sc::IntCoorGen(3)

💖 NAME 💖

sc::IntCoorGen(3) is serving from the MPQC manual, and IntCoorGen generates a set of simple internal coordinates for a molecule. That's literally the whole NAME section, bestie — short, iconic, periodt. ✨

🌸 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 🛠

These are the protected helper functions — same names, same signatures, no extra description on the page:

• 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 🦋

This page also has an Additional Inherited Members section. That's all it says — inherited members, not re-listed here. 🫶

💫 Detailed Description 💫

IntCoorGen generates a set of simple internal coordinates for a molecule. That's the assignment, and it ate. 💅

🎀 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.

⚠️ Ownership tea alert: IntCoorGen keeps a reference to extra and deletes it when the destructor is called. Do not forget this, bestie. 😭

🔑 sc::IntCoorGen::IntCoorGen (const Ref< KeyVal > &)

The KeyVal constructor. Here are the keywords it reads:

• 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. 🤖 (The robots did the paperwork; the vibes are still ours.)

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🎀 Cute sign-off: this page is from MPQC version 2.3.1, dated Sun Oct 4 2020. That's the footer tea, bestie — bye! 💖💅