Classes | |
class | ELE |
Element Class This class has a nested enum for all elements. More... | |
class | 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 | 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 | 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 | 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 | 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 | MOL |
MOL Class Class MOL can be used to copy molecules. More... | |
class | PhoenixError |
errors class for phoenix
All errors thrown in namespace phoenix are of this type. More... | |
class | 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. More... | |
class | 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 | Float_t |
floating point number type. | |
typedef Vec3f | Vec3_t |
general purpose 3d vector (osg::Vec3d Class). | |
typedef Quat | Quat_t |
general purpose quaternion (osg::Quat Class). | |
typedef Matrixf | Matrix_t |
general purpose 4x4 matrix (osg::Matrixd Class). | |
typedef vector< ChainKey > | ChainList |
container to store "ChainKey"s. Some functions expect this container for in/output. | |
typedef vector< ResidueKey > | ResidueList |
container to store "ResidueKey"s. Some functions expect this container for in/output. | |
typedef vector< AtomKey > | AtomList |
container to store "AtomKey"s. Some functions expect this container for in/output. | |
typedef vector< BondKey > | BondList |
container to store "BondKey"s. Some functions expect this container for in/output. | |
Functions | |
ostream & | operator<< (ostream &os, const ELE &e) |
operator << for class ELE | |
ostream & | operator<< (ostream &os, const GEO &g) |
operator << for class GEO | |
ostream & | operator<< (ostream &os, const BT &bt) |
operator << for class BT | |
ChainKey | cCreate (string n) |
Create a new chain. | |
void | cDelete (ChainKey c) |
Delete a chain. | |
void | clDelete (const ChainList &cl) |
Delete several chains. | |
ResidueKey | rCreate (ChainKey p, RT rt) |
Create a new residue. | |
void | rDelete (ResidueKey r) |
Delete a residue. | |
void | rlDelete (const ResidueList &rl) |
Delete several residues. | |
AtomKey | aCreate (ResidueKey p, ELE e, Vec3_t c, GEO g) |
Create a new atom. | |
void | aDelete (AtomKey a) |
Delete an atom. | |
void | alDelete (const AtomList &al) |
Delete several atoms. | |
BondKey | bCreate (AtomKey a1, AtomKey a2, BT bt) |
Create a new bond. | |
void | bDelete (BondKey b) |
Delete a bond. | |
void | blDelete (const BondList &bl) |
Delete several bonds. | |
ChainList | Chains () |
Return all chains. | |
ResidueList | cResidues (ChainKey c) |
Return the residues of a chain. | |
ResidueList | clResidues (const ChainList &cl) |
Return the residues of several chains. | |
AtomList | cAtoms (ChainKey c) |
Return the atoms of a chain. | |
AtomList | clAtoms (const ChainList &cl) |
Return the atoms of several chains. | |
ResidueList | Residues () |
Return all residues. | |
ChainKey | rChain (ResidueKey r) |
ChainList | rlChain (const ResidueList &rl) |
Return the parent chain of several residues. | |
AtomList | rAtoms (ResidueKey r) |
Return the atoms of a residue. | |
AtomList | rlAtoms (ResidueList rl) |
Return the atoms of several residues. | |
AtomList | Atoms () |
Return all atoms. | |
ChainKey | aChain (AtomKey a) |
ChainList | alChains (const AtomList &al) |
Return the parent chain of several atoms. | |
ResidueKey | aResidue (AtomKey a) |
ResidueList | alResidues (const AtomList &al) |
Return the parent residues of several atoms. | |
BondList | aBonds (AtomKey a) |
Return the bonds of an atom. | |
BondList | alBonds (const AtomList &al) |
Return the bonds of several atoms. | |
AtomList | aAdjAtoms (AtomKey a) |
Return the adjacent atoms of a. | |
BondList | aaFormBond (AtomKey a1, AtomKey a2) |
Return the bond between a1 and a2. | |
AtomList | abAdjAtom (AtomKey a1, BondKey b) |
Return the adjacent atom of a connected by b. | |
BondList | Bonds () |
AtomList | bAtoms (BondKey b) |
AtomList | blAtoms (const BondList &bl) |
Return the atoms of several bonds. | |
bool | isRingBond (BondKey b) |
Return true if bond b is in a ring. | |
bool | isXRingBond (BondKey b, unsigned int x) |
Return true if bond b is in a ring with x atoms. | |
bool | isRingAtom (AtomKey a) |
Return true if atom a is in a ring. | |
bool | isXRingAtom (AtomKey a, unsigned int x) |
Return true if atom a is in a ring with x atoms. | |
AtomList | aExtendConnected (AtomKey a) |
AtomList | alExtendConnected (AtomList al) |
unsigned int | aHeavyCount (AtomKey a) |
unsigned int | aHCount (AtomKey a) |
unsigned int | aLPCount (AtomKey a) |
Return the number of lonepairs(explicit). | |
bool | aPolar (AtomKey a) |
Return true if not all adjacent atoms C or H. | |
bool | aMetall (AtomKey a) |
Return true if a is a metall atom. | |
void | CorrectGraphByTopology (ChainList cl) |
Fix small problems in the graph, so that type perception works well. | |
ChainList | ReadMOL2 (string file) |
int | GraphDistance (AtomKey a1, AtomKey a2) |
AtomKey | aAdjacentAtom (AtomKey a1, BondKey b) |
search for subgraphs matching query | |
ostream & | operator<< (ostream &os, const Vec3_t &v) |
operator<< for Vec3_t | |
ostream & | operator<< (ostream &os, const Quat_t &v) |
operator<< for Quat_t | |
void | normalize (Quat_t &r) |
normalize Quat_t | |
ostream & | operator<< (ostream &os, const RT &rt) |
operator << for class RT |
AtomList phoenix::alExtendConnected | ( | AtomList | al | ) |
Return all atoms which are connected to any atom in al.
ChainList phoenix::ReadMOL2 | ( | string | file | ) |
read a Tripos mol2 file
int phoenix::GraphDistance | ( | AtomKey | a1, | |
AtomKey | a2 | |||
) |
return the distance in bonds between atom a1 and a2
AtomKey phoenix::aAdjacentAtom | ( | AtomKey | a1, | |
BondKey | b | |||
) |
search for subgraphs matching query
return the atom adjacent to a1, connected by b