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
- CASRN
str
CASRN [-]
- CASRN
- Returns
- RG
float
Radius of gyration, [m]
- RG
- Other Parameters
- method
str
,optional
A string for the method name to use, as defined by constants in RG_methods
- method
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
- CASRN
str
CASRN, [-]
- CASRN
- Returns
See also
- 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
- CASRN
str
CASRN [-]
- CASRN
- Returns
- linearbool
Whether or not the chemical is linear, [-]
- Other Parameters
- method
str
,optional
A string for the method name to use, as defined by constants in linear_methods
- method
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
- CASRN
str
CASRN, [-]
- CASRN
- Returns
See also
- chemicals.molecular_geometry.linear_all_methods = ('PSI4_2022A',)¶
Tuple of method name keys. See the linear for the actual references