   9.160   1.530  1.00  0.00            
+ATOM     86 HH12 ARG     5      33.360   7.750   1.810  1.00  0.00            
 ATOM     87  NH2 ARG     5      33.250   6.840  -0.530  1.00  0.00            
-ATOM     88 1HH2 ARG     5      33.110   6.550  -1.470  1.00  0.00            
-ATOM     89 2HH2 ARG     5      33.760   6.260   0.100  1.00  0.00            
+ATOM     88 HH21 ARG     5      33.110   6.550  -1.470  1.00  0.00            
+ATOM     89 HH22 ARG     5      33.760   6.260   0.100  1.00  0.00            
 ATOM     90  C   ARG     5      34.670  12.730  -1.560  1.00  0.00            
 ATOM     91  O   ARG     5      34.670  13.650  -0.700  1.00  0.00            
 ATOM     92  N   CYS     6      35.670  11.850  -1.610  1.00  0.00            
@@ -150,13 +150,13 @@ ATOM    124  HB2 LEU     8      34.060  16.330  -1.530  1.00  0.00
 ATOM    125  CG  LEU     8      33.720  18.350  -1.310  1.00  0.00            
 ATOM    126  HG  LEU     8      33.780  18.420  -0.310  1.00  0.00            
 ATOM    127  CD1 LEU     8      34.300  19.660  -1.840  1.00  0.00            
-ATOM    128 1HD1 LEU     8      33.760  20.430  -1.500  1.00  0.00            
-ATOM    129 2HD1 LEU     8      35.240  19.750  -1.530  1.00  0.00            
-ATOM    130 3HD1 LEU     8      34.270  19.650  -2.840  1.00  0.00            
+ATOM    128 HD11 LEU     8      33.760  20.430  -1.500  1.00  0.00            
+ATOM    129 HD12 LEU     8      35.240  19.750  -1.530  1.00  0.00            
+ATOM    130 HD13 LEU     8      34.270  19.650  -2.840  1.00  0.00            
 ATOM    131  CD2 LEU     8      32.250  18.140  -1.600  1.00  0.00            
-ATOM    132 1HD2 LEU     8      31.720  18.930  -1.260  1.00  0.00            
-ATOM    133 2HD2 LEU     8      32.110  18.050  -2.580  1.00  0.00            
-ATOM    134 3HD2 LEU     8      31.930  17.310  -1.140  1.00  0.00            
+ATOM    132 HD21 LEU     8      31.720  18.930  -1.260  1.00  0.00            
+ATOM    133 HD22 LEU     8      32.110  18.050  -2.580  1.00  0.00            
+ATOM    134 HD23 LEU     8      31.930  17.310  -1.140  1.00  0.00            
 ATOM    135  C   LEU     8      36.050  17.130   0.270  1.00  0.00            
 ATOM    136  O   LEU     8      36.160  18.170   0.920  1.00  0.00            
 ATOM    137  N   ALA     9      35.750  15.980   0.830  1.00  0.00            

diff --git a/src/testutils/simulationdatabase/lysozyme.pdb b/src/testutils/simulationdatabase/lysozyme.pdb
index d82163b43dc5b663248fae87346aac748ee2ddb9..ab0d63590c3f11bd67780abe55fe739bb4f2ec0d 100644 (file)
--- a/src/testutils/simulationdatabase/lysozyme.pdb
+++ b/src/testutils/simulationdatabase/lysozyme.pdb
@@ -33,13 +33,13 @@ 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     32 HG11 VAL B   2      31.770  15.470 -11.060  1.00  0.00           H
+ATOM     33 HG12 VAL B   2      32.820  15.550  -9.810  1.00  0.00           H
+ATOM     34 HG13 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     36 HG21 VAL B   2      31.830  17.020 -12.840  1.00  0.00           H
+ATOM     37 HG22 VAL B   2      31.620  18.300 -11.850  1.00  0.00           H
+ATOM     38 HG23 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
@@ -86,11 +86,11 @@ 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     85 HH11 ARG B   5      32.390   9.160   1.530  1.00  0.00           H
+ATOM     86 HH12 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     88 HH21 ARG B   5      33.110   6.550  -1.470  1.00  0.00           H
+ATOM     89 HH22 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
@@ -129,13 +129,13 @@ 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    128 HD11 LEU B   8      33.760  20.430  -1.500  1.00  0.00           H
+ATOM    129 HD12 LEU B   8      35.240  19.750  -1.530  1.00  0.00           H
+ATOM    130 HD13 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    132 HD21 LEU B   8      31.720  18.930  -1.260  1.00  0.00           H
+ATOM    133 HD22 LEU B   8      32.110  18.050  -2.580  1.00  0.00           H
+ATOM    134 HD23 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