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sc::IntCoorGen(3) MPQC sc::IntCoorGen(3) NAME sc::IntCoorGen - IntCoorGen generates a set of simple internal coordinates for a molecule. SYNOPSIS #include <coor.h> Inherits sc::SavableState. 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. virtual void save_data_state (StateOut &) Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them. 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. virtual void print (std::ostream &=ExEnv::out0()) const Print the object. 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) Detailed Description IntCoorGen generates a set of simple internal coordinates for a molecule. Constructor & Destructor Documentation 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. Member Function Documentation 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. Author Generated automatically by Doxygen for MPQC from the source code. Version 2.3.1 Tue May 13 2025 sc::IntCoorGen(3)
NAME | SYNOPSIS | Detailed Description | Constructor & Destructor Documentation | Member Function Documentation | Author
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