Package: psiresp
PsiRESP😪-RESPLatest releaseInstallationStatusCommunityPsiRESP is a package for calculating atomic partial charges from
restrained and unrestrained electrostatic potential fits using Psi4.
It is highly flexible, configurable, easy to use, and totally written in Python.
It supports fitting to multiple orientations and conformers,
as well as both intra-molecular and inter-molecular charge constraints for
multi-molecule fits.
It is written to correspond closely with existing tools such as theRESP ESP charge Derive (R.E.D.)tools.As of now, the following implementations are well-tested to reproduce results from existing tools, primarily R.E.D.:standard 2-stage RESP (convenience class: psiresp.configs.TwoStageRESP)standard 1-stage RESP (convenience class: psiresp.configs.OneStageRESP)standard unrestrained ESP (convenience class: psiresp.configs.ESP)These implementations are not as well-tested:ESP using HF/STO-3G (convenience class: psiresp.configs.WeinerESP) -- Psi4 seems to minimize to a relatively different geometry than GAMESS with STO-3G.psiresp.configs.ATBRESP, mimicking the method used by theAutomated Topology Builderis not tested at all. The published methods do not indicate the point density, moreover, the results generated seem to have changed since the original paper.Use at your own risk.psiresp.configs.RESP2, as the methods are expensiveInstallationThe recommended way to install PsiRESP is viaanaconda,
as the required dependencies are most easily installed distributed throughconda.For the fully featured version, install:conda install -c conda-forge -c psi4 psiresp psi4This will pull in all dependencies necessary for full functionality, includingRDKit,Psi4andQCFractal.For minimal functionality, install:conda install -c conda-forge psiresp-basepsiresp-baseinstalls the package with minimal dependencies, so that
only functionality that does not depend on RDKit, Psi4,or QCFractal is available.The library can also be installed with minimal dependencies via Pypi:pip install psirespAlternatively, to build from source:clone this repositorycreate a new environment with dependenciesbuild the packagegit clone https://github.com/lilyminium/psiresp.git
cd psiresp
conda env create -f devtools/conda-envs/environment.yaml
conda activate psiresp
pip install .Please seethe Installation docsfor more information on installation and dependencies.ExampleExamples for PsiRESP are provided as tutorials bothonlineand as downloadable Jupyter notebooks in theexamples folder.
More information can also be found in thedocumentation.A minimal example is provided below, running a standard 2-stage restrained electrostatic potential fit (Bayly et al., 1993).
This requires the full installation ofpsiresp, instead of the minimalpsiresp-base,
as it makes use of RDKit, Psi4 and QCFractal.importpsirespfrompsiresp.testingimportFractalSnowflakeimportqcfractal.interfaceasptl# set up server and clientserver=FractalSnowflake()client=ptl.FractalClient(server)# set up moleculedmso=psiresp.Molecule.from_smiles("CS(=O)C")# set up jobjob=psiresp.Job(molecules=[dmso])charges=job.run(client=client)ContributingAll contributions are welcomed! This can include sharing bug reports, bug fixes, requesting or adding new features, or improving the documentation.
If you notice any issues or have feature requests, please open an issue on theIssue tracker.
Otherwise, please check out theContributingpage in the documentation.CopyrightCopyright (c) 2020, Lily WangAcknowledgementsProject based on theComputational Molecular Science Python Cookiecutterversion 1.2.Pre-configured models and reorientation algorithm are written to directly match results fromRESP ESP charge Derive (R.E.D.).
Dupradeau, F.-Y. et al. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. Phys. Chem. Chem. Phys. 12, 7821 (2010).ATBRESP tries to match results fromAutomated Topology Builder (A.T.B.).
Malde, A. K. et al. An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. J. Chem. Theory Comput. 7, 4026–4037 (2011).RESP2 tries to match results fromRESP2.
Schauperl, M. et al. Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2). Commun Chem 3, 1–11 (2020).Some tests compare results to output fromresp, the current RESP plugin
for Psi4.
Alenaizan, A., Burns, L. A. & Sherrill, C. D. Python implementation of the restrained electrostatic potential charge model. International Journal of Quantum Chemistry 120, e26035 (2020).