mmcif_info.hh

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//------------------------------------------------------------------------------
// 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 <map>
#include <boost/shared_ptr.hpp>
#include <ost/seq/sequence_list.hh>
#include <ost/geom/geom.hh>
#include <ost/string_ref.hh>
#include <ost/io/module_config.hh>

namespace ost { namespace io {

class DLLEXPORT_OST_IO MMCifInfoStructDetails {
public:
  MMCifInfoStructDetails(): entry_id_(""), title_(""), casp_flag_('\0'),
    descriptor_(""), mass_(0.0), mass_method_(""), model_details_(""),
    model_type_details_("") {};

  void SetEntryID(String id) { entry_id_ = id; }
  String GetEntryID() const { return entry_id_; }

  void SetCASPFlag(char flag) { casp_flag_ = flag; }
  char GetCASPFlag() const { return casp_flag_; }

  void SetDescriptor(String desc) { descriptor_ = desc; }
  String GetDescriptor() const { return descriptor_; }

  void SetMass(Real mass) { mass_ = mass; }
  Real GetMass() const { return mass_; }

  void SetMassMethod(String method) { mass_method_ = method; }
  String GetMassMethod() const { return mass_method_; }

  void SetModelDetails(String desc) { model_details_ = desc; }
  String GetModelDetails() const { return model_details_; }

  void SetModelTypeDetails(String desc) { model_type_details_ = desc; }
  String GetModelTypeDetails() const { return model_type_details_; }

  void SetTitle(String title) { title_ = title; }
  String GetTitle() const { return title_; }

  bool operator==(const MMCifInfoStructDetails& sd) const {
    if (this->entry_id_ != sd.entry_id_) {
      return false;
    }
    if (this->casp_flag_ != sd.casp_flag_) {
      return false;
    }
    if (this->descriptor_ != sd.descriptor_) {
      return false;
    }
    if (this->mass_ != sd.mass_) {
      return false;
    }
    if (this->mass_method_ != sd.mass_method_) {
      return false;
    }
    if (this->model_details_ != sd.model_details_) {
      return false;
    }
    if (this->model_type_details_ != sd.model_type_details_) {
      return false;
    }
    if (this->title_ != sd.title_) {
      return false;
    }

    return true;
  }

  bool operator!=(const MMCifInfoStructDetails& sd) const {
    return !this->operator == (sd);
  }

private:
  String entry_id_;
  String title_;
  char   casp_flag_;
  String descriptor_;
  Real   mass_;
  String mass_method_;
  String model_details_;
  String model_type_details_;
};

class DLLEXPORT_OST_IO MMCifInfoTransOp {
public:
  MMCifInfoTransOp(): id_(""), type_("")
  {
    translation_ = geom::Vec3();
  };

  void SetID(String id) { id_ = id; }
  String GetID() const { return id_; }

  void SetType(String type) { type_ = type; }
  String GetType() const { return type_; }

  void SetVector(Real x, Real y, Real z)
  {
    translation_.SetX(x);
    translation_.SetY(y);
    translation_.SetZ(z);
  }
  geom::Vec3 GetVector() const { return translation_; }

  void SetMatrix(Real i00, Real i01, Real i02,
                 Real i10, Real i11, Real i12,
                 Real i20, Real i21, Real i22)
  {
    rotation_ = geom::Mat3(i00,i01,i02, i10,i11,i12, i20,i21,i22);
  }
  geom::Mat3 GetMatrix() const { return rotation_; }

  bool operator==(const MMCifInfoTransOp& op) const {
    if (this->id_ != op.id_) {
      return false;
    }
    if (this->type_ != op.type_) {
      return false;
    }
    if (this->translation_ != op.translation_) {
      return false;
    }
    if (this->rotation_ != op.rotation_) {
      return false;
    }

    return true;
  }

  bool operator!=(const MMCifInfoTransOp& op) const {
    return !this->operator==(op);
  }

private:
  String id_;              
  String type_;            
  geom::Vec3 translation_; 
  geom::Mat3 rotation_;    
};
typedef boost::shared_ptr<MMCifInfoTransOp> MMCifInfoTransOpPtr;


class DLLEXPORT_OST_IO MMCifInfoBioUnit {
public:
  MMCifInfoBioUnit(): id_(""), details_("") {};

  void Merge(MMCifInfoBioUnit& from);

  void SetID(String id) { id_ = id; }
  String GetID() const { return id_; }

  void SetDetails(String details) { details_ = details; }
  String GetDetails() const { return details_; }

  void SetMethodDetails(String method_details) {
    method_details_ = method_details;
  }
  String GetMethodDetails() const { return method_details_; }

  void AddChain(String chain);

  void SetChainList(std::vector<String> chains);

  const std::vector<String>& GetChainList() const { return chains_; }

  const std::vector<std::pair<int, int> >& GetChainIntervalList()
  {
    return tr_chains_;
  }

  void AddOperations(std::vector<MMCifInfoTransOpPtr> operations);

  const std::vector<std::pair<int, int> >& GetOperationsIntervalList()
  {
    return tr_operations_;
  }

  const std::vector<std::vector<MMCifInfoTransOpPtr> >& GetOperations()
  {
    return operations_;
  }

  bool operator==(const MMCifInfoBioUnit& bu) const {
    if (this->id_ != bu.id_) {
      return false;
    }
    if (this->details_ != bu.details_) {
      return false;
    }
    if (this->chains_ != bu.chains_) {
      return false;
    }
    if (this->tr_chains_ != bu.tr_chains_) {
      return false;
    }
    if (this->tr_operations_ != bu.tr_operations_) {
      return false;
    }
    if (this->operations_.size() == bu.operations_.size()) {
      std::vector<std::vector<MMCifInfoTransOpPtr> >::const_iterator th_ops_it;
      std::vector<std::vector<MMCifInfoTransOpPtr> >::const_iterator bu_ops_it;
      std::vector<MMCifInfoTransOpPtr>::const_iterator th_op_it;
      std::vector<MMCifInfoTransOpPtr>::const_iterator bu_op_it;

      for (th_ops_it = this->operations_.begin(),
             bu_ops_it = bu.operations_.begin();
           th_ops_it != this->operations_.end();
           ++th_ops_it, ++bu_ops_it) {
        if (th_ops_it->size() == bu_ops_it->size()) {
          for (th_op_it = th_ops_it->begin(), bu_op_it = bu_ops_it->begin();
               th_op_it != th_ops_it->end();
               ++th_op_it, ++bu_op_it) {
            if (*th_op_it != *bu_op_it) {
              return false;
            }
          }
        } else {
          return false;
        }
      }
    } else {
      return false;
    }

    return true;
  }

  bool operator!=(const MMCifInfoBioUnit& bu) const {
    return !this->operator==(bu);
  }

private:
  String id_;                  
  String details_;             
  String method_details_;      
  std::vector<String> chains_; 
  std::vector<std::pair<int, int> > tr_chains_; //< chains of a transformation
  std::vector<std::vector<MMCifInfoTransOpPtr> > operations_;
  std::vector<std::pair<int, int> > tr_operations_; //< ops. of a transformation
};

class DLLEXPORT_OST_IO MMCifInfoCitation {
public:
  MMCifInfoCitation(): id_(""), where_(UNKNOWN), cas_(""), published_in_(""),
    volume_(""), page_first_(""), page_last_(""), doi_(""), pubmed_(0),
    year_(0), title_("") {};

  void SetID(String id) { id_ = id; }
  String GetID() const { return id_; }

  void SetCAS(String id) { cas_ = id; }
  String GetCAS() const { return cas_; }

  void SetISBN(String code) { isbn_ = code; }

  String GetISBN() const { return isbn_; }

  void SetPublishedIn(String title) { published_in_ = title; }

  String GetPublishedIn() const { return published_in_; }

  void SetVolume(String volume) { volume_ = volume; }

  String GetVolume() const { return volume_; }

  void SetPageFirst(String first) { page_first_ = first; }

  String GetPageFirst() const { return page_first_; }

  void SetPageLast(String last) { page_last_ = last; }

  String GetPageLast() const { return page_last_; }

  void SetDOI(String doi) { doi_ = doi; }


  String GetDOI() const { return doi_; }

  void SetPubMed(int no) { pubmed_ = no; }

  int GetPubMed() const { return pubmed_; }

  void SetYear(int year) { year_ = year; }


  int GetYear() const { return year_; }


  void SetTitle(String title) { title_ = title; }

  String GetTitle() const { return title_; }

  void SetAuthorList(std::vector<String> list) { authors_ = 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:
  typedef enum {
    JOURNAL,
    BOOK,
    UNKNOWN
  } MMCifInfoCType;

  String              id_;           
  MMCifInfoCType      where_;        
  String              cas_;          
  String              isbn_;         
  String              published_in_; 
  String              volume_;       
  String              page_first_;   
  String              page_last_;    
  String              doi_;          
  int                 pubmed_;       
  int                 year_;         
  String              title_;        
  std::vector<String> authors_;       
};

class DLLEXPORT_OST_IO MMCifInfoObsolete {
public:
  MMCifInfoObsolete(): date_(""), id_(UNKNOWN), pdb_id_(""),
    replaced_pdb_id_("") {};

  void SetDate(String date) { date_ = date; }

  String GetDate() { return date_; }

  void SetID(StringRef type)
  {
    if (type == StringRef("OBSLTE", 6)) {
      id_ = OBSLTE;
    }
    else if (type == StringRef("SPRSDE", 6)) {
      id_ = SPRSDE;
    }
  }

  String GetID()
  {
    if (id_ == OBSLTE) {
      return "Obsolete";
    }
    if (id_ == SPRSDE) {
      return "Supersede";
    }
    return "Unknown";
  }

  void SetPDBID(String id) { pdb_id_ = id; }

  String GetPDBID() { return pdb_id_; }

  void SetReplacedPDBID(String id) { replaced_pdb_id_ = id; }

  String GetReplacedPDBID() { return replaced_pdb_id_; }

private:
  typedef enum {
    OBSLTE,
    SPRSDE,
    UNKNOWN
  } MMCifObsoleteType;

  String date_;            
  MMCifObsoleteType id_;   
  String pdb_id_;          
  String replaced_pdb_id_; 
};

class DLLEXPORT_OST_IO MMCifInfoRevisions {
public:
  MMCifInfoRevisions(): date_original_("?"), first_release_(0) {};

  void SetDateOriginal(String date) { date_original_ = date; }

  String GetDateOriginal() const { return date_original_; }

  void AddRevision(int num, String date, String status)
  {
    if (num_.size() && (num_.back() >= num)) {
      std::stringstream ss;
      ss << "Unique ID of revision has to increase with every revision, "
         << "last was " << num_.back() << ", trying to add " << num;
      throw IOException(ss.str());
    }
    num_.push_back(num);
    date_.push_back(date);
    status_.push_back(status);
    // set first release date if not already occupied
    if (first_release_ == 0) {
      if (status == "full release" || status == "Initial release") {
        first_release_ = status_.size();
      }
    }
  }

  size_t GetSize() const { return num_.size(); }

  String GetDate(size_t i) const { return date_.at(i); }

  int GetNum(size_t i) const { return num_.at(i); }

  String GetStatus(size_t i) const { return status_.at(i); }

  String GetLastDate() const {
    if (date_.empty()) return "?";
    else               return date_.back();
  }

  size_t GetFirstRelease() const
  {
    return first_release_;
  }

private:
  String date_original_;       
  size_t first_release_;          
  std::vector<int> num_;       
  std::vector<String> date_;   
  std::vector<String> status_; 
};


class MMCifInfoStructRef;
class MMCifInfoStructRefSeq;
class MMCifInfoStructRefSeqDif;


typedef boost::shared_ptr<MMCifInfoStructRef> MMCifInfoStructRefPtr;
typedef boost::shared_ptr<MMCifInfoStructRefSeq> MMCifInfoStructRefSeqPtr;
typedef boost::shared_ptr<MMCifInfoStructRefSeqDif> MMCifInfoStructRefSeqDifPtr;

typedef std::vector<MMCifInfoStructRefPtr> MMCifInfoStructRefs;
typedef std::vector<MMCifInfoStructRefSeqPtr> MMCifInfoStructRefSeqs;
typedef std::vector<MMCifInfoStructRefSeqDifPtr> MMCifInfoStructRefSeqDifs;
class DLLEXPORT_OST_IO MMCifInfoStructRef {
public:
  MMCifInfoStructRef(const String& id, const String& ent_id, 
                     const String& db_name, 
                     const String& db_ident, const String& db_access):
    id_(id), ent_id_(ent_id), db_name_(db_name), db_ident_(db_ident), 
    db_access_(db_access)
  { }
  const String& GetID() const { return id_; }
  const String& GetDBName() const { return db_name_; }
  const String& GetDBID() const { return db_ident_; }
  const String& GetEntityID() const { return ent_id_; }
  const String& GetDBAccess() const { return db_access_; }
  MMCifInfoStructRefSeqPtr AddAlignedSeq(const String& align_id, 
                                         const String& chain_name, int seq_begin, 
                                         int seq_end, int db_begin, int db_end);
  MMCifInfoStructRefSeqPtr GetAlignedSeq(const String& align_id) const;
  MMCifInfoStructRefSeqs GetAlignedSeqs() const
  {
    MMCifInfoStructRefSeqs seqs;
    seqs.reserve(seqs_.size());
    for (std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator
         i=seqs_.begin(), e=seqs_.end(); i!=e; ++i) {
      seqs.push_back(i->second);
    }
    return seqs;
  }
private:
  String  id_;
  String  ent_id_;
  String  db_name_;
  String  db_ident_;
  String  db_access_;
  std::map<String, MMCifInfoStructRefSeqPtr> seqs_;
};

class DLLEXPORT_OST_IO MMCifInfoStructRefSeq {
public:
  MMCifInfoStructRefSeq(const String& align_id, const String& chain_name, 
                        int seq_begin, int seq_end, 
                        int db_begin, int db_end):
    id_(align_id), chain_name_(chain_name), 
    seq_begin_(seq_begin), seq_end_(seq_end), db_begin_(db_begin), db_end_(db_end)
  { }

  const String& GetID() const { return id_; }
  const String& GetChainName() const { return chain_name_; }
  int GetSeqBegin() const { return seq_begin_; }
  int GetSeqEnd() const { return seq_end_; }
  int GetDBBegin() const { return db_begin_; }
  int GetDBEnd() const { return db_end_; }
  MMCifInfoStructRefSeqDifPtr AddDif(int seq_num, const String& db_rnum, 
                                     const String& details);
  const std::vector<MMCifInfoStructRefSeqDifPtr>& GetDifs() const { return difs_; }
private:
  String   id_;
  String   chain_name_;
  int      seq_begin_;
  int      seq_end_;
  int      db_begin_;
  int      db_end_;
  std::vector<MMCifInfoStructRefSeqDifPtr> difs_;
};

class DLLEXPORT_OST_IO MMCifInfoStructRefSeqDif {
public:
  MMCifInfoStructRefSeqDif(int seq_rnum, const String& db_rnum, const String& details): 
    seq_rnum_(seq_rnum), db_rnum_(db_rnum), details_(details) {}
  int GetSeqRNum() const { return seq_rnum_;}
  const String& GetDBRNum() const { return db_rnum_; }
  const String& GetDetails() const { return details_; }
private:
  int    seq_rnum_;
  String db_rnum_;
  String details_;
};

class DLLEXPORT_OST_IO MMCifInfo {
public:
  MMCifInfo(): exptl_method_(""), resolution_(0), r_free_(0), r_work_(0) { }

  void AddCitation(MMCifInfoCitation citation) // unit test
  {
    citations_.push_back(citation);
  }

  void AddAuthorsToCitation(StringRef id, std::vector<String> list); //unit test

  const std::vector<MMCifInfoCitation>& GetCitations() const
  {
    return citations_;
  }

  void SetMethod(String method) { exptl_method_ = method; }

  const StringRef GetMethod() const
  { 
    return StringRef(exptl_method_.c_str(), exptl_method_.length());
  }

  void SetResolution(Real res) { resolution_ = res; }

  Real GetResolution() const { return resolution_; }

  void SetRFree(Real r_free) { r_free_ = r_free; }

  Real GetRFree() const { return r_free_; }

  void SetRWork(Real r_work) { r_work_ = r_work; }

  Real GetRWork() const { return r_work_; }

  void AddMMCifPDBChainTr(String cif, String pdb);

  String GetMMCifPDBChainTr(String cif) const;

  void AddPDBMMCifChainTr(String pdb, String cif);

  String GetPDBMMCifChainTr(String pdb) const;

  void AddMMCifEntityIdTr(String cif, String ent_id);

  String GetMMCifEntityIdTr(String cif) const;

  void AddBioUnit(MMCifInfoBioUnit bu);

  const std::vector<MMCifInfoBioUnit>& GetBioUnits() const
  {
    return biounits_;
  }

  void AddOperation(MMCifInfoTransOpPtr op) // unit test
  {
    transops_.push_back(op);
  }

  const std::vector<MMCifInfoTransOpPtr>& GetOperations() const
  {
    return transops_;
  }

  void SetStructDetails(MMCifInfoStructDetails details)
  {
    struct_details_ = details;
  }

  const MMCifInfoStructDetails GetStructDetails() const
  {
    return struct_details_;
  }

  void SetObsoleteInfo(MMCifInfoObsolete obsolete)
  {
    obsolete_ = obsolete;
  }

  MMCifInfoObsolete GetObsoleteInfo() const
  {
    return obsolete_;
  }
  const MMCifInfoStructRefs& GetStructRefs() const { return struct_refs_; }
  void SetStructRefs(const MMCifInfoStructRefs& sr) { struct_refs_=sr; }

  void SetRevisionsDateOriginal(String date)
  {
    // only set once
    if (revisions_.GetDateOriginal() == "?") {
      revisions_.SetDateOriginal(date);
    }
  }

  void AddRevision(int num, String date, String status)
  {
    revisions_.AddRevision(num, date, status);
  }

  MMCifInfoRevisions GetRevisions() const 
  {
    return revisions_;
  }
//protected:

private:
  // members
  String exptl_method_;
  Real resolution_;
  Real r_free_;
  Real r_work_;
  MMCifInfoStructDetails struct_details_;     
  MMCifInfoObsolete obsolete_;                
  MMCifInfoRevisions revisions_;              
  std::vector<MMCifInfoCitation> citations_;  
  std::vector<MMCifInfoBioUnit>  biounits_;   
  std::vector<MMCifInfoTransOpPtr> transops_;
  MMCifInfoStructRefs            struct_refs_;
  std::map<String, String> cif_2_pdb_chain_id_;
  std::map<String, String> pdb_2_cif_chain_id_;
  std::map<String, String> cif_2_entity_id_;
};


}} // ns

#endif