#include <gcu/molecule.h>
List of all members.
Detailed Description
Represents molecules.
Definition at line 42 of file gcu/molecule.h.
Constructor & Destructor Documentation
- 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.
Reimplemented in gcp::Molecule.
- 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. |
Member Function Documentation
- Parameters:
-
Adds an atom to the molecule.
Reimplemented in gcp::Molecule.
- Parameters:
-
Adds a bond to the molecule.
Reimplemented in gcp::Molecule.
- 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.
- Parameters:
-
i | an uninitialized iterator. |
- Returns:
- the first atom of the molecule.
- Parameters:
-
i | an uninitialized iterator. |
- Returns:
- the first bond of the molecule.
- Parameters:
-
convention | a naming convention. |
- Returns:
- the molecule name using convention if known.
- Parameters:
-
- Returns:
- the next atom of the molecule or NULL if all atoms have been previously returned.
- Parameters:
-
- Returns:
- the next bond of the molecule or NULL if all bonds have been previously returned.
- 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.
- 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.
- Parameters:
-
pObject | an atom or a bond in the molecule. |
Removes an atom or a bond from a molecule.
Reimplemented in gcp::Molecule.
- 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.
- Parameters:
-
pBond | a bond in the molecule. |
Updates the cycles list after a change, starting the exploration from pBond.
Updates the cycles list after a change.
Member Data Documentation
The non cyclic chains contained in the molecules (not used at the moment).
Definition at line 179 of file gcu/molecule.h.
The cycles contained in the molecules.
Definition at line 175 of file gcu/molecule.h.
The documentation for this class was generated from the following file: