MPQC 2.3.1
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IntCoorGen generates a set of simple internal coordinates for a molecule. More...
#include <coor.h>
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) |
IntCoorGen generates a set of simple internal coordinates for a molecule.
Create an IntCoorGen given a Molecule and, optionally, extra bonds.
IntCoorGen keeps a reference to extra and deletes it when the destructor is called.
Referenced by IntCoorGen().
The KeyVal constructor.
A Molecule object. There is no default.
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.
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.
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.
Generate BendSimpleCo objects to describe linear bends. The default is false.
Generate pairs of LinIPSimpleCo and LinIPSimpleCo objects to describe linear bends. The default is true.
Generate TorsSimpleCo objects to described linear torsions. The default is false.
Generate ScaledTorsSimpleCo objects to described linear torsions. The default is true.
This is a vector of atom numbers, where elements
References IntCoorGen().
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virtual |
Print out information about this.
Reimplemented from sc::DescribedClass.
References sc::ExEnv::out0().
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virtual |
Standard member.
Reimplemented from sc::SavableState.