BALL
1.4.1
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#include <BALL/KERNEL/fragment.h>
Public Member Functions | |
bool | operator== (const Fragment &fragment) const |
bool | operator!= (const Fragment &fragment) const |
Constructors and Destructors | |
Fragment () | |
Fragment (const Fragment &fragment, bool deep=true) | |
Fragment (const String &name) | |
virtual | ~Fragment () |
Persistence | |
void | persistentWrite (PersistenceManager &pm, const char *name=0) const |
void | persistentRead (PersistenceManager &pm) |
Assignment | |
Fragment & | operator= (const Fragment &fragment) |
Debugging and Diagnostics | |
virtual void | dump (std::ostream &s=std::cout, Size depth=0) const |
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AtomContainer () | |
AtomContainer (const AtomContainer &atom_container, bool deep=true) | |
AtomContainer (const String &name) | |
virtual | ~AtomContainer () |
virtual void | clear () |
virtual void | destroy () |
void | set (const AtomContainer &atom_container, bool deep=true) |
AtomContainer & | operator= (const AtomContainer &atom_container) |
void | get (AtomContainer &atom_container, bool deep=true) const |
void | swap (AtomContainer &atom_container) |
bool | operator== (const AtomContainer &atom_container) const |
bool | operator!= (const AtomContainer &atom_container) const |
bool | isSubAtomContainerOf (const AtomContainer &atom_container) const |
bool | isSuperAtomContainerOf (const AtomContainer &atom_container) const |
void | setName (const String &name) |
const String & | getName () const |
AtomContainer * | getSuperAtomContainer () |
const AtomContainer * | getSuperAtomContainer () const |
AtomContainer * | getAtomContainer (Position position) |
const AtomContainer * | getAtomContainer (Position position) const |
Atom * | getAtom (Position position) |
const Atom * | getAtom (Position position) const |
Atom * | getAtom (const String &name) |
const Atom * | getAtom (const String &name) const |
Size | countAtomContainers () const |
Size | countAtoms () const |
Size | countBonds () const |
Size | countInterBonds () const |
Size | countIntraBonds () const |
void | prepend (Atom &atom) |
void | append (Atom &atom) |
void | insert (Atom &atom) |
void | insertBefore (Atom &atom, Composite &before) |
void | insertAfter (Atom &atom, Composite &after) |
bool | remove (Atom &atom) |
Size | removeHavingProperty (BALL::Property p) |
Size | removeNotHavingProperty (BALL::Property p) |
Size | removeHavingProperty (const string &name) |
Size | removeNotHavingProperty (const string &name) |
void | prepend (AtomContainer &atom_container) |
void | append (AtomContainer &atom_container) |
void | insert (AtomContainer &atom_container) |
void | insertBefore (AtomContainer &atom_container, Composite &before) |
void | insertAfter (AtomContainer &atom_container, Composite &after) |
void | spliceBefore (AtomContainer &atom_container) |
void | spliceAfter (AtomContainer &atom_container) |
void | splice (AtomContainer &atom_container) |
bool | remove (AtomContainer &atom_container) |
void | destroyBonds () |
virtual bool | isValid () const |
bool | applyIntraBond (UnaryProcessor< Bond > &processor) |
Apply to all bonds connecting two atoms inside this AtomContainer. | |
bool | applyInterBond (UnaryProcessor< Bond > &processor) |
Apply to all bonds connected to atoms outside this AtomContainer. | |
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AncestorIterator | beginAncestor () |
AncestorIterator | endAncestor () |
AncestorConstIterator | beginAncestor () const |
AncestorConstIterator | endAncestor () const |
ChildCompositeIterator | beginChildComposite () |
ChildCompositeIterator | endChildComposite () |
ChildCompositeConstIterator | beginChildComposite () const |
ChildCompositeConstIterator | endChildComposite () const |
ChildCompositeReverseIterator | rbeginChildComposite () |
ChildCompositeReverseIterator | rendChildComposite () |
ChildCompositeConstReverseIterator | rbeginChildComposite () const |
ChildCompositeConstReverseIterator | rendChildComposite () const |
CompositeIterator | beginComposite () |
CompositeIterator | endComposite () |
CompositeConstIterator | beginComposite () const |
CompositeConstIterator | endComposite () const |
CompositeReverseIterator | rbeginComposite () |
CompositeReverseIterator | rendComposite () |
CompositeConstReverseIterator | rbeginComposite () const |
CompositeConstReverseIterator | rendComposite () const |
void | deleteChildrenList_ (std::list< Composite * > &composites) |
Composite () | |
Composite (const Composite &composite, bool deep=true) | |
virtual | ~Composite () |
void | destroy (bool virtual_destroy) |
void * | clone (Composite &root) const |
bool | operator== (const Composite &composite) const |
bool | operator!= (const Composite &composite) const |
bool | isEmpty () const |
bool | isRoot () const |
bool | isRootOf (const Composite &composite) const |
bool | isInterior () const |
bool | hasChild () const |
bool | isChildOf (const Composite &composite) const |
bool | isFirstChild () const |
bool | isFirstChildOf (const Composite &composite) const |
bool | isLastChild () const |
bool | isLastChildOf (const Composite &composite) const |
bool | hasParent () const |
bool | isParentOf (const Composite &composite) const |
bool | hasSibling () const |
bool | isSiblingOf (const Composite &composite) const |
bool | hasPreviousSibling () const |
bool | isPreviousSiblingOf (const Composite &composite) const |
bool | hasNextSibling () const |
bool | isNextSiblingOf (const Composite &composite) const |
bool | isDescendantOf (const Composite &composite) const |
template<typename T > | |
bool | hasAncestor (const T &dummy) const |
bool | isAncestorOf (const Composite &composite) const |
bool | isRelatedWith (const Composite &composite) const |
bool | isHomomorph (const Composite &composite) const |
bool | containsSelection () const |
void | host (Visitor< Composite > &visitor) |
template<typename T > | |
bool | applyAncestor (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyChild (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyDescendantPreorder (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyDescendantPostorder (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyDescendant (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyPreorder (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyPostorder (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | apply (UnaryProcessor< T > &processor) |
template<typename T > | |
bool | applyLevel (UnaryProcessor< T > &processor, long level) |
void | set (const Composite &composite, bool deep=true) |
Composite & | operator= (const Composite &composite) |
void | get (Composite &composite, bool deep=true) const |
Size | getDegree () const |
Size | count (const KernelPredicateType &predicate) const |
Size | countDescendants () const |
Size | getPathLength (const Composite &composite) const |
Size | getDepth () const |
Size | getHeight () const |
Composite & | getRoot () |
const Composite & | getRoot () const |
Composite * | getLowestCommonAncestor (const Composite &composite) |
const Composite * | getLowestCommonAncestor (const Composite &composite) const |
template<typename T > | |
T * | getAncestor (const T &) |
template<typename T > | |
const T * | getAncestor (const T &) const |
template<typename T > | |
T * | getPrevious (const T &) |
template<typename T > | |
const T * | getPrevious (const T &dummy) const |
template<typename T > | |
T * | getNext (const T &) |
template<typename T > | |
const T * | getNext (const T &dummy) const |
Composite * | getParent () |
const Composite * | getParent () const |
Composite * | getChild (Index index) |
const Composite * | getChild (Index index) const |
Composite * | getSibling (Index index) |
const Composite * | getSibling (Index index) const |
Composite * | getFirstChild () |
const Composite * | getFirstChild () const |
Composite * | getLastChild () |
const Composite * | getLastChild () const |
const PreciseTime & | getModificationTime () const |
const PreciseTime & | getSelectionTime () const |
void | stamp (StampType stamp=BOTH) |
void | prependChild (Composite &composite) |
void | appendChild (Composite &composite) |
void | insertBefore (Composite &composite) |
void | insertAfter (Composite &composite) |
void | spliceBefore (Composite &composite) |
void | spliceAfter (Composite &composite) |
void | splice (Composite &composite) |
bool | removeChild (Composite &child) |
Size | removeSelected () |
Size | removeUnselected () |
void | replace (Composite &composite) |
void | swap (Composite &composite) |
virtual void | select () |
virtual void | deselect () |
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PersistentObject () | |
virtual | ~PersistentObject () |
PersistenceManager & | operator>> (PersistenceManager &pm) const |
virtual void | finalize () |
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Object () | |
Default constructor. | |
Object (const Object &object) | |
Copy constructor. | |
virtual | ~Object () |
Destructor. | |
const Object & | operator= (const Object &) |
bool | operator== (const Object &object) const |
bool | operator!= (const Object &object) const |
bool | operator< (const Object &object) const |
bool | operator<= (const Object &object) const |
bool | operator>= (const Object &object) const |
bool | operator> (const Object &object) const |
int | compare (const Object &object) const |
virtual void | dump (::std::ostream &s=std::cout, Size depth=0) const |
Handle | getHandle () const |
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virtual | ~AutoDeletable () |
void * | operator new (size_t size) |
void | operator delete (void *ptr) |
void * | operator new (size_t size, void *ptr) |
void | operator delete (void *ptr, void *) |
bool | isAutoDeletable () const |
void | setAutoDeletable (bool enable) |
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Selectable () | |
Selectable (const Selectable &selectable, bool deep=true) | |
virtual | ~Selectable () |
void | set (const Selectable &selectable, bool deep=true) |
const Selectable & | operator= (const Selectable &selectable) |
void | get (Selectable &selectable, bool deep=true) const |
void | swap (Selectable &selectable) |
virtual void | setSelected (bool selected) |
bool | isSelected () const |
bool | operator== (const Selectable &selectable) const |
bool | operator!= (const Selectable &selectable) const |
void | write (PersistenceManager &pm) const |
bool | read (PersistenceManager &pm) |
virtual void | dump (::std::ostream &s=std::cout, Size depth=0) const |
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BALL_INLINE | PropertyManager () |
Default constructor. | |
BALL_INLINE | PropertyManager (const PropertyManager &property_manager) |
Copy constructor. | |
virtual | ~PropertyManager () |
Destructor. | |
void | set (const PropertyManager &property_manager) |
const PropertyManager & | operator= (const PropertyManager &property_manager) |
void | get (PropertyManager &property_manager) const |
void | swap (PropertyManager &property_manager) |
BitVector & | getBitVector () |
const BitVector & | getBitVector () const |
operator BitVector & () | |
void | setProperty (Property property) |
void | clearProperty (Property property) |
void | toggleProperty (Property property) |
Size | countProperties () const |
const NamedProperty & | getNamedProperty (Position index) const |
NamedProperty & | getNamedProperty (Position index) |
void | setProperty (const NamedProperty &property) |
void | setProperty (const string &name) |
void | setProperty (const string &name, bool value) |
void | setProperty (const string &name, int value) |
void | setProperty (const string &name, unsigned int value) |
void | setProperty (const string &name, float value) |
void | setProperty (const string &name, double value) |
void | setProperty (const string &name, const string &value) |
void | setProperty (const string &name, const PersistentObject &value) |
const NamedProperty & | getProperty (const string &name) const |
NamedPropertyIterator | beginNamedProperty () |
NamedPropertyIterator | endNamedProperty () |
void | clearProperty (const string &name) |
Size | countNamedProperties () const |
bool | hasProperty (Property property) const |
Query for an unnamed property. | |
bool | hasProperty (const string &name) const |
Query for a named property. | |
bool | operator== (const PropertyManager &pm) const |
bool | operator!= (const PropertyManager &pm) const |
Inequality operator. | |
void | write (PersistenceManager &pm) const |
Persistent stream writing. | |
bool | read (PersistenceManager &pm) |
Persistent stream reading. |
Additional Inherited Members | |
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static bool | insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true) |
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static Handle | getNextHandle () |
static Handle | getNewHandle () |
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static void | clearLastPtr () |
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static UnaryProcessor< Composite > | DEFAULT_PROCESSOR |
static KernelPredicateType | DEFAULT_UNARY_PREDICATE |
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AutoDeletable () | |
AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false) | |
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bool | selected_ |
Fragment class. Fragments are used to represent parts of molecules (for example functional groups, monomers in larger polymers).
Definition at line 20 of file fragment.h.
Definition at line 32 of file fragment.h.
BALL::Fragment::Fragment | ( | ) |
Default constructor
BALL::Fragment::Fragment | ( | const String & | name | ) |
Constructor
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virtual |
Destructor
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virtual |
Internal state dump. Dump the current internal state to the output ostream s with dumping depth depth .
s | - output stream where to output the internal state |
depth | - the dumping depth |
Reimplemented from BALL::AtomContainer.
Reimplemented in BALL::Residue, and BALL::Nucleotide.
Inequality operator
Equality operator. Two fragments are equal if they have the same handle.
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Reads a Fragment object from a persistent stream.
pm | the persistence manager |
Reimplemented from BALL::AtomContainer.
Reimplemented in BALL::Residue, and BALL::Nucleotide.
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virtual |
Writes a Fragment object to a persistent stream.
pm | the persistence manager |
Reimplemented from BALL::AtomContainer.
Reimplemented in BALL::Residue, and BALL::Nucleotide.