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structural_analysis

Codes for the generation and analysis of molecular representations.

https://github.com/bernadette-mohr/structural_analysis

Science Score: 77.0%

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    Links to: arxiv.org
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Repository

Codes for the generation and analysis of molecular representations.

Basic Info
  • Host: GitHub
  • Owner: Bernadette-Mohr
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 447 KB
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  • Stars: 1
  • Watchers: 1
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Created over 3 years ago · Last pushed over 2 years ago
Metadata Files
Readme Citation

README.md

Condensed-phase molecular representation to link structure and thermodynamics in molecular dynamics

Code accompanying the publication at https://doi.org/10.1021/acs.jctc.3c00201

The scripts were created specifically for this project, with specific expectations for directory paths and some hard-coded filenames and other settings. * Python version >= 3.9 * package list requirements.txt

Inserting angles and constraints into the GROMACS topology files for small molecule graphs:

  • isomorphism_find_unique.py
    • A small number of structures make up the entire set, the variations between the small molecules are based on different combinations of coarse-grained bead types.
  • make_template_file.py
    • Suitable angles and constraints are manually optimized for one example of each of the recurring structures and subsequently used as a template.
  • isomorphs_insert_constraints.py
    • Iterating over the entire set of small molecule graphs, identifiying the correct template and inserting the settings for angles and constraints.

Generating the SLATM representations:

The Spectrum of London and Axilrod-Teller-Muto (SLATM) potential was defined by Huang, Symonds and von Lilienfeld, https://arxiv.org/abs/1807.04259. * analyze_structures.py * Handles loading of trajectory files and the required steps to translate the coarse-grained MD trajectories into SLATM representations. * clean_trajectories.py * Corrects for periodic boundary conditions, centers systems around the solutes, selects frames by solute position. * preprocessing.py * Selects solutes and environment particles within the long-range interaction cutoff distance around the solutes' center of mass. * generate_representations.py * Handles the generation of the list of possible many-body interactions and unique particle identifiers required by the QML SLATM method. * Generates the SLATM representations. * Saves the results as pickled pandas dataframes.

Analyzing a set of SLATM representations with PCA:

  • analyze_SLATMs.py
    • Loads the SLATM representations and required additional files,
    • Handles preprocessing of SLATM representations including normalization for PCA
    • PCA embedding of the SLATM representations

Visualizing the PCA results:

  • generate_labels.py
    • Loads principal components and additional information, generates descriptors for further analysis.
  • plot_cross_correlations.py
    • Cross-correlates a descriptor to principal components, performs linear regression.
  • correlate_loadings_interactions.py
    • Visualizes the most relevant interactions selected by their loading values (eigenvecor * sqrt(eigenvalue)) to provide an idea about 3D structural aspects.
  • biplot_scores_weights.py
    • Plots most pairs of principal components and their most relevant eigenvector coefficients. Colored by a previously generated descriptor.

Owner

  • Name: bernadette
  • Login: Bernadette-Mohr
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use/expand on this code, please cite it as below."
authors:
- family-names: "Mohr"
  given-names: "Bernadette"
  orcid: "https://orcid.org/0000-0003-0903-0073"
- family-names: "Van der Mast"
  given-names: "Diego"
- family-names: "Bereau"
  given-names: "Tristan"
  orcid: "https://orcid.org/0000-0001-9945-1271"
title: "STRUCTURAL_ANALYSIS"
version: 1.0.0
doi: 10.5281/zenodo.1234
date-released: 2023-02-14
url: "https://github.com/Bernadette-Mohr/STRUCTURAL_ANALYSIS"

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