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Deemian DSL

Documentation Status codecov release os

Deemian is a Domain Specific Language (DSL) that serves as a tool and programming language for molecular interaction analysis. The language uses the vocabulary of cheminformatics and bioinformatics domains, making it simple and intuitive. Despite its simplicity, it is a powerful tool that allows for systematic analysis. The script is easy to read and modify, which enhances readability, reproducibility, and reusability in molecular interaction studies.

Feature

At the moment Deemian only have minimum feature, in the future more feature will be added as decribed in the Roadmap.

Here is the list of current Deemian feature:

  • PDB file processing, both single (X-ray crystal structure) and multimodel (NMR solution structure).
  • Molecule bond assignment based on SMILES template.
  • Electrostatic interaction analysis.
  • Allows both apparent and ionizable charge identification.
  • Interaction calculation between two selection.
  • Present interaction in detailed, clustered, and summarized mode.
  • Generate Deemian data which can be viewed with Deemian Viewer.

Quick Tour

Here is an example of Deemian script to analyze the interaction between oseltamivir and neuraminidase in a crystal structure (PDB ID: 5nzn)

molecule 5nzn.pdb [
    select protein_A = chain A and protein
    select oseltamivir = chain A and resname G39
    assign bond oseltamivir template CCC(CC)O[C@@H]1C=C(C[C@@H]([C@H]1NC(=O)C)N)C(=O)O
]

measure protein_ligand [
    interactions all
    ionizable positive true
    ionizable negative true
    between oseltamivir and protein_A
]

present protein_ligand [
    interactions protein_ligand.txt
    deemiandata protein_ligand.dd
]

Which will generate this readable output

Deemian version: 0.1.0

interaction for "oseltamivir:protein_A":
conf          1
    ELECTROSTATIC as_cation:

                         oseltamivir protein_A

    id                   4           562     563     1053
    atom_name            N4          OE1     OE2     OD1
    res_name             G39         GLU     GLU     ASP
    res_num.chain        503.A       119.A   119.A   151.A
    distance                         4.206   2.744   3.157

    ELECTROSTATIC as_anion:

                         oseltamivir protein_A

    id                   0           539     540     541     4295    4296    4297
    atom_name            O1A         CZ      NH1     NH2     CZ      NH1     NH2
    res_name             G39         ARG     ARG     ARG     ARG     ARG     ARG
    res_num.chain        503.A       118.A   118.A   118.A   368.A   368.A   368.A
    distance                         3.646   2.800   3.584   3.625   2.832   3.523

    id                   1           3182    3183    3184    4295    4296    4297
    atom_name            O1B         CZ      NH1     NH2     CZ      NH1     NH2
    res_name             G39         ARG     ARG     ARG     ARG     ARG     ARG
    res_num.chain        503.A       293.A   293.A   293.A   368.A   368.A   368.A
    distance                         3.547   3.181   3.015   3.702   3.677   2.833

And Deemian Data file which can be viewed with Deemian Viewer

gettingstartedDeemianViewer.mp4

Installation

To install Deemian, download the latest version from the Deemian release page. Extract the zip / tar.gz file and run the pip install command, using the directory name as the last argument:

pip install deemian-0.1.0

Check the documentation for more detailed instruction.

Usage

For more detailed usage checkout the Getting Started guide and Tutorial pages on Documentation.

Contributing

Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.

License

deemian was created by Muhammad Radifar. It is licensed under the terms of the Apache License 2.0 license.

Credits

deemian was created with cookiecutter and the py-pkgs-cookiecutter template.