MPQC  3.0.0-alpha
sc::IntCoorGen Class Reference

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

#include <chemistry/molecule/coor.h>

Inheritance diagram for sc::IntCoorGen:
sc::SavableState sc::DescribedClass sc::RefCount

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
SavableStateoperator= (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 &)
 
DescribedClassoperator= (const DescribedClass &)
 
ClassDescclass_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< DescribedClassref ()
 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 SavableStaterestore_state (StateIn &si)
 Restores objects saved with save_state. More...
 
static SavableStatekey_restore_state (StateIn &si, const char *keyword)
 Like restore_state, but keyword is used to override values while restoring.
 
static SavableStatedir_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 &)
 
RefCountoperator= (const RefCount &)
 

Protected Attributes

Ref< Moleculemolecule_
 
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:

Generated at Sun Jan 26 2020 23:24:06 for MPQC 3.0.0-alpha using the documentation package Doxygen 1.8.16.