More changes from char* to std::string to accomodate variable size of…

… chain id and resnames in hierarchy. Necessary test adjustments. At this point PDB format output will be not valid for longer ids - they won't be trimmed, rather outputted in full.

iotbx/pdb/hierarchy.cpp

@@ -705,21 +705,22 @@ namespace {
 
 } // namespace <anonymous>
 
-  void
+  std::string
   atom::format_atom_record_serial_label_columns(
-    char* result,
     atom_label_columns_formatter* label_formatter) const
   {
+    std::string result;
     char blank = ' ';
-    data->serial.copy_right_justified(result+6, 5U, blank);
-    result[11] = blank;
+    result += (boost::format("%5s") % data->serial.elems).str();
+    result += blank;
     if (label_formatter == 0) {
-      atom_label_columns_formatter().format(result+12, *this);
+      result += atom_label_columns_formatter().format(*this);
     }
     else {
       label_formatter->name = data->name.elems;
-      label_formatter->format(result+12);
+      result += label_formatter->format();
     }
+    return result;
   }
 
   unsigned
@@ -838,20 +839,22 @@ namespace {
   {
     char blank = ' ';
     std::memcpy(result, (data->hetero ? "HETATM" : "ATOM  "), 6U);
-    format_atom_record_serial_label_columns(result, label_formatter);
+    std::string far = format_atom_record_serial_label_columns(label_formatter);
+    std::memcpy(result+6, far.c_str(), far.size());
     unsigned segid_start;
     unsigned blanks_start_at;
+    size_t far_plus = far.size() + 6;
     if (replace_floats_with != 0) {
-      segid_start = 27U;
+      segid_start = far_plus;
       unsigned i=0;
       while (replace_floats_with[i] != '\0' && segid_start != 72U) {
         result[segid_start++] = replace_floats_with[i++];
       }
       blanks_start_at = segid_start + 8U;
     }
     else {
-      copy_left_justified(result+27, 3U, 0, 0U, blank);
-      char *r = result + 30;
+      copy_left_justified(result+far_plus, 3U, 0, 0U, blank);
+      char *r = result + far_plus + 3;
       // the buffer size in std::snprintf is limited to 640 bytes for
       // the 80 column PDB format
       for(unsigned i=0;i<3;i++) {
@@ -860,7 +863,7 @@ namespace {
           throw std::runtime_error(
             std::string("atom ") + "XYZ"[i] + " coordinate value"
             " does not fit into F8.3 format:\n"
-            + "  \"" + std::string(result, 27U) + "\"\n"
+            + "  \"" + std::string(result, far_plus) + "\"\n"
             + "  value: " + (boost::format("%.3f") % data->xyz[i]).str());
         }
         r += 8;
@@ -869,22 +872,21 @@ namespace {
       if (r[6] != '\0' && r[4] != '.' && r[5] != '.') {
         throw std::runtime_error(
           std::string("atom occupancy factor does not fit into F6.2 format:\n")
-          + "  \"" + std::string(result, 27U) + "\"\n"
+          + "  \"" + std::string(result, far_plus) + "\"\n"
           + "  occupancy factor: " + (boost::format("%.2f") % data->occ).str());
       }
       r += 6;
       std::snprintf(r, 640U, "%6.2f", std::min(std::max(-1.e5, data->b), 1.e6));
       if (r[6] != '\0' && r[4] != '.' && r[5] != '.') {
         throw std::runtime_error(
           std::string("atom B-factor does not fit into F6.2 format:\n")
-          + "  \"" + std::string(result, 27U) + "\"\n"
+          + "  \"" + std::string(result, far_plus) + "\"\n"
           + "  B-factor: " + (boost::format("%.2f") % data->b).str());
       }
-      segid_start = 72U;
-      blanks_start_at = 66U;
+      blanks_start_at = 39+far_plus;
+      segid_start = blanks_start_at+6;
     }
-    return format_atom_record_segid_element_charge_columns(
-      result, segid_start, blanks_start_at);
+    return format_atom_record_segid_element_charge_columns(result, segid_start, blanks_start_at);
   }
 
   unsigned
@@ -894,16 +896,18 @@ namespace {
   {
     char blank = ' ';
     std::memcpy(result, "SIGATM", 6U);
-    format_atom_record_serial_label_columns(result, label_formatter);
-    copy_left_justified(result+27, 3U, 0, 0U, blank);
-    char *r = result + 30;
+    std::string far = format_atom_record_serial_label_columns(label_formatter);
+    size_t far_plus = far.size() + 6;
+    std::memcpy(result+6, far.c_str(), far.size());
+    copy_left_justified(result+far_plus, 3U, 0, 0U, blank);
+    char *r = result + far_plus + 3;
     for(unsigned i=0;i<3;i++) {
       std::snprintf(r, 640U, "%8.3f", std::min(std::max(-1.e7, data->sigxyz[i]),1.e8));
       if (r[8] != '\0' && r[5] != '.' && r[6] != '.' && r[7] != '.') {
         throw std::runtime_error(
           std::string("atom sigma ") + "XYZ"[i] + " coordinate value"
           " does not fit into F8.3 format:\n"
-          + "  \"" + std::string(result, 27U) + "\"\n"
+          + "  \"" + std::string(result, far_plus) + "\"\n"
           + "  value: " + (boost::format("%.3f") % data->sigxyz[i]).str());
       }
       r += 8;
@@ -912,7 +916,7 @@ namespace {
     if (r[6] != '\0' && r[4] != '.' && r[5] != '.') {
       throw std::runtime_error(std::string(
           "atom sigma occupancy factor does not fit into F6.2 format:\n")
-        + "  \"" + std::string(result, 27U) + "\"\n"
+        + "  \"" + std::string(result, far_plus) + "\"\n"
         + "  sigma occupancy factor: "
         + (boost::format("%.2f") % data->sigocc).str());
     }
@@ -921,11 +925,11 @@ namespace {
     if (r[6] != '\0' && r[4] != '.' && r[5] != '.') {
       throw std::runtime_error(std::string(
           "atom sigma B-factor does not fit into F6.2 format:\n")
-        + "  \"" + std::string(result, 27U) + "\"\n"
+        + "  \"" + std::string(result, far_plus) + "\"\n"
         + "  sigma B-factor: "
         + (boost::format("%.2f") % data->sigb).str());
     }
-    return format_atom_record_segid_element_charge_columns(result, 72U, 66U);
+    return format_atom_record_segid_element_charge_columns(result, 45+far_plus, 39+far_plus);
   }
 
 namespace {
@@ -955,16 +959,18 @@ namespace {
   {
     char blank = ' ';
     std::memcpy(result, "ANISOU", 6U);
-    format_atom_record_serial_label_columns(result, label_formatter);
-    result[27] = blank;
-    char *r = result + 28;
+    std::string far = format_atom_record_serial_label_columns(label_formatter);
+    std::memcpy(result+6, far.c_str(), far.size());
+    size_t far_plus=far.size() + 6;
+    result[far_plus] = blank;
+    char *r = result + far_plus + 1;
     for(unsigned i=0;i<6;i++) {
       double value = data->uij[i]*10000.;
       std::snprintf(r, 640U, "%7.0f", std::min(std::max(-1.e7, value), 1.e8));
       r += 7;
       if (*r != '\0') throw_f70_error(i, value, result, "");
     }
-    return format_atom_record_segid_element_charge_columns(result, 72U, 70U);
+    return format_atom_record_segid_element_charge_columns(result, 45+far_plus, 43+far_plus);
   }
 
   unsigned
@@ -974,9 +980,11 @@ namespace {
   {
     char blank = ' ';
     std::memcpy(result, "SIGUIJ", 6U);
-    format_atom_record_serial_label_columns(result, label_formatter);
-    result[27] = blank;
-    char *r = result + 28;
+    std::string far = format_atom_record_serial_label_columns(label_formatter);
+    std::memcpy(result+6, far.c_str(), far.size());
+    size_t far_plus=far.size() + 6;
+    result[far_plus] = blank;
+    char *r = result + far_plus +1;
     for(unsigned i=0;i<6;i++) {
       double value =
 #ifdef IOTBX_PDB_ENABLE_ATOM_DATA_SIGUIJ
@@ -989,7 +997,7 @@ namespace {
       r += 7;
       if (*r != '\0') throw_f70_error(i, value, result, "sigma ");
     }
-    return format_atom_record_segid_element_charge_columns(result, 72U, 70U);
+    return format_atom_record_segid_element_charge_columns(result, 45+far_plus, 43+far_plus);
   }
 
   std::string

iotbx/pdb/hierarchy.h

@@ -692,13 +692,8 @@ namespace hierarchy {
       }
 
       //! Not available in Python.
-      /*! result must point to an array of size 27 (or greater).
-          The first 6 characters are not modified.
-          On return, result is NOT null-terminated.
-       */
-      void
+      std::string
       format_atom_record_serial_label_columns(
-        char* result,
         atom_label_columns_formatter* label_formatter=0) const;
 
       //! Not available in Python.

iotbx/regression/tst_hierarchy_long_chain_ids_1.py

@@ -260,9 +260,10 @@ def test1():
   o_pdb_str = h.as_pdb_string()
   # Note here incorrect/trimmed chain id
   # There's no way to correctly output chain ids longer than 2 char in PDB format
+  print(o_pdb_str)
   assert_lines_in_text(o_pdb_str, """\
-ATOM     61  C   SERA-   2      72.898  71.361  62.393  1.00 67.20           C
-ATOM     62  O   SERA-   2      73.055  70.333  61.737  1.00 65.10           O
+ATOM     61  C   SERA-2   2      72.898  71.361  62.393  1.00 67.20           C
+ATOM     62  O   SERA-2   2      73.055  70.333  61.737  1.00 65.10           O
     """)
 
   o_cif_str = "%s" % h.as_cif_block()

iotbx/regression/tst_hierarchy_long_resname_1.py

@@ -103,8 +103,8 @@ def test1():
 ATOM      9  NZ  LYS A 279      -3.209 -12.856  44.100  1.00 54.19           N
 TER
 HETATM   10 CA    CA A 301     -17.362 -22.385  28.047  1.00 15.20          CA
-HETATM   11  C10 7ZT A 302      -7.646  -6.965   5.796  1.00 22.62           C
-HETATM   12  C2  7ZT A 302      -8.462  -5.534   9.265  1.00 16.68           C
+HETATM   11  C10 7ZTVU A 302      -7.646  -6.965   5.796  1.00 22.62           C
+HETATM   12  C2  7ZTVU A 302      -8.462  -5.534   9.265  1.00 16.68           C
     """)
 
   o_cif_str = "%s" % h.as_cif_block()

iotbx/regression/tst_hierarchy_long_resname_2.py

@@ -132,7 +132,7 @@ def test1():
   # print(model_pdb)
   for l in [
       'LINK         NZ  LYS A 279                 O   longHOH A 401 ',
-      'HETATM   10  O   lon A 401      -3.209 -12.856  46.100  1.00 30.11           O']:
+      'HETATM   10  O   longHOH A 401      -3.209 -12.856  46.100  1.00 30.11           O']:
     assert_lines_in_text(model_pdb, l)
 
 if (__name__ == "__main__"):

iotbx/regression/tst_hierarchy_long_resname_3.py

@@ -6,6 +6,7 @@
 import mmtbx.model
 from mmtbx import monomer_library
 from libtbx.utils import Sorry
+from six.moves import cStringIO as StringIO
 
 # ------------------------------------------------------------------------------
 
@@ -178,16 +179,17 @@
 def test1():
   """
   Creating restraints for long residue name
-  Not finished yet.
   """
   #dumping to disk if needed:
-  # for name, s in [('model', model_cif), ('restr', ligand_cif)]:
+  # for name, s in [('model', mm_cif), ('restr', ligand_cif)]:
   #   with open('%s.cif' % name, 'w') as f:
   #     f.write(s)
   inp = iotbx.pdb.input(lines=mm_cif.split("\n"), source_info=None)
   cif_object = iotbx.cif.reader(input_string = ligand_cif).model()
   cif_objects = [('bla.cif', cif_object)]
-  model = mmtbx.model.manager(model_input = inp, restraint_objects = cif_objects)
+  model = mmtbx.model.manager(
+      model_input = inp,
+      restraint_objects = cif_objects)
   try:
     model.process(make_restraints=True)
     geo_str = model.restraints_as_geo()
@@ -211,12 +213,37 @@ def test1():
     ]:
     assert_lines_in_text(model_cif, l)
   model_pdb = model.model_as_pdb()
-  # print(model_pdb)
+  print(model_pdb)
   for l in [
-    'HETATM   10  C10 7ZT A 302      -7.646  -6.965   5.796  1.00 22.62           C',
+    'HETATM   10  C10 7ZTVU A 302      -7.646  -6.965   5.796  1.00 22.62           C',
     ]:
     assert_lines_in_text(model_pdb, l)
 
+def test2():
+  """
+  Try creating restraints for long residue name without cif.
+  Check error message formatting (atom.quote() function)
+  """
+  #dumping to disk if needed:
+  # for name, s in [('model', mm_cif), ('restr', ligand_cif)]:
+  #   with open('%s.cif' % name, 'w') as f:
+  #     f.write(s)
+  inp = iotbx.pdb.input(lines=mm_cif.split("\n"), source_info=None)
+  cif_object = iotbx.cif.reader(input_string = ligand_cif).model()
+  cif_objects = [('bla.cif', cif_object)]
+  mlog = StringIO()
+  model = mmtbx.model.manager(
+      model_input = inp,
+      log = mlog)
+  try:
+    model.process(make_restraints=True)
+  except Sorry as e:
+    mlog_txt = mlog.getvalue()
+    # print(str(e))
+    # print(mlog_txt)
+    assert_lines_in_text(mlog_txt, """ "HETATM   15  C7  7ZTVU A 302 .*.     C  " """)
+
+
 if (__name__ == "__main__"):
   t0 = time.time()
   mon_lib_srv = None
@@ -226,4 +253,5 @@ def test1():
     print("Can not initialize monomer_library, skipping test.")
   if mon_lib_srv is not None:
     test1()
+    test2()
   print("OK. Time: %8.3f"%(time.time()-t0))