/usr/include/BALL/STRUCTURE/peptideBuilder.h is in libball1.4-dev 1.4.1+20111206-3.
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//
#ifndef BALL_STRUCTURE_PEPTIDEBUILDER_H
#define BALL_STRUCTURE_PEPTIDEBUILDER_H
#ifndef BALL_STRUCTURE_PEPTIDES_H
# include <BALL/STRUCTURE/peptides.h>
#endif
namespace BALL
{
class FragmentDB;
namespace Peptides
{
/** This class represents one amino acid in the sequence.
\ingroup StructurePeptideBuilder
*/
class BALL_EXPORT AminoAcidDescriptor
{
public:
/** Default constructor.
*/
AminoAcidDescriptor();
/** Detailed constructor. Here, type is considered to be
* either a three - letter or a one letter string for the
* amino acid type, phi is the torsion angle phi, psi is
* the psi torsion angle and omega is the angle of the peptide
* bond. By default, a standard alpha-helical geometry is constructed.
*/
AminoAcidDescriptor(const String& type, const Angle& phi=Angle(-47.,false),
const Angle& psi=Angle(-58.,false), const Angle& omega=Angle(180.,false));
/// Default angles: sheet ????
/** Destructor.
*/
virtual ~AminoAcidDescriptor();
/** copy constructor
*/
AminoAcidDescriptor(const AminoAcidDescriptor& aad);
/** Set the type of the amino acid. type is considered to be a
* one - or three letter code.
*/
void setAminoAcidType(const String& type);
/** Set the torsion angle phi.
*/
void setPhi(const Angle& phi);
/** Set the torsion angle psi.
*/
void setPsi(const Angle& psi);
/** Set the peptide bond angle omega.
*/
void setOmega(const Angle& omega);
/** Returns the type of this amino acid.
*/
const String& getType() const;
/** Returns the torsion angle phi.
*/
const Angle& getPhi() const;
/** Returns the torsion angle psi.
*/
const Angle& getPsi() const;
/** Returns the angle of the peptide bond omega.
*/
const Angle& getOmega() const;
protected:
String type_;
Angle phi_;
Angle psi_;
Angle omega_;
};
/** Build a Peptide from a sequence and the corresponing angles.
Dont forget to call setFragmentDB() before using this class.
\ingroup StructurePeptideBuilder
*/
class BALL_EXPORT PeptideBuilder
{
public:
/** Default constructor.
*/
PeptideBuilder();
/** Detailed constructor. This constructor takes a vector of
* AminoAcidDescriptors and prepares everything for the construction
* process.
*/
PeptideBuilder(const std::vector<AminoAcidDescriptor>& sequence);
/** Construct a peptide from a one-letter code sequence.
*/
PeptideBuilder(const String& sequence, const Angle& phi = Angle(-47., false),
const Angle& psi = Angle(-58., false), const Angle& omega = Angle(180., false));
/** copy constructor
*/
PeptideBuilder(const PeptideBuilder& pc);
/** Destructor.
*/
virtual ~PeptideBuilder();
/** Adds another amino acid to the sequence.
*/
void addAminoAcid(const String& type, const Angle& phi=Angle(-47.,false),
const Angle& psi=Angle(-58.,false), const Angle& omega=Angle(180.,false));
// Sheet angles ???
/** Adds another amino acid to the sequence.
*/
void addAminoAcid(const AminoAcidDescriptor& aad);
/** Sets the name of the chain.
*/
void setChainName(const String& name);
/** Returns the name of the chain.
*/
const String& getChainName() const;
/** Sets the name of the protein.
*/
void setProteinName(const String& name);
/** Returns the name of the protein.
*/
const String& getProteinName() const;
/** Constructs the peptide and returns it.
*/
Protein* construct();
///
void setFragmentDB(const FragmentDB* db)
;
///
const FragmentDB* getFragmentDB() const
;
protected:
std::vector<AminoAcidDescriptor> sequence_;
String chainname_;
String proteinname_;
/// The proline flag
bool is_proline_;
FragmentDB* fragment_db_;
/** some helper functions for the construction of the residue; for internal use only
* omega is not yet implemented
*/
Residue* createResidue_(const String& type, const int id);
void insert_(Residue& resnew, Residue& resold);
void transform_(const Angle& phi, const Angle& psi, Residue& resold, Residue& resnew);
void peptide_(Residue& resold, Residue& resnew);
void setOmega_(Residue& resold, Residue& residue, const Angle& omega);
PDBAtom* getAtomByName_(Residue& res, const String& name);
};
} // namespace Peptides
} // namespace BALL
#endif // BALL_STRUCTURE_PEPTIDEBUILDER_H
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