Index

M

mdk (C++ type), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29] mdk::AAAtomInfo (C++ struct), [1] mdk::AAAtomInfo::inBackbone (C++ member), [1] mdk::AAAtomInfo::radius (C++ member), [1] mdk::AminoAcid (C++ class), [1] mdk::AminoAcid::AminoAcid (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9] mdk::AminoAcid::aminoAcids (C++ function), [1] mdk::AminoAcid::codes (C++ function), [1] mdk::AminoAcid::info (C++ function), [1] mdk::AminoAcid::isProper (C++ function), [1] mdk::AminoAcid::N (C++ member), [1] mdk::AminoAcid::names (C++ function), [1] mdk::AminoAcid::operator AminoAcidIdx const& (C++ function), [1] mdk::AminoAcid::operator char const& (C++ function), [1] mdk::AminoAcid::operator int8_t (C++ function), [1] mdk::AminoAcid::operator std::string (C++ function), [1] mdk::AminoAcid::operator!= (C++ function), [1] mdk::AminoAcid::operator< (C++ function), [1] mdk::AminoAcid::operator<= (C++ function), [1] mdk::AminoAcid::operator== (C++ function), [1] mdk::AminoAcid::operator> (C++ function), [1] mdk::AminoAcid::operator>= (C++ function), [1] mdk::AminoAcid::type (C++ member), [1] mdk::AminoAcid::types (C++ function), [1] mdk::AminoAcidIdx (C++ enum), [1] mdk::AminoAcidIdx::ALA (C++ enumerator), [1] mdk::AminoAcidIdx::ARG (C++ enumerator), [1] mdk::AminoAcidIdx::ASN (C++ enumerator), [1] mdk::AminoAcidIdx::ASP (C++ enumerator), [1] mdk::AminoAcidIdx::CYS (C++ enumerator), [1] mdk::AminoAcidIdx::GLN (C++ enumerator), [1] mdk::AminoAcidIdx::GLU (C++ enumerator), [1] mdk::AminoAcidIdx::GLY (C++ enumerator), [1] mdk::AminoAcidIdx::HIS (C++ enumerator), [1] mdk::AminoAcidIdx::ILE (C++ enumerator), [1] mdk::AminoAcidIdx::LEU (C++ enumerator), [1] mdk::AminoAcidIdx::LYS (C++ enumerator), [1] mdk::AminoAcidIdx::MET (C++ enumerator), [1] mdk::AminoAcidIdx::PHE (C++ enumerator), [1] mdk::AminoAcidIdx::PRO (C++ enumerator), [1] mdk::AminoAcidIdx::SER (C++ enumerator), [1] mdk::AminoAcidIdx::THR (C++ enumerator), [1] mdk::AminoAcidIdx::TRP (C++ enumerator), [1] mdk::AminoAcidIdx::TYR (C++ enumerator), [1] mdk::AminoAcidIdx::VAL (C++ enumerator), [1] mdk::AminoAcidInfo (C++ struct), [1] mdk::AminoAcidInfo::atomInfo (C++ member), [1] mdk::AminoAcidInfo::heavyAtoms (C++ member), [1] mdk::AminoAcidInfo::mass (C++ member), [1] mdk::Ampere (C++ member), [1] mdk::angle (C++ function) mdk::angstrom (C++ member), [1] mdk::asphericity (C++ function) mdk::atom (C++ member), [1] mdk::au (C++ member), [1] mdk::BondAngles (C++ class), [1] mdk::BondAngles::asyncPart (C++ function), [1] mdk::BondAngles::bind (C++ function), [1] mdk::BondAngles::heurBA (C++ member), [1] mdk::BondAngles::inRange (C++ member), [1] mdk::BondAngles::natBA (C++ member), [1] mdk::Bytes (C++ type), [1] mdk::Chains (C++ class), [1] mdk::Chains::chainIdx (C++ member), [1] mdk::Chains::Chains (C++ function), [1], [2], [3] mdk::Chains::isTerminal (C++ member), [1] mdk::Chains::model (C++ member), [1] mdk::Chains::nativeQuads (C++ member), [1] mdk::Chains::nativeTriples (C++ member), [1] mdk::Chains::nativeTuples (C++ function), [1] mdk::Chains::pairs (C++ member), [1] mdk::Chains::quads (C++ member), [1] mdk::Chains::sepByAtLeastN (C++ function), [1] mdk::Chains::triples (C++ member), [1] mdk::Chains::tuples (C++ function), [1] mdk::Charges (C++ class), [1] mdk::Charges::Charges (C++ function), [1], [2], [3] mdk::Chirality (C++ class), [1] mdk::Chirality::asyncPart (C++ function), [1] mdk::Chirality::bind (C++ function), [1] mdk::Chirality::C_nat (C++ member), [1] mdk::Chirality::d0_cube_inv (C++ member), [1] mdk::Chirality::e_chi (C++ member), [1] mdk::Chirality::inRange (C++ member), [1] mdk::cmap (C++ type) mdk::cmap::ContactMap (C++ class), [1] mdk::cmap::ContactMap::angle (C++ member), [1] mdk::cmap::ContactMap::Contact (C++ struct), [1] mdk::cmap::ContactMap::Contact::dist0 (C++ member), [1] mdk::cmap::ContactMap::Contact::res (C++ member), [1] mdk::cmap::ContactMap::contacts (C++ member), [1] mdk::cmap::ContactMap::dihedral (C++ member), [1] mdk::cmap::ContactMap::len (C++ member), [1] mdk::cmap::ContactMap::offset (C++ member), [1] mdk::cmap::LegacyParser (C++ class), [1] mdk::cmap::LegacyParser::read (C++ function), [1] mdk::cmap::LegacyParser::write (C++ function), [1] mdk::ComplexNativeDihedral (C++ class), [1] mdk::ComplexNativeDihedral::bind (C++ function), [1] mdk::ComplexNativeDihedral::CDA (C++ member), [1] mdk::ComplexNativeDihedral::CDB (C++ member), [1] mdk::ComplexNativeDihedral::term (C++ function), [1] mdk::ConstDH (C++ class), [1] mdk::ConstDH::asyncPart (C++ function), [1] mdk::ConstDH::permittivity (C++ member), [1] mdk::ConstDH::screeningDist (C++ member), [1] mdk::ConstDH::spec (C++ function), [1] mdk::ContactType (C++ class), [1] mdk::ContactType::code (C++ member), [1] mdk::ContactType::ContactType (C++ function), [1], [2], [3], [4], [5], [6], [7] mdk::ContactType::operator ContactTypeIdx const& (C++ function), [1] mdk::ContactType::operator int8_t (C++ function), [1] mdk::ContactType::operator std::string (C++ function), [1] mdk::ContactTypeIdx (C++ enum), [1] mdk::ContactTypeIdx::NAT (C++ enumerator), [1] mdk::ContactTypeIdx::NAT_BB (C++ enumerator), [1] mdk::ContactTypeIdx::NAT_BS (C++ enumerator), [1] mdk::ContactTypeIdx::NAT_SB (C++ enumerator), [1] mdk::ContactTypeIdx::NAT_SS (C++ enumerator), [1] mdk::ContactTypeIdx::SSBOND (C++ enumerator), [1] mdk::Coulomb (C++ member), [1] mdk::cspeed (C++ member), [1] mdk::DataFactory (C++ class), [1] mdk::DataFactory::create (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] mdk::DataFactory::data (C++ function), [1] mdk::DataFactory::DataFactory (C++ function), [1] mdk::DataFactory::model (C++ member), [1] mdk::DataFactory::params (C++ member), [1] mdk::DataFactory::savedData (C++ member), [1] mdk::degree (C++ member), [1] mdk::dihedral (C++ function) mdk::DihedralAngles (C++ class), [1] mdk::DihedralAngles::asyncPart (C++ function), [1] mdk::DihedralAngles::bind (C++ function), [1] mdk::DihedralAngles::heurDih (C++ member), [1] mdk::DihedralAngles::inRange (C++ member), [1] mdk::DihedralAngles::natDih (C++ member), [1] mdk::Dynamics (C++ struct) mdk::Dynamics::F (C++ member) mdk::Dynamics::V (C++ member) mdk::Dynamics::zero (C++ function) mdk::echarge (C++ member), [1] mdk::eps (C++ member), [1] mdk::eps_kB (C++ member), [1] mdk::epsilon_0 (C++ member), [1] mdk::ESBase (C++ class), [1] mdk::ESBase::bind (C++ function), [1] mdk::ESBase::charge (C++ member), [1] mdk::ESBase::Contact (C++ struct), [1] mdk::ESBase::Contact::i1 (C++ member), [1] mdk::ESBase::Contact::i2 (C++ member), [1] mdk::ESBase::Contact::q1_x_q2 (C++ member), [1] mdk::ESBase::pairs (C++ member), [1] mdk::ESBase::vlUpdateHook (C++ function), [1] mdk::ExportPDB (C++ class), [1] mdk::ExportPDB::base (C++ member), [1] mdk::ExportPDB::bind (C++ function), [1] mdk::ExportPDB::data (C++ member), [1] mdk::ExportPDB::execute (C++ function), [1] mdk::ExportPDB::ExportPDB (C++ function), [1] mdk::ExportPDB::modelIdx (C++ member), [1] mdk::ExportPDB::modelPath (C++ member), [1] mdk::ExportPDB::period (C++ member), [1] mdk::ExportPDB::state (C++ member), [1] mdk::ExportPDB::tprev (C++ member), [1] mdk::ExportPDB::~ExportPDB (C++ function), [1] mdk::f77mass (C++ member), [1] mdk::f77unit (C++ member), [1] mdk::Force (C++ class), [1] mdk::Force::asyncPart (C++ function), [1] mdk::Force::bind (C++ function), [1] mdk::Force::state (C++ member), [1] mdk::Force::syncPart (C++ function), [1] mdk::Harmonic (C++ class), [1] mdk::Harmonic::computeF (C++ function), [1] mdk::Harmonic::computeV (C++ function), [1] mdk::Harmonic::H1 (C++ member), [1] mdk::Harmonic::H2 (C++ member), [1] mdk::Harmonic::Harmonic (C++ function), [1], [2], [3] mdk::Henry (C++ member), [1] mdk::HeuresticBA (C++ class), [1] mdk::HeuresticBA::angleTypes (C++ member), [1] mdk::HeuresticBA::bind (C++ function), [1] mdk::HeuresticBA::coeff (C++ member), [1] mdk::HeuresticBA::D (C++ member), [1] mdk::HeuresticBA::term (C++ function), [1] mdk::HeuresticDihedral (C++ class), [1] mdk::HeuresticDihedral::angleTypes (C++ member), [1] mdk::HeuresticDihedral::bind (C++ function), [1] mdk::HeuresticDihedral::coeff (C++ member), [1] mdk::HeuresticDihedral::term (C++ function), [1] mdk::Hook (C++ class), [1] mdk::Hook::execute (C++ function), [1] mdk::Integers (C++ type), [1] mdk::Integrator (C++ class), [1] mdk::Integrator::bind (C++ function), [1] mdk::Integrator::init (C++ function), [1] mdk::Integrator::integrate (C++ function), [1] mdk::Integrator::state (C++ member), [1] mdk::Joule (C++ member), [1] mdk::kB (C++ member), [1] mdk::kcal (C++ member), [1] mdk::Kelvin (C++ member), [1] mdk::kg (C++ member), [1] mdk::LambdaPeak (C++ class), [1] mdk::LambdaPeak::alpha (C++ member), [1] mdk::LambdaPeak::cosineVersion (C++ member), [1] mdk::LambdaPeak::eval (C++ function), [1] mdk::LambdaPeak::psi0 (C++ member), [1] mdk::LambdaPeak::supp (C++ function), [1] mdk::LangPredictorCorrector (C++ class), [1] mdk::LangPredictorCorrector::bind (C++ function), [1] mdk::LangPredictorCorrector::dt (C++ member), [1] mdk::LangPredictorCorrector::gamma (C++ member), [1] mdk::LangPredictorCorrector::gaussianNoise (C++ member), [1] mdk::LangPredictorCorrector::generateNoise (C++ function), [1] mdk::LangPredictorCorrector::init (C++ function), [1] mdk::LangPredictorCorrector::initialized (C++ member), [1] mdk::LangPredictorCorrector::integrate (C++ function), [1] mdk::LangPredictorCorrector::LangPredictorCorrector (C++ function), [1] mdk::LangPredictorCorrector::m (C++ member), [1] mdk::LangPredictorCorrector::random (C++ member), [1] mdk::LangPredictorCorrector::rngs (C++ member), [1] mdk::LangPredictorCorrector::temperature (C++ member), [1] mdk::LangPredictorCorrector::y0 (C++ member), [1] mdk::LangPredictorCorrector::y1 (C++ member), [1] mdk::LangPredictorCorrector::y2 (C++ member), [1] mdk::LangPredictorCorrector::y3 (C++ member), [1] mdk::LangPredictorCorrector::y4 (C++ member), [1] mdk::LangPredictorCorrector::y5 (C++ member), [1] mdk::Leapfrog (C++ class), [1] mdk::Leapfrog::a_prev (C++ member), [1] mdk::Leapfrog::bind (C++ function), [1] mdk::Leapfrog::dt (C++ member), [1] mdk::Leapfrog::init (C++ function), [1] mdk::Leapfrog::integrate (C++ function), [1] mdk::Leapfrog::Leapfrog (C++ function), [1] mdk::Leapfrog::m (C++ member), [1] mdk::LennardJones (C++ class), [1] mdk::LennardJones::computeF (C++ function), [1] mdk::LennardJones::computeV (C++ function), [1] mdk::LennardJones::cutoff (C++ function), [1] mdk::LennardJones::depth (C++ member), [1] mdk::LennardJones::LennardJones (C++ function), [1], [2], [3] mdk::LennardJones::r_min (C++ member), [1] mdk::line (C++ function) mdk::lineStream (C++ function) mdk::ltrim (C++ function) mdk::Masses (C++ class), [1] mdk::Masses::Masses (C++ function), [1], [2], [3] mdk::meter (C++ member), [1] mdk::microsecond (C++ member), [1] mdk::millisecond (C++ member), [1] mdk::Model (C++ class), [1] mdk::Model::addChain (C++ function), [1] mdk::Model::addCMapContacts (C++ function), [1] mdk::Model::addContact (C++ function), [1] mdk::Model::addContactMap (C++ function), [1] mdk::Model::addResidue (C++ function), [1] mdk::Model::addSP (C++ function), [1] mdk::Model::Chain (C++ struct), [1] mdk::Model::Chain::end (C++ member), [1] mdk::Model::Chain::idx (C++ member), [1] mdk::Model::Chain::start (C++ member), [1] mdk::Model::Chain::structuredParts (C++ member), [1] mdk::Model::chains (C++ member), [1] mdk::Model::Contact (C++ struct), [1] mdk::Model::Contact::dist0 (C++ member), [1] mdk::Model::Contact::idx (C++ member), [1] mdk::Model::Contact::res (C++ member), [1] mdk::Model::Contact::type (C++ member), [1] mdk::Model::contacts (C++ member), [1] mdk::Model::exactLegacySAW (C++ function), [1] mdk::Model::initVelocity (C++ function), [1] mdk::Model::legacyMorphIntoSAW (C++ function), [1] mdk::Model::morphIntoLine (C++ function), [1] mdk::Model::morphIntoSAW (C++ function), [1] mdk::Model::n (C++ member), [1] mdk::Model::nonlocalPairs (C++ function), [1] mdk::Model::Residue (C++ struct), [1] mdk::Model::Residue::chainIdx (C++ member), [1] mdk::Model::Residue::idx (C++ member), [1] mdk::Model::Residue::mass (C++ member), [1] mdk::Model::Residue::nat_r (C++ member), [1] mdk::Model::Residue::r (C++ member), [1] mdk::Model::Residue::type (C++ member), [1] mdk::Model::Residue::v (C++ member), [1] mdk::Model::residues (C++ member), [1] mdk::Model::StructuredPart (C++ struct), [1] mdk::Model::StructuredPart::angle (C++ member), [1] mdk::Model::StructuredPart::dihedral (C++ member), [1] mdk::Model::StructuredPart::idx (C++ member), [1] mdk::Model::StructuredPart::len (C++ member), [1] mdk::Model::StructuredPart::off (C++ member), [1] mdk::Model::structuredParts (C++ member), [1] mdk::Model::top (C++ member), [1] mdk::Model::useAverageMasses (C++ function), [1] mdk::mol (C++ member), [1] mdk::mu_0 (C++ member), [1] mdk::nanometer (C++ member), [1] mdk::nanosecond (C++ member), [1] mdk::NativeBA (C++ class), [1] mdk::NativeBA::bind (C++ function), [1] mdk::NativeBA::CBA (C++ member), [1] mdk::NativeBA::isNative (C++ member), [1] mdk::NativeBA::term (C++ function), [1] mdk::NativeBA::theta0 (C++ member), [1] mdk::NativeContacts (C++ class), [1] mdk::NativeContacts::allContacts (C++ member), [1] mdk::NativeContacts::asyncPart (C++ function), [1] mdk::NativeContacts::bind (C++ function), [1] mdk::NativeContacts::Contact (C++ struct), [1] mdk::NativeContacts::Contact::i1 (C++ member), [1] mdk::NativeContacts::Contact::i2 (C++ member), [1] mdk::NativeContacts::Contact::r_min (C++ member), [1] mdk::NativeContacts::curPairs (C++ member), [1] mdk::NativeContacts::depth (C++ member), [1] mdk::NativeContacts::newVL (C++ member), [1] mdk::NativeContacts::spec (C++ function), [1] mdk::NativeContacts::vlUpdateHook (C++ function), [1] mdk::NativeDihedralBase (C++ class), [1] mdk::NativeDihedralBase::bind (C++ function), [1] mdk::NativeDihedralBase::isNative (C++ member), [1] mdk::NativeDihedralBase::phi0 (C++ member), [1] mdk::NonlocalForce (C++ class), [1] mdk::NonlocalForce::bind (C++ function), [1] mdk::NonlocalForce::installIntoVL (C++ function), [1] mdk::NonlocalForce::savedSpec (C++ member), [1] mdk::NonlocalForce::spec (C++ function), [1] mdk::NonlocalForce::vl (C++ member), [1] mdk::NonlocalForce::vlUpdateHook (C++ function), [1] mdk::numOfPTs (C++ member), [1] mdk::Pairs (C++ type), [1] mdk::PairType (C++ enum), [1] mdk::pairType (C++ function), [1] mdk::PairType::GG (C++ enumerator), [1] mdk::PairType::GP (C++ enumerator), [1] mdk::PairType::GX (C++ enumerator), [1] mdk::PairType::PG (C++ enumerator), [1] mdk::PairType::PP (C++ enumerator), [1] mdk::PairType::PX (C++ enumerator), [1] mdk::PairType::XG (C++ enumerator), [1] mdk::PairType::XP (C++ enumerator), [1] mdk::PairType::XX (C++ enumerator), [1] mdk::pairTypes (C++ function), [1] mdk::param (C++ type) mdk::param::LegacyParser (C++ class), [1] mdk::param::LegacyParser::read (C++ function), [1] mdk::param::LegacyParser::write (C++ function), [1] mdk::param::Parameters (C++ class), [1] mdk::param::Parameters::angleParams (C++ member), [1] mdk::param::Parameters::Coeffs (C++ type), [1] mdk::param::Parameters::defAngleParams (C++ member), [1] mdk::param::Parameters::dihedralParams (C++ member), [1] mdk::param::Parameters::mjMatrix (C++ member), [1] mdk::param::Parameters::pairwiseMinDist (C++ member), [1] mdk::param::Parameters::Parameters (C++ function), [1] mdk::param::Parameters::PerAcidData (C++ type), [1] mdk::param::Parameters::PerPairData (C++ type), [1] mdk::param::Parameters::PerPTData (C++ type), [1] mdk::param::Parameters::radius (C++ member), [1] mdk::param::Parameters::specificity (C++ member), [1] mdk::param::Parameters::SpecificityParams (C++ struct), [1] mdk::param::Parameters::SpecificityParams::maxHydrophobicSS (C++ member), [1] mdk::param::Parameters::SpecificityParams::maxPolarSS (C++ member), [1] mdk::param::Parameters::SpecificityParams::maxSidechain (C++ member), [1] mdk::param::Parameters::SpecificityParams::polarization (C++ member), [1] mdk::param::Polarization (C++ enum) mdk::param::Polarization::GLY_PRO (C++ enumerator) mdk::param::Polarization::HYDROPHOBIC (C++ enumerator) mdk::param::Polarization::MISSING (C++ enumerator) mdk::param::Polarization::POLAR (C++ enumerator) mdk::param::Polarization::POLAR_NEG (C++ enumerator) mdk::param::Polarization::POLAR_POS (C++ enumerator) mdk::PauliExclusion (C++ class), [1] mdk::PauliExclusion::asyncPart (C++ function), [1] mdk::PauliExclusion::bind (C++ function), [1] mdk::PauliExclusion::exclPairs (C++ member), [1] mdk::PauliExclusion::PauliExclusion (C++ function), [1] mdk::PauliExclusion::spec (C++ function), [1] mdk::PauliExclusion::stlj (C++ member), [1] mdk::PauliExclusion::vlUpdateHook (C++ function), [1] mdk::pdb (C++ type), [1], [2] mdk::pdb::AtomParser (C++ class), [1] mdk::pdb::AtomParser::AtomParser (C++ function), [1] mdk::pdb::Char (C++ class), [1] mdk::pdb::Char::Char (C++ function), [1] mdk::pdb::Char::i (C++ member), [1] mdk::pdb::Char::read (C++ function), [1] mdk::pdb::Char::v (C++ member), [1] mdk::pdb::Char::write (C++ function), [1] mdk::pdb::Cryst1Parser (C++ class), [1] mdk::pdb::Cryst1Parser::Cryst1Parser (C++ function), [1] mdk::pdb::Data (C++ class), [1] mdk::pdb::Data::asModel (C++ function), [1] mdk::pdb::Data::Data (C++ function), [1], [2], [3] mdk::pdb::Data::onlyAtoms (C++ function), [1] mdk::pdb::Data::operator<< (C++ function), [1], [2], [3] mdk::pdb::Data::records (C++ member), [1] mdk::pdb::EndmdlParser (C++ class), [1] mdk::pdb::EndmdlParser::EndmdlParser (C++ function), [1] mdk::pdb::EndParser (C++ class), [1] mdk::pdb::EndParser::EndParser (C++ function), [1] mdk::pdb::Field (C++ class), [1] mdk::pdb::Field::read (C++ function), [1] mdk::pdb::Field::write (C++ function), [1] mdk::pdb::HetatmParser (C++ class), [1] mdk::pdb::HetatmParser::HetatmParser (C++ function), [1] mdk::pdb::Integer (C++ class), [1] mdk::pdb::Integer::i (C++ member), [1] mdk::pdb::Integer::Integer (C++ function), [1] mdk::pdb::Integer::j (C++ member), [1] mdk::pdb::Integer::offset (C++ member), [1] mdk::pdb::Integer::read (C++ function), [1] mdk::pdb::Integer::v (C++ member), [1] mdk::pdb::Integer::write (C++ function), [1] mdk::pdb::LinkParser (C++ class), [1] mdk::pdb::LinkParser::LinkParser (C++ function), [1] mdk::pdb::Literal (C++ class), [1] mdk::pdb::Literal::i (C++ member), [1] mdk::pdb::Literal::j (C++ member), [1] mdk::pdb::Literal::lit (C++ member), [1]

mdk::pdb::Literal::Literal (C++ function), [1] mdk::pdb::Literal::read (C++ function), [1] mdk::pdb::Literal::write (C++ function), [1] mdk::pdb::Mode (C++ enum), [1] mdk::pdb::Mode::Exact (C++ enumerator), [1] mdk::pdb::Mode::Left (C++ enumerator), [1] mdk::pdb::Mode::Right (C++ enumerator), [1] mdk::pdb::Mode::Trim (C++ enumerator), [1] mdk::pdb::Model (C++ class), [1] mdk::pdb::Model::addAtom (C++ function), [1] mdk::pdb::Model::addChain (C++ function), [1] mdk::pdb::Model::addContact (C++ function), [1] mdk::pdb::Model::addContactsFromAtomOverlap (C++ function), [1] mdk::pdb::Model::addContactsFromResOverlap (C++ function), [1] mdk::pdb::Model::addResidue (C++ function), [1] mdk::pdb::Model::Atom (C++ struct), [1] mdk::pdb::Model::Atom::idxInRes (C++ member), [1] mdk::pdb::Model::Atom::r (C++ member), [1] mdk::pdb::Model::Atom::res (C++ member), [1] mdk::pdb::Model::Atom::serial (C++ member), [1] mdk::pdb::Model::Atom::type (C++ member), [1] mdk::pdb::Model::atoms (C++ member), [1] mdk::pdb::Model::Chain (C++ struct), [1] mdk::pdb::Model::Chain::residues (C++ member), [1] mdk::pdb::Model::Chain::serial (C++ member), [1] mdk::pdb::Model::chains (C++ member), [1] mdk::pdb::Model::coarsen (C++ function), [1] mdk::pdb::Model::Contact (C++ struct), [1] mdk::pdb::Model::Contact::atom (C++ member), [1] mdk::pdb::Model::Contact::dist0 (C++ member), [1] mdk::pdb::Model::Contact::idx (C++ member), [1] mdk::pdb::Model::Contact::type (C++ member), [1] mdk::pdb::Model::contacts (C++ member), [1] mdk::pdb::Model::Model (C++ function), [1], [2], [3] mdk::pdb::Model::Residue (C++ struct), [1] mdk::pdb::Model::Residue::atoms (C++ member), [1] mdk::pdb::Model::Residue::chain (C++ member), [1] mdk::pdb::Model::Residue::find (C++ function), [1] mdk::pdb::Model::Residue::idxInChain (C++ member), [1] mdk::pdb::Model::Residue::serial (C++ member), [1] mdk::pdb::Model::Residue::type (C++ member), [1] mdk::pdb::Model::residues (C++ member), [1] mdk::pdb::Model::top (C++ member), [1] mdk::pdb::ModelParser (C++ class), [1] mdk::pdb::ModelParser::ModelParser (C++ function), [1] mdk::pdb::operator<< (C++ function), [1] mdk::pdb::Parser (C++ class), [1] mdk::pdb::Parser::Parser (C++ function), [1] mdk::pdb::Parser::parsers (C++ member), [1] mdk::pdb::Parser::read (C++ function), [1] mdk::pdb::Parser::write (C++ function), [1] mdk::pdb::Real (C++ class), [1] mdk::pdb::Real::i (C++ member), [1] mdk::pdb::Real::j (C++ member), [1] mdk::pdb::Real::m (C++ member), [1] mdk::pdb::Real::n (C++ member), [1] mdk::pdb::Real::read (C++ function), [1] mdk::pdb::Real::Real (C++ function), [1] mdk::pdb::Real::scalar (C++ member), [1] mdk::pdb::Real::v (C++ member), [1] mdk::pdb::Real::write (C++ function), [1] mdk::pdb::RecordParser (C++ class), [1] mdk::pdb::RecordParser::fields (C++ member), [1] mdk::pdb::RecordParser::record (C++ member), [1] mdk::pdb::RecordParser::tryParse (C++ function), [1] mdk::pdb::RecordParser::write (C++ function), [1] mdk::pdb::records (C++ type), [1] mdk::pdb::records::Atom (C++ class), [1] mdk::pdb::records::Atom::altLocation (C++ member), [1] mdk::pdb::records::Atom::atomName (C++ member), [1] mdk::pdb::records::Atom::chainID (C++ member), [1] mdk::pdb::records::Atom::charge (C++ member), [1] mdk::pdb::records::Atom::element (C++ member), [1] mdk::pdb::records::Atom::insertionCode (C++ member), [1] mdk::pdb::records::Atom::occupancy (C++ member), [1] mdk::pdb::records::Atom::pos (C++ member), [1] mdk::pdb::records::Atom::residueName (C++ member), [1] mdk::pdb::records::Atom::residueSeqNum (C++ member), [1] mdk::pdb::records::Atom::serialNum (C++ member), [1] mdk::pdb::records::Atom::tempFactor (C++ member), [1] mdk::pdb::records::Cryst1 (C++ class), [1] mdk::pdb::records::Cryst1::angles (C++ member), [1] mdk::pdb::records::Cryst1::size (C++ member), [1] mdk::pdb::records::Cryst1::spaceGroup (C++ member), [1] mdk::pdb::records::Cryst1::z (C++ member), [1] mdk::pdb::records::End (C++ class), [1] mdk::pdb::records::Endmdl (C++ class), [1] mdk::pdb::records::Link (C++ class), [1] mdk::pdb::records::Link::linkLength (C++ member), [1] mdk::pdb::records::Link::PerResidueData (C++ struct), [1] mdk::pdb::records::Link::PerResidueData::altLocation (C++ member), [1] mdk::pdb::records::Link::PerResidueData::atomName (C++ member), [1] mdk::pdb::records::Link::PerResidueData::chainId (C++ member), [1] mdk::pdb::records::Link::PerResidueData::insertionCode (C++ member), [1] mdk::pdb::records::Link::PerResidueData::residueName (C++ member), [1] mdk::pdb::records::Link::PerResidueData::residueSeqNum (C++ member), [1] mdk::pdb::records::Link::PerResidueData::symmetryOp (C++ member), [1] mdk::pdb::records::Link::res (C++ member), [1] mdk::pdb::records::Model (C++ class), [1] mdk::pdb::records::Model::serialNum (C++ member), [1] mdk::pdb::records::Record (C++ type), [1] mdk::pdb::records::Remark (C++ class), [1] mdk::pdb::records::Remark::number (C++ member), [1] mdk::pdb::records::Remark::text (C++ member), [1] mdk::pdb::records::SSBond (C++ class), [1] mdk::pdb::records::SSBond::dist0 (C++ member), [1] mdk::pdb::records::SSBond::PerResidueData (C++ struct), [1] mdk::pdb::records::SSBond::PerResidueData::chainId (C++ member), [1] mdk::pdb::records::SSBond::PerResidueData::insertionCode (C++ member), [1] mdk::pdb::records::SSBond::PerResidueData::residueSeqNum (C++ member), [1] mdk::pdb::records::SSBond::PerResidueData::symmetryOp (C++ member), [1] mdk::pdb::records::SSBond::res (C++ member), [1] mdk::pdb::records::SSBond::serialNum (C++ member), [1] mdk::pdb::records::Ter (C++ class), [1] mdk::pdb::records::Ter::chainId (C++ member), [1] mdk::pdb::records::Ter::insertionCode (C++ member), [1] mdk::pdb::records::Ter::residueName (C++ member), [1] mdk::pdb::records::Ter::residueSeqNum (C++ member), [1] mdk::pdb::records::Ter::serialNum (C++ member), [1] mdk::pdb::RemarkParser (C++ class), [1] mdk::pdb::RemarkParser::RemarkParser (C++ function), [1] mdk::pdb::SSBondParser (C++ class), [1] mdk::pdb::SSBondParser::SSBondParser (C++ function), [1] mdk::pdb::String (C++ class), [1] mdk::pdb::String::i (C++ member), [1] mdk::pdb::String::j (C++ member), [1] mdk::pdb::String::mode (C++ member), [1] mdk::pdb::String::read (C++ function), [1] mdk::pdb::String::String (C++ function), [1] mdk::pdb::String::v (C++ member), [1] mdk::pdb::String::write (C++ function), [1] mdk::pdb::SymOp (C++ class), [1] mdk::pdb::SymOp::i (C++ member), [1] mdk::pdb::SymOp::j (C++ member), [1] mdk::pdb::SymOp::read (C++ function), [1] mdk::pdb::SymOp::SymOp (C++ function), [1] mdk::pdb::SymOp::v (C++ member), [1] mdk::pdb::SymOp::write (C++ function), [1] mdk::pdb::TerParser (C++ class), [1] mdk::pdb::TerParser::TerParser (C++ function), [1] mdk::PositionDiff (C++ class), [1] mdk::PositionDiff::bind (C++ function), [1] mdk::PositionDiff::execute (C++ function), [1] mdk::PositionDiff::inputPath (C++ member), [1] mdk::PositionDiff::output (C++ member), [1] mdk::PositionDiff::PositionDiff (C++ function), [1] mdk::PositionDiff::refPositions (C++ member), [1] mdk::PositionDiff::state (C++ member), [1] mdk::ProgressBar (C++ class), [1] mdk::ProgressBar::bind (C++ function), [1] mdk::ProgressBar::execute (C++ function), [1] mdk::ProgressBar::prevTime (C++ member), [1] mdk::ProgressBar::ProgressBar (C++ function), [1] mdk::ProgressBar::realTime0 (C++ member), [1] mdk::ProgressBar::simul (C++ member), [1] mdk::ProgressBar::state (C++ member), [1] mdk::ProgressBar::time_point (C++ type), [1] mdk::ProgressBar::totalTime (C++ member), [1] mdk::ProgressBar::updatePeriod (C++ member), [1] mdk::ProgressBar::width (C++ member), [1] mdk::PseudoImproperDihedral (C++ class), [1] mdk::PseudoImproperDihedral::asyncPart (C++ function), [1] mdk::PseudoImproperDihedral::bb_neg (C++ member), [1] mdk::PseudoImproperDihedral::bb_neg_lj (C++ member), [1] mdk::PseudoImproperDihedral::bb_pos (C++ member), [1] mdk::PseudoImproperDihedral::bb_pos_lj (C++ member), [1] mdk::PseudoImproperDihedral::bind (C++ function), [1] mdk::PseudoImproperDihedral::deriveAngles (C++ function), [1] mdk::PseudoImproperDihedral::pairs (C++ member), [1] mdk::PseudoImproperDihedral::seqs (C++ member), [1] mdk::PseudoImproperDihedral::spec (C++ function), [1] mdk::PseudoImproperDihedral::ss (C++ member), [1] mdk::PseudoImproperDihedral::ss_ljs (C++ member), [1] mdk::PseudoImproperDihedral::types (C++ member), [1] mdk::PseudoImproperDihedral::vlUpdateHook (C++ function), [1] mdk::QAContact (C++ struct), [1] mdk::QAContact::i1 (C++ member), [1] mdk::QAContact::i2 (C++ member), [1] mdk::QAContact::Status (C++ enum), [1] mdk::QAContact::status (C++ member), [1] mdk::QAContact::Status::BREAKING (C++ enumerator), [1] mdk::QAContact::Status::FORMING (C++ enumerator), [1] mdk::QAContact::Status::REMOVED (C++ enumerator), [1] mdk::QAContact::t0 (C++ member), [1] mdk::QAContact::type (C++ member), [1] mdk::QADiff (C++ struct), [1] mdk::QADiff::cont (C++ member), [1] mdk::QADiff::oldIdx (C++ member), [1] mdk::QADiff::operator< (C++ function), [1] mdk::QADiff::statDiffs (C++ member), [1] mdk::QAFreePair (C++ struct), [1] mdk::QAFreePair::i1 (C++ member), [1] mdk::QAFreePair::i2 (C++ member), [1] mdk::QAFreePair::Status (C++ enum), [1] mdk::QAFreePair::status (C++ member), [1] mdk::QAFreePair::Status::FREE (C++ enumerator), [1] mdk::QAFreePair::Status::TAKEN (C++ enumerator), [1] mdk::QuasiAdiabatic (C++ class), [1] mdk::QuasiAdiabatic::asyncPart (C++ function), [1] mdk::QuasiAdiabatic::bb_lj (C++ member), [1] mdk::QuasiAdiabatic::bind (C++ function), [1] mdk::QuasiAdiabatic::breakingTime (C++ member), [1] mdk::QuasiAdiabatic::breakingTolerance (C++ member), [1] mdk::QuasiAdiabatic::bs_lj (C++ member), [1] mdk::QuasiAdiabatic::chains (C++ member), [1] mdk::QuasiAdiabatic::computeNH (C++ function), [1] mdk::QuasiAdiabatic::formationMaxDistSq (C++ member), [1] mdk::QuasiAdiabatic::formationTime (C++ member), [1] mdk::QuasiAdiabatic::formationTolerance (C++ member), [1] mdk::QuasiAdiabatic::freePairs (C++ member), [1] mdk::QuasiAdiabatic::geometryPhase (C++ function), [1] mdk::QuasiAdiabatic::h (C++ member), [1] mdk::QuasiAdiabatic::hh_abs_min (C++ member), [1] mdk::QuasiAdiabatic::hr_abs_min (C++ member), [1] mdk::QuasiAdiabatic::n (C++ member), [1] mdk::QuasiAdiabatic::nr_max (C++ member), [1] mdk::QuasiAdiabatic::oldPairs (C++ member), [1] mdk::QuasiAdiabatic::pairs (C++ member), [1] mdk::QuasiAdiabatic::qaDiffs (C++ member), [1] mdk::QuasiAdiabatic::qaDiffsMutex (C++ member), [1] mdk::QuasiAdiabatic::spec (C++ function), [1] mdk::QuasiAdiabatic::ss_ljs (C++ member), [1] mdk::QuasiAdiabatic::stats (C++ member), [1] mdk::QuasiAdiabatic::syncPart (C++ function), [1] mdk::QuasiAdiabatic::types (C++ member), [1] mdk::QuasiAdiabatic::vlUpdateHook (C++ function), [1] mdk::rad (C++ member), [1] mdk::Random (C++ class), [1] mdk::Random::getNewRandom (C++ function), [1] mdk::Random::normal (C++ function), [1], [2], [3] mdk::Random::Random (C++ function), [1], [2], [3], [4], [5] mdk::Random::sphere (C++ function), [1] mdk::Random::state (C++ member), [1] mdk::Random::two_normals (C++ function), [1] mdk::Random::uniform (C++ function), [1], [2], [3] mdk::RelativeDH (C++ class), [1] mdk::RelativeDH::asyncPart (C++ function), [1] mdk::RelativeDH::r0 (C++ member), [1] mdk::RelativeDH::screeningDist (C++ member), [1] mdk::RelativeDH::spec (C++ function), [1] mdk::ResType (C++ class), [1] mdk::ResType::code (C++ member), [1] mdk::ResType::mass (C++ function), [1] mdk::ResType::operator int8_t (C++ function), [1] mdk::ResType::operator ResTypeIdx const& (C++ function), [1] mdk::ResType::operator std::string (C++ function), [1] mdk::ResType::ResType (C++ function), [1], [2], [3], [4], [5], [6], [7] mdk::ResTypeIdx (C++ enum), [1] mdk::ResTypeIdx::ALA (C++ enumerator), [1] mdk::ResTypeIdx::ARG (C++ enumerator), [1] mdk::ResTypeIdx::ASN (C++ enumerator), [1] mdk::ResTypeIdx::ASP (C++ enumerator), [1] mdk::ResTypeIdx::CYS (C++ enumerator), [1] mdk::ResTypeIdx::GLN (C++ enumerator), [1] mdk::ResTypeIdx::GLU (C++ enumerator), [1] mdk::ResTypeIdx::GLY (C++ enumerator), [1] mdk::ResTypeIdx::HIS (C++ enumerator), [1] mdk::ResTypeIdx::ILE (C++ enumerator), [1] mdk::ResTypeIdx::LEU (C++ enumerator), [1] mdk::ResTypeIdx::LYS (C++ enumerator), [1] mdk::ResTypeIdx::MET (C++ enumerator), [1] mdk::ResTypeIdx::PHE (C++ enumerator), [1] mdk::ResTypeIdx::PRO (C++ enumerator), [1] mdk::ResTypeIdx::SER (C++ enumerator), [1] mdk::ResTypeIdx::THR (C++ enumerator), [1] mdk::ResTypeIdx::TRP (C++ enumerator), [1] mdk::ResTypeIdx::TYR (C++ enumerator), [1] mdk::ResTypeIdx::VAL (C++ enumerator), [1] mdk::rtrim (C++ function) mdk::Scalars (C++ type), [1] mdk::second (C++ member), [1] mdk::seq (C++ type) mdk::seq::LegacyParser (C++ class), [1] mdk::seq::LegacyParser::read (C++ function), [1] mdk::seq::Sequence (C++ class), [1] mdk::seq::Sequence::asModel (C++ function), [1] mdk::seq::Sequence::Chain (C++ struct), [1] mdk::seq::Sequence::Chain::codes (C++ member), [1] mdk::seq::Sequence::Chain::contactMaps (C++ member), [1] mdk::seq::Sequence::chains (C++ member), [1] mdk::seq::Sequence::contactMaps (C++ member), [1] mdk::seq::Sequence::screeningDist (C++ member), [1] mdk::ShiftedTruncatedLJ (C++ class), [1] mdk::ShiftedTruncatedLJ::computeF (C++ function), [1] mdk::ShiftedTruncatedLJ::computeV (C++ function), [1] mdk::ShiftedTruncatedLJ::cutoff (C++ function), [1] mdk::ShiftedTruncatedLJ::depth (C++ member), [1] mdk::ShiftedTruncatedLJ::r_cut (C++ member), [1] mdk::ShiftedTruncatedLJ::ShiftedTruncatedLJ (C++ function), [1], [2], [3] mdk::SidechainLJ (C++ class), [1] mdk::SidechainLJ::computeF (C++ function), [1] mdk::SidechainLJ::computeV (C++ function), [1] mdk::SidechainLJ::cutoff (C++ function), [1] mdk::SidechainLJ::depth (C++ member), [1] mdk::SidechainLJ::SidechainLJ (C++ function), [1], [2], [3] mdk::SidechainLJ::sink_max (C++ member), [1] mdk::SimpleNativeDihedral (C++ class), [1] mdk::SimpleNativeDihedral::bind (C++ function), [1] mdk::SimpleNativeDihedral::CDH (C++ member), [1] mdk::SimpleNativeDihedral::term (C++ function), [1] mdk::Simulation (C++ class), [1] mdk::Simulation::add (C++ function), [1] mdk::Simulation::addAsyncTask (C++ function), [1] mdk::Simulation::asyncTasks (C++ member), [1] mdk::Simulation::calcForces (C++ function), [1] mdk::Simulation::data (C++ function), [1] mdk::Simulation::df (C++ member), [1] mdk::Simulation::forces (C++ member), [1] mdk::Simulation::hooks (C++ member), [1] mdk::Simulation::init (C++ function), [1] mdk::Simulation::initialized (C++ member), [1] mdk::Simulation::integrator (C++ member), [1] mdk::Simulation::model (C++ member), [1] mdk::Simulation::nonlocalForces (C++ member), [1] mdk::Simulation::params (C++ member), [1] mdk::Simulation::Simulation (C++ function), [1] mdk::Simulation::step (C++ function), [1], [2], [3] mdk::Simulation::step_nr (C++ member), [1] mdk::Simulation::var (C++ function), [1] mdk::Simulation::vars (C++ member), [1] mdk::SimulVar (C++ class), [1] mdk::SimulVar::bind (C++ function), [1] mdk::skipLine (C++ function) mdk::SolidWall (C++ class) mdk::SolidWall::asyncPart (C++ function) mdk::SolidWall::wall (C++ member) mdk::Stat (C++ struct), [1] mdk::Stat::backbone (C++ member), [1] mdk::Stat::hydrophobicSS (C++ member), [1] mdk::Stat::operator+ (C++ function), [1] mdk::Stat::operator+= (C++ function), [1] mdk::Stat::operator- (C++ function), [1], [2], [3] mdk::Stat::operator-= (C++ function), [1] mdk::Stat::polarSS (C++ member), [1] mdk::Stat::sidechain (C++ member), [1] mdk::Stat::valid (C++ function), [1] mdk::State (C++ class), [1] mdk::State::bind (C++ function), [1] mdk::State::dyn (C++ member), [1] mdk::State::exportTo (C++ function), [1] mdk::State::n (C++ member), [1] mdk::State::prepareDyn (C++ function), [1] mdk::State::r (C++ member), [1] mdk::State::t (C++ member), [1] mdk::State::top (C++ member), [1] mdk::State::updateWithDyn (C++ function), [1] mdk::State::v (C++ member), [1] mdk::Stats (C++ class), [1] mdk::Stats::bind (C++ function), [1] mdk::Stats::creationDiffs (C++ function), [1] mdk::Stats::polarization (C++ member), [1] mdk::Stats::stats (C++ member), [1] mdk::Stats::Type (C++ enum), [1] mdk::Stats::Type::BB (C++ enumerator), [1] mdk::Stats::Type::BS (C++ enumerator), [1] mdk::Stats::Type::SB (C++ enumerator), [1] mdk::Stats::Type::SS (C++ enumerator), [1] mdk::Stats::types (C++ member), [1] mdk::tau (C++ member), [1] mdk::Tether (C++ class), [1] mdk::Tether::asyncPart (C++ function), [1] mdk::Tether::bind (C++ function), [1] mdk::Tether::dist0 (C++ member), [1] mdk::Tether::fromNative (C++ member), [1] mdk::Tether::harm (C++ member), [1] mdk::Tether::isConnected (C++ member), [1] mdk::Tether::n (C++ member), [1] mdk::Tether::Tether (C++ function), [1] mdk::Topology (C++ class), [1] mdk::Topology::cell (C++ member), [1] mdk::Topology::cellInv (C++ member), [1] mdk::Topology::fix (C++ function), [1] mdk::Topology::operator() (C++ function), [1] mdk::Topology::setCell (C++ function), [1] mdk::Topology::use (C++ member), [1] mdk::trim (C++ function) mdk::Types (C++ class), [1] mdk::Types::Types (C++ function), [1], [2], [3] mdk::Vector (C++ type), [1] mdk::VectorBase (C++ type), [1] mdk::Vectors (C++ class), [1] mdk::Vectors::operator[] (C++ function), [1], [2], [3] mdk::Vectors::size (C++ function), [1] mdk::Vectors::Vectors (C++ function), [1], [2], [3], [4], [5] mdk::Vectors::vectorwise (C++ function), [1], [2], [3] mdk::view (C++ function), [1] mdk::vl (C++ type) mdk::vl::List (C++ class), [1] mdk::vl::List::bind (C++ function), [1] mdk::vl::List::chains (C++ member), [1] mdk::vl::List::check (C++ function), [1] mdk::vl::List::cutoff (C++ member), [1] mdk::vl::List::effCutoff (C++ member), [1] mdk::vl::List::effCutoffSq (C++ member), [1] mdk::vl::List::first (C++ member), [1] mdk::vl::List::forces (C++ member), [1] mdk::vl::List::grid (C++ member), [1] mdk::vl::List::indexOf (C++ function), [1] mdk::vl::List::initial (C++ member), [1] mdk::vl::List::last (C++ member), [1] mdk::vl::List::minBondSep (C++ member), [1] mdk::vl::List::needToReset (C++ function), [1] mdk::vl::List::next (C++ member), [1] mdk::vl::List::pad (C++ member), [1] mdk::vl::List::pairs (C++ member), [1] mdk::vl::List::perCell (C++ function), [1] mdk::vl::List::perPair (C++ function), [1] mdk::vl::List::r0 (C++ member), [1] mdk::vl::List::registerNF (C++ function), [1] mdk::vl::List::state (C++ member), [1] mdk::vl::List::t0 (C++ member), [1] mdk::vl::List::top0 (C++ member), [1] mdk::vl::List::update (C++ function), [1] mdk::vl::List::updateGrid (C++ function), [1] mdk::vl::PairInfo (C++ struct) mdk::vl::PairInfo::i1 (C++ member) mdk::vl::PairInfo::i2 (C++ member) mdk::vl::PairInfo::norm (C++ member) mdk::vl::PairInfo::unit (C++ member) mdk::vl::Spec (C++ struct), [1] mdk::vl::Spec::cutoffSq (C++ member), [1] mdk::vl::Spec::minBondSep (C++ member), [1] mdk::VRef (C++ type), [1]

S

std (C++ type), [1], [2] std::hash<mdk::AminoAcid> (C++ struct) std::hash<mdk::AminoAcid>::operator() (C++ function) std::hash<mdk::ContactType> (C++ struct)

std::hash<mdk::ContactType>::operator() (C++ function) std::hash<mdk::ResType> (C++ struct) std::hash<mdk::ResType>::operator() (C++ function) std::PhonyNameDueToError::operator() (C++ function), [1], [2]

U

Unit (C macro)