.TH "sc::IntCoorGen" 3 "Sun Oct 4 2020" "Version 2.3.1" "MPQC" \" -*- nroff -*-
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.SH NAME
sc::IntCoorGen \- \fBIntCoorGen\fP generates a set of simple internal coordinates for a molecule\&.  

.SH SYNOPSIS
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.PP
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\fC#include <coor\&.h>\fP
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Inherits \fBsc::SavableState\fP\&.
.SS "Public Member Functions"

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.RI "\fBIntCoorGen\fP (const \fBRef\fP< \fBMolecule\fP > &, int nextra=0, int *extra=0)"
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.RI "Create an \fBIntCoorGen\fP given a \fBMolecule\fP and, optionally, extra bonds\&. "
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.RI "\fBIntCoorGen\fP (const \fBRef\fP< \fBKeyVal\fP > &)"
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.RI "The \fBKeyVal\fP constructor\&. "
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.RI "\fBIntCoorGen\fP (\fBStateIn\fP &)"
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.RI "void \fBsave_data_state\fP (\fBStateOut\fP &)"
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.RI "Standard member\&. "
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.RI "virtual void \fBgenerate\fP (const \fBRef\fP< \fBSetIntCoor\fP > &)"
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.RI "This generates a set of internal coordinates\&. "
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.RI "virtual void \fBprint\fP (std::ostream &out=\fBExEnv::out0\fP()) const"
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.RI "Print out information about this\&. "
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.SS "Protected Member Functions"

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.RI "void \fBinit_constants\fP ()"
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.RI "double \fBcos_ijk\fP (\fBMolecule\fP &m, int i, int j, int k)"
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.RI "int \fBhterminal\fP (\fBMolecule\fP &m, \fBBitArrayLTri\fP &bonds, int i)"
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.RI "int \fBnearest_contact\fP (int i, \fBMolecule\fP &m)"
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.RI "void \fBadd_bonds\fP (const \fBRef\fP< \fBSetIntCoor\fP > &list, \fBBitArrayLTri\fP &bonds, \fBMolecule\fP &m)"
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.RI "void \fBadd_bends\fP (const \fBRef\fP< \fBSetIntCoor\fP > &list, \fBBitArrayLTri\fP &bonds, \fBMolecule\fP &m)"
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.RI "void \fBadd_tors\fP (const \fBRef\fP< \fBSetIntCoor\fP > &list, \fBBitArrayLTri\fP &bonds, \fBMolecule\fP &m)"
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.RI "void \fBadd_out\fP (const \fBRef\fP< \fBSetIntCoor\fP > &list, \fBBitArrayLTri\fP &bonds, \fBMolecule\fP &m)"
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.SS "Protected Attributes"

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.RI "\fBRef\fP< \fBMolecule\fP > \fBmolecule_\fP"
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.RI "int \fBlinear_bends_\fP"
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.RI "int \fBlinear_lbends_\fP"
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.RI "int \fBlinear_tors_\fP"
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.RI "int \fBlinear_stors_\fP"
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.RI "int \fBnextra_bonds_\fP"
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.RI "int * \fBextra_bonds_\fP"
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.RI "double \fBlinear_bend_thres_\fP"
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.RI "double \fBlinear_tors_thres_\fP"
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.RI "double \fBradius_scale_factor_\fP"
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.SS "Additional Inherited Members"
.SH "Detailed Description"
.PP 
\fBIntCoorGen\fP generates a set of simple internal coordinates for a molecule\&. 
.SH "Constructor & Destructor Documentation"
.PP 
.SS "sc::IntCoorGen::IntCoorGen (const \fBRef\fP< \fBMolecule\fP > &, int nextra = \fC0\fP, int * extra = \fC0\fP)"

.PP
Create an \fBIntCoorGen\fP given a \fBMolecule\fP and, optionally, extra bonds\&. \fBIntCoorGen\fP keeps a reference to extra and deletes it when the destructor is called\&. 
.SS "sc::IntCoorGen::IntCoorGen (const \fBRef\fP< \fBKeyVal\fP > &)"

.PP
The \fBKeyVal\fP constructor\&. 
.IP "\fB\fCmolecule\fP\fP" 1c
A \fBMolecule\fP object\&. There is no default\&.
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.IP "\fB\fCradius_scale_factor\fP\fP" 1c
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\&.
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.IP "\fB\fClinear_bend_threshold\fP\fP" 1c
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\&.
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.IP "\fB\fClinear_tors_threshold\fP\fP" 1c
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\&.
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.IP "\fB\fClinear_bend\fP\fP" 1c
Generate \fBBendSimpleCo\fP objects to describe linear bends\&. The default is false\&.
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.IP "\fB\fClinear_lbend\fP\fP" 1c
Generate pairs of \fBLinIPSimpleCo\fP and \fBLinIPSimpleCo\fP objects to describe linear bends\&. The default is true\&.
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.IP "\fB\fClinear_tors\fP\fP" 1c
Generate \fBTorsSimpleCo\fP objects to described linear torsions\&. The default is false\&.
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.IP "\fB\fClinear_stors\fP\fP" 1c
Generate \fBScaledTorsSimpleCo\fP objects to described linear torsions\&. The default is true\&.
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.IP "\fB\fCextra_bonds\fP\fP" 1c
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\&.
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.SH "Author"
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Generated automatically by Doxygen for MPQC from the source code\&.