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        "author": "DRP Project",
        "author_email": "darkreactionproject@haverford.edu",
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        "description": "# chemdescriptor - Molecular descriptor generator\nGeneric molecular descriptor generator wrapper around various software packages to simplify the process of getting descriptors\n\n## To install\nType:\n\n```pip install chemdescriptor```\n\n## Requirements\n1. Pandas\n2. Working copy of ChemAxon cxcalc\n\n## Usage\nCurrently only supports ChemAxon cxcalc. The module can be expanded to cover other generators as well.\nExample input files can be found in the examples/ folder of this repo as well as the pip installed package.\n\n**Important! The code requires an environment variable CXCALC_PATH to be set, which points to the folder where cxcalc is installed!**\n\n### Command Line\n```\nchemdescriptor-cx -m /path/to/SMILES/file -d /path/to/descriptor/whitelist/json -p 6.8 7.0 7.2 -o output.csv\n```\n\n```\nusage: chemdescriptor-cx [-h] -m MOLECULE -d DESCRIPTORS -p PH [PH ...]\n                         [-c COMMANDS] [-pc PHCOMMANDS] -o OUTPUT\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -m MOLECULE, --molecule MOLECULE\n                        Path to input SMILES file\n  -d DESCRIPTORS, --descriptors DESCRIPTORS\n                        Path to descriptor white list json file\n  -p PH [PH ...], --pH PH [PH ...]\n                        List of pH values at which to calculate descriptors\n  -c COMMANDS, --commands COMMANDS\n                        Optional command stems for descriptors in json format\n  -pc PHCOMMANDS, --phcommands PHCOMMANDS\n                        Optional command stems for pH dependent descriptorsin\n                        json format\n  -o OUTPUT, --output OUTPUT\n                        Path to output file\n```\n\n### In code\nSet CXCALC_PATH\n\n```\nimport os\nos.environ['CXCALC_PATH'] = '/path/to/cxcalc'\n```\n\nImport the generator class\n\n``` from chemdescriptor import ChemAxonDescriptorGenerator ```\n\nInstantiate a generator\n``` \ncag = ChemAxonDescriptorGenerator('/path/to/SMILES/file',\n                                  '/path/to/descriptor/whitelist/json',\n                                  ph_values=[6, 7, 8],\n                                  command_stems=None,\n                                  ph_command_stems=None)\n```\n\nGenerate csv output\n``` cag.generate('output.csv', dataframe=False, lec=False) ```\n\nOptional keyword arguments for `generate` include `dataframe` boolean (default False) which returns a pandas dataframe in addition to writing a csv if True\nand `lec` boolean (default False) which converts the Smiles code to an intermediate \"Low Energy Conformer (LEC)\" representation before generating descriptors.\nA license is most likely required to generate LECs.\n\n## Notes:\n\nInput SMILES file has a SMILES code in each line.\n\nDescriptor whitelist is a json file of the form:\n```\n{\n    \"descriptors\": [\n        \"refractivity\",\n        \"maximalprojectionarea\",\n        \"maximalprojectionradius\",\n        \"maximalprojectionsize\",\n        \"minimalprojectionarea\",\n        \"minimalprojectionradius\",\n        \"minimalprojectionsize\"\n    ],\n    \"ph_descriptors\": [\n        \"avgpol\",\n        \"molpol\",\n        \"vanderwaals\",\n        \"asa\",\n        \"asa+\",\n        \"asa-\",\n        \"asa_hydrophobic\",\n        \"asa_polar\",\n        \"hbda_acc\",\n        \"hbda_don\",\n        \"polar_surface_area\"\n    ]\n}\n```\n\nchemdescriptor expects 2 keys where \"descriptors\" are generic and \"ph_descriptors\" are ph dependent descriptors\n\n2 optional dictionaries can be passed to the ChemAxonDescriptorGenerator, \"command_stems\" and \"ph_command_stems\".\nThese dictionaries \"translate\" the above descriptors into commands that ChemAxon cxcalc can understand.\n\nFor example, if no value is passed to the ph_command_stems, the following dictionary is used:\n\n```\n_default_ph_command_stems = {\n        'avgpol': 'avgpol',\n        'molpol': 'molpol',\n        'vanderwaals': 'vdwsa',\n        'asa': ['molecularsurfacearea', '-t', 'ASA'],\n        'asa+': ['molecularsurfacearea', '-t', 'ASA+'],\n        'asa-': ['molecularsurfacearea', '-t', 'ASA-'],\n        'asa_hydrophobic': ['molecularsurfacearea', '-t', 'ASA_H'],\n        'asa_polar': ['molecularsurfacearea', '-t', 'ASA_P'],\n        'hbda_acc': 'acceptorcount',\n        'hbda_don': 'donorcount',\n        'polar_surface_area': 'polarsurfacearea',\n    }\n```\n\nNote that commands with multiple words are entries in a list. For example, the command \n\n```molecularsurfacearea -t ASA```\n\nis represented in the dictionary as ```['molecularsurfacearea', '-t', 'ASA']```\n\n# To Do\n[ ] Test on different machines\n\n[ ] Get feedback on what needs to be changed/improved\n\n[ ] Expand to cover other descriptor generators\n\n\n",
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