| addAminoAcid(const String &type, const Angle &phi=Angle(-47., false), const Angle &psi=Angle(-58., false), const Angle &omega=Angle(180., false)) | Peptides::PeptideBuilder | |
| addAminoAcid(const AminoAcidDescriptor &aad) | Peptides::PeptideBuilder | |
| chainname_ (defined in Peptides::PeptideBuilder) | Peptides::PeptideBuilder | [protected] |
| construct() | Peptides::PeptideBuilder | |
| createResidue_(const String &type, const int id) | Peptides::PeptideBuilder | [protected] |
| fragment_db_ (defined in Peptides::PeptideBuilder) | Peptides::PeptideBuilder | [protected] |
| getAtomByName_(Residue &res, const String &name) (defined in Peptides::PeptideBuilder) | Peptides::PeptideBuilder | [protected] |
| getChainName() const | Peptides::PeptideBuilder | |
| getFragmentDB() const (defined in Peptides::PeptideBuilder) | Peptides::PeptideBuilder | |
| getProteinName() const | Peptides::PeptideBuilder | |
| insert_(Residue &resnew, Residue &resold) (defined in Peptides::PeptideBuilder) | Peptides::PeptideBuilder | [protected] |
| is_proline_ | Peptides::PeptideBuilder | [protected] |
| peptide_(Residue &resold, Residue &resnew) (defined in Peptides::PeptideBuilder) | Peptides::PeptideBuilder | [protected] |
| PeptideBuilder() | Peptides::PeptideBuilder | |
| PeptideBuilder(const std::vector< AminoAcidDescriptor > &sequence) | Peptides::PeptideBuilder | |
| PeptideBuilder(const String &sequence, const Angle &phi=Angle(-47., false), const Angle &psi=Angle(-58., false), const Angle &omega=Angle(180., false)) | Peptides::PeptideBuilder | |
| PeptideBuilder(const PeptideBuilder &pc) | Peptides::PeptideBuilder | |
| proteinname_ (defined in Peptides::PeptideBuilder) | Peptides::PeptideBuilder | [protected] |
| sequence_ (defined in Peptides::PeptideBuilder) | Peptides::PeptideBuilder | [protected] |
| setChainName(const String &name) | Peptides::PeptideBuilder | |
| setFragmentDB(const FragmentDB *db) (defined in Peptides::PeptideBuilder) | Peptides::PeptideBuilder | |
| setOmega_(Residue &resold, Residue &residue, const Angle &omega) (defined in Peptides::PeptideBuilder) | Peptides::PeptideBuilder | [protected] |
| setProteinName(const String &name) | Peptides::PeptideBuilder | |
| transform_(const Angle &phi, const Angle &psi, Residue &resold, Residue &resnew) (defined in Peptides::PeptideBuilder) | Peptides::PeptideBuilder | [protected] |
| ~PeptideBuilder() | Peptides::PeptideBuilder | [virtual] |