Functions | |
ChainList | phoenix::Chains () |
Return all chains. | |
ResidueList | phoenix::cResidues (ChainKey c) |
Return the residues of a chain. | |
ResidueList | phoenix::clResidues (const ChainList &cl) |
Return the residues of several chains. | |
AtomList | phoenix::cAtoms (ChainKey c) |
Return the atoms of a chain. | |
AtomList | phoenix::clAtoms (const ChainList &cl) |
Return the atoms of several chains. | |
ResidueList | phoenix::Residues () |
Return all residues. | |
ChainKey | phoenix::rChain (ResidueKey r) |
ChainList | phoenix::rlChain (const ResidueList &rl) |
Return the parent chain of several residues. | |
AtomList | phoenix::rAtoms (ResidueKey r) |
Return the atoms of a residue. | |
AtomList | phoenix::rlAtoms (ResidueList rl) |
Return the atoms of several residues. | |
AtomList | phoenix::Atoms () |
Return all atoms. | |
ChainKey | phoenix::aChain (AtomKey a) |
ChainList | phoenix::alChains (const AtomList &al) |
Return the parent chain of several atoms. | |
ResidueKey | phoenix::aResidue (AtomKey a) |
ResidueList | phoenix::alResidues (const AtomList &al) |
Return the parent residues of several atoms. | |
BondList | phoenix::aBonds (AtomKey a) |
Return the bonds of an atom. | |
BondList | phoenix::alBonds (const AtomList &al) |
Return the bonds of several atoms. | |
AtomList | phoenix::aAdjAtoms (AtomKey a) |
Return the adjacent atoms of a. | |
BondList | phoenix::aaFormBond (AtomKey a1, AtomKey a2) |
Return the bond between a1 and a2. | |
AtomList | phoenix::abAdjAtom (AtomKey a1, BondKey b) |
Return the adjacent atom of a connected by b. | |
BondList | phoenix::Bonds () |
AtomList | phoenix::bAtoms (BondKey b) |
AtomList | phoenix::blAtoms (const BondList &bl) |
Return the atoms of several bonds. | |
bool | phoenix::isRingBond (BondKey b) |
Return true if bond b is in a ring. | |
bool | phoenix::isXRingBond (BondKey b, unsigned int x) |
Return true if bond b is in a ring with x atoms. | |
bool | phoenix::isRingAtom (AtomKey a) |
Return true if atom a is in a ring. | |
bool | phoenix::isXRingAtom (AtomKey a, unsigned int x) |
Return true if atom a is in a ring with x atoms. | |
AtomList | phoenix::aExtendConnected (AtomKey a) |
ChainList phoenix::Chains | ( | ) |
Return all chains.
Return all chains in the order they are stored in the global container.
ResidueList phoenix::cResidues | ( | ChainKey | c | ) |
Return the residues of a chain.
Return the residues of chain c in the order they are stored in the chain.
ResidueList phoenix::clResidues | ( | const ChainList & | cl | ) |
Return the residues of several chains.
Return the residues of all chains in cl. The residues are simply concatenated. This list is not uniq if one chain appears twice.
AtomList phoenix::cAtoms | ( | ChainKey | c | ) |
Return the atoms of a chain.
Return the atoms of chain c by concatenating the atoms of all residue in c.
AtomList phoenix::clAtoms | ( | const ChainList & | cl | ) |
Return the atoms of several chains.
Return the atoms of all chains in cl. The atoms are simply concatenated. This list is not uniq if one chain appears twice.
ResidueList phoenix::Residues | ( | ) |
Return all residues.
Return all residues in the order they are stored in the chains. This is done by concatenating all residues of all chains.
ChainKey phoenix::rChain | ( | ResidueKey | r | ) |
Return the parent chain.
ChainList phoenix::rlChain | ( | const ResidueList & | rl | ) |
Return the parent chain of several residues.
Return the parent chain of several residues. The result will have one chain for every residue in cl.
AtomList phoenix::rAtoms | ( | ResidueKey | r | ) |
Return the atoms of a residue.
Return the atoms of residue r in the order they are stored in the residue.
AtomList phoenix::rlAtoms | ( | ResidueList | rl | ) |
Return the atoms of several residues.
Return the atoms of all residues in rl. The atoms are simply concatenated. This list is not uniq if one residue appears twice.
AtomList phoenix::Atoms | ( | ) |
Return all atoms.
Return all atoms.This is done by concatenating all atoms of all residues of all chains.
ChainKey phoenix::aChain | ( | AtomKey | a | ) |
Return the parent chain of the parent residue.
ChainList phoenix::alChains | ( | const AtomList & | al | ) |
Return the parent chain of several atoms.
Return the parent chain of all the parent residues of all atoms in al. The result will have one chain for every atom in al.
ResidueKey phoenix::aResidue | ( | AtomKey | a | ) |
Return the parent residue.
ResidueList phoenix::alResidues | ( | const AtomList & | al | ) |
Return the parent residues of several atoms.
Return the parent residues of all atoms in al. The result will have one residue for every atom in al.
BondList phoenix::aBonds | ( | AtomKey | a | ) |
Return the bonds of an atom.
Return the bonds of atom a.
BondList phoenix::alBonds | ( | const AtomList & | al | ) |
Return the bonds of several atoms.
Return the bonds of all atoms in al. The result is uniq.
AtomList phoenix::aAdjAtoms | ( | AtomKey | a | ) |
Return the adjacent atoms of a.
Return the adjacent atoms of a. The order of the result is the same like the result from aBonds.
BondList phoenix::aaFormBond | ( | AtomKey | a1, | |
AtomKey | a2 | |||
) |
Return the bond between a1 and a2.
If atom a1 and atom a2 form a bond it will be in the result. Otherwise it will be empty.
AtomList phoenix::abAdjAtom | ( | AtomKey | a1, | |
BondKey | b | |||
) |
Return the adjacent atom of a connected by b.
Return the adjacent atom of a connected by b. If there is no atom connected to a by b the result will be empty.
BondList phoenix::Bonds | ( | ) |
Return all bonds.
AtomList phoenix::bAtoms | ( | BondKey | b | ) |
Return the atoms of the bond.
AtomList phoenix::blAtoms | ( | const BondList & | bl | ) |
Return the atoms of several bonds.
Return the atoms of the several bonds. The result is uniq.
bool phoenix::isRingBond | ( | BondKey | b | ) |
Return true if bond b is in a ring.
Return true if bond b is in a ring. The size of the ring doesn't matter.
bool phoenix::isXRingBond | ( | BondKey | b, | |
unsigned int | x | |||
) |
Return true if bond b is in a ring with x atoms.
Return true if bond b is in a ring with x atoms. Note: b can also be in a ring of different size.
bool phoenix::isRingAtom | ( | AtomKey | a | ) |
Return true if atom a is in a ring.
Return true if atom a is in a ring. The size of the ring doesn't matter.
bool phoenix::isXRingAtom | ( | AtomKey | a, | |
unsigned int | x | |||
) |
Return true if atom a is in a ring with x atoms.
Return true if atom a is in a ring with x atoms. Note: a can also be in a ring of different size.
AtomList phoenix::aExtendConnected | ( | AtomKey | a | ) |
Return all atoms which are connected to atom a.