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Man Pages


Manual Reference Pages  -  SC_INTCOORGEN (3)

NAME

sc::IntCoorGen - IntCoorGen generates a set of simple internal coordinates for a molecule.

CONTENTS

Synopsis

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.

    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 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

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.

Author

Generated automatically by Doxygen for MPQC from the source code.

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Version 2.3.1 SC::INTCOORGEN (3) Sun Apr 3 2016

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