rdkit/Code/GraphMol/MonomerInfo.h

//
//  Copyright (C) 2013 Greg Landrum
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
/*! \file MonomerInfo.h

  \brief Defines Monomer information classes

*/  
#ifndef _RD_MONOMERINFO_H
#define _RD_MONOMERINFO_H

#include <string>
#include <boost/shared_ptr.hpp>

namespace RDKit{

  //! The abstract base class for atom-level monomer info
  class AtomMonomerInfo {
  public:
    typedef enum {
      UNKNOWN=0,
      PDBRESIDUE,
      OTHER
    } AtomMonomerType;

    virtual ~AtomMonomerInfo() {};

    AtomMonomerInfo() : d_monomerType(UNKNOWN), d_name("") {};
    AtomMonomerInfo(AtomMonomerType typ,const std::string &nm="") : d_monomerType(typ), d_name(nm)  {};
    AtomMonomerInfo(const AtomMonomerInfo &other) : d_monomerType(other.d_monomerType),d_name(other.d_name)  {};
    
    const std::string & getName() const { return d_name; };
    void setName(const std::string &nm) { d_name=nm; };
    AtomMonomerType getMonomerType() const { return d_monomerType; };
    void setMonomerType(AtomMonomerType typ) { d_monomerType=typ; };

    virtual AtomMonomerInfo *copy() const {
      return new AtomMonomerInfo(*this);
    }
  private:
    AtomMonomerType d_monomerType;
    std::string d_name;
  };

  //! Captures atom-level information about peptide residues
  class AtomPDBResidueInfo : public AtomMonomerInfo {
  public:
    AtomPDBResidueInfo() : AtomMonomerInfo(PDBRESIDUE) {};
    AtomPDBResidueInfo(const AtomPDBResidueInfo &other) : AtomMonomerInfo(other),
                                                          d_serialNumber(other.d_serialNumber),
                                                          d_altLoc(other.d_altLoc),
                                                          d_residueName(other.d_residueName),
                                                          d_residueNumber(other.d_residueNumber),
                                                          d_chainId(other.d_chainId),
                                                          d_insertionCode(other.d_insertionCode),
                                                          d_occupancy(other.d_occupancy),
                                                          d_tempFactor(other.d_tempFactor),
                                                          df_heteroAtom(other.df_heteroAtom),
                                                          d_secondaryStructure(other.d_secondaryStructure),
                                                          d_segmentNumber(other.d_segmentNumber){};

    AtomPDBResidueInfo(std::string atomName,
                       int serialNumber=0,
                       std::string altLoc="",
                       std::string residueName="",
                       int residueNumber=0,
                       std::string chainId="",
                       std::string insertionCode="",
                       double occupancy=1.0,
                       double tempFactor=0.0,
                       bool isHeteroAtom=false,
                       unsigned int secondaryStructure=0,
                       unsigned int segmentNumber=0 ) :  AtomMonomerInfo(PDBRESIDUE,atomName),
                                                         d_serialNumber(serialNumber),
                                                         d_altLoc(altLoc),
                                                         d_residueName(residueName),
                                                         d_residueNumber(residueNumber),
                                                         d_chainId(chainId),
                                                         d_insertionCode(insertionCode),
                                                         d_occupancy(occupancy),
                                                         d_tempFactor(tempFactor),
                                                         df_heteroAtom(isHeteroAtom),
                                                         d_secondaryStructure(secondaryStructure),
                                                         d_segmentNumber(segmentNumber) {};
    
    int getSerialNumber() const { return d_serialNumber; };
    void setSerialNumber(int val) { d_serialNumber=val; };
    const std::string &getAltLoc() const { return d_altLoc; };
    void setAltLoc(const std::string &val) { d_altLoc=val; };
    const std::string &getResidueName() const { return d_residueName; };
    void setResidueName(const std::string &val) { d_residueName=val; };
    int getResidueNumber() const { return d_residueNumber; };
    void setResidueNumber(int val) { d_residueNumber=val; };
    const std::string &getChainId() const { return d_chainId; };
    void setChainId(const std::string &val) { d_chainId=val; };
    const std::string &getInsertionCode() const { return d_insertionCode; };
    void setInsertionCode(const std::string &val) { d_insertionCode=val; };
    double getOccupancy() const { return d_occupancy; };
    void setOccupancy(double val) { d_occupancy=val; };
    double getTempFactor() const { return d_tempFactor; };
    void setTempFactor(double val) { d_tempFactor=val; };
    bool getIsHeteroAtom() const { return df_heteroAtom; };
    void setIsHeteroAtom(bool val) { df_heteroAtom=val; };
    unsigned int getSecondaryStructure() const {return d_secondaryStructure;};
    void setSecondaryStructure(unsigned int val) { d_secondaryStructure=val; };
    unsigned int getSegmentNumber() const {return d_segmentNumber;};
    void setSegmentNumber(unsigned int val) { d_segmentNumber=val; };
    
    
    AtomMonomerInfo *copy() const {
      return static_cast<AtomMonomerInfo *>(new AtomPDBResidueInfo(*this));
    }
    
  private:
    // the fields here are from the PDB definition 
    // (http://www.wwpdb.org/documentation/format33/sect9.html#ATOM) [9 Aug, 2013]
    // element and charge are not present since the atom itself stores that information
    unsigned int d_serialNumber;
    std::string d_altLoc;
    std::string d_residueName;
    int d_residueNumber;
    std::string d_chainId;
    std::string d_insertionCode;
    double d_occupancy;
    double d_tempFactor;
    // additional, non-PDB fields:
    bool df_heteroAtom;  // is this from a HETATM record?
    unsigned int d_secondaryStructure;
    unsigned int d_segmentNumber;

  };
    
};
//! allows AtomPDBResidueInfo objects to be dumped to streams
std::ostream & operator<<(std::ostream& target, const RDKit::AtomPDBResidueInfo &apri);

#endif