#include <gcu/molecule.h>
List of all members.
Detailed Description
Represents molecules.
Definition at line 43 of file gcu/molecule.h.
Constructor & Destructor Documentation
gcu::Molecule::Molecule |
( |
TypeId |
Type = MoleculeType , |
|
|
ContentType |
ct = ContentType3D |
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) |
| |
- Parameters:
-
Type | the type id of a derived class |
The constructor. The type id may be changed in derived classes, otherwise the argument is not needed, since the default value is enough.
- Parameters:
-
pAtom | Builds a molecule from an atom. If the atom has bonds, the connectivity will be explored and all atoms and bonds found will be added to the molecule. |
virtual gcu::Molecule::~Molecule |
( |
| ) |
[virtual] |
Member Function Documentation
virtual void gcu::Molecule::AddAtom |
( |
Atom * |
pAtom | ) |
[virtual] |
- Parameters:
-
Adds an atom to the molecule.
Reimplemented in gcp::Molecule.
virtual void gcu::Molecule::AddBond |
( |
Bond * |
pBond | ) |
[virtual] |
- Parameters:
-
Adds a bond to the molecule.
Reimplemented in gcp::Molecule.
void gcu::Molecule::AddChild |
( |
Object * |
object | ) |
[virtual] |
- Parameters:
-
object | an object, generally an atom or a bond. |
Adds an object (which might be an atom or a bond) to the molecule.
Reimplemented from gcu::Object.
Reimplemented in gcp::Molecule.
void gcu::Molecule::Clear |
( |
| ) |
[virtual] |
virtual unsigned gcu::Molecule::GetAtomsNumber |
( |
| ) |
const [inline, virtual] |
Atom const* gcu::Molecule::GetFirstAtom |
( |
std::list< Atom * >::const_iterator & |
i | ) |
const |
- Parameters:
-
i | an uninitialized iterator. |
- Returns:
- the first atom of the molecule.
Bond const* gcu::Molecule::GetFirstBond |
( |
std::list< Bond * >::const_iterator & |
i | ) |
const |
- Parameters:
-
i | an uninitialized iterator. |
- Returns:
- the first bond of the molecule.
std::string const& gcu::Molecule::GetInChI |
( |
| ) |
|
char const* gcu::Molecule::GetName |
( |
char const * |
convention = NULL | ) |
|
- Parameters:
-
convention | a naming convention. |
- Returns:
- the molecule name using convention if known.
Atom const* gcu::Molecule::GetNextAtom |
( |
std::list< Atom * >::const_iterator & |
i | ) |
const |
- Parameters:
-
- Returns:
- the next atom of the molecule or NULL if all atoms have been previously returned.
Bond const* gcu::Molecule::GetNextBond |
( |
std::list< Bond * >::const_iterator & |
i | ) |
const |
- Parameters:
-
- Returns:
- the next bond of the molecule or NULL if all bonds have been previously returned.
static Molecule* gcu::Molecule::MoleculeFromFormula |
( |
Document * |
Doc, |
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Formula const & |
formula, |
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bool |
add_pseudo = true |
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) |
| [static] |
- Parameters:
-
Doc | a document. |
formula | a formula |
add_pseudo | tells if a pseudo atom (with Z = 0) has to be added (used when building a gcu::Residue instance). |
Tries to build a molecule from a formula, adding bonds between atoms. Atoms coordinates are not calculated.
- Returns:
- a molecule on success or NULL.
std::string gcu::Molecule::Name |
( |
| ) |
[virtual] |
- Returns:
- the localized object generic name.
Reimplemented from gcu::Object.
bool gcu::Molecule::operator== |
( |
Molecule const & |
molecule | ) |
const |
- Parameters:
-
- Returns:
- true if the molecules have identical atoms and the connection framework between the atoms.
virtual void gcu::Molecule::Remove |
( |
gcu::Object * |
pObject | ) |
[virtual] |
- Parameters:
-
pObject | an atom or a bond in the molecule. |
Removes an atom or a bond from a molecule.
Reimplemented in gcp::Molecule.
void gcu::Molecule::SetName |
( |
char const * |
name, |
|
|
char const * |
convention |
|
) |
| |
- Returns:
- the localized object generic name.
- Parameters:
-
name | a name. |
convention | a naming convention, might be NULL. |
Adds a molecule name following convention. Only one name can be stored for a given convention.
void gcu::Molecule::UpdateCycles |
( |
| ) |
|
Updates the cycles list after a change.
void gcu::Molecule::UpdateCycles |
( |
Bond * |
pBond | ) |
|
- Parameters:
-
pBond | a bond in the molecule. |
Updates the cycles list after a change, starting the exploration from pBond.
Member Data Documentation
The non cyclic chains contained in the molecules (not used at the moment).
Definition at line 189 of file gcu/molecule.h.
The cycles contained in the molecules.
Definition at line 185 of file gcu/molecule.h.
The documentation for this class was generated from the following file: