gcu::Chain Class Reference
#include <gcu/chain.h>
List of all members.
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) |
Protected Attributes |
std::map< Atom *, ChainElt > | m_Bonds |
Molecule * | m_Molecule |
Detailed Description
This class is used to represent chains of atoms.
Definition at line 59 of file chain.h.
Constructor & Destructor Documentation
gcu::Chain::Chain |
( |
Bond * |
pBond, |
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|
Atom * |
pAtom = NULL , |
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|
TypeId |
Type = ChainType | |
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) |
| | |
- Parameters:
-
| 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.
- Parameters:
-
| 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.
- Parameters:
-
| 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 |
( |
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) |
[virtual] |
Member Function Documentation
void gcu::Chain::AddBond |
( |
Atom * |
start, |
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Atom * |
end | |
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) |
| | |
- Parameters:
-
| 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 |
( |
Bond * |
pBond |
) |
|
- Parameters:
-
- Returns:
- true if pBond is in the chain.
bool gcu::Chain::Contains |
( |
Atom * |
pAtom |
) |
|
- Parameters:
-
- Returns:
- true if pAtom is in the chain.
virtual void gcu::Chain::Erase |
( |
Atom * |
pAtom1, |
|
|
Atom * |
pAtom2 | |
|
) |
| | [virtual] |
- Parameters:
-
| 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.
void gcu::Chain::Extract |
( |
Atom * |
pAtom1, |
|
|
Atom * |
pAtom2, |
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Chain & |
chain | |
|
) |
| | |
- Parameters:
-
| 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.
bool gcu::Chain::FindCycle |
( |
Atom * |
pAtom, |
|
|
Bond * |
pBond | |
|
) |
| | |
- Parameters:
-
| 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.
- Returns:
- true on success, false otherwise.
void gcu::Chain::FindCycles |
( |
Atom * |
pAtom |
) |
|
- Parameters:
-
Searches all cycles in a molecule starting from Atom pAtom. Found cycles are added to the molecule cycles list.
unsigned gcu::Chain::GetHeteroatoms |
( |
|
) |
|
- Returns:
- the number of heteroatoms in the chain.
unsigned gcu::Chain::GetLength |
( |
|
) |
|
- Returns:
- the number of bonds in the chain
double gcu::Chain::GetMeanBondLength |
( |
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) |
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- Returns:
- the mean bond length in the chain.
Atom* gcu::Chain::GetNextAtom |
( |
Atom * |
pAtom |
) |
|
- Parameters:
-
| pAtom | an atom in the chain. |
- Returns:
- the next atom in the chain or NULL if pAtom is the last one.
unsigned gcu::Chain::GetUnsaturations |
( |
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) |
|
- Returns:
- the number of multiple bonds in the chain so not really the unsaturations number.
virtual void gcu::Chain::Insert |
( |
Atom * |
pAtom1, |
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Atom * |
pAtom2, |
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Chain & |
chain | |
|
) |
| | [virtual] |
- Parameters:
-
| 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.
void gcu::Chain::Reverse |
( |
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) |
|
Reverses the chain order.
Member Data Documentation
The molecule which owns the chain.
Definition at line 189 of file chain.h.
The documentation for this class was generated from the following file: