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. More...

	IntCoorGen (const Ref< KeyVal > &)
	The KeyVal constructor. More...

	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. More...

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. More...

virtual void	save_vbase_state (StateOut &)
	Save the virtual bases for the object. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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.

The documentation for this class was generated from the following file:

src/lib/chemistry/molecule/coor.h

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ IntCoorGen() [1/2]

◆ IntCoorGen() [2/2]