Chemical Geometry (chemicals.molecular_geometry)

This module contains various radius of gyration functions.

For reporting bugs, adding feature requests, or submitting pull requests, please use the GitHub issue tracker.

Lookup Functions

chemicals.molecular_geometry.RG(CASRN, method=None)[source]

This function handles the retrieval of a chemical’s radius of gyration. Lookup is based on CASRNs. Will automatically select a data source to use if no method is provided; returns None if the data is not available.

Function has data for approximately 670 chemicals.

Parameters
CASRNstr

CASRN [-]

Returns
RGfloat

Radius of gyration, [m]

Other Parameters
methodstr, optional

A string for the method name to use, as defined by constants in RG_methods

Notes

The available sources are as follows:

  • ‘PSI4_2022A’, values computed using the Psi4 version 1.3.2 quantum chemistry software, with initialized positions from rdkit’s EmbedMolecule method, the basis set 6-31G** and the method mp2 [1].

  • ‘CHEMSEP’, from the databank included and distributed with the licence notice ChemSep v8.1 pure component data - Copyright (c) Harry Kooijman and Ross Taylor (2018) - http://www.perlfoundation.org/artistic_license_2_0. A small portion of the data is used.

References

1

Turney, Justin M., Andrew C. Simmonett, Robert M. Parrish, Edward G. Hohenstein, Francesco A. Evangelista, Justin T. Fermann, Benjamin J. Mintz, et al. “Psi4: An Open-Source Ab Initio Electronic Structure Program.” WIREs Computational Molecular Science 2, no. 4 (2012): 556-65. https://doi.org/10.1002/wcms.93.

2

Kooijman, Harry A., and Ross Taylor. The ChemSep Book. Books on Demand Norderstedt, Germany, 2000.

Examples

>>> RG(CASRN='64-17-5')
2.225e-10
chemicals.molecular_geometry.RG_methods(CASRN)[source]

Return all methods available to obtain the radius of gyration for the desired chemical.

Parameters
CASRNstr

CASRN, [-]

Returns
methodslist[str]

Methods which can be used to obtain the RG with the given inputs.

See also

RG
chemicals.molecular_geometry.RG_all_methods = ('PSI4_2022A', 'CHEMSEP')

Tuple of method name keys. See the RG for the actual references

chemicals.molecular_geometry.linear(CASRN, method=None)[source]

This function handles the retrieval whether or not a chemical is linear. Lookup is based on CASRNs. Will automatically select a data source to use if no method is provided; returns None if the data is not available.

Function has data for approximately 300 chemicals.

Parameters
CASRNstr

CASRN [-]

Returns
linearbool

Whether or not the chemical is linear, [-]

Other Parameters
methodstr, optional

A string for the method name to use, as defined by constants in linear_methods

Notes

The available sources are as follows:

  • ‘PSI4_2022A’, values computed using the Psi4 version 1.3.2 quantum chemistry software, with initialized positions from rdkit’s EmbedMolecule method, the basis set 6-31G** and the method mp2 [1].

Warning

This function does not yet have a reliable data source.

References

1

Turney, Justin M., Andrew C. Simmonett, Robert M. Parrish, Edward G. Hohenstein, Francesco A. Evangelista, Justin T. Fermann, Benjamin J. Mintz, et al. “Psi4: An Open-Source Ab Initio Electronic Structure Program.” WIREs Computational Molecular Science 2, no. 4 (2012): 556-65. https://doi.org/10.1002/wcms.93.

Examples

>>> linear(CASRN='64-17-5')
False
chemicals.molecular_geometry.linear_methods(CASRN)[source]

Return all methods available to obtain whether or not the desired chemical is linear.

Parameters
CASRNstr

CASRN, [-]

Returns
methodslist[str]

Methods which can be used to obtain the linear with the given inputs.

See also

linear
chemicals.molecular_geometry.linear_all_methods = ('PSI4_2022A',)

Tuple of method name keys. See the linear for the actual references