{
    "info": {
        "author": "Vlachos Research Group",
        "author_email": "vlachos@udel.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Chemistry"
        ],
        "description": "python Group Additivity (pgradd)\n================================\n\nA Python package and database, developed by the Vlachos Research Group at the University of Delaware implements the **F**\\ irst-**P**\\ rinciples **S**\\ emi-**E**\\ mpirical (FPSE) **G**\\ roup **A**\\ dditivity\n(GA) method for estimating thermodynamic properties of molecules. First introduced by Benson et al. for gas molecules and\nwas later extended by Kua et al. to species adsorbed on catalytic surfaces. GA relies on graph theory defining each molecule\nas a collection of groups and their frequency of occurrence. The values of GA groups are determined from DFT-calculated\nthermodynamic properties of a (training) set of molecules by linear regression to minimize the difference of thermodynamic\nproperties of molecules predicted by the GA from those estimated via DFT. This package implements four group additivity\nschemes in six databases (See below) and will convert a molecule entered as a **S**\\ implified **M**\\ olecular-**I**\\ nput\n**L**\\ ine-**E**\\ ntry **S**\\ ystem (`SMILES`_) providing the constituent groups, their frequency of occurrence, and estimated\nthermodynamic properties for that molecule. pgradd also provides a general GA framework for implementing a custom group additivity\nscheme from your *ab initio*\\  data and regression to groups.\n\n-  Benson's gas molecule group additivity (BensonGA)\n-  Salciccioli et al. (2012) adsorbate on Pt(111) group additivity scheme (SalciccioliGA2012)\n-  Gu et al. (2017) solvated adsorbate on Pt(111) group additivity scheme (GuSolventGA2017Aq, GuSolventGA2017Vac)\n-  Wittreich (2018) adsorbate on Pt(111). Subset of Gu et al. including only surface species, group values regressed with OLS/GLS (Maximum Likelihood) and DFT data processed with `pmutt`_ (GRWSurface2018)\n-  Wittreich (2018) solvated adsorbate on Pt(111). Subset of Gu et al. including only surface species, group values regressed with OLS/GLS (Maximum Likelihood) and DFT data processed with `pmutt`_ (GRWAqueous2018)\n\nDevelopers\n----------\n\n-  Gerhard R Wittreich, P.E.\n-  Geun Ho Gu\n-  Michael Salciccioli\n-  Stephen M. Edie\n\nRequired Packages\n-----------------\n\n-  Python2/Python3\n-  `pmutt`_ >= 1.2.5\n-  `rdkit`_ >= 2018.03.4.0\n-  ipython >= 7.0.0\n-  `numpy`_ >= 1.15.1\n-  `pyyaml`_ >= 3.0\n-  `scipy`_ >= 1.1.0\n\nGetting Started\n---------------\n\n1. Install using pip::\n\n    pip install --user pgradd\n\n2. Run the unit tests. Navigate to the **tests**\\  directory, input the command shown below, and look for an **OK**\\  response. (**Note:**\\  The number of tests/time may change with subsequent versions)::\n\n    python -m unittest\n\n    ..................................\n    ----------------------------------------------------------------------\n    Ran 36 tests in 4.389s\n\n    OK\n\n3. Look at examples below\n\nLicense\n-------\n\nThis project is licensed under the MIT License - see the `LICENSE`_ file for details.\n\nContributing\n------------\n\nIf you have a suggestion, please post to our `Issues page`_ with the ``enhancement`` tag. Similarly, if you encounter a bug, please post to our `Issues page`_ with the ``bug`` tag. Finally, if you would like to add to the body of code, please check our documentation to make sure the new code is consistent with the relevant page and submit a `pull request`_.\n\nQuestions\n---------\n\nIf you are having issues, please post to our `Issues page`_ with the ``help wanted`` or ``question`` tag. We \nwill do our best to assist.\n\nSpecial Thanks\n--------------\n\n-  Dr. Jeffrey Frey (pip and conda compatibility)\n\nCitations\n---------\n\n-  Rangarajan et al. \"Language-oriented rule-based reaction network generation and analysis: Algorithms of RING\", Comput. Chem. Eng. 2014, 64, 124\n-  Rangarajan et al. \"Language-oriented rule-based reaction network generation and analysis: Descrpition of RING\", Comput. Chem. Eng. 2012, 45, 114\n-  Benson et al. \"Additivity rules for the estimation of thermochemical properties.\" Chem. Rev., 1969, 69 (3), 279-324\n-  Salciccioli et al. \"Density Functional Theory-Derived Group Additivity and Linear Scaling Methods for Prediction of Oxygenate Stability on Metal Catalysts: Adsorption of Open-Ring Alcohol and Polyol Dehydrogenation Intermediates on Pt-Based Metals.\" J. Phys. Chem. C, 2010, 114 (47) 20155-20166\n-  Kua J, Goddard WA (1998) Chemisorption of Organics on Platinum. 2. Chemisorption of C 2 H x and CH x on Pt(111). J Phys Chem B 102:9492\u00e2\u20ac\u201c9500\n-  Kua J, Faglioni F, Goddard WA (2000) Thermochemistry for hydrocarbon intermediates chemisorbed on metal surfaces: CH(n-m)(CH3)(m) with n = 1, 2, 3 and m \u00e2\u2030\u00a4 n on Pt, Ir, Os, Pd, Rh, and Ru. J Am Chem Soc 122:2309\u00e2\u20ac\u201c2321\n-  Salciccioli et al. \"Adsorption of Acid, Ester, and Ether Functional Groups on Pt: Fast Prediction of Thermochemical Properties of Adsorbed Oxygenates via DFT-Based Group Additivity Methods.\" J. Phys. Chem. C, 2012, 116(2), 1873-1886\n-  Vorotnikov et al. \"Group Additivity for Estimating Thermochemical Properties of Furanic Compounds on Pd(111).\" Ind. Eng. Chem. Res., 2014, 53 (30), 11929-11938\n-  Vorotnikov et al. \"Group Additivity and Modified Linear Scaling Relations for Estimating Surface Thermochemistry on Transition Metal Surfaces: Application to Furanics.\" J. Phys. Chem. C, 2015, 119 (19), 10417-10426\n-  Gu et al. \"Group Additivity for Thermochemical Property Estimation of Lignin Monomers on Pt(111).\" J. Phys. Chem. C, 2016, 120 (34), 19234-19241\n-  Gu GH, Schweitzer B, Michel C, et al (2017) Group additivity for aqueous phase thermochemical properties of alcohols on Pt(111). J Phys Chem C 121:21510\u00e2\u20ac\u201c21519\n\nExamples\n--------\n\n**Benson's Gas Group Additivity Example**::\n\n    In:\n    from pgradd.GroupAdd.Library import GroupLibrary\n    import pgradd.ThermoChem\n    lib = GroupLibrary.Load('BensonGA')\n    descriptors = lib.GetDescriptors('C1CO1')\n    print(descriptors)\n    thermochem = lib.Estimate(descriptors,'thermochem')\n    print(thermochem.get_HoRT(298.15))\n\n    Out:\n    defaultdict(int, {'C(C)(H)2(O)': 2, 'O(C)2': 1, 'Oxirane': 1})\n    -21.09467743150278\n\n\n**Salciccioli et al. J. Phys. Chem. C, 2012, 116 (2), pp 1873-1886 Example**::\n\n    In:\n    from pgradd.GroupAdd.Library import GroupLibrary\n    import pgradd.ThermoChem\n    lib = GroupLibrary.Load('SalciccioliGA2012')\n    descriptors = lib.GetDescriptors('C([Pt])C[Pt]')\n    print(descriptors)\n    thermochem = lib.Estimate(descriptors,'thermochem')\n    print(thermochem.get_HoRT(298.15))\n\n    Out:\n    defaultdict(<class 'int'>, {'C(C)(H)2(Pt)': 2, 'surface-ring strain': 0.217})\n    37.62494617247582\n\n**Gu et al. J. Phys. Chem. C, 2017, 121 pp 21510\u00e2\u20ac\u201c21519 Example**::\n\n    In:\n    from pgradd.GroupAdd.Library import GroupLibrary\n    import pgradd.ThermoChem\n    lib = GroupLibrary.Load('GuSolventGA2017Aq')\n    descriptors = lib.GetDescriptors('C(=O)([Pt])O')\n    print(descriptors)\n    thermochem = lib.Estimate(descriptors,'thermochem')\n    print(thermochem.get_HoRT(500))\n\n    Out:\n    defaultdict(<class 'int'>, {'CO(O)(Pt)+O(CO)(H)': 1.0})\n    -109.86212002776878\n\n\n**Wittreich Surface Example**::\n\n    In:\n    from pgradd.GroupAdd.Library import GroupLibrary\n    import pgradd.ThermoChem\n    lib = GroupLibrary.Load('GRWSurface2018')\n    descriptors = lib.GetDescriptors('[Pt]C([Pt])C([Pt])([Pt])C=O')\n    print(descriptors)\n    thermochem = lib.Estimate(descriptors,'thermochem')\n    print(thermochem.get_HoRT(750), '[Dimensionless]')\n    print(thermochem.get_H(750, 'kcal/mol'), '[kcal/mol]')\n\n    Out:\n    defaultdict(<class 'int'>, {'C(C)(H)(Pt)2': 1, 'C(C)(CO)(Pt)2': 1, 'CO(C)(H)': 1,\n                                'CPt2CPt2': 1, 'CCPt2': 1, 'surface-ring strain': 0.392})\n    -13.423119203382337 [Dimensionless]\n    -20.005853103142883 [kcal/mol]\n\n**Wittreich Solvated Surface Example**::\n\n    In:\n    from pgradd.GroupAdd.Library import GroupLibrary\n    import pgradd.ThermoChem\n    lib = GroupLibrary.Load('GRWAqueous2018')\n    descriptors = lib.GetDescriptors('C(=O)([Pt])O')\n    print(descriptors)\n    thermochem = lib.Estimate(descriptors,'thermochem')\n    print(thermochem.get_HoRT(500), '[Dimensionless]')\n    print(thermochem.get_H(500, 'kJ/mol'), '[kJ/mol]')\n\n    Out:\n    defaultdict(<class 'int'>, {'CO(O)(Pt)+O(CO)(H)': 1.0})\n    -107.57909464133714 [Dimensionless]\n    -447.23102885789655 [kJ/mol]\n\n.. _`scipy`: https://www.scipy.org/\n.. _`rdkit`: https://www.rdkit.org/\n.. _`numpy`: http://www.numpy.org/\n.. _`pyyaml`: https://pyyaml.org/\n.. _`SMILES`: https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system\n.. _`pmutt`: https://github.com/VlachosGroup/pMuTT\n.. _`LICENSE`: https://github.com/VlachosGroup/VlachosGroupAdditivity/blob/master/LICENSE.md\n.. _`Issues page`: https://github.com/VlachosGroup/VlachosGroupAdditivity/issues\n.. _`pull request`: https://github.com/VlachosGroup/VlachosGroupAdditivity/pulls\n\n\n",
        "description_content_type": "text/x-rst",
        "docs_url": null,
        "download_url": "",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://github.com/VlachosGroup/PythonGroupAdditivity",
        "keywords": "",
        "license": "",
        "maintainer": "",
        "maintainer_email": "",
        "name": "pgradd",
        "package_url": "https://pypi.org/project/pgradd/",
        "platform": "",
        "project_url": "https://pypi.org/project/pgradd/",
        "project_urls": {
            "Homepage": "https://github.com/VlachosGroup/PythonGroupAdditivity"
        },
        "release_url": "https://pypi.org/project/pgradd/1.5/",
        "requires_dist": [
            "pmutt (>=1.2.5)",
            "scipy (>=1.1.0)",
            "numpy (>=1.15.1)",
            "IPython (>=7.0.0)",
            "PyYAML (>=3.0)"
        ],
        "requires_python": "",
        "summary": "Python package implements the Group Additivity (GA) method for estimating thermodynamic properties",
        "version": "1.5"
    },
    "last_serial": 5396249,
    "releases": {
        "1.3.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "68f0f897701880bcd3b70495923132ee",
                    "sha256": "21b780bcce9914d9ffbdc4ba369bfd7e1af9e7f3b7249b28bed3122e3276844d"
                },
                "downloads": -1,
                "filename": "pGrAdd-1.3.5-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "68f0f897701880bcd3b70495923132ee",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 76468,
                "upload_time": "2019-05-15T16:55:46",
                "url": "https://files.pythonhosted.org/packages/a1/84/b7960832d4cc6ff024ba12baf0847c25fc8437ee6860e89983f95a38c9aa/pGrAdd-1.3.5-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "d3e030a6323df80fb92212cf4a2587a7",
                    "sha256": "f86b2ad646b22f4ddb4341c03f04a9a1a82474b78561f2901e1d0bfbe82f6e56"
                },
                "downloads": -1,
                "filename": "pGrAdd-1.3.5.tar.gz",
                "has_sig": false,
                "md5_digest": "d3e030a6323df80fb92212cf4a2587a7",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 60185,
                "upload_time": "2019-05-15T16:55:49",
                "url": "https://files.pythonhosted.org/packages/f4/18/80b18a50c25762a8be8665ed5083687401a7b9b4bd2c3b0f62d16729a4a4/pGrAdd-1.3.5.tar.gz"
            }
        ],
        "1.3.7": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "f40be7030c8fb2bbc83b8e771d7ae156",
                    "sha256": "f3d7fa3acd9c687ce09de8d43d48dfccc7abf8b68666fb2ddff13e2c0135486f"
                },
                "downloads": -1,
                "filename": "pGrAdd-1.3.7-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "f40be7030c8fb2bbc83b8e771d7ae156",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 5579,
                "upload_time": "2019-05-15T20:28:09",
                "url": "https://files.pythonhosted.org/packages/de/dd/d9f82a5e5db2320ebc71c1b259d72bda563f69f41987abb07d4492dd5c33/pGrAdd-1.3.7-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "ff966d1e3bc8b3081dc3a49e099a5757",
                    "sha256": "c1d92a7d292782843d85b519b29bb98aeed9caa1dc5d9aa4f6ded8098ebcc26c"
                },
                "downloads": -1,
                "filename": "pGrAdd-1.3.7.tar.gz",
                "has_sig": false,
                "md5_digest": "ff966d1e3bc8b3081dc3a49e099a5757",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5281,
                "upload_time": "2019-05-15T20:28:11",
                "url": "https://files.pythonhosted.org/packages/24/f0/71dec1db2faf0f1c08b5e44ece3a40ca12b15135f6a8a9eddfe835fd4937/pGrAdd-1.3.7.tar.gz"
            }
        ],
        "1.3.8": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "117b6472c59c1149a3b4ae92e03898e3",
                    "sha256": "eecfc94786959dd460d4dba399db5531fdf63b876fa2cfb3287e973cec54b4c8"
                },
                "downloads": -1,
                "filename": "pGrAdd-1.3.8-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "117b6472c59c1149a3b4ae92e03898e3",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 76467,
                "upload_time": "2019-05-15T20:43:07",
                "url": "https://files.pythonhosted.org/packages/f8/89/d00e9387844391552756896a72db6e090ec6f02c5739a1f739672890476b/pGrAdd-1.3.8-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "b62f256f8de01d6e924fc4f65d51a6c8",
                    "sha256": "632c6c0740777db7db1ef2e2924966d08bd4feeeec68f5db438c0117c7d4dac4"
                },
                "downloads": -1,
                "filename": "pGrAdd-1.3.8.tar.gz",
                "has_sig": false,
                "md5_digest": "b62f256f8de01d6e924fc4f65d51a6c8",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 60405,
                "upload_time": "2019-05-15T20:43:09",
                "url": "https://files.pythonhosted.org/packages/be/4c/7a7f033a67e59650f907f61193a8d89be5ba28f5b04623641054e6bbb80e/pGrAdd-1.3.8.tar.gz"
            }
        ],
        "1.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "e5fb9d96ae37ca050a4e54b3a8cd46ed",
                    "sha256": "218437b665a525263512796a572bfd6df50fbe440a4f0b7a193a21686206e9cb"
                },
                "downloads": -1,
                "filename": "pGrAdd-1.4-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "e5fb9d96ae37ca050a4e54b3a8cd46ed",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 206503,
                "upload_time": "2019-05-15T21:25:54",
                "url": "https://files.pythonhosted.org/packages/c4/fc/1795d3ef3a89d83d2a057cee7140624f8bcde3545e6673523e972e310541/pGrAdd-1.4-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "9973776de6b137ec1c099d5998be0b3a",
                    "sha256": "87957f325b841917239c1e3ac05806f221de5b2b8ce1a96fd790abb3cb9e7cc8"
                },
                "downloads": -1,
                "filename": "pGrAdd-1.4.tar.gz",
                "has_sig": false,
                "md5_digest": "9973776de6b137ec1c099d5998be0b3a",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 175236,
                "upload_time": "2019-05-15T21:25:57",
                "url": "https://files.pythonhosted.org/packages/e8/89/0ff6fefd16b42ded49adb43432ea94cef2393c2304c72b605df667efa7c5/pGrAdd-1.4.tar.gz"
            }
        ],
        "1.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "eb95de18d78b2d8aca4f453ae5ff5175",
                    "sha256": "9759c064100a71dd3e5f9d1fb7a8e20d5c5614f4a0071587770dad5d24444176"
                },
                "downloads": -1,
                "filename": "pgradd-1.5-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "eb95de18d78b2d8aca4f453ae5ff5175",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 187362,
                "upload_time": "2019-06-13T14:54:34",
                "url": "https://files.pythonhosted.org/packages/26/7e/39c0e975d032d9db20fd9c44df3da95a990130ae2ac7d5bc47cdd4f7760e/pgradd-1.5-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "6473d8902362acd75e7dab6053e8242f",
                    "sha256": "a43e48316faed6b763f77e4f789b65d7449042816baf8939c2b052227825e93d"
                },
                "downloads": -1,
                "filename": "pgradd-1.5.tar.gz",
                "has_sig": false,
                "md5_digest": "6473d8902362acd75e7dab6053e8242f",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 157450,
                "upload_time": "2019-06-13T14:54:35",
                "url": "https://files.pythonhosted.org/packages/ca/72/99b11fd2ca83ce2472ca1a48537ecdde20b1da1eb6e7896f0a8b771ed829/pgradd-1.5.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "eb95de18d78b2d8aca4f453ae5ff5175",
                "sha256": "9759c064100a71dd3e5f9d1fb7a8e20d5c5614f4a0071587770dad5d24444176"
            },
            "downloads": -1,
            "filename": "pgradd-1.5-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "eb95de18d78b2d8aca4f453ae5ff5175",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": null,
            "size": 187362,
            "upload_time": "2019-06-13T14:54:34",
            "url": "https://files.pythonhosted.org/packages/26/7e/39c0e975d032d9db20fd9c44df3da95a990130ae2ac7d5bc47cdd4f7760e/pgradd-1.5-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "6473d8902362acd75e7dab6053e8242f",
                "sha256": "a43e48316faed6b763f77e4f789b65d7449042816baf8939c2b052227825e93d"
            },
            "downloads": -1,
            "filename": "pgradd-1.5.tar.gz",
            "has_sig": false,
            "md5_digest": "6473d8902362acd75e7dab6053e8242f",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 157450,
            "upload_time": "2019-06-13T14:54:35",
            "url": "https://files.pythonhosted.org/packages/ca/72/99b11fd2ca83ce2472ca1a48537ecdde20b1da1eb6e7896f0a8b771ed829/pgradd-1.5.tar.gz"
        }
    ]
}