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The Gnome Chemistry Utils 0.12.8
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#include <gcu/chain.h>
Public Member Functions | |
| Chain (Bond *pBond, Atom *pAtom=NULL, TypeId Type=ChainType) | |
| Chain (Molecule *molecule, Bond *pBond, TypeId Type=ChainType) | |
| Chain (Molecule *molecule, Atom *pAtom, TypeId Type=ChainType) | |
| virtual | ~Chain () |
| void | FindCycles (Atom *pAtom) |
| bool | FindCycle (Atom *pAtom, Bond *pBond) |
| virtual void | Erase (Atom *pAtom1, Atom *pAtom2) |
| virtual void | Insert (Atom *pAtom1, Atom *pAtom2, Chain &chain) |
| void | Extract (Atom *pAtom1, Atom *pAtom2, Chain &chain) |
| void | Reverse () |
| void | AddBond (Atom *start, Atom *end) |
| unsigned | GetUnsaturations () |
| unsigned | GetHeteroatoms () |
| bool | Contains (Atom *pAtom) |
| bool | Contains (Bond *pBond) |
| unsigned | GetLength () |
| double | GetMeanBondLength () |
| Atom * | GetNextAtom (Atom *pAtom) |
| std::string | Name () |
Protected Attributes | |
| std::map< Atom *, ChainElt > | m_Bonds |
| Molecule * | m_Molecule |
| pBond | a bond. |
| pAtom | an atom. |
| Type | an optional type id used when constructing a derived type (i. e. a cycle). |
Constructs a Chain starting from a bond and an optional atom. Choosing the atom forces the direction of the chain, otherwise, the first atom will be the first atom of the bond.
| molecule | a molecule. |
| pBond | a bond in the molecule or NULL. |
| Type | an optional type id used when constructing a derived type |
Explores a molecule and find all cycles, starting from pBond or an empty chain if pBond is NULL.
| molecule | a molecule. |
| pAtom | an atom in the molecule. |
| Type | an optional type id used when constructing a derived type |
Explores a molecule and find all cycles, starting from pAtom or an empty chain if pAtom is NULL.
| virtual gcu::Chain::~Chain | ( | ) | [virtual] |
The destructor.
| start | an atom. |
| end | an atom. |
Adds the two atoms and the bond between them to the chain. The two atoms must be bonded.
| bool gcu::Chain::Contains | ( | Atom * | pAtom | ) |
| pAtom | an atom. |
| bool gcu::Chain::Contains | ( | Bond * | pBond | ) |
| pBond | a bond. |
| pAtom1 | an atom in the source chain. |
| pAtom2 | an atom in the source chain. |
Erases a sub-chain. One of the atoms must already be one of the chain ends.
Reimplemented in gcu::Cycle.
| pAtom1 | an atom in the chain. |
| pAtom2 | an atom in the chain. |
| chain | the target chain. |
Extracts a sub-chain to the chain variable which should be empty before the call.
| pAtom | an atom. |
| pBond | a bond. |
Searches for a cycle containing the atom pAtom and the bond pBond. pAtom must be one of the ends of pBond. If a cycle is found, it is added to the molecule cycles list.
| void gcu::Chain::FindCycles | ( | Atom * | pAtom | ) |
| pAtom | an atom. |
Searches all cycles in a molecule starting from Atom pAtom. Found cycles are added to the molecule cycles list.
| unsigned gcu::Chain::GetHeteroatoms | ( | ) |
| unsigned gcu::Chain::GetLength | ( | ) |
| double gcu::Chain::GetMeanBondLength | ( | ) |
| pAtom | an atom in the chain. |
| unsigned gcu::Chain::GetUnsaturations | ( | ) |
| pAtom1 | an atom in the source chain. |
| pAtom2 | an atom in the source chain. |
| chain | the source chain. |
Inserts a chain. One of the atoms must already be in the target chain.
Reimplemented in gcu::Cycle.
| std::string gcu::Chain::Name | ( | ) | [virtual] |
Reimplemented from gcu::Object.
Reimplemented in gcu::Cycle.
| void gcu::Chain::Reverse | ( | ) |
Reverses the chain order.
std::map<Atom*, ChainElt> gcu::Chain::m_Bonds [protected] |
The gcu::ChainElt elements in the chain indexed by their common atom.
Molecule* gcu::Chain::m_Molecule [protected] |
1.7.4