Graph/Tree Types and Classes


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

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