| phoenix::Atom | Atom Class Class Atom represents the nodes in the molecular graph and the last layer in the hirachical tree. An Atom has an parent Residue, an Element (class ELE), a Geometry (class GEO), 3d coordinates (Vec3_t) and a list of bonds. It can also have a name, a forcefield type, a charge and a formal charge |
| phoenix::Bond | Bond Class Class Bond represents the edges in a molecular graph. A Bond has two AtomKeys for the atoms, which are connected by the bond, and a bondtype (class BT). The atoms are named Atom1 and Atom2. Its also possible to store a forcefield type (unsigned int) in the bond |
| phoenix::BT | Bond Type Class This class has a nested enum for different bondtypes. Supported bondtypes are: BT::s - single bond BT::re - bond involved in resonance stabilized system eg. carboxylate, peptide but not aromatic BT::ar - aromatic bond BT::d - double bond BT::t - triple bond BT::UNK - unknown |
| phoenix::Chain | Chain Class This class is the top level in the molecular tree structure. It has a name, a ResidueList with all residues and a tag |
| phoenix::ELE | Element Class This class has a nested enum for all elements |
| paradocks::Fitness | Fitness class. Virtual base class interface definition for all Fitness class implementations |
| paradocks::FitnessError | Fitness error class. This class should be thrown by all implemented Fitness classes in case of an error. Derived from std::runtime_error |
| phoenix::GEO | Geometry Class This class has a nested enum for geometries. Supported geometries are: GEO::none - atoms with no or one bond eg. H, Fl, Cl GEO::lin - linear geometry for atoms with 2 bonds eg. sp carbon GEO::tri - trigonal planar geometry eg. sp2 carbon/nitrogen, carboxylate oxygen(lonepairs also count) GEO::tet - tetrahedral geometry eg. sp3 carbon but also hydroxy oxygen GEO::bip - trigonal bipyramidal GEO::oct - octahedral GEO::UNK - unknown geometry |
| paradocks::Grid | Grid class. This class can be used to aproximate the energie value within a grid by linear triangulation |
| phoenix::MOL | MOL Class Class MOL can be used to copy molecules |
| paradocks::Optimizer | Optimizer class. Virtual base class interface definition for all Optimizer class implementations |
| paradocks::OptimizerError | Optimizer error class. This class should be thrown by all implemented Optimizer classes in case of an error |
| paradocks::ParadocksConfig | Class to hold configuration data. This class parses the configuration file and holds the configuration data. With the help of this object, data is transmitted between participating nodes |
| phoenix::PhoenixError | Errors class for phoenix All errors thrown in namespace phoenix are of this type |
| paradocks::PSO | Particle Swarm Optimization class. This class implements particle swarm optimization from: J. Kennedy and R. Eberhart Particle swarm optimization Proc. of the IEEE Int. Conf. on Neural Networks, Piscataway, NJ, pp. 1942-1948, 1995. an example input section looks like this: |
| phoenix::Residue | Residue Class This is a container to group atoms in small organising units. It has a parent Chain, a residue type (class RT) and a AtomList with all atoms of the residue. It can also have a name and a id |
| phoenix::RT | Residue Type Class This class has a nested enum for different residues types. Supported residues types are: standard as ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL modified standard as ASZ, ASH - neutral ASP GLZ, GLH - neutral GLU HID - neutral HIS, H at ND1, converted to HIS HIE - neutral HIS, H at NE2 HIP - positive HIS LYZ, LYN - neutral LYS CYM - negative CYS CYX - half cystine, CYS in disulfide bridges TYM - negative TYR N and C terminus AMN - N-terminus ammonium AMI - N-terminus amin CXL - C-terminus carboxylate CXC - C-terminus carbon acid UNK - unspecified type |
| paradocks::StaticNeighborhood | StaticNeighborhood class. This class provides a static neighborhood list for atoms |
| paradocks::SWLS | Local search optimizer Solis, JF and Wets, RJ, Math Oper Res (1981) vol. 6 (1) pp. 19-30 this class makes a local search starting at the input conformation |
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