Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
phoenix::AtomAtom 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::BondBond 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::BTBond 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::ChainChain 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::ELEElement Class This class has a nested enum for all elements
paradocks::FitnessFitness class. Virtual base class interface definition for all Fitness class implementations
paradocks::FitnessErrorFitness error class. This class should be thrown by all implemented Fitness classes in case of an error. Derived from std::runtime_error
phoenix::GEOGeometry 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::GridGrid class. This class can be used to aproximate the energie value within a grid by linear triangulation
phoenix::MOLMOL Class Class MOL can be used to copy molecules
paradocks::OptimizerOptimizer class. Virtual base class interface definition for all Optimizer class implementations
paradocks::OptimizerErrorOptimizer error class. This class should be thrown by all implemented Optimizer classes in case of an error
paradocks::ParadocksConfigClass 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::PhoenixErrorErrors class for phoenix

All errors thrown in namespace phoenix are of this type

paradocks::PSOParticle 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::ResidueResidue 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::RTResidue 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::StaticNeighborhoodStaticNeighborhood class. This class provides a static neighborhood list for atoms
paradocks::SWLSLocal 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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