First changes in MMCifParser

modules/io/pymod/export_mmcif_io.cc

+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+#include <boost/python.hpp>
+using namespace boost::python;
+
+#include <ost/io/mol/io_profile.hh>
+#include <ost/io/mol/mmcif_reader.hh>
+using namespace ost;
+using namespace ost::io;
+using namespace ost::mol;
+
+void export_mmcif_io()
+{
+  class_<MMCifParser, boost::noncopyable>("MMCifParser", init<const String&, EntityHandle&, const IOProfile&>())
+    .def("Parse", &MMCifParser::Parse)
+    .def("SetRestrictChains", &MMCifParser::SetRestrictChains)
+    .add_property("restrict_chains",
+                  make_function(&MMCifParser::GetRestrictChains,
+                                return_value_policy<copy_const_reference>()),
+                  &MMCifParser::SetRestrictChains)
+  ;
+}

modules/io/src/mol/mmcif_reader.cc

@@ -53,7 +53,6 @@ void MMCifParser::Init()
   warned_name_mismatch_ = false;
   category_             = DONT_KNOW;
   chain_count_          = 0;
-  record_type_          = "";
   atom_count_           = 0;
   residue_count_        = 0;
   auth_chain_id_        = false;
@@ -72,7 +71,6 @@ void MMCifParser::ClearState()
   residue_count_        = 0;
   atom_count_           = 0;
   category_             = DONT_KNOW;
-  record_type_          = "";
   warned_name_mismatch_ = false;
 }
 
@@ -170,11 +168,6 @@ bool MMCifParser::ParseAtomIdent(const std::vector<StringRef>& columns,
                                  StringRef& atom_name,
                                  char& alt_loc)
 {
-  // is checking really neccessary? just by using OnBeginData, enough columns
-  // should be available!
-  if (!this->EnsureEnoughColumns(columns, 12)) {
-    return false;
-  }
   // ATOM name
   atom_name = columns[indices_[LABEL_ATOM_ID]];
   if (profile_.calpha_only) { // unit test profile
@@ -187,12 +180,12 @@ bool MMCifParser::ParseAtomIdent(const std::vector<StringRef>& columns,
     chain_name = columns[indices_[AUTH_ASYM_ID]].str();
   } else {
     chain_name = columns[indices_[LABEL_ASYM_ID]].str();
-    if (restrict_chains_.size() > 0 && // unit test
-        restrict_chains_.find(chain_name) == String::npos) { // unit test
-      return false;
-    }
   }
- 
+  if (restrict_chains_.size() > 0 && // unit test
+      restrict_chains_.find(chain_name) == String::npos) { // unit test
+    return false;
+  } 
+
   std::pair<bool, int> a_num = this->TryGetInt(columns[indices_[ID]],
                                                "_atom_site.id",
                                           profile_.fault_tolerant); // unit test
@@ -236,7 +229,7 @@ void MMCifParser::ParseAndAddAtom(const std::vector<StringRef>& columns)
                             alt_loc)) {
     return;                            
   }
-  Real occ, temp;
+  Real occ = 1.00f, temp = 0;
   geom::Vec3 apos;
   
   for (int i = CARTN_X; i <= CARTN_Z; ++i) {
@@ -253,14 +246,10 @@ void MMCifParser::ParseAndAddAtom(const std::vector<StringRef>& columns)
 
   if (indices_[OCCUPANCY] != -1) { // unit test
     occ = this->TryGetReal(columns[indices_[OCCUPANCY]], "atom_site.occupancy");
-  } else {
-    occ = 1.00f;
   }
   if (indices_[B_ISO_OR_EQUIV] != -1) { // unit test
     temp = this->TryGetReal(columns[indices_[B_ISO_OR_EQUIV]],
                             "atom_site.B_iso_or_equiv");
-  } else {
-    temp = 0;
   }
 
   // determine element
@@ -370,20 +359,14 @@ void MMCifParser::ParseAndAddAtom(const std::vector<StringRef>& columns)
     ah = editor.InsertAtom(curr_residue_, aname, apos, s_ele);
     ++atom_count_;
   }
-  if (indices_[B_ISO_OR_EQUIV] != -1) {// unit test
-    ah.SetBFactor(temp);
-  }
-  if (indices_[OCCUPANCY] != -1) {// unit test
-    ah.SetOccupancy(occ);
-  }
+  ah.SetBFactor(temp);
+
+  ah.SetOccupancy(occ);
 
   // record type
-  if (indices_[GROUP_PDB] != -1) {
-    record_type_ = columns[indices_[GROUP_PDB]].str();
-  } else {
-    record_type_ = "ATOM";
-  }
-  ah.SetHetAtom(record_type_[0]=='H');
+  ah.SetHetAtom(indices_[GROUP_PDB] == -1 ? false :  
+                columns[indices_[GROUP_PDB]][0]=='H');
+
 }
 
 void MMCifParser::OnDataRow(const StarLoopDesc& header, 

modules/io/src/mol/mmcif_reader.hh

@@ -29,13 +29,6 @@
 
 namespace ost { namespace io {
 
-/// \enum categories of the mmcif format
-typedef enum {
-  ATOM_SITE,
-  DONT_KNOW
-} MMCifCategory;
-
-
 /// \brief reader for the mmcif file format
 /// 
 /// \section mmcif_format mmcif format description/ coverage
@@ -183,6 +176,12 @@ private:
     GROUP_PDB          ///< record name
   } AtomSiteItems;
 
+  /// \enum categories of the mmcif format
+  typedef enum {
+    ATOM_SITE,
+    DONT_KNOW
+  } MMCifCategory;
+
   // members
   MMCifCategory category_;
   int           indices_[MAX_ITEMS_IN_ROW]; ///< map items to values in loops
@@ -196,7 +195,6 @@ private:
   int residue_count_;
   int atom_count_;
   bool warned_name_mismatch_;
-  String record_type_;
   bool go_on_; ///< flow control within the parser hooks
   //from pdbdreader
   //entity als member, fill in ondatarow