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// SPDX-License-Identifier: LGPL-3.0-or-later
// Author: Kristian Lytje
#include <constants/Constants.h>
#include <constants/vdwTable.h>
#include <utility/StringUtils.h>
#include <io/ExistingFile.h>
#include <stdexcept>
using namespace ausaxs;
namespace ausaxs::constants {
const saxs::detail::SimpleMap<char> name_1symbol_map = std::unordered_map<std::string, char>{
{"glycine", 'G'}, {"alanine", 'A'}, {"valine", 'V'}, {"leucine", 'L'}, {"isoleucine", 'I'}, {"phenylalanine", 'F'}, {"tyrosine", 'Y'},
{"tryptophan", 'W'}, {"aspartic_acid", 'D'}, {"glutamic_acid", 'E'}, {"serine", 'S'}, {"threonine", 'T'}, {"asparagine", 'N'},
{"glutamine", 'Q'}, {"lysine", 'K'}, {"arginine", 'R'}, {"histidine", 'H'}, {"methionine", 'M'}, {"cysteine", 'C'}, {"proline", 'P'}
};
const saxs::detail::SimpleMap<std::string> name_3symbol_map = std::unordered_map<std::string, std::string>{
{"glycine", "GLY"}, {"alanine", "ALA"}, {"valine", "VAL"}, {"leucine", "LEU"}, {"isoleucine", "ILE"}, {"phenylalanine", "PHE"}, {"tyrosine", "TYR"},
{"tryptophan", "TRP"}, {"aspartic_acid", "ASP"}, {"glutamic_acid", "GLU"}, {"serine", "SER"}, {"threonine", "THR"}, {"asparagine", "ASN"},
{"glutamine", "GLN"}, {"lysine", "LYS"}, {"arginine", "ARG"}, {"histidine", "HIS"}, {"methionine", "MET"}, {"cysteine", "CYS"}, {"proline", "PRO"}
};
const saxs::detail::SimpleMap<double> volume::amino_acids = std::unordered_map<std::string, double>{
{"GLY", 66.4}, {"ALA", 91.5}, {"VAL", 141.7}, {"LEU", 167.9}, {"ILE", 168.8}, {"PHE", 203.5}, {"TYR", 203.6}, {"TRP", 237.6},
{"ASP", 113.6}, {"GLU", 140.6}, {"SER", 99.1}, {"THR", 122.1}, {"ASN", 135.2}, {"GLN", 161.1}, {"LYS", 176.2}, {"ARG", 180.8},
{"HIS", 167.3}, {"MET", 170.8}, {"CYS", 105.6}, {"PRO", 129.3}
};
double radius::detail::dummy_radius = 1;
void radius::set_dummy_radius(double radius) {
radius::detail::dummy_radius = radius;
}
std::string symbols::hydrogen = "H";
std::string symbols::carbon = "C";
std::string symbols::nitrogen = "N";
std::string symbols::oxygen = "O";
const saxs::detail::SimpleMap<constants::atom_t> symbols::detail::string_to_atomt_map = std::unordered_map<std::string, constants::atom_t>{
{"H", atom_t::H}, {"He", atom_t::He},
{"Li", atom_t::Li}, {"Be", atom_t::Be}, {"B", atom_t::B}, {"C", atom_t::C}, {"N", atom_t::N}, {"O", atom_t::O}, {"F", atom_t::F}, {"Ne", atom_t::Ne},
{"Na", atom_t::Na}, {"Mg", atom_t::Mg}, {"Al", atom_t::Al}, {"Si", atom_t::Si}, {"P", atom_t::P}, {"S", atom_t::S}, {"Cl", atom_t::Cl}, {"Ar", atom_t::Ar},
{"K", atom_t::K}, {"Ca", atom_t::Ca}, {"Sc", atom_t::Sc}, {"Ti", atom_t::Ti}, {"V", atom_t::V}, {"Cr", atom_t::Cr}, {"Mn", atom_t::Mn}, {"Fe", atom_t::Fe},
{"Co", atom_t::Co}, {"Ni", atom_t::Ni}, {"Cu", atom_t::Cu}, {"Zn", atom_t::Zn}, {"Ga", atom_t::Ga}, {"Ge", atom_t::Ge}, {"As", atom_t::As}, {"Se", atom_t::Se},
{"Br", atom_t::Br}, {"Kr", atom_t::Kr},
{"Rb", atom_t::Rb}, {"Sr", atom_t::Sr}, {"Y", atom_t::Y}, {"Zr", atom_t::Zr}, {"Nb", atom_t::Nb}, {"Mo", atom_t::Mo}, {"Tc", atom_t::Tc}, {"Ru", atom_t::Ru},
{"Rh", atom_t::Rh}, {"Pd", atom_t::Pd}, {"Ag", atom_t::Ag}, {"Cd", atom_t::Cd}, {"In", atom_t::In}, {"Sn", atom_t::Sn}, {"Sb", atom_t::Sb}, {"Te", atom_t::Te},
{"I", atom_t::I}, {"Xe", atom_t::Xe},
{"Cs", atom_t::Cs}, {"Ba", atom_t::Ba}, {"Hf", atom_t::Hf}, {"Ta", atom_t::Ta}, {"W", atom_t::W}, {"Re", atom_t::Re}, {"Os", atom_t::Os}, {"Ir", atom_t::Ir},
{"Pt", atom_t::Pt}, {"Au", atom_t::Au}, {"Tl", atom_t::Tl}, {"Pb", atom_t::Pb}, {"Bi", atom_t::Bi}, {"Po", atom_t::Po},
{"M", atom_t::M}
};
residue::ResidueStorage hydrogen_atoms::residues;
}
constants::atomic_group_t constants::symbols::get_atomic_group(const std::string& residue_name, const std::string& atom_name, constants::atom_t atom_type) {
return hydrogen_atoms::residues.get_atomic_group(residue_name, atom_name, atom_type);
}
constants::atom_t constants::symbols::parse_element_string(const std::string& element_string) {
return constants::symbols::detail::string_to_atomt_map.get(element_string);
}
constants::atomic_group_t constants::symbols::get_atomic_group(constants::atom_t atom_type, unsigned int hydrogens) {
if (hydrogens == 0) {return constants::atomic_group_t::unknown;}
switch (atom_type) {
case constants::atom_t::C:
switch (hydrogens) {
case 1: return constants::atomic_group_t::CH;
case 2: return constants::atomic_group_t::CH2;
case 3: return constants::atomic_group_t::CH3;
default: break;
}
break;
case constants::atom_t::N:
switch (hydrogens) {
case 1: return constants::atomic_group_t::NH;
case 2: return constants::atomic_group_t::NH2;
case 3: return constants::atomic_group_t::NH3;
default: break;
}
break;
case constants::atom_t::O:
switch (hydrogens) {
case 1: return constants::atomic_group_t::OH;
default: break;
}
break;
case constants::atom_t::S:
switch (hydrogens) {
case 1: return constants::atomic_group_t::SH;
default: break;
}
break;
default: break;
}
return constants::atomic_group_t::unknown;
}
unsigned int constants::charge::nuclear::get_charge(atom_t atom) {
switch(atom) {
case atom_t::H: return 1;
case atom_t::He: return 2;
case atom_t::Li: return 3;
case atom_t::Be: return 4;
case atom_t::B: return 5;
case atom_t::C: return 6;
case atom_t::N: return 7;
case atom_t::O: return 8;
case atom_t::F: return 9;
case atom_t::Ne: return 10;
case atom_t::Na: return 11;
case atom_t::Mg: return 12;
case atom_t::Al: return 13;
case atom_t::Si: return 14;
case atom_t::P: return 15;
case atom_t::S: return 16;
case atom_t::Cl: return 17;
case atom_t::Ar: return 18;
case atom_t::K: return 19;
case atom_t::Ca: return 20;
case atom_t::Sc: return 21;
case atom_t::Ti: return 22;
case atom_t::V: return 23;
case atom_t::Cr: return 24;
case atom_t::Mn: return 25;
case atom_t::Fe: return 26;
case atom_t::Co: return 27;
case atom_t::Ni: return 28;
case atom_t::Cu: return 29;
case atom_t::Zn: return 30;
case atom_t::Ga: return 31;
case atom_t::Ge: return 32;
case atom_t::As: return 33;
case atom_t::Se: return 34;
case atom_t::Br: return 35;
case atom_t::Kr: return 36;
case atom_t::Rb: return 37;
case atom_t::Sr: return 38;
case atom_t::Y: return 39;
case atom_t::Zr: return 40;
case atom_t::Nb: return 41;
case atom_t::Mo: return 42;
case atom_t::Tc: return 43;
case atom_t::Ru: return 44;
case atom_t::Rh: return 45;
case atom_t::Pd: return 46;
case atom_t::Ag: return 47;
case atom_t::Cd: return 48;
case atom_t::In: return 49;
case atom_t::Sn: return 50;
case atom_t::Sb: return 51;
case atom_t::Te: return 52;
case atom_t::I: return 53;
case atom_t::Xe: return 54;
case atom_t::Cs: return 55;
case atom_t::Ba: return 56;
case atom_t::Hf: return 72;
case atom_t::Ta: return 73;
case atom_t::W: return 74;
case atom_t::Re: return 75;
case atom_t::Os: return 76;
case atom_t::Ir: return 77;
case atom_t::Pt: return 78;
case atom_t::Au: return 79;
case atom_t::Tl: return 81;
case atom_t::Pb: return 82;
case atom_t::Bi: return 83;
case atom_t::Po: return 84;
case atom_t::M: return 0;
case atom_t::dummy: return 1;
case atom_t::unknown: return 1;
default: throw std::runtime_error("constants::charge::nuclear::get_charge: Unknown atom type \"" + constants::symbols::to_string(atom) + "\"");
}
}
unsigned int constants::charge::ionic::get_charge(atom_t atom) {
switch (atom) {
case atom_t::Ca: return 2;
case atom_t::Cl: return -1;
case atom_t::Zn: return 2;
default: throw std::runtime_error("constants::charge::ionic::get_charge: Unknown atom type \"" + constants::symbols::to_string(atom) + "\"");
}
}
unsigned int constants::valence::get_valence(atom_t atom) {
switch(atom) {
case atom_t::H: return 1;
case atom_t::C: return 4;
case atom_t::N: return 3;
case atom_t::O: return 2;
case atom_t::F: return 1;
case atom_t::Ne: return 0;
case atom_t::S: return 2;
case atom_t::P: return 1;
case atom_t::Cl: return 1;
case atom_t::Fe: return 4;
case atom_t::Se: return 2;
case atom_t::M: return 0;
default: throw std::runtime_error("constants::valence::get_valence: Unknown atom type \"" + constants::symbols::to_string(atom) + "\"");
}
}
double constants::radius::get_vdw_radius(atom_t atom) {
switch(atom) {
case atom_t::H: return vdw::H;
case atom_t::He: return vdw::He;
case atom_t::Ne: return vdw::Ne;
case atom_t::Ar: return vdw::Ar;
case atom_t::Li: return vdw::Li;
case atom_t::Be: return vdw::Be;
case atom_t::B: return vdw::B;
case atom_t::C: return vdw::C;
case atom_t::N: return vdw::N;
case atom_t::O: return vdw::O;
case atom_t::F: return vdw::F;
case atom_t::Na: return vdw::Na;
case atom_t::Mg: return vdw::Mg;
case atom_t::Al: return vdw::Al;
case atom_t::Si: return vdw::Si;
case atom_t::P: return vdw::P;
case atom_t::S: return vdw::S;
case atom_t::Cl: return vdw::Cl;
case atom_t::K: return vdw::K;
case atom_t::Ca: return vdw::Ca;
case atom_t::Sc: return vdw::Sc;
case atom_t::Ti: return vdw::Ti;
case atom_t::V: return vdw::V;
case atom_t::Cr: return vdw::Cr;
case atom_t::Mn: return vdw::Mn;
case atom_t::Fe: return vdw::Fe;
case atom_t::Co: return vdw::Co;
case atom_t::Ni: return vdw::Ni;
case atom_t::Cu: return vdw::Cu;
case atom_t::Zn: return vdw::Zn;
case atom_t::Ga: return vdw::Ga;
case atom_t::Ge: return vdw::Ge;
case atom_t::As: return vdw::As;
case atom_t::Se: return vdw::Se;
case atom_t::Br: return vdw::Br;
case atom_t::Rb: return vdw::Rb;
case atom_t::Sr: return vdw::Sr;
case atom_t::Y: return vdw::Y;
case atom_t::Zr: return vdw::Zr;
case atom_t::Nb: return vdw::Nb;
case atom_t::Mo: return vdw::Mo;
case atom_t::Tc: return vdw::Tc;
case atom_t::Ru: return vdw::Ru;
case atom_t::Rh: return vdw::Rh;
case atom_t::Pd: return vdw::Pd;
case atom_t::Ag: return vdw::Ag;
case atom_t::Cd: return vdw::Cd;
case atom_t::In: return vdw::In;
case atom_t::Sn: return vdw::Sn;
case atom_t::Sb: return vdw::Sb;
case atom_t::Te: return vdw::Te;
case atom_t::I: return vdw::I;
case atom_t::Cs: return vdw::Cs;
case atom_t::Ba: return vdw::Ba;
case atom_t::Hf: return vdw::Hf;
case atom_t::Ta: return vdw::Ta;
case atom_t::W: return vdw::W;
case atom_t::Re: return vdw::Re;
case atom_t::Os: return vdw::Os;
case atom_t::Ir: return vdw::Ir;
case atom_t::Pt: return vdw::Pt;
case atom_t::Au: return vdw::Au;
case atom_t::Tl: return vdw::Tl;
case atom_t::Pb: return vdw::Pb;
case atom_t::Bi: return vdw::Bi;
// fake elements
case atom_t::M: return 0;
case atom_t::dummy: {return radius::detail::dummy_radius;}
default: throw std::runtime_error("constants::radius::get_vdw_radius: Unknown atom type \"" + constants::symbols::to_string(atom) + "\"");
}
}
std::string ausaxs::constants::symbols::to_string(atom_t atom) {
switch(atom) {
case atom_t::H: return "H";
case atom_t::He: return "He";
case atom_t::Li: return "Li";
case atom_t::Be: return "Be";
case atom_t::B: return "B";
case atom_t::C: return "C";
case atom_t::N: return "N";
case atom_t::O: return "O";
case atom_t::F: return "F";
case atom_t::Ne: return "Ne";
case atom_t::Na: return "Na";
case atom_t::Mg: return "Mg";
case atom_t::Al: return "Al";
case atom_t::Si: return "Si";
case atom_t::P: return "P";
case atom_t::S: return "S";
case atom_t::Cl: return "Cl";
case atom_t::Ar: return "Ar";
case atom_t::K: return "K";
case atom_t::Ca: return "Ca";
case atom_t::Sc: return "Sc";
case atom_t::Ti: return "Ti";
case atom_t::V: return "V";
case atom_t::Cr: return "Cr";
case atom_t::Mn: return "Mn";
case atom_t::Fe: return "Fe";
case atom_t::Co: return "Co";
case atom_t::Ni: return "Ni";
case atom_t::Cu: return "Cu";
case atom_t::Zn: return "Zn";
case atom_t::Ga: return "Ga";
case atom_t::Ge: return "Ge";
case atom_t::As: return "As";
case atom_t::Se: return "Se";
case atom_t::Br: return "Br";
case atom_t::Rb: return "Rb";
case atom_t::Sr: return "Sr";
case atom_t::Y: return "Y";
case atom_t::Zr: return "Zr";
case atom_t::Nb: return "Nb";
case atom_t::Mo: return "Mo";
case atom_t::Tc: return "Tc";
case atom_t::Ru: return "Ru";
case atom_t::Rh: return "Rh";
case atom_t::Pd: return "Pd";
case atom_t::Ag: return "Ag";
case atom_t::Cd: return "Cd";
case atom_t::In: return "In";
case atom_t::Sn: return "Sn";
case atom_t::Sb: return "Sb";
case atom_t::Te: return "Te";
case atom_t::I: return "I";
case atom_t::Xe: return "Xe";
case atom_t::Cs: return "Cs";
case atom_t::Ba: return "Ba";
case atom_t::Hf: return "Hf";
case atom_t::Ta: return "Ta";
case atom_t::W: return "W";
case atom_t::Re: return "Re";
case atom_t::Os: return "Os";
case atom_t::Ir: return "Ir";
case atom_t::Pt: return "Pt";
case atom_t::Au: return "Au";
case atom_t::Tl: return "Tl";
case atom_t::Pb: return "Pb";
case atom_t::Bi: return "Bi";
case atom_t::Po: return "Po";
case atom_t::M: return "M";
case atom_t::dummy: return "#";
default: throw std::runtime_error("constants::symbols::to_string: Unknown atom type \"" + std::to_string(static_cast<int>(atom)) + "\"");
}
}
std::string ausaxs::constants::symbols::to_string(atomic_group_t group) {
switch(group) {
case atomic_group_t::CH: return "CH";
case atomic_group_t::CH2: return "CH2";
case atomic_group_t::CH3: return "CH3";
case atomic_group_t::NH: return "NH";
case atomic_group_t::NH2: return "NH2";
case atomic_group_t::NH3: return "NH3";
case atomic_group_t::OH: return "OH";
case atomic_group_t::SH: return "SH";
case atomic_group_t::unknown: return "unknown";
default: throw std::runtime_error("constants::symbols::to_string: Unknown atomic group \"" + std::to_string(static_cast<int>(group)) + "\"");
}
}
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