Class monomer

Inheritance Relationships

Base Type

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.

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.