diff --git a/modules/base/pymod/wrap_base.cc b/modules/base/pymod/wrap_base.cc
index 1ba0b15718baec2fbf014e9301583d052a3d2205..1c305685bba1800c9f4b10d0efc42dcd5707b526 100644
--- a/modules/base/pymod/wrap_base.cc
+++ b/modules/base/pymod/wrap_base.cc
@@ -21,6 +21,7 @@
#include <vector>
#include <ost/geom/export_helper/vector.hh>
#include <ost/base.hh>
+#include <ost/string_ref.hh>
#include <ost/platform.hh>
#include <ost/message.hh>
#include <ost/version.hh>
@@ -38,8 +39,48 @@ void translator(const ost::Error& x) {
}
+struct stringref_to_python_string
+{
+ static PyObject* convert(ost::StringRef const& s)
+ {
+ return boost::python::incref(boost::python::object(s.str()).ptr());
+ }
+};
+
+struct stringref_from_python_string
+{
+ stringref_from_python_string()
+ {
+ boost::python::converter::registry::push_back(&convertible,
+ &construct,
+ boost::python::type_id<ost::StringRef>());
+ }
+
+ static void* convertible(PyObject* obj_ptr)
+ {
+ if (!PyString_Check(obj_ptr)) return 0;
+ return obj_ptr;
+ }
+
+ static void construct(PyObject* obj_ptr,
+ boost::python::converter::rvalue_from_python_stage1_data* data)
+ {
+ const char* value = PyString_AsString(obj_ptr);
+ if (value == 0) boost::python::throw_error_already_set();
+ void* storage = (
+ (boost::python::converter::rvalue_from_python_storage<ost::StringRef>*)
+ data)->storage.bytes;
+ new (storage) ost::StringRef(value, strlen(value));
+ data->convertible = storage;
+ }
+};
+
+
BOOST_PYTHON_MODULE(_ost_base)
{
+ boost::python::to_python_converter<ost::StringRef,
+ stringref_to_python_string>();
+ stringref_from_python_string();
register_exception_translator<ost::Error>(&translator);
def("SetPrefixPath", &ost::SetPrefixPath);
@@ -67,5 +108,5 @@ BOOST_PYTHON_MODULE(_ost_base)
class_<std::vector<int> >("IntList", init<>())
.def(vector_indexing_suite<std::vector<int> >())
.def(geom::VectorAdditions<IntList>())
- ;
+ ;
}
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index 4746f452cf6e72287c54e2e05012fd775d7be3d3..41759d1987ef149bd53ed942fc21814b22ba43c0 100644
--- a/modules/io/doc/io.rst
+++ b/modules/io/doc/io.rst
@@ -5,6 +5,7 @@
:hidden:
formats
+ mmcif
profile
.. module:: ost.io
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
new file mode 100644
index 0000000000000000000000000000000000000000..da840874e29de801134a25a648a83eca6911499a
--- /dev/null
+++ b/modules/io/doc/mmcif.rst
@@ -0,0 +1,237 @@
+MMCif File Format
+--------------------------------------------------------------------------------
+
+The MMCif file format is an alternate container for structural entities, also
+provided by the PDB. Here we describe how to load those files and how to deal
+with information provided above the common PDB format.
+
+
+Loading MMCif Files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. autofunction:: ost.io.LoadMMCIF
+
+
+Categories Available
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+
+Info Classes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Information from MMCif files which goes beyond structural data, is kept in a
+special container, the :class:`MMCifInfo` class. Here is a detailed description
+of the annotation available.
+
+.. class:: MMCifInfo
+
+ This is the container for all bits of non-molecular data pulled from a MMCif
+ file.
+
+ .. attribute:: citations
+
+ Stores a list of citations (:class:`MMCifInfoCitation`).
+
+ Also available as :meth:`GetCitations`.
+
+ .. method:: AddCitation(citation)
+
+ Add a citation to the citation list of an info object.
+
+ :param citation: Citation to be added.
+ :type citation: :class:`MMCifInfoCitation`
+
+ .. method:: AddAuthorsToCitation(id, authors)
+
+ Adds a list of authors to a specific citation.
+
+ :param id: identifier of the citation
+ :type id: :class:`str`
+ :param authors: List of authors.
+ :type authors: :class:`~ost.StringList`
+
+ .. method:: GetCitations()
+
+ See :attr:`citations`
+
+.. class:: MMCifInfoCitation
+
+ This stores citation information from an input file.
+
+ .. attribute:: id
+
+ Stores an internal identifier for a citation. If not provided, resembles an
+ empty string.
+
+ Also available as :meth:`GetID`. May also be modified by :meth:`SetID`.
+
+ .. attribute:: cas
+
+ Stores a Chemical Abstract Service identifier, if available. If not
+ provided, resembles an empty string.
+
+ Also available as :meth:`GetCAS`. May also be modified by :meth:`SetCas`.
+
+ .. attribute:: isbn
+
+ Stores the ISBN code, presumably for cited books. If not
+ provided, resembles an empty string.
+
+ Also available as :meth:`GetISBN`. May also be modified by :meth:`SetISBN`.
+
+ .. attribute:: published_in
+
+ Stores the book or journal title of a publication. Should take the full
+ title, no abbreviations. If not provided, resembles an empty string.
+
+ Also available as :meth:`GetPublishedIn`. May also be modified by
+ :meth:`SetPublishedIn`.
+
+ .. attribute:: volume
+
+ Supposed to store volume information for journals. Since the volume number
+ is not always a simple integer, it is stored as a string. If not provided,
+ resembles an empty string.
+
+ Also available as :meth:`GetVolume`. May also be modified by
+ :meth:`SetVolume`.
+
+ .. attribute:: page_first
+
+ Stores the first page of a publication. Since the page numbers are not
+ always a simple integers, they are stored as strings. If not provided,
+ resembles empty strings.
+
+ Also available as :meth:`GetPageFirst`. May also be modified by
+ :meth:`SetPageFirst`.
+
+ .. attribute:: page_last
+
+ Stores the last page of a publication. Since the page numbers are not
+ always a simple integers, they are stored as strings. If not provided,
+ resembles empty strings.
+
+ Also available as :meth:`GetPageLast`. May also be modified by
+ :meth:`SetPageLast`.
+
+ .. attribute:: doi
+
+ Stores the Document Object Identifier as used by doi.org for a cited
+ document. If not provided, resembles a empty strings.
+
+ Also available as :meth:`GetDOI`. May also be modified by :meth:`SetDOI`.
+
+ .. attribute:: pubmed
+
+ Stores the PubMed accession number. If not provided, is set to 0.
+
+ Also available as :meth:`GetPubMed`. May also be modified by
+ :meth:`SetPubmed`.
+
+ .. attribute:: year
+
+ Stores the publication year. If not provided, is set to 0.
+
+ Also available as :meth:`GetYear`. May also be modified by :meth:`SetYear`.
+
+ .. attribute:: title
+
+ Stores a title. If not provided, is set to an empty string.
+
+ Also available as :meth:`GetTitle`. May also be modified by
+ :meth:`SetTitle`.
+
+ .. attribute:: authors
+
+ Stores a :class:`~ost.StringList` of authors.
+
+ Also available as :meth:`GetAuthorList`. May also be modified by
+ :meth:`SetAuthorList`.
+
+ .. method:: GetCAS()
+
+ See :attr:`cas`
+
+ .. method:: SetCAS(cas)
+
+ See :attr:`cas`
+
+ .. method:: GetISBN()
+
+ See :attr:`isbn`
+
+ .. method:: SetISBN(isbn)
+
+ See :attr:`isbn`
+
+ .. method:: GetPublishedIn()
+
+ See :attr:`published_in`
+
+ .. method:: SetPublishedIn(title)
+
+ See :attr:`published_in`
+
+ .. method:: GetVolume()
+
+ See :attr:`volume`
+
+ .. method:: SetVolume(volume)
+
+ See :attr:`volume`
+
+ .. method:: GetPageFirst()
+
+ See :attr:`page_first`
+
+ .. method:: SetPageFirst(first)
+
+ See :attr:`page_first`
+
+ .. method:: GetPageLast()
+
+ See :attr:`page_last`
+
+ .. method:: SetPageLast(last)
+
+ See :attr:`page_last`
+
+ .. method:: GetDOI()
+
+ See :attr:`doi`
+
+ .. method:: SetDOI(doi)
+
+ See :attr:`doi`
+
+ .. method:: GetPubMed()
+
+ See :attr:`pubmed`
+
+ .. method:: SetPubMed(no)
+
+ See :attr:`pubmed`
+
+ .. method:: GetYear()
+
+ See :attr:`year`
+
+ .. method:: SetYear(year)
+
+ See :attr:`year`
+
+ .. method:: GetTitle()
+
+ See :attr:`title`
+
+ .. method:: SetTitle(title)
+
+ See :attr:`title`
+
+ .. method:: GetAuthorList()
+
+ See :attr:`authors`
+
+ .. method:: SetAuthorList(list)
+
+ See :attr:`authors`
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 1eb524a2f8cd65dc81a73eb6b1b2ab1de69031d4..87e060687a8e590f87d5b198e90199f3cf1f7bf9 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -264,7 +264,7 @@ def LoadCHARMMTraj(crd, dcd_file=None, profile='CHARMM',
raise ValueError("No DCD filename given")
return LoadCHARMMTraj_(crd, dcd_file, stride, lazy_load)
-def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=None, profile='DEFAULT', remote=False, strict_hydrogens=None, seqres=False):
+def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=None, profile='DEFAULT', remote=False, strict_hydrogens=None, seqres=False, info=False):
"""
Load MMCIF file from disk and return one or more entities. Several options
allow to customize the exact behaviour of the MMCIF import. For more
@@ -283,13 +283,16 @@ def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=Non
pdb id.
:rtype: :class:`~ost.mol.EntityHandle`.
-
- :param seqres: Whether to read SEQRES records. If set to true, the loaded
- entity and seqres entry will be returned as a tuple.
:param strict_hydrogens: If set, overrides the value of
:attr:`IOProfile.strict_hydrogens`.
+ :param seqres: Whether to read SEQRES records. If set to true, the loaded
+ entity and seqres entry will be returned as second item.
+
+ :param info: Whether to return an info container with the other output.
+ Returns a :class:`MMCifInfo` object as last item.
+
:raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous
or inexistent file
"""
@@ -328,8 +331,12 @@ def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=Non
conop_inst.ConnectAll(builder, ent, 0)
#else:
# raise IOError("File doesn't contain any entities")
+ if seqres and info:
+ return ent, reader.seqres, reader.info
if seqres:
return ent, reader.seqres
+ if info:
+ return ent, reader.info
return ent
except:
raise
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 9fb3740887f4e7c4f3122be992a6416c692474ec..4e1a7e60af45d51fa8b03c2ab92c887eb5f42374 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -17,10 +17,12 @@
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#include <boost/python.hpp>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
using namespace boost::python;
#include <ost/io/mol/io_profile.hh>
#include <ost/io/mol/mmcif_reader.hh>
+#include <ost/io/mol/mmcif_info.hh>
using namespace ost;
using namespace ost::io;
using namespace ost::mol;
@@ -32,6 +34,8 @@ void export_mmcif_io()
.def("SetRestrictChains", &MMCifParser::SetRestrictChains)
.def("SetReadCanonicalSeqRes", &MMCifParser::SetReadCanonicalSeqRes)
.def("GetSeqRes", &MMCifParser::GetSeqRes)
+ .def("GetInfo", make_function(&MMCifParser::GetInfo,
+ return_value_policy<copy_const_reference>()))
.add_property("restrict_chains",
make_function(&MMCifParser::GetRestrictChains,
return_value_policy<copy_const_reference>()),
@@ -39,5 +43,71 @@ void export_mmcif_io()
.add_property("seqres", &MMCifParser::GetSeqRes)
.add_property("read_seqres", &MMCifParser::GetReadSeqRes,
&MMCifParser::SetReadSeqRes)
+ .add_property("info", make_function(&MMCifParser::GetInfo,
+ return_value_policy<copy_const_reference>()))
+ ;
+
+ class_<MMCifInfoCitation, boost::noncopyable>("MMCifInfoCitation", init<>())
+ .def("SetID", &MMCifInfoCitation::SetID)
+ .def("GetID", &MMCifInfoCitation::GetID)
+ .def("SetCAS", &MMCifInfoCitation::SetCAS)
+ .def("GetCAS", &MMCifInfoCitation::GetCAS)
+ .def("SetISBN", &MMCifInfoCitation::SetISBN)
+ .def("GetISBN", &MMCifInfoCitation::GetISBN)
+ .def("SetPublishedIn", &MMCifInfoCitation::SetPublishedIn)
+ .def("GetPublishedIn", &MMCifInfoCitation::GetPublishedIn)
+ .def("SetVolume", &MMCifInfoCitation::SetVolume)
+ .def("GetVolume", &MMCifInfoCitation::GetVolume)
+ .def("SetPageFirst", &MMCifInfoCitation::SetPageFirst)
+ .def("GetPageFirst", &MMCifInfoCitation::GetPageFirst)
+ .def("SetPageLast", &MMCifInfoCitation::SetPageLast)
+ .def("GetPageLast", &MMCifInfoCitation::GetPageLast)
+ .def("SetDOI", &MMCifInfoCitation::SetDOI)
+ .def("GetDOI", &MMCifInfoCitation::GetDOI)
+ .def("SetPubMed", &MMCifInfoCitation::SetPubMed)
+ .def("GetPubMed", &MMCifInfoCitation::GetPubMed)
+ .def("SetYear", &MMCifInfoCitation::SetYear)
+ .def("GetYear", &MMCifInfoCitation::GetYear)
+ .def("SetTitle", &MMCifInfoCitation::SetTitle)
+ .def("GetTitle", &MMCifInfoCitation::GetTitle)
+ .def("SetAuthorList", &MMCifInfoCitation::SetAuthorList)
+ .def("GetAuthorList", make_function(&MMCifInfoCitation::GetAuthorList,
+ return_value_policy<copy_const_reference>()))
+ .add_property("id", &MMCifInfoCitation::GetID, &MMCifInfoCitation::SetID)
+ .add_property("cas", &MMCifInfoCitation::GetCAS, &MMCifInfoCitation::SetCAS)
+ .add_property("isbn", &MMCifInfoCitation::GetISBN,
+ &MMCifInfoCitation::SetISBN)
+ .add_property("published_in", &MMCifInfoCitation::GetPublishedIn,
+ &MMCifInfoCitation::SetPublishedIn)
+ .add_property("volume", &MMCifInfoCitation::GetVolume,
+ &MMCifInfoCitation::SetVolume)
+ .add_property("page_first", &MMCifInfoCitation::GetPageFirst,
+ &MMCifInfoCitation::SetPageFirst)
+ .add_property("page_last", &MMCifInfoCitation::GetPageLast,
+ &MMCifInfoCitation::SetPageLast)
+ .add_property("doi", &MMCifInfoCitation::GetDOI, &MMCifInfoCitation::SetDOI)
+ .add_property("pubmed", &MMCifInfoCitation::GetPubMed,
+ &MMCifInfoCitation::SetPubMed)
+ .add_property("year", &MMCifInfoCitation::GetYear,
+ &MMCifInfoCitation::SetYear)
+ .add_property("title", &MMCifInfoCitation::GetTitle,
+ &MMCifInfoCitation::SetTitle)
+ .add_property("authors", make_function(&MMCifInfoCitation::GetAuthorList,
+ return_value_policy<copy_const_reference>()),
+ &MMCifInfoCitation::SetAuthorList)
+ ;
+
+ typedef std::vector<MMCifInfoCitation> MMCifInfoCitationList;
+ class_<std::vector<MMCifInfoCitation> >("MMCifInfoCitationList", init<>())
+ .def(vector_indexing_suite<std::vector<MMCifInfoCitation> >())
+ ;
+
+ class_<MMCifInfo, boost::noncopyable>("MMCifInfo", init<>())
+ .def("AddCitation", &MMCifInfo::AddCitation)
+ .def("GetCitations", make_function(&MMCifInfo::GetCitations,
+ return_value_policy<copy_const_reference>()))
+ .def("AddAuthorsToCitation", &MMCifInfo::AddAuthorsToCitation)
+ .add_property("citations", make_function(&MMCifInfo::GetCitations,
+ return_value_policy<copy_const_reference>()))
;
}
diff --git a/modules/io/src/mol/CMakeLists.txt b/modules/io/src/mol/CMakeLists.txt
index db328bb9c366cdba2a6d6354348e78213773dfef..05c813456155e14b540e7f00b3848932124db523 100644
--- a/modules/io/src/mol/CMakeLists.txt
+++ b/modules/io/src/mol/CMakeLists.txt
@@ -16,6 +16,7 @@ io_profile.cc
dcd_io.cc
star_parser.cc
mmcif_reader.cc
+mmcif_info.cc
PARENT_SCOPE
)
@@ -23,6 +24,7 @@ set(OST_IO_MOL_HEADERS
chemdict_parser.hh
star_parser.hh
mmcif_reader.hh
+mmcif_info.hh
io_profile.hh
dcd_io.hh
entity_io_crd_handler.hh
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
new file mode 100644
index 0000000000000000000000000000000000000000..1e4c8928123b010f211564635cfa5a1e9ba3189d
--- /dev/null
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -0,0 +1,39 @@
+//------------------------------------------------------------------------------
+// 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 <ost/io/io_exception.hh>
+#include <ost/io/mol/mmcif_info.hh>
+
+namespace ost { namespace io {
+
+void MMCifInfo::AddAuthorsToCitation(StringRef id, std::vector<String> list)
+{
+ // find citation
+ std::vector<MMCifInfoCitation>::iterator cit_it;
+ for (cit_it = citations_.begin(); cit_it != citations_.end(); ++cit_it) {
+ if (id == StringRef(cit_it->GetID().c_str(), cit_it->GetID().length())) {
+ cit_it->SetAuthorList(list);
+ return;
+ }
+ }
+
+ throw IOException("No citation for identifier '" + id.str() + "' found.");
+}
+
+}} //ns
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
new file mode 100644
index 0000000000000000000000000000000000000000..70624d4f74eb0356f8f618cc2d496357451fa90e
--- /dev/null
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -0,0 +1,281 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+#ifndef OST_MMCIF_INFO_HH
+#define OST_MMCIF_INFO_HH
+
+#include <vector>
+#include <ost/string_ref.hh>
+#include <ost/io/module_config.hh>
+
+namespace ost { namespace io {
+
+class DLLEXPORT_OST_IO MMCifInfoCitation {
+public:
+ /// \brief Create a citation.
+ MMCifInfoCitation(): id_(""), where_(UNKNOWN), cas_(""), published_in_(""),
+ volume_(""), page_first_(""), page_last_(""), doi_(""), pubmed_(0),
+ year_(0), title_("") {};
+
+ /// \brief Set ID
+ ///
+ /// \param id ID
+ void SetID(String id) { id_ = id; }
+ /// \brief Get ID
+ ///
+ /// \return ID
+ String GetID() const { return id_; }
+
+ /// \brief Set a CAS identifier
+ ///
+ /// \param id CAS identifier
+ void SetCAS(String id) { cas_ = id; }
+ /// \brief Get a CAS identifier
+ ///
+ /// \return CAS identifier
+ String GetCAS() const { return cas_; }
+
+ /// \brief Set an ISBN code
+ ///
+ /// \param code ISBN code
+ void SetISBN(String code) { isbn_ = code; }
+
+ /// \brief Get an ISBN code
+ ///
+ /// \return ISBN code
+ String GetISBN() const { return isbn_; }
+
+ /// \brief Set a book title or journal name
+ ///
+ /// \param title where published
+ void SetPublishedIn(String title) { published_in_ = title; }
+
+ /// \brief Get a book title or journal name
+ ///
+ /// \return title
+ String GetPublishedIn() const { return published_in_; }
+
+ /// \brief Set a journal volume
+ ///
+ /// \param volume
+ void SetVolume(String volume) { volume_ = volume; }
+
+ /// \brief Get a journal volume
+ ///
+ /// \return volume
+ String GetVolume() const { return volume_; }
+
+ /// \brief Set the start page for a publication
+ ///
+ /// \param start
+ void SetPageFirst(String first) { page_first_ = first; }
+
+ /// \brief Get the start page of a publication
+ ///
+ /// \return first page
+ String GetPageFirst() const { return page_first_; }
+
+ /// \brief Set the end page for a publication
+ ///
+ /// \param end
+ void SetPageLast(String last) { page_last_ = last; }
+
+ /// \brief Get the last page of a publication
+ ///
+ /// \return last page
+ String GetPageLast() const { return page_last_; }
+
+ /// \brief Set the DOI of a document
+ ///
+ /// \param doi
+ void SetDOI(String doi) { doi_ = doi; }
+
+
+ /// \brief Get the DOI of a document
+ ///
+ /// \return DOI
+ String GetDOI() const { return doi_; }
+
+ /// \brief Set the PubMed accession number
+ ///
+ /// \param no
+ void SetPubMed(int no) { pubmed_ = no; }
+
+ /// \brief Get the PubMed accession number
+ ///
+ /// \return PubMed accession
+ int GetPubMed() const { return pubmed_; }
+
+ /// \brief Set the year of a publication
+ ///
+ /// \param year
+ void SetYear(int year) { year_ = year; }
+
+
+ /// \brief Get the year of a publication
+ ///
+ /// \return year
+ int GetYear() const { return year_; }
+
+
+ /// \brief Set the title of a publication
+ ///
+ /// \param title
+ void SetTitle(String title) { title_ = title; }
+
+ /// \brief Get the title of a publication
+ ///
+ /// \return title
+ String GetTitle() const { return title_; }
+
+ /// \brief Set the list of authors
+ ///
+ /// \param list
+ void SetAuthorList(std::vector<String> list) { authors_ = list; }
+
+ /// \brief Get the list of authors
+ ///
+ /// \return list
+ const std::vector<String>& GetAuthorList() const { return authors_; }
+
+ bool operator==(const MMCifInfoCitation& cit) const {
+ if (this->year_ != cit.year_) {
+ return false;
+ }
+ if (this->pubmed_ != cit.pubmed_) {
+ return false;
+ }
+ if (this->where_ != cit.where_) {
+ return false;
+ }
+ if (StringRef(this->id_.c_str(), this->id_.length()) !=
+ StringRef(cit.id_.c_str(), cit.id_.length())) {
+ return false;
+ }
+ if (StringRef(this->cas_.c_str(), this->cas_.length()) !=
+ StringRef(cit.cas_.c_str(), cit.cas_.length())) {
+ return false;
+ }
+ if (StringRef(this->isbn_.c_str(), this->isbn_.length()) !=
+ StringRef(cit.isbn_.c_str(), cit.isbn_.length())) {
+ return false;
+ }
+ if (StringRef(this->published_in_.c_str(), this->published_in_.length()) !=
+ StringRef(cit.published_in_.c_str(), cit.published_in_.length())) {
+ return false;
+ }
+ if (StringRef(this->volume_.c_str(), this->volume_.length()) !=
+ StringRef(cit.volume_.c_str(), cit.volume_.length())) {
+ return false;
+ }
+ if (StringRef(this->page_first_.c_str(), this->page_first_.length()) !=
+ StringRef(cit.page_first_.c_str(), cit.page_first_.length())) {
+ return false;
+ }
+ if (StringRef(this->page_last_.c_str(), this->page_last_.length()) !=
+ StringRef(cit.page_last_.c_str(), cit.page_last_.length())) {
+ return false;
+ }
+ if (StringRef(this->doi_.c_str(), this->doi_.length()) !=
+ StringRef(cit.doi_.c_str(), cit.doi_.length())) {
+ return false;
+ }
+ if (StringRef(this->title_.c_str(), this->title_.length()) !=
+ StringRef(cit.title_.c_str(), cit.title_.length())) {
+ return false;
+ }
+ if (this->authors_ != cit.authors_) {
+ return false;
+ }
+
+ return true;
+ }
+
+ bool operator!=(const MMCifInfoCitation& cit) const {
+ return !this->operator==(cit);
+ }
+
+private:
+ /// \enum types of citations
+ typedef enum {
+ JOURNAL,
+ BOOK,
+ UNKNOWN
+ } MMCifInfoCType;
+
+ //CITATION_ID
+ String id_; ///< internal identifier
+ MMCifInfoCType where_; ///< journal or book?
+ String cas_; ///< CAS identifier
+ String isbn_; ///< ISBN no. of medium
+ String published_in_; ///< book title or full journal name
+ String volume_; ///< journal volume
+ String page_first_; ///< first page
+ String page_last_; ///< last page
+ String doi_; ///< DOI identifier
+ int pubmed_; ///< accession no.
+ int year_; ///< year of publication
+ String title_; ///< title of the publication
+ std::vector<String> authors_; ///< author information
+};
+
+/// \brief container class for additional information from MMCif files
+///
+/// \section mmcif annotation information
+///
+/// MMCif files contain loads of additional information beside coordinates.
+/// This class is set up to capture some of it. In detail, we have:
+///
+/// \li citations
+class DLLEXPORT_OST_IO MMCifInfo {
+public:
+ /// \brief Create an info object.
+ MMCifInfo() {};
+
+ /// \brief Add an item to the list of citations
+ ///
+ /// \param citation to be added
+ void AddCitation(MMCifInfoCitation citation) // unit test
+ {
+ citations_.push_back(citation);
+ }
+
+ /// \brief Add a list of authors to a specific citation.
+ ///
+ /// \param id identifier of the citation to be modified.
+ /// \param list list of authors to be added.
+ void AddAuthorsToCitation(StringRef id, std::vector<String> list); //unit test
+
+ /// \brief Get the list of citations stored in an info object.
+ ///
+ /// \return vector of MMCifInfoCitation objects
+ const std::vector<MMCifInfoCitation>& GetCitations() const
+ {
+ return citations_;
+ }
+
+//protected:
+
+private:
+ // members
+ std::vector<MMCifInfoCitation> citations_; ///< list of citations
+};
+
+}} // ns
+
+#endif
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index dc384b57f8de98163474437056824d442f6ba5cf..5b85c1340ec990377e9f66deea17ea5620f2ecfe 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -62,6 +62,7 @@ void MMCifParser::Init()
seqres_ = seq::CreateSequenceList();
read_seqres_ = false;
warned_rule_based_ = false;
+ info_ = MMCifInfo();
}
void MMCifParser::ClearState()
@@ -74,7 +75,9 @@ void MMCifParser::ClearState()
category_ = DONT_KNOW;
warned_name_mismatch_ = false;
seqres_ = seq::CreateSequenceList();
+ info_ = MMCifInfo();
entity_desc_map_.clear();
+ authors_map_.clear();
}
void MMCifParser::SetRestrictChains(const String& restrict_chains)
@@ -160,7 +163,7 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
} else if (header.GetCategory() == "entity_poly") {
category_ = ENTITY_POLY;
// mandatory
- this->TryStoreIdx(ENTITY_ID, "entity_id", header);
+ this->TryStoreIdx(ENTITY_ID, "entity_id", header);
// optional
indices_[EP_TYPE] = header.GetIndex("type");
indices_[PDBX_SEQ_ONE_LETTER_CODE] =
@@ -171,7 +174,7 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
} else if (header.GetCategory() == "citation") {
category_ = CITATION;
// mandatory items
- this->TryStoreIdx(CITATION_ID, "id", header);
+ this->TryStoreIdx(CITATION_ID, "id", header);
// optional
indices_[ABSTRACT_ID_CAS] = header.GetIndex("abstract_id_CAS");
indices_[BOOK_ID_ISBN] = header.GetIndex("book_id_ISBN");
@@ -186,9 +189,15 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
indices_[PDBX_DATABASE_ID_PUBMED] =
header.GetIndex("pdbx_database_id_PubMed");
cat_available = true;
- }
- /*else if (header.GetCategory()=="pdbx_poly_seq_scheme") {
- } else if (header.GetCategory()=="pdbx_struct_assembly") {
+ } else if (header.GetCategory()=="citation_author") {
+ category_ = CITATION_AUTHOR;
+ // mandatory items
+ this->TryStoreIdx(AUTHOR_CITATION_ID, "citation_id", header);
+ this->TryStoreIdx(AUTHOR_NAME, "name", header);
+ this->TryStoreIdx(ORDINAL, "ordinal", header);
+ cat_available = true;
+ } /*
+else if (header.GetCategory()=="pdbx_struct_assembly") {
} else if (header.GetCategory()=="struct_conf") {
}*/
category_counts_[category_]++;
@@ -590,7 +599,109 @@ String MMCifParser::ConvertSEQRES(const String& seqres,
void MMCifParser::ParseCitation(const std::vector<StringRef>& columns)
{
- // fetch dependencies from dscription, like article requires year
+ // create citation object
+ MMCifInfoCitation cit = MMCifInfoCitation();
+ // just add info
+ cit.SetID(columns[indices_[CITATION_ID]].str());
+ if (indices_[ABSTRACT_ID_CAS] != -1) {
+ cit.SetCAS(columns[indices_[ABSTRACT_ID_CAS]].str());
+ }
+ if (indices_[BOOK_ID_ISBN] != -1) {
+ cit.SetISBN(columns[indices_[BOOK_ID_ISBN]].str());
+ }
+ if (indices_[BOOK_TITLE] != -1) {
+ if (columns[indices_[BOOK_TITLE]] != StringRef(".", 1)) {
+ cit.SetPublishedIn(columns[indices_[BOOK_TITLE]].str());
+ }
+ }
+ if (indices_[JOURNAL_FULL] != -1) {
+ if (columns[indices_[JOURNAL_FULL]] != StringRef(".", 1)) {
+ if (cit.GetPublishedIn().length() > 0) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_WARNING,
+ "citation.book_title already occupies the 'published_in' field of this citation, cannot add " +
+ columns[indices_[JOURNAL_FULL]].str() +
+ ".",
+ this->GetCurrentLinenum()));
+ } else {
+ cit.SetPublishedIn(columns[indices_[JOURNAL_FULL]].str());
+ }
+ }
+ }
+ if (indices_[JOURNAL_VOLUME] != -1) {
+ cit.SetVolume(columns[indices_[JOURNAL_VOLUME]].str());
+ }
+ if (indices_[PAGE_FIRST] != -1) {
+ cit.SetPageFirst(columns[indices_[PAGE_FIRST]].str());
+ }
+ if (indices_[PAGE_LAST] != -1) {
+ cit.SetPageLast(columns[indices_[PAGE_LAST]].str());
+ }
+ if (indices_[PDBX_DATABASE_ID_DOI] != -1) {
+ cit.SetDOI(columns[indices_[PDBX_DATABASE_ID_DOI]].str());
+ }
+ if (indices_[PDBX_DATABASE_ID_PUBMED] != -1) {
+ cit.SetPubMed(this->TryGetInt(columns[indices_[PDBX_DATABASE_ID_PUBMED]],
+ "citation.pdbx_database_id_PubMed"));
+ }
+ if (indices_[YEAR] != -1) {
+ cit.SetPubMed(this->TryGetInt(columns[indices_[YEAR]], "citation.year"));
+ }
+ if (indices_[TITLE] != -1) {
+ cit.SetTitle(columns[indices_[TITLE]].str());
+ }
+
+ // store citation (wo author, yet)
+ info_.AddCitation(cit);
+}
+
+void MMCifParser::ParseCitationAuthor(const std::vector<StringRef>& columns)
+{
+ // get/ pack values
+ MMCifCitationAuthorMap::iterator atm_it;
+ std::vector<String> at_vec;
+ std::vector<int> pos_vec;
+ atm_it = authors_map_.find(columns[indices_[AUTHOR_CITATION_ID]].str());
+ if (atm_it != authors_map_.end()) {
+ at_vec = atm_it->second.second;
+ pos_vec = atm_it->second.first;
+ }
+ at_vec.push_back(columns[indices_[AUTHOR_NAME]].str());
+ pos_vec.push_back(this->TryGetInt(columns[indices_[ORDINAL]],
+ "citation_author.ordinal"));
+
+ // sort new author into right position
+ std::vector<int>::iterator pos_it;
+ std::vector<String>::iterator atv_it;
+ int ti;
+ String ts;
+ pos_it = pos_vec.end();
+ atv_it = at_vec.end();
+ --pos_it;
+ --atv_it;
+ for (; pos_it != pos_vec.begin(); --pos_it, --atv_it) {
+ if (*pos_it < *(pos_it-1)) {
+ ti = *pos_it;
+ *pos_it = *(pos_it-1);
+ *(pos_it-1) = ti;
+ ts = *atv_it;
+ *atv_it = *(atv_it-1);
+ *(atv_it-1) = ts;
+ }
+ else {
+ break;
+ }
+ }
+
+ // store new values in map
+ if (atm_it != authors_map_.end()) {
+ atm_it->second.second = at_vec;
+ atm_it->second.first = pos_vec;
+ } else {
+ authors_map_.insert(MMCifCitationAuthorMap::value_type(
+ columns[indices_[AUTHOR_CITATION_ID]].str(),
+ std::pair<std::vector<int>, std::vector<String> >(pos_vec, at_vec)
+ ));
+ }
}
void MMCifParser::OnDataRow(const StarLoopDesc& header,
@@ -610,9 +721,13 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
this->ParseEntityPoly(columns);
break;
case CITATION:
- LOG_TRACE("processing citation entry")
+ LOG_TRACE("processing citation entry");
this->ParseCitation(columns);
break;
+ case CITATION_AUTHOR:
+ LOG_TRACE("processing citation_author entry")
+ this->ParseCitationAuthor(columns);
+ break;
default:
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
"Uncatched category '"+ header.GetCategory() +"' found.",
@@ -621,141 +736,6 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
}
}
- /*
-void PDBReader::Import(mol::EntityHandle& ent,
- const String& restrict_chains)
-{
- do {
- switch(curr_line[0]) {
- case 'A':
- case 'a':
- if (IEquals(curr_line.substr(0, 6), StringRef("ANISOU", 6))) {
- if (!charmm_style_) {
- LOG_TRACE("processing ANISOU entry");
- this->ParseAnisou(curr_line, line_num_, ent);
- }
- }
- break;
- case 'C':
- case 'c':
- if (curr_line.size()<20) {
- LOG_TRACE("skipping entry");
- continue;
- }
- if (IEquals(curr_line.substr(0, 6), StringRef("COMPND", 6))) {
- LOG_TRACE("processing COMPND entry");
- this->ParseCompndEntry(curr_line, line_num_);
- }
- break;
- case 'E':
- case 'e':
- if (curr_line.size()<3) {
- continue;
- }
- if (IEquals(curr_line.rtrim(), StringRef("END", 3))) {
- hard_end_=true;
- go_on=false;
- break;
- }
- if (curr_line.size()<6) {
- continue;
- }
- if (IEquals(curr_line.substr(0, 6), StringRef("ENDMDL", 6))) {
- go_on=false;
- num_model_records_=0;
- break;
- }
- case 'H':
- case 'h':
- if (curr_line.size()<6) {
- continue;
- }
- if (IEquals(curr_line.substr(0, 6), StringRef("HETATM", 6))) {
- if (profile_.no_hetatms)
- continue;
- LOG_TRACE("processing HETATM entry");
- this->ParseAndAddAtom(curr_line, line_num_, ent,
- StringRef("HETATM", 6));
- } else if (IEquals(curr_line.substr(0, 6), StringRef("HELIX ", 6))) {
- if (!charmm_style_) {
- this->ParseHelixEntry(curr_line);
- }
- } else if (IEquals(curr_line.substr(0, 6), StringRef("HET ", 6))) {
- // remember het entry to mark the residues as ligand during ATOM import
- char chain=curr_line[12];
- std::pair<bool, int> num=curr_line.substr(13, 4).ltrim().to_int();
- if (!num.first) {
- if (profile_.fault_tolerant) {
- LOG_WARNING("Invalid HET entry on line " << line_num_);
- continue;
- } else {
- String msg=str(format("Invalid HET entry on line %d")%line_num_);
- throw IOException(msg);
- }
- }
- hets_.push_back(HetEntry(chain, to_res_num(num.second,
- curr_line[17])));
- }
- break;
- case 'M':
- case 'm':
- if (curr_line.size()<6) {
- continue;
- }
- if (IEquals(curr_line.substr(0, 6), StringRef("MODEL ", 6))) {
- ++num_model_records_;
- if (num_model_records_<2) {
- continue;
- }
- if (profile_.fault_tolerant) {
- go_on=false;
- num_model_records_=1;
- break;
- }
- String msg=str(format("MODEL record without matching ENDMDL on line %d")%line_num_);
- throw IOException(msg);
- }
- break;
- case 'S':
- case 's':
- if (curr_line.size()<6) {
- continue;
- }
- if (IEquals(curr_line.substr(0, 6), StringRef("SHEET ", 6))) {
- if (!charmm_style_) {
- this->ParseStrandEntry(curr_line);
- }
- }
- break;
- default:
- break;
- }
- } while (std::getline(in_, curr_line_) && ++line_num_ && go_on);
- LOG_INFO("imported "
- << chain_count_ << " chains, "
- << residue_count_ << " residues, "
- << atom_count_ << " atoms; with "
- << helix_list_.size() << " helices and "
- << strand_list_.size() << " strands");
- this->AssignSecStructure(ent);
- this->AssignMolIds(ent);
- for (HetList::const_iterator i=hets_.begin(), e=hets_.end(); i!=e; ++i) {
- mol::ResidueHandle res=ent.FindResidue(String(1, i->chain), i->num);
- if (res.IsValid()) {
- res.SetIsLigand(true);
- }
- }
-}
- */
-
-
- /*
- virtual void OnEndLoop() { }
-
- virtual void OnDataItem(const StarDataItem& item) { }
-
- };*/
-
void MMCifParser::OnEndData()
{
mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT);
@@ -779,6 +759,17 @@ void MMCifParser::OnEndData()
}
}
+ // process citations (couple with authors
+ // iterate citations
+ MMCifCitationAuthorMap::const_iterator atm_it;
+ std::vector<String>::const_iterator atv_it;
+ std::vector<int>::const_iterator pos_it;
+ for (atm_it = authors_map_.begin(); atm_it != authors_map_.end(); ++atm_it) {
+ info_.AddAuthorsToCitation(StringRef(atm_it->first.c_str(),
+ atm_it->first.length()),
+ atm_it->second.second);
+ }
+
LOG_INFO("imported "
<< chain_count_ << " chains, "
<< residue_count_ << " residues, "
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index d82b9fb103d8dcf269af4463f9d6b51ab2106e57..ecd9f31a39a0982dc8d0f5f65f8001056bbce00f 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -31,6 +31,7 @@
#include <ost/io/mol/io_profile.hh>
#include <ost/io/io_exception.hh>
#include <ost/io/mol/star_parser.hh>
+#include <ost/io/mol/mmcif_info.hh>
namespace ost { namespace io {
@@ -43,6 +44,9 @@ namespace ost { namespace io {
/// parser:
///
/// \li atom_site
+/// \li entity
+/// \li entity_poly
+/// \li citation
class DLLEXPORT_OST_IO MMCifParser : public StarParser {
public:
/// \brief create a MMCifParser
@@ -133,7 +137,12 @@ public:
return read_seqres_;
}
- protected:
+ /// \brief Get additional information of the MMCif file.
+ ///
+ /// \return MMCitfInfo object
+ const MMCifInfo& GetInfo() { return info_; }
+
+protected:
/// \brief Store an item index from loop header in preparation for reading a
/// row. Throws an exception if the item does not exist.
///
@@ -171,6 +180,8 @@ public:
/// \param[out] res_name fetches atom_site.label_comp_id
/// \param[out] resnum gets atom_site.label_seq_id if available, consecutive
/// numbers, otherwise
+ /// \param[out] valid_res_num shows if we have a valid residue number or if
+ /// we have to invent our own
/// \param[out] atom_name corresponds to label_atom_id
/// \param[out] alt_loc gets first letter of atom_site.label_alt_id
bool ParseAtomIdent(const std::vector<StringRef>& columns,
@@ -210,6 +221,11 @@ public:
/// to some of the residues. To be consistent, we have to do the conversion on
/// our own.
String ConvertSEQRES(const String& seqres, conop::CompoundLibPtr compound_lib);
+ /// \brief Fetch MMCif citation_author information
+ ///
+ /// \param columns data row
+ void ParseCitationAuthor(const std::vector<StringRef>& columns);
+
private:
/// \enum magic numbers of this class
typedef enum {
@@ -270,12 +286,20 @@ private:
TITLE ///< title of the citation
} CitationItems;
+ /// \enum items of the citation_author category
+ typedef enum {
+ AUTHOR_CITATION_ID, ///< link to CITATION_ID
+ AUTHOR_NAME, ///< name of an author
+ ORDINAL ///< position in author list
+ } CitationAuthorItems;
+
/// \enum categories of the mmcif format
typedef enum {
ATOM_SITE,
ENTITY,
ENTITY_POLY,
CITATION,
+ CITATION_AUTHOR,
DONT_KNOW
} MMCifCategory;
@@ -287,6 +311,9 @@ private:
} MMCifEntityDesc;
typedef std::map<String, MMCifEntityDesc> MMCifEntityDescMap;
+ //typedef std::map<String, std::pair<std::vector<int>, std::vector<String> > >
+ typedef std::map<String, std::pair<std::vector<int>, std::vector<String> > >
+ MMCifCitationAuthorMap;
// members
MMCifCategory category_;
@@ -312,6 +339,8 @@ private:
MMCifEntityDescMap entity_desc_map_; ///< stores entity items
seq::SequenceList seqres_;
bool read_seqres_;
+ MMCifInfo info_; ///< info container
+ MMCifCitationAuthorMap authors_map_;
};
}}
diff --git a/modules/io/tests/CMakeLists.txt b/modules/io/tests/CMakeLists.txt
index bcad4b24e6e76e55b6c08f40bcd9ea69670ca704..c4b3486d52aeb26db1865488f61e42c750f9c67c 100644
--- a/modules/io/tests/CMakeLists.txt
+++ b/modules/io/tests/CMakeLists.txt
@@ -1,5 +1,6 @@
set(OST_IO_UNIT_TESTS
test_io_pdb.py
+ test_io_mmcif.py
test_clustal.cc
test_io_pdb.cc
test_io_crd.cc
@@ -9,6 +10,7 @@ set(OST_IO_UNIT_TESTS
tests.cc
test_star_parser.cc
test_mmcif_reader.cc
+ test_mmcif_info.cc
)
if (ENABLE_IMG)
list(APPEND OST_IO_UNIT_TESTS test_io_img.cc)
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
new file mode 100644
index 0000000000000000000000000000000000000000..47c52b7ece410092f5e4f46464680f143be3af1f
--- /dev/null
+++ b/modules/io/tests/test_io_mmcif.py
@@ -0,0 +1,64 @@
+import unittest
+from ost import *
+
+class TestPDB(unittest.TestCase):
+ def setUp(self):
+ pass
+
+ def test_mmcifinfo(self):
+ c = io.MMCifInfoCitation()
+ # test ID setting/ getting
+ c.SetID('ID')
+ self.assertEquals(c.GetID(), 'ID')
+ # test CAS setting/ getting
+ c.SetCAS('FOO')
+ self.assertEquals(c.GetCAS(), 'FOO')
+ # test ISBN setting/ getting
+ c.SetISBN('0-0-0-0-0-0')
+ self.assertEquals(c.GetISBN(), '0-0-0-0-0-0')
+ # test published_in setting/ getting
+ c.SetPublishedIn('Best Book Ever')
+ self.assertEquals(c.GetPublishedIn(), 'Best Book Ever')
+ # test volume setting/ getting
+ c.SetVolume('3')
+ self.assertEquals(c.GetVolume(), '3')
+ # test page setting/ getting
+ c.SetPageFirst('1')
+ self.assertEquals(c.GetPageFirst(), '1')
+ c.SetPageLast('10')
+ self.assertEquals(c.GetPageLast(), '10')
+ # test doi setting/ getting
+ c.SetDOI('HERE')
+ self.assertEquals(c.GetDOI(), 'HERE')
+ # test PubMed setting/ getting
+ c.SetPubMed(815)
+ self.assertEquals(c.GetPubMed(), 815)
+ # test year setting/ getting
+ c.SetYear(815)
+ self.assertEquals(c.GetYear(), 815)
+ # test title setting/ getting
+ c.SetTitle('Foo')
+ self.assertEquals(c.GetTitle(), 'Foo')
+ # test auhtors setting/ getting
+ s = ost.StringList()
+ s.append('Foo')
+ c.SetAuthorList(s)
+ s2 = c.GetAuthorList()
+ self.assertEquals(s2[0], 'Foo')
+
+ i = io.MMCifInfo()
+ i.AddCitation(c)
+ s.append('Bar')
+ i.AddAuthorsToCitation('ID', s)
+
+ cl = i.GetCitations()
+ self.assertEquals(len(cl), 1)
+ al = cl[0].GetAuthorList()
+ self.assertEquals(len(al), 2)
+ self.assertEquals(al[0], 'Foo')
+ self.assertEquals(al[1], 'Bar')
+
+if __name__== '__main__':
+ unittest.main()
+
+
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
new file mode 100644
index 0000000000000000000000000000000000000000..97346d7ff5ee6b6bbc090822497b3d391a634da9
--- /dev/null
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -0,0 +1,82 @@
+//------------------------------------------------------------------------------
+// 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 <ost/io/io_exception.hh>
+#include <ost/io/mol/mmcif_info.hh>
+
+#define BOOST_AUTO_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+
+using namespace ost;
+using namespace ost::io;
+
+BOOST_AUTO_TEST_SUITE( io );
+
+BOOST_AUTO_TEST_CASE(mmcif_info_citation)
+{
+ BOOST_MESSAGE(" Running mmcif_info_citation tests...");
+
+ MMCifInfoCitation cit = MMCifInfoCitation();
+ std::vector<String> author_list;
+
+ author_list.push_back("Kabel, H.");
+
+ cit.SetID("ID");
+ cit.SetCAS("FOO");
+ cit.SetISBN("0-0-0-0-0");
+ cit.SetPublishedIn("Journal of Uncanny Science");
+ cit.SetVolume("3");
+ cit.SetPageFirst("1");
+ cit.SetPageLast("10");
+ cit.SetDOI("HERE");
+ cit.SetPubMed(815);
+ cit.SetYear(815);
+ cit.SetTitle("Foo");
+ cit.SetAuthorList(author_list);
+ author_list.clear();
+
+ BOOST_CHECK(cit.GetID() == "ID");
+ BOOST_CHECK(cit.GetCAS() == "FOO");
+ BOOST_CHECK(cit.GetISBN() == "0-0-0-0-0");
+ BOOST_CHECK(cit.GetPublishedIn() == "Journal of Uncanny Science");
+ BOOST_CHECK(cit.GetVolume() == "3");
+ BOOST_CHECK(cit.GetPageFirst() == "1");
+ BOOST_CHECK(cit.GetPageLast() == "10");
+ BOOST_CHECK(cit.GetDOI() == "HERE");
+ BOOST_CHECK(cit.GetPubMed() == 815);
+ BOOST_CHECK(cit.GetYear() == 815);
+ BOOST_CHECK(cit.GetTitle() == "Foo");
+ author_list = cit.GetAuthorList();
+ BOOST_CHECK(author_list.back() == "Kabel, H.");
+
+ BOOST_MESSAGE(" done.");
+ BOOST_MESSAGE(" trying to add everything to an info object");
+ MMCifInfo info = MMCifInfo();
+ info.AddCitation(cit);
+ std::vector<MMCifInfoCitation> citations = info.GetCitations();
+ BOOST_CHECK(citations.size() == 1);
+ BOOST_CHECK(citations.back() == cit);
+ BOOST_CHECK_THROW(info.AddAuthorsToCitation(StringRef("Foo", 3),
+ author_list),
+ IOException);
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 08b3a8bc972e1e53b0f2d06eae5e81795c237559..d534e834a072416f086dc85cd5e8201483424d12 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -53,6 +53,7 @@ public:
using MMCifParser::ParseAndAddAtom;
using MMCifParser::ParseEntity;
using MMCifParser::ParseEntityPoly;
+ using MMCifParser::ParseCitation;
using MMCifParser::TryStoreIdx;
using MMCifParser::SetReadSeqRes;
using MMCifParser::SetReadCanonicalSeqRes;
@@ -507,6 +508,65 @@ columns.push_back(StringRef("polydeoxyribonucleotide/polyribonucleotide hybrid",
conop::Conopology::Instance().SetDefaultBuilder("HEURISTIC");
}
+BOOST_AUTO_TEST_CASE(mmcif_citation_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_citation_tests...");
+ //build dummy citation
+ mol::EntityHandle eh;
+ TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ StarLoopDesc tmmcif_h;
+ std::vector<StringRef> columns;
+
+ tmmcif_h.SetCategory(StringRef("citation", 8));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("book_title", 10));
+ tmmcif_h.Add(StringRef("journal_full", 12));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.push_back(StringRef("Foo", 3));
+ columns.push_back(StringRef("The Guide", 9));
+ columns.push_back(StringRef(".", 1));
+
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseCitation(columns));
+
+ columns.pop_back();
+ columns.pop_back();
+ columns.push_back(StringRef(".", 1));
+ columns.push_back(StringRef("Hitch", 5));
+
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseCitation(columns));
+
+ columns.pop_back();
+ columns.pop_back();
+ columns.push_back(StringRef("The Guide", 9));
+ columns.push_back(StringRef("Hitch", 5));
+
+ BOOST_CHECK_THROW(tmmcif_p.ParseCitation(columns), IOException);
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_citation_author_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_citation_author_tests...");
+
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::ifstream s("testfiles/mmcif/atom_site.mmcif");
+ IOProfile profile;
+ MMCifParser mmcif_p(s, eh, profile);
+ BOOST_CHECK_NO_THROW(mmcif_p.Parse());
+
+ std::vector<String> authors =
+ mmcif_p.GetInfo().GetCitations().back().GetAuthorList();
+
+ BOOST_CHECK(authors.size() == 3);
+ BOOST_CHECK(authors[0] == "Whiskers, P.D.");
+ BOOST_CHECK(authors[1] == "McCheese, B.M.");
+ BOOST_CHECK(authors[2] == "Van Hummel, J.F.");
+
+ BOOST_MESSAGE(" done.");
+}
+
BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
{
BOOST_MESSAGE(" Running mmcif_parseatomident tests...");
@@ -520,6 +580,8 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
String chain_name;
StringRef res_name;
mol::ResNum resnum(0);
+ bool valid_res_num = false;
+ char alt_loc;
//StringRef atom_name;
BOOST_MESSAGE(" testing valid line");
diff --git a/modules/io/tests/testfiles/mmcif/atom_site.mmcif b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
index eaa46793866696ac28513af3c1c467f7dfe005fa..2d2322af617a75d450de0f054869b5dbe5d38830 100644
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -21,6 +21,28 @@ _entity_poly.nstd_linkage no
_entity_poly.nstd_monomer no
_entity_poly.pdbx_seq_one_letter_code 'VTI'
+loop_
+_citation.id
+_citation.abstract_id_CAS
+_citation.title
+_citation.journal_volume
+_citation.journal_full
+_citation.page_first
+_citation.page_last
+_citation.pdbx_database_id_DOI
+_citation.pdbx_database_id_PubMed
+_citation.year
+primary 58-08-2 'Very important, but we won't tell' 1 'Some Journal' 0 10 0815 0815 2011
+
+# the authors are not ordered on purpose for unit tests
+loop_
+_citation_author.citation_id
+_citation_author.ordinal
+_citation_author.name
+ primary 1 'Whiskers, P.D.'
+ primary 3 'Van Hummel, J.F.'
+ primary 2 'McCheese, B.M.'
+
loop_
_atom_site.group_PDB
_atom_site.type_symbol