Parameter files

class mdk::param::Parameters

A POD representing the parameters from the parameter file. Arguably the legacy file could be split so that everything wouldn’t be in one structure.

Public Types

using Coeffs = std::vector<double>

template<typename T>
using PerPTData = std::unordered_map<PairType, T>

template<typename T>
using PerAcidData = std::unordered_map<AminoAcid, T>

template<typename T>
using PerPairData = std::unordered_map<std::pair<AminoAcid, AminoAcid>, T>

Public Functions

Parameters()

Public Members

Coeffs defAngleParams

“Default” angle parameters. These are I assume for the simplified angle potential (option lsimpang).

PerPTData<Coeffs> angleParams

A set of bond angle parameters (for heurestic potential) for each pair of types of residues i, i+1 in a triple (i-1, i, i+1).

PerPTData<Coeffs> dihedralParams

A set of dihedral angle parameters (for heurestic potential) for each pair of types of residues i-1, i in a quadruple (i-2, i-1, i, i+1).

PerAcidData<SpecificityParams> specificity

Specificity parameters for every amino acid type.

PerAcidData<double> radius

Radii of amino acids (for use in non-full-atomic derivation of a contact map from the native structure).

PerPairData<double> pairwiseMinDist

A maximum in a distribution of sidechain-sidechain contacts between two given amino acids.

std::optional<PerPairData<double>> mjMatrix

An optional MJ matrix of Lennard-Jones potential depths depending on the amino acid types in the pair.

struct SpecificityParams

Specificity parameters POD.

Public Members

Polarization polarization

Polarization of an amino acid.

int maxSidechain

Maximum number of sidechain contacts an amino acid can form.

int maxHydrophobicSS

Maximum number of sidechain contacts an amino acid can form with hydrophobic amino acids.

int maxPolarSS

Maximum number of sidechain contacts an amino acid can form with polar amino acids.

class mdk::param::LegacyParser

A parser of parameter files in the legacy format (as described in legacy README.txt).

Public Functions

Parameters read(std::istream &is)

Read parameter file from a stream.

Parameters

is – Input stream wherefrom to read the contact map

Returns

Parsed parameter file.

std::ostream &write(std::ostream &os, Parameters const &data)

Write parameter file to a stream.

Parameters

• os – Output stream whereto to write the contact map

• data – Parameter file to write

Returns

os