Class monomer

Defined in File model.hpp

Inheritance Relationships

Base Type

public cif::mm::residue (Class residue)

Class Documentation

class monomer : public cif::mm::residue 

a monomer models a single residue in a protein chain

Public Functions

monomer(const monomer &rhs) = delete

monomer &operator=(const monomer &rhs) = delete

monomer(monomer &&rhs): Move constructor.

monomer &operator=(monomer &&rhs): Move assignment operator.

monomer(const polymer &polymer, std::size_t index, int seqID, const std::string &authSeqID, const std::string &pdbInsCode, const std::string &compoundID): constructor with actual values

bool is_first_in_chain() const: Return if this residue is the first residue in the chain.

bool is_last_in_chain() const: Return if this residue is the last residue in the chain.

bool has_alpha() const: Return if a alpha value can be calculated (depends on location in chain)

bool has_kappa() const: Return if a kappa value can be calculated (depends on location in chain)

float phi() const: Return the phi value for this residue.

float psi() const: Return the psi value for this residue.

float alpha() const: Return the alpha value for this residue.

float kappa() const: Return the kappa value for this residue.

float tco() const: Return the tco value for this residue.

float omega() const: Return the omega value for this residue.

std::size_t nr_of_chis() const: Return how many torsion angles can be calculated.

float chi(std::size_t i) const: Return torsion angle i.

bool is_cis() const: Return true if this residue is in a cis conformation.

bool is_complete() const: Returns true if the four atoms C, CA, N and O are present.

bool has_alternate_backbone_atoms() const: Returns true if any of the backbone atoms has an alternate.

inline atom CAlpha() const: Return the CAlpha atom.

inline atom C() const: Return the C atom.

inline atom N() const: Return the N atom.

inline atom O() const: Return the O atom.

inline atom H() const: Return the H atom.

inline bool is_bonded_to(const monomer &rhs) const: Return true if this monomer is bonded to monomer rhs.

float chiral_volume() const: Return the chiral volume, only for LEU and VAL.

inline bool operator==(const monomer &rhs) const: Compare this monomer with rhs.

virtual atom create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation) override

Create a new atom and add it to the list.

Returns: newly created atom

Public Static Functions

static bool are_bonded(const monomer &a, const monomer &b, float errorMargin = 0.5f)

Return true if the distance between the CA atoms of the two monomers a and b are within the expected range with an error margin of errorMargin.

The expected distance is 3.0 ångström for a cis conformation and 3.8 ångström for trans.

static bool is_cis(const monomer &a, const monomer &b): Return true if the bond between a and b is cis.

static float omega(const monomer &a, const monomer &b): Return the omega angle between a and b.