PROFASI
Version 1.5
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#include <histidine.hh>
Additional Inherited Members | |
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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. | |
Specification of histidine side chain, the pentagonal tip is regarded as rigid. It's geometry is treated in the HistidineTip class.