{"id":21739287,"url":"https://github.com/skyeav/orcafunctionalhub","last_synced_at":"2026-05-01T21:32:40.127Z","repository":{"id":259344190,"uuid":"877039525","full_name":"SkyeAv/OrcaFunctionalHub","owner":"SkyeAv","description":"OrcaFunctionalHub facilitates molecular modeling and computational chemistry tasks using the Orca quantum chemistry package. 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The script automates the conversion of SMILES representations of molecules into 3D coordinates, performs geometry optimization, and executes time-dependent density functional theory (TDDFT) calculations. \n\n## Features\n\n- **3D Coordinate Generation**: Converts SMILES formulas into 3D coordinates using RDKit.\n- **Query Generation**: Creates and writes Orca input files for different computational tasks.\n- **Output Parsing**: Parses output files from Orca to extract relevant information such as optimized coordinates and spectra data.\n- **Data Visualization**: Generates and saves absorbance spectra graphs based on TDDFT calculations.\n- **Configurable Input**: Uses YAML configuration files to specify molecular properties and calculation parameters.\n\n## Requirements\n\n- **Julia**: The script is written in Julia and requires a Julia environment.\n- **Packages**: The following Julia packages are needed:\n  - `FilePathsBase`\n  - `LaTeXStrings`\n  - `DataFrames`\n  - `PyCall`\n  - `Plots`\n  - `YAML`\n  - `CSV`\n- **RDKit**: The RDKit library must be installed and accessible through Python.\n\n## Installation\n\n1. **Install Julia**: Download and install Julia from [the official website](https://julialang.org/downloads/).\n2. **Install Required Packages**: Use the Julia package manager to install the required packages:\n   ```julia\n   using Pkg\n   Pkg.add(\"FilePathsBase\")\n   Pkg.add(\"LaTeXStrings\")\n   Pkg.add(\"DataFrames\")\n   Pkg.add(\"PyCall\")\n   Pkg.add(\"Plots\")\n   Pkg.add(\"YAML\")\n   Pkg.add(\"CSV\")\n   ```\n3. **The RDKit library must be installed and accessible through Python** You can install RDKit using conda:\n```bash\nconda install -c conda-forge rdkit\n```\nConfirm that RDKit is installed correctly by opening a Python session and importing the library:\n```python\nimport rdkit\nprint(rdkit.__version__)\n```\n## Usage\n\n### Create a YAML Configuration File\n\nSpecify the molecules and calculation parameters in a YAML file. An example is provided below:\n\n```yaml\n# Skye Goetz (CalPoly) 10/22/2024\n\nMolecules : \n# [[ list of molecules and attributes ]]\n  # smiles formulas REQUIRE explicit hydrogens\n\n - SmilesFormula : \"[CH3][CH3]\"\n   MolecularCharge : 0 \n   MolecularMultiplicity : 1\n\nTightOpt : \n# [[ TightOpt Query Parameters ]]\n\n Functional : PBE0\n BasisSet : Def2-SVPD\n SolventModel : SMD\n SolventToUse : ethanol\n\nScanAngle : \n# [[ Scan Angle Query Parameters ]]\n\n Functional : PBE0\n BasisSet : Def2-SVPD\n SolventModel : SMD\n SolventToUse : ethanol\n\n ScanType : D\n Angles : \n # [[ List Of Angles For Geometry Scan ]]\n\n   - 0\n   - 1\n   - 4\n   - 6\n\n Advanced : \n\n   ScanRange :\n   # [[ In Degrees ]]\n     \n     - 0\n     - 90\n\n   NumberOfScans : 10\n\nTDDFT : \n# [[ TDDFT Query Parameters ]]\n\n Functional : CAM-B3LYP\n BasisSet : Def2-TZVPD\n SolventModel : CPCM\n SolventToUse : ethanol\n\n Advanced : \n\n   Nroots : 10\n   Maxdim : 100\n\nAdvancedSettings : \n# [[ Configures OrcaFunctionalHub ]]\n \n NumberOfGeometryScansPerTDDFTCalculation : 1\n```\n\n## Run the Script\n\nExecute the Julia script with the path to your YAML file:\n\n```bash\njulia OrcaFunctionalHub.jl path/to/config.yaml\n```\n\n## Output\n\nThe script generates several output files, including:\n\n- Orca input files for each calculation.\n- XYZ files containing molecular coordinates.\n- Output files containing results from Orca.\n- Graphs of absorbance spectra saved as PNG files.\n\n### Author\n\nSkye Goetz (CalPoly)  \nDate: 10/22/2024\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fskyeav%2Forcafunctionalhub","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fskyeav%2Forcafunctionalhub","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fskyeav%2Forcafunctionalhub/lists"}