diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
new file mode 100644
index 0000000000000000000000000000000000000000..4e0a47240f088518b582896862528703935aca64
--- /dev/null
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -0,0 +1,38 @@
+//------------------------------------------------------------------------------
+// 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)
+ ;
+}
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 535aedbfa8fc6bbcd2f2ee41859a332a82798a81..6ed02b70651e1eaf9858e7142943de5d639034b5 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/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,
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 20f7bacd9d5a482526ad19ec9a273a2d65fa5617..93322dd267aac35220d579b0d9c68294cedbb554 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/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