IntCoorGen generates a set of simple internal coordinates for a molecule. More...

#include <chemistry/molecule/coor.h>

Inheritance diagram for sc::IntCoorGen:

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 MPQC__NOEXCEPT
	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.

Ref< DescribedClass >	ref ()
	Return this object wrapped up in a Ref smart pointer.

Public Member Functions inherited from sc::RefCount
size_t	identifier () const
	Return the unique identifier for this object that can be compared for different objects of different types.

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
	Return 1 if the object is managed. Otherwise return 0.

Static Public Member Functions
static BitArrayLTri	adjacency_matrix (const Molecule &mol, double radius_scaling_factor=1.1)
	computes the adjacency matrix for this molecule using atomic radii and the scaling_factor

static std::vector< std::set< int > >	find_disconnected_subgraphs (const BitArrayLTri &adjmat)
	given the adjacency matrix find all disconnected subgraphs, each subgraph is specified by a set of vertex indices

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)

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)

void	connect_subgraphs (const Molecule &mol, BitArrayLTri &adjacency_matrix)
	(potentially) modifies the adjacency matrix to make sure that there are no disconnected subgraphs

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_

Detailed Description

IntCoorGen generates a set of simple internal coordinates for a molecule.

Constructor & Destructor Documentation

◆ IntCoorGen() [1/2]

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.

◆ IntCoorGen() [2/2]

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.