#include <tyrosine.hh>
Inheritance diagram for prf::Tyrosine:
Additional Inherited Members | |
 Public Member Functions inherited from prf::AminoAcid | |
| Atom & | Nitrogen () |
| Reference to backbone nitrogen. | |
| Atom & | Calpha () |
| Reference to Calpha. | |
| Atom & | Cprime () |
| Reference to C' atom. | |
| Atom & | Hca () |
| Reference to H alpha, or first H attached to C alpha. | |
| Atom & | Cbeta () |
| Reference to C beta. | |
| Atom & | Oc () |
| Reference to O attached to C'. | |
| Atom & | sidechain_atom (int i) |
| Reference to i'th side chain atom. | |
| Atom * | labeled_atom (std::string alabel) |
| Reference to any atom in the amino acid through its PDB label. | |
| Atom & | at (std::string alabel) |
| Look up and return reference to Atom with a certain label. | |
| double | Chi (int i) const |
| Side chain torsional DOF numbered from 0. | |
| double | Phi () const |
| Ramachandran Phi angle about the bond N-CA in the residue. | |
| double | Psi () const |
| Ramachandran Psi angle about the bond CA-C in the residue. | |
| double | Omega () const |
| Peptide bond angle between this and the next residue. | |
| void | Chi (int i, double x) |
| Set side chain torsional DOF. | |
| void | Phi (double x) |
| Set Ramachandran Phi angle. | |
| void | Psi (double x) |
| Set Ramachandran Psi angle. | |
| void | Omega (double x) |
| Set omega angle between this and the next residue. | |
| void | calcPhiPsi (double &phv, double &psv) const |
| Calculate Ramachandran angles from current 3D coordinates. | |
| bool | is_helical () const |
| Do the current backbone angles fall in the helix region ? | |
| bool | is_strand () const |
| Do the current backbone angles fall in the beta strand region ? | |
| void | WritePDB (int &atindx, char ch_id, int aaindx, FILE *fp) |
| Writes into a PDB file. | |
| void | WritePDB2 (int &atindx, char ch_id, int aaindx, FILE *fp) |
| Write PDB with heavy atoms first. | |
| double | get_coord (int i) |
| phi, psi, omega and side chain chi angles | |
| void | set_coord (int i, double x) |
| Assign to i'th DOF in amino acid. | |
| int | n_coord () const |
| 3+number of side chain angles | |
| double | get_dof (int i) |
| True degrees of freedom in the residue. | |
| void | set_dof (int i, double x) |
| Assign to i'th true DOF in amino acid. | |
| int | n_dof () const |
| Number of true degrees of freedom in the residue. | |
| int | rotDof_assign_and_reconstruct (int il, double mgd, int &a0, int &a1) |
| Assign to (sidechain) dof i, and return the range of moved atoms. | |
| int | rotDof_assign (int il, double mgd) |
| Assign to (sidechain) dof i, but don't recalculate any coordinates. | |
| double | get_rotDof (int il) |
| Value of the i'th (sidechain) dof. | |
| void | nodes_reconnect () |
| Reassign atom offsets to the nodes. | |
Detailed Description
Specification of tyrosine side chain. Here we use an MPhenylGroup which creates a phenyl ring, but the atoms attached to the ring carbon atoms could be connected with bonds of different length. This feature is used for the OH group attached to the ring.
The documentation for this class was generated from the following files:
- model/AA/tyrosine.hh
- model/AA/tyrosine.cc