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@ATB-UQ Automated Topology Builder (ATB)

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    35 repositories

    • QUBIC_Molecules_Theme

      Public
      Monthly meeting schedule for the QUBIC Molecules Theme
      JavaScript
      •1•0•0•0•Updated May 20, 2025May 20, 2025

    • ATB-UQ.github.io

      Public
      JavaScript
      •1•0•0•0•Updated Apr 23, 2025Apr 23, 2025

    • volume_occupancy

      Public
      Code for calculating the volume occupancy of ligands in binding pockets
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 2, 2025Apr 2, 2025

    • atb_docs

      Public
      Documentation for ATB
      0•1•0•0•Updated Mar 12, 2025Mar 12, 2025

    • PyThinFilm

      Public
      Python
      •
      GNU General Public License v3.0
      •1•8•1•0•Updated Feb 21, 2025Feb 21, 2025

    • pmx-pytf

      Public
      pmx (https://github.com/dseeliger/pmx) with modifications required by PyThinFilm
      Python
      •
      GNU Lesser General Public License v3.0
      •71•0•0•0•Updated Feb 21, 2025Feb 21, 2025

    • md-group-resources

      Public
      Information and documentation for the Molecular Dynamics group at UQ.
      0•0•0•0•Updated Dec 24, 2024Dec 24, 2024

    • csc-tools

      Public
      Python
      •0•2•0•0•Updated Dec 24, 2024Dec 24, 2024

    • atb_api_public

      Public
      Public Python API client for the ATB API.
      Python
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Jun 18, 2024Jun 18, 2024

    • chemical_equivalence

      Public
      Predicting chemical equivalence of atoms in molecules using graph automorphisms (nauty) and chemical symmetry constraints.
      Python
      •0•5•0•0•Updated May 23, 2024May 23, 2024

    • atb_outputs

      Public
      Automated Topology Builder (ATB) molecule data object and output modules (PDB, YML, PICKLE, LGF, GRAPH)
      Python
      •1•1•0•0•Updated May 23, 2024May 23, 2024

    • ACSC_promotion

      Public
      Promotional materials for the Australasian Computational and Simulation Commons
      0•0•0•0•Updated Dec 4, 2023Dec 4, 2023

    • ATB3.0_validation_data

      Public
      Supplementary data for "The Automated Topology Builder Version 3.0 (ATB3.0): Prediction of Solvation Free Enthalpies in Water and Hexane."
      0•0•0•0•Updated Nov 23, 2023Nov 23, 2023

    • chemistry_helpers

      Public
      Various chemistry related helpers.
      Python
      •
      MIT License
      •1•0•0•0•Updated Oct 25, 2023Oct 25, 2023

    • Blind_RMSD

      Public
      A new structural distance metric that is completely independent of the arbitrary representation of a molecule in a given molecular format.
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•0•0•0•Updated Oct 25, 2023Oct 25, 2023

    • HPC_scripts

      Public
      Templates for Running Simulations on HPC Systems
      Shell
      •0•0•0•0•Updated Oct 6, 2023Oct 6, 2023

    • md-docker

      Public
      Experimental Docker Image for MD Tutorials
      Dockerfile
      •0•0•0•0•Updated Jul 3, 2023Jul 3, 2023

    • dihedral_fragments

      Public
      Generalised description of torsion (dihedral) fragments in a molecule.
      Python
      •2•0•0•0•Updated Jun 20, 2023Jun 20, 2023

    • fragment_capping

      Public
      Combinatorial, graph-based fragment capping algorithm.
      Python
      •
      MIT License
      •1•1•0•0•Updated Jun 19, 2023Jun 19, 2023

    • gromos2amber

      Public
      A command line tool for converting GROMOS simulation inputs to AMBER formats
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 8, 2023Jun 8, 2023

    • discourse-custom-embed

      Public
      Customise the embed view for Discourse
      HTML
      •1•0•0•0•Updated May 22, 2023May 22, 2023

    • OFraMP

      Public
      OFraMP - The tool for Online Fragment-based Molecule Parameterisation
      JavaScript
      •
      MIT License
      •2•0•0•0•Updated Mar 22, 2023Mar 22, 2023

    • CYANA-Examples

      Public
      Example use of ATB CYANA library files.
      LOLCODE
      •0•0•1•0•Updated Feb 20, 2023Feb 20, 2023

    • fixnom

      Public
      Standardise the atoms names of amino acids
      Perl
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 20, 2023Feb 20, 2023

    • CYSX

      Public
      0•0•0•0•Updated Feb 17, 2023Feb 17, 2023

    • APP-RCM-CNS-Files

      Public
      Inputs and results for CNS water refinement of the APP-RCM protein
      Prolog
      •0•0•0•0•Updated Feb 17, 2023Feb 17, 2023

    • ATB_repository

      Public
      A web-based repository for molecular simulation trajectories based on CKAN
      Python
      •
      MIT License
      •1•1•6•1•Updated Aug 15, 2022Aug 15, 2022

    • trapz_errors

      Public
      Error analysis for the trapezoidal integration method.
      Python
      •
      MIT License
      •2•2•0•0•Updated Feb 21, 2022Feb 21, 2022

    • amber_wiener_example

      Public
      Example job submission script and inputs for an Amber simulation on the Wiener cluster at the University of Queensland
      Shell
      •0•1•0•0•Updated Nov 5, 2019Nov 5, 2019

    • gromos2amber_tests

      Public
      Tests for the gromos2amber topology conversion tool
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 11, 2019Jul 11, 2019
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