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export_mmcif_io.cc 18.08 KiB
//------------------------------------------------------------------------------
// 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>
#include <boost/shared_ptr.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
using namespace boost::python;
#include <ost/export_helper/pair_to_tuple_conv.hh>
#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;
void export_mmcif_io()
{
class_<MMCifReader, boost::noncopyable>("MMCifReader", init<const String&, EntityHandle&, const IOProfile&>())
.def("Parse", &MMCifReader::Parse)
.def("SetRestrictChains", &MMCifReader::SetRestrictChains)
.def("SetReadCanonicalSeqRes", &MMCifReader::SetReadCanonicalSeqRes)
.def("GetSeqRes", &MMCifReader::GetSeqRes)
.def("GetInfo", make_function(&MMCifReader::GetInfo,
return_value_policy<copy_const_reference>()))
.add_property("restrict_chains",
make_function(&MMCifReader::GetRestrictChains,
return_value_policy<copy_const_reference>()),
&MMCifReader::SetRestrictChains)
.add_property("seqres", &MMCifReader::GetSeqRes)
.add_property("read_seqres", &MMCifReader::GetReadSeqRes,
&MMCifReader::SetReadSeqRes)
.add_property("info", make_function(&MMCifReader::GetInfo,
return_value_policy<copy_const_reference>()))
;
class_<MMCifInfoCitation>("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_<MMCifInfoTransOp, MMCifInfoTransOpPtr>("MMCifInfoTransOp", init<>())
.def("SetID", &MMCifInfoTransOp::SetID)
.def("GetID", &MMCifInfoTransOp::GetID)
.def("SetType", &MMCifInfoTransOp::SetType)
.def("GetType", &MMCifInfoTransOp::GetType)
.def("SetVector", &MMCifInfoTransOp::SetVector)
.def("GetVector", &MMCifInfoTransOp::GetVector)
.def("SetMatrix", &MMCifInfoTransOp::SetMatrix)
.def("GetMatrix", &MMCifInfoTransOp::GetMatrix)
.add_property("id", &MMCifInfoTransOp::GetID,
&MMCifInfoTransOp::SetID)
.add_property("type", &MMCifInfoTransOp::GetType,
&MMCifInfoTransOp::SetType)
.add_property("translation", &MMCifInfoTransOp::GetVector,
&MMCifInfoTransOp::SetVector)
.add_property("rotation", &MMCifInfoTransOp::GetMatrix,
&MMCifInfoTransOp::SetMatrix)
;
typedef std::vector<MMCifInfoTransOp> MMCifInfoTransOpList;
class_<std::vector<MMCifInfoTransOp> >("MMCifInfoTransOpList", init<>())
.def(vector_indexing_suite<std::vector<MMCifInfoTransOp> >())
;
typedef std::vector<MMCifInfoTransOpPtr> MMCifInfoTransOpPtrList;
class_<std::vector<MMCifInfoTransOpPtr> >("MMCifInfoTransOpPtrList", init<>())
.def(vector_indexing_suite<std::vector<MMCifInfoTransOpPtr>, true >())
;
typedef std::vector<MMCifInfoTransOpPtrList > MMCifInfoTransOpPtrListList;
class_<std::vector<MMCifInfoTransOpPtrList > >("MMCifInfoTransOpPtrListList",
init<>())
.def(vector_indexing_suite<std::vector<MMCifInfoTransOpPtrList >, true >()) ;
class_<MMCifInfoStructRef, MMCifInfoStructRefPtr>("MMCifInfoStructRef", no_init)
.add_property("id", make_function(&MMCifInfoStructRef::GetID,
return_value_policy<copy_const_reference>()))
.add_property("db_name", make_function(&MMCifInfoStructRef::GetDBName,
return_value_policy<copy_const_reference>()))
.add_property("db_id", make_function(&MMCifInfoStructRef::GetDBID,
return_value_policy<copy_const_reference>()))
.add_property("entity_id", make_function(&MMCifInfoStructRef::GetEntityID,
return_value_policy<copy_const_reference>()))
.add_property("db_access", make_function(&MMCifInfoStructRef::GetDBAccess,
return_value_policy<copy_const_reference>()))
.def("GetAlignedSeq", &MMCifInfoStructRef::GetAlignedSeq, arg("align_id"))
.def("GetAlignedSeqs", &MMCifInfoStructRef::GetAlignedSeqs)
.add_property("aligned_seqs", &MMCifInfoStructRef::GetAlignedSeqs)
;
class_<MMCifInfoStructRefSeq, MMCifInfoStructRefSeqPtr>("MMCifInfoStructRefSeq", no_init)
.add_property("align_id", make_function(&MMCifInfoStructRefSeq::GetID,
return_value_policy<copy_const_reference>()))
.add_property("chain_name", make_function(&MMCifInfoStructRefSeq::GetChainName,
return_value_policy<copy_const_reference>()))
.add_property("seq_begin", &MMCifInfoStructRefSeq::GetSeqBegin)
.add_property("seq_end", &MMCifInfoStructRefSeq::GetSeqEnd)
.add_property("db_begin", &MMCifInfoStructRefSeq::GetDBBegin)
.add_property("db_end", &MMCifInfoStructRefSeq::GetDBEnd)
.add_property("difs", make_function(&MMCifInfoStructRefSeq::GetDifs,
return_value_policy<copy_const_reference>()))
;
class_<MMCifInfoStructRefSeqDif,
MMCifInfoStructRefSeqDifPtr>("MMCifInfoStructRefSeqDif", no_init)
.add_property("details", make_function(&MMCifInfoStructRefSeqDif::GetDetails,
return_value_policy<copy_const_reference>()))
.add_property("seq_rnum", &MMCifInfoStructRefSeqDif::GetSeqRNum)
.add_property("db_rnum", &MMCifInfoStructRefSeqDif::GetDBRNum)
;
typedef std::pair<int, int> IntPair;
to_python_converter<IntPair, PairToTupleConverter<int, int> >();
typedef std::vector<IntPair> VectorIntPair;
class_<VectorIntPair>("VectorIntPair", init<>())
.def(vector_indexing_suite<VectorIntPair, true>())
;
class_<MMCifInfoBioUnit>("MMCifInfoBioUnit", init<>())
.def("SetDetails", &MMCifInfoBioUnit::SetDetails)
.def("GetDetails", &MMCifInfoBioUnit::GetDetails)
.def("AddChain", &MMCifInfoBioUnit::AddChain)
.def("SetChainList", &MMCifInfoBioUnit::SetChainList)
.def("GetChainList", make_function(&MMCifInfoBioUnit::GetChainList,
return_value_policy<copy_const_reference>()))
.def("GetChainIntervalList",
make_function(&MMCifInfoBioUnit::GetChainIntervalList,
return_value_policy<copy_const_reference>()))
.def("AddOperations", &MMCifInfoBioUnit::AddOperations)
.def("GetOperations", make_function(&MMCifInfoBioUnit::GetOperations,
return_value_policy<copy_const_reference>()))
.def("GetOperationsIntervalList",
make_function(&MMCifInfoBioUnit::GetOperationsIntervalList,
return_value_policy<copy_const_reference>()))
.def("SetID", &MMCifInfoBioUnit::SetID)
.def("GetID", &MMCifInfoBioUnit::GetID)
.add_property("details", &MMCifInfoBioUnit::GetDetails,
&MMCifInfoBioUnit::SetDetails)
.add_property("chains", make_function(&MMCifInfoBioUnit::GetChainList,
return_value_policy<copy_const_reference>()))
.add_property("chainintervalls", make_function(
&MMCifInfoBioUnit::GetChainIntervalList,
return_value_policy<copy_const_reference>()))
.add_property("operations", make_function(&MMCifInfoBioUnit::GetOperations,
return_value_policy<copy_const_reference>())) .add_property("operationsintervalls", make_function(
&MMCifInfoBioUnit::GetOperationsIntervalList,
return_value_policy<copy_const_reference>()))
.add_property("id", &MMCifInfoBioUnit::GetID, &MMCifInfoBioUnit::SetID)
;
class_<MMCifInfoStructRefs>("MMCifInfoStructRefs", init<>())
.def(vector_indexing_suite<MMCifInfoStructRefs, true>())
;
class_<MMCifInfoStructRefSeqs>("MMCifInfoStructRefSeqs", init<>())
.def(vector_indexing_suite<MMCifInfoStructRefSeqs, true>())
;
class_<MMCifInfoStructRefSeqDifs>("MMCifInfoStructRefSeqDifs", init<>())
.def(vector_indexing_suite<MMCifInfoStructRefSeqDifs, true>())
;
typedef std::vector<MMCifInfoBioUnit> MMCifInfoBioUnitList;
class_<std::vector<MMCifInfoBioUnit> >("MMCifInfoBioUnitList", init<>())
.def(vector_indexing_suite<std::vector<MMCifInfoBioUnit> >())
;
class_<MMCifInfoStructDetails>("MMCifInfoStructDetails", init<>())
.def("SetEntryID", &MMCifInfoStructDetails::SetEntryID)
.def("GetEntryID", &MMCifInfoStructDetails::GetEntryID)
.def("SetTitle", &MMCifInfoStructDetails::SetTitle)
.def("GetTitle", &MMCifInfoStructDetails::GetTitle)
.def("SetCASPFlag", &MMCifInfoStructDetails::SetCASPFlag)
.def("GetCASPFlag", &MMCifInfoStructDetails::GetCASPFlag)
.def("SetDescriptor", &MMCifInfoStructDetails::SetDescriptor)
.def("GetDescriptor", &MMCifInfoStructDetails::GetDescriptor)
.def("SetMass", &MMCifInfoStructDetails::SetMass)
.def("GetMass", &MMCifInfoStructDetails::GetMass)
.def("SetMassMethod", &MMCifInfoStructDetails::SetMassMethod)
.def("GetMassMethod", &MMCifInfoStructDetails::GetMassMethod)
.def("SetModelDetails", &MMCifInfoStructDetails::SetModelDetails)
.def("GetModelDetails", &MMCifInfoStructDetails::GetModelDetails)
.def("SetModelTypeDetails", &MMCifInfoStructDetails::SetModelTypeDetails)
.def("GetModelTypeDetails", &MMCifInfoStructDetails::GetModelTypeDetails)
.add_property("entry_id", &MMCifInfoStructDetails::GetEntryID,
&MMCifInfoStructDetails::SetEntryID)
.add_property("title", &MMCifInfoStructDetails::GetTitle,
&MMCifInfoStructDetails::SetTitle)
.add_property("casp_flag", &MMCifInfoStructDetails::GetCASPFlag,
&MMCifInfoStructDetails::SetCASPFlag)
.add_property("descriptor", &MMCifInfoStructDetails::GetDescriptor,
&MMCifInfoStructDetails::SetDescriptor)
.add_property("mass", &MMCifInfoStructDetails::GetMass,
&MMCifInfoStructDetails::SetMass)
.add_property("mass_method", &MMCifInfoStructDetails::GetMassMethod,
&MMCifInfoStructDetails::SetMassMethod)
.add_property("model_details", &MMCifInfoStructDetails::GetModelDetails,
&MMCifInfoStructDetails::SetModelDetails)
.add_property("model_type_details",
&MMCifInfoStructDetails::GetModelTypeDetails,
&MMCifInfoStructDetails::SetModelTypeDetails)
;
class_<MMCifInfoObsolete>("MMCifInfoObsolete", init<>())
.def("SetDate", &MMCifInfoObsolete::SetDate)
.def("GetDate", &MMCifInfoObsolete::GetDate)
.def("SetID", &MMCifInfoObsolete::SetID)
.def("GetID", &MMCifInfoObsolete::GetID)
.def("SetPDBID", &MMCifInfoObsolete::SetPDBID)
.def("GetPDBID", &MMCifInfoObsolete::GetPDBID)
.def("SetReplacedPDBID", &MMCifInfoObsolete::SetReplacedPDBID)
.def("GetReplacedPDBID", &MMCifInfoObsolete::GetReplacedPDBID)
.add_property("date", &MMCifInfoObsolete::GetDate,
&MMCifInfoObsolete::SetDate)
.add_property("id", &MMCifInfoObsolete::GetID,
&MMCifInfoObsolete::SetID)
.add_property("pdb_id", &MMCifInfoObsolete::GetPDBID, &MMCifInfoObsolete::SetPDBID)
.add_property("replace_pdb_id", &MMCifInfoObsolete::GetReplacedPDBID,
&MMCifInfoObsolete::SetReplacedPDBID)
;
class_<MMCifInfoRevisions>("MMCifInfoRevisions", init<>())
.def("SetDateOriginal", &MMCifInfoRevisions::SetDateOriginal)
.def("GetDateOriginal", &MMCifInfoRevisions::GetDateOriginal)
.def("AddRevision", &MMCifInfoRevisions::AddRevision)
.def("GetSize", &MMCifInfoRevisions::GetSize)
.def("GetDate", &MMCifInfoRevisions::GetDate)
.def("GetNum", &MMCifInfoRevisions::GetNum)
.def("GetStatus", &MMCifInfoRevisions::GetStatus)
.def("GetLastDate", &MMCifInfoRevisions::GetLastDate)
.def("GetFirstRelease", &MMCifInfoRevisions::GetFirstRelease)
.add_property("date_original", &MMCifInfoRevisions::GetDateOriginal,
&MMCifInfoRevisions::SetDateOriginal)
.add_property("first_release", &MMCifInfoRevisions::GetFirstRelease)
;
class_<MMCifInfo>("MMCifInfo", init<>())
.def("AddCitation", &MMCifInfo::AddCitation)
.def("GetCitations", make_function(&MMCifInfo::GetCitations,
return_value_policy<copy_const_reference>()))
.def("AddBioUnit", &MMCifInfo::AddBioUnit)
.def("GetBioUnits", make_function(&MMCifInfo::GetBioUnits,
return_value_policy<copy_const_reference>()))
.def("SetMethod", &MMCifInfo::SetMethod)
.def("GetMethod", &MMCifInfo::GetMethod)
.def("SetResolution", &MMCifInfo::SetResolution)
.def("GetResolution", &MMCifInfo::GetResolution)
.def("AddAuthorsToCitation", &MMCifInfo::AddAuthorsToCitation)
.def("AddOperation", &MMCifInfo::AddOperation)
.def("GetOperations", make_function(&MMCifInfo::GetOperations,
return_value_policy<copy_const_reference>()))
.def("SetStructDetails", &MMCifInfo::SetStructDetails)
.def("GetStructDetails", &MMCifInfo::GetStructDetails)
.def("SetObsoleteInfo", &MMCifInfo::SetObsoleteInfo)
.def("GetObsoleteInfo", &MMCifInfo::GetObsoleteInfo)
.def("AddMMCifPDBChainTr", &MMCifInfo::AddMMCifPDBChainTr)
.def("GetMMCifPDBChainTr", &MMCifInfo::GetMMCifPDBChainTr)
.def("AddPDBMMCifChainTr", &MMCifInfo::AddPDBMMCifChainTr)
.def("GetPDBMMCifChainTr", &MMCifInfo::GetPDBMMCifChainTr)
.def("SetRevisionsDateOriginal", &MMCifInfo::SetRevisionsDateOriginal)
.def("AddRevision", &MMCifInfo::AddRevision)
.def("GetRevisions", &MMCifInfo::GetRevisions)
.add_property("citations", make_function(&MMCifInfo::GetCitations,
return_value_policy<copy_const_reference>()))
.add_property("biounits", make_function(&MMCifInfo::GetBioUnits,
return_value_policy<copy_const_reference>()))
.add_property("method", &MMCifInfo::GetMethod, &MMCifInfo::SetMethod)
.add_property("resolution", &MMCifInfo::GetResolution,
&MMCifInfo::SetResolution)
.add_property("operations", make_function(&MMCifInfo::GetOperations,
return_value_policy<copy_const_reference>()))
.add_property("struct_details", &MMCifInfo::GetStructDetails,
&MMCifInfo::SetStructDetails)
.add_property("struct_refs", make_function(&MMCifInfo::GetStructRefs,
return_value_policy<copy_const_reference>()))
.add_property("obsolete", &MMCifInfo::GetObsoleteInfo,
&MMCifInfo::SetObsoleteInfo)
.add_property("revisions", &MMCifInfo::GetRevisions)
;
}