Public Member Functions

IntCoorGen (const Ref< Molecule > &, int nextra=0, int *extra=0)
Create an IntCoorGen given a Molecule and, optionally, extra bonds. IntCoorGen (const Ref< KeyVal > &)
The KeyVal constructor. IntCoorGen (StateIn &)
void save_data_state (StateOut &)
Standard member. virtual void generate (const Ref< SetIntCoor > &)
This generates a set of internal coordinates. virtual void print (std::ostream &out=ExEnv::out0()) const
Print out information about this.

Public Member Functions inherited from sc::SavableState
SavableState & operator= (const SavableState &)
void save_state (StateOut &)
Save the state of the object as specified by the StateOut object. void save_object_state (StateOut &)
This can be used for saving state when the exact type of the object is known for both the save and the restore. virtual void save_vbase_state (StateOut &)
Save the virtual bases for the object.

Public Member Functions inherited from sc::DescribedClass
DescribedClass (const DescribedClass &)
DescribedClass & operator= (const DescribedClass &)
ClassDesc * class_desc () const throw ()
This returns the unique pointer to the ClassDesc corresponding to the given type_info object. const char * class_name () const
Return the name of the object's exact type. int class_version () const
Return the version of the class.

Public Member Functions inherited from sc::RefCount
int lock_ptr () const
Lock this object. int unlock_ptr () const
Unlock this object. void use_locks (bool inVal)
start and stop using locks on this object refcount_t nreference () const
Return the reference count. refcount_t reference ()
Increment the reference count and return the new count. refcount_t dereference ()
Decrement the reference count and return the new count. int managed () const
void unmanage ()
Turn off the reference counting mechanism for this object. int managed () const
Return 1 if the object is managed. Otherwise return 0.

Public Member Functions inherited from sc::Identity
Identifier identifier ()
Return the Identifier for this argument.

Protected Member Functions

void init_constants ()
double cos_ijk (Molecule &m, int i, int j, int k)
int hterminal (Molecule &m, BitArrayLTri &bonds, int i)
int nearest_contact (int i, Molecule &m)
void add_bonds (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m)
void add_bends (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m)
void add_tors (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m)
void add_out (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m)

Protected Member Functions inherited from sc::SavableState
SavableState (const SavableState &)
SavableState (StateIn &)
Each derived class StateIn CTOR handles the restore corresponding to calling save_object_state, save_vbase_state, and save_data_state listed above.

Protected Member Functions inherited from sc::RefCount
RefCount (const RefCount &)
RefCount & operator= (const RefCount &)

Protected Attributes

Ref< Molecule > molecule_
int linear_bends_
int linear_lbends_
int linear_tors_
int linear_stors_
int nextra_bonds_
int * extra_bonds_
double linear_bend_thres_
double linear_tors_thres_
double radius_scale_factor_

Additional Inherited Members

Static Public Member Functions inherited from sc::SavableState
static void save_state (SavableState *s, StateOut &)
static SavableState * restore_state (StateIn &si)
Restores objects saved with save_state. static SavableState * key_restore_state (StateIn &si, const char *keyword)
Like restore_state, but keyword is used to override values while restoring. static SavableState * dir_restore_state (StateIn &si, const char *objectname, const char *keyword=0)

sc::IntCoorGen::IntCoorGen (const Ref< Molecule > &, int nextra = 0, int * extra = 0)

Create an IntCoorGen given a Molecule and, optionally, extra bonds. IntCoorGen keeps a reference to extra and deletes it when the destructor is called.

sc::IntCoorGen::IntCoorGen (const Ref< KeyVal > &)

The KeyVal constructor.

molecule

A Molecule object. There is no default.

radius_scale_factor

If the distance between two atoms is less than the radius scale factor times the sum of the atoms' atomic radii, then a bond is placed between the two atoms for the purpose of finding internal coordinates. The default is 1.1.

linear_bend_threshold

A bend angle in degress greater than 180 minus this keyword's floating point value is considered a linear bend. The default is 1.0.

linear_tors_threshold

The angles formed by atoms a-b-c and b-c-d are checked for near linearity. If an angle in degrees is greater than 180 minus this keyword's floating point value, then the torsion is classified as a linear torsion. The default is 1.0.

linear_bend

Generate BendSimpleCo objects to describe linear bends. The default is false.

linear_lbend

Generate pairs of LinIPSimpleCo and LinIPSimpleCo objects to describe linear bends. The default is true.

linear_tors

Generate TorsSimpleCo objects to described linear torsions. The default is false.

linear_stors

Generate ScaledTorsSimpleCo objects to described linear torsions. The default is true.

extra_bonds

This is a vector of atom numbers, where elements $2 (i-1) + 1$ and $2 i$ specify the atoms which are bound in extra bond $i$. The extra_bonds keyword should only be needed for weakly interacting fragments, otherwise all the needed bonds will be found.

virtual void sc::IntCoorGen::print (std::ostream & out = ExEnv::out0()) const [virtual]

Print out information about this.

Reimplemented from sc::DescribedClass.

void sc::IntCoorGen::save_data_state (StateOut &) [virtual]

Standard member.

Reimplemented from sc::SavableState.