Classes | |
class | phoenix::ELE |
Element Class This class has a nested enum for all elements. More... | |
class | 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. More... | |
class | 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. More... | |
class | 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. More... | |
class | 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. More... | |
class | 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. More... | |
class | phoenix::PhoenixError |
errors class for phoenix
All errors thrown in namespace phoenix are of this type. More... | |
class | 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. More... | |
Typedefs | |
typedef float | phoenix::Float_t |
floating point number type. | |
typedef Vec3f | phoenix::Vec3_t |
general purpose 3d vector (osg::Vec3d Class). | |
typedef Quat | phoenix::Quat_t |
general purpose quaternion (osg::Quat Class). | |
typedef Matrixf | phoenix::Matrix_t |
general purpose 4x4 matrix (osg::Matrixd Class). | |
typedef vector< ChainKey > | phoenix::ChainList |
container to store "ChainKey"s. Some functions expect this container for in/output. | |
typedef vector< ResidueKey > | phoenix::ResidueList |
container to store "ResidueKey"s. Some functions expect this container for in/output. | |
typedef vector< AtomKey > | phoenix::AtomList |
container to store "AtomKey"s. Some functions expect this container for in/output. | |
typedef vector< BondKey > | phoenix::BondList |
container to store "BondKey"s. Some functions expect this container for in/output. | |
Functions | |
ostream & | phoenix::operator<< (ostream &os, const Vec3_t &v) |
operator<< for Vec3_t | |
ostream & | phoenix::operator<< (ostream &os, const Quat_t &v) |
operator<< for Quat_t | |
void | phoenix::normalize (Quat_t &r) |
normalize Quat_t |