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peptideBuilder.h
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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#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
{
class BALL_EXPORT AminoAcidDescriptor
{
public:
AminoAcidDescriptor();
AminoAcidDescriptor(const String& type, const Angle& phi=Angle(-47.,false),
const Angle& psi=Angle(-58.,false), const Angle& omega=Angle(180.,false));
virtual ~AminoAcidDescriptor();
AminoAcidDescriptor(const AminoAcidDescriptor& aad);
void setAminoAcidType(const String& type);
void setPhi(const Angle& phi);
void setPsi(const Angle& psi);
void setOmega(const Angle& omega);
const String& getType() const;
const Angle& getPhi() const;
const Angle& getPsi() const;
const Angle& getOmega() const;
protected:
String type_;
Angle phi_;
Angle psi_;
Angle omega_;
};
class BALL_EXPORT PeptideBuilder
{
public:
PeptideBuilder();
PeptideBuilder(const std::vector<AminoAcidDescriptor>& sequence);
PeptideBuilder(const String& sequence, const Angle& phi = Angle(-47., false),
const Angle& psi = Angle(-58., false), const Angle& omega = Angle(180., false));
PeptideBuilder(const PeptideBuilder& pc);
virtual ~PeptideBuilder();
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 ???
void addAminoAcid(const AminoAcidDescriptor& aad);
void setChainName(const String& name);
const String& getChainName() const;
void setProteinName(const String& name);
const String& getProteinName() const;
Protein* construct();
void setFragmentDB(const FragmentDB* db)
;
const FragmentDB* getFragmentDB() const
;
protected:
std::vector<AminoAcidDescriptor> sequence_;
String chainname_;
String proteinname_;
bool is_proline_;
FragmentDB* fragment_db_;
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
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
db
db
Definition GAFFTypeProcessor.h:74
BALL::FragmentDB
Definition fragmentDB.h:45
BALL::PDBAtom
Definition PDBAtom.h:40
BALL::Peptides::AminoAcidDescriptor
Definition peptideBuilder.h:22
BALL::Peptides::AminoAcidDescriptor::phi_
Angle phi_
Definition peptideBuilder.h:83
BALL::Peptides::AminoAcidDescriptor::~AminoAcidDescriptor
virtual ~AminoAcidDescriptor()
Default angles: sheet ????
BALL::Peptides::AminoAcidDescriptor::getType
const String & getType() const
BALL::Peptides::AminoAcidDescriptor::AminoAcidDescriptor
AminoAcidDescriptor()
BALL::Peptides::AminoAcidDescriptor::getOmega
const Angle & getOmega() const
BALL::Peptides::AminoAcidDescriptor::omega_
Angle omega_
Definition peptideBuilder.h:85
BALL::Peptides::AminoAcidDescriptor::setOmega
void setOmega(const Angle &omega)
BALL::Peptides::AminoAcidDescriptor::getPhi
const Angle & getPhi() const
BALL::Peptides::AminoAcidDescriptor::setPhi
void setPhi(const Angle &phi)
BALL::Peptides::AminoAcidDescriptor::type_
String type_
Definition peptideBuilder.h:82
BALL::Peptides::AminoAcidDescriptor::AminoAcidDescriptor
AminoAcidDescriptor(const String &type, const Angle &phi=Angle(-47., false), const Angle &psi=Angle(-58., false), const Angle &omega=Angle(180., false))
BALL::Peptides::AminoAcidDescriptor::AminoAcidDescriptor
AminoAcidDescriptor(const AminoAcidDescriptor &aad)
BALL::Peptides::AminoAcidDescriptor::setAminoAcidType
void setAminoAcidType(const String &type)
BALL::Peptides::AminoAcidDescriptor::setPsi
void setPsi(const Angle &psi)
BALL::Peptides::AminoAcidDescriptor::getPsi
const Angle & getPsi() const
BALL::Peptides::AminoAcidDescriptor::psi_
Angle psi_
Definition peptideBuilder.h:84
BALL::Peptides::PeptideBuilder::getAtomByName_
PDBAtom * getAtomByName_(Residue &res, const String &name)
BALL::Peptides::PeptideBuilder::setFragmentDB
void setFragmentDB(const FragmentDB *db)
BALL::Peptides::PeptideBuilder::proteinname_
String proteinname_
Definition peptideBuilder.h:160
BALL::Peptides::PeptideBuilder::PeptideBuilder
PeptideBuilder(const String &sequence, const Angle &phi=Angle(-47., false), const Angle &psi=Angle(-58., false), const Angle &omega=Angle(180., false))
BALL::Peptides::PeptideBuilder::insert_
void insert_(Residue &resnew, Residue &resold)
BALL::Peptides::PeptideBuilder::PeptideBuilder
PeptideBuilder(const std::vector< AminoAcidDescriptor > &sequence)
BALL::Peptides::PeptideBuilder::addAminoAcid
void addAminoAcid(const String &type, const Angle &phi=Angle(-47., false), const Angle &psi=Angle(-58., false), const Angle &omega=Angle(180., false))
BALL::Peptides::PeptideBuilder::construct
Protein * construct()
BALL::Peptides::PeptideBuilder::~PeptideBuilder
virtual ~PeptideBuilder()
BALL::Peptides::PeptideBuilder::PeptideBuilder
PeptideBuilder()
BALL::Peptides::PeptideBuilder::addAminoAcid
void addAminoAcid(const AminoAcidDescriptor &aad)
BALL::Peptides::PeptideBuilder::setOmega_
void setOmega_(Residue &resold, Residue &residue, const Angle &omega)
BALL::Peptides::PeptideBuilder::peptide_
void peptide_(Residue &resold, Residue &resnew)
BALL::Peptides::PeptideBuilder::getProteinName
const String & getProteinName() const
BALL::Peptides::PeptideBuilder::is_proline_
bool is_proline_
The proline flag.
Definition peptideBuilder.h:163
BALL::Peptides::PeptideBuilder::setProteinName
void setProteinName(const String &name)
BALL::Peptides::PeptideBuilder::chainname_
String chainname_
Definition peptideBuilder.h:159
BALL::Peptides::PeptideBuilder::sequence_
std::vector< AminoAcidDescriptor > sequence_
Definition peptideBuilder.h:158
BALL::Peptides::PeptideBuilder::getFragmentDB
const FragmentDB * getFragmentDB() const
BALL::Peptides::PeptideBuilder::setChainName
void setChainName(const String &name)
BALL::Peptides::PeptideBuilder::transform_
void transform_(const Angle &phi, const Angle &psi, Residue &resold, Residue &resnew)
BALL::Peptides::PeptideBuilder::createResidue_
Residue * createResidue_(const String &type, const int id)
BALL::Peptides::PeptideBuilder::PeptideBuilder
PeptideBuilder(const PeptideBuilder &pc)
BALL::Peptides::PeptideBuilder::fragment_db_
FragmentDB * fragment_db_
Definition peptideBuilder.h:164
BALL::Peptides::PeptideBuilder::getChainName
const String & getChainName() const
BALL::Protein
Definition protein.h:30
BALL::Residue
Definition residue.h:38
BALL::String
Definition string.h:57
BALL::Peptides
Definition peptideBuilder.h:17
BALL
Definition constants.h:13
BALL::Angle
TAngle< float > Angle
Definition angle.h:697
peptides.h