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        "author": "Daniel P. Russo",
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        "description": "# CIIProMol\n## ciipro.rutgers.edu\n\n### Outline - \n\n1. From a set of SMILES\n\t* obtain CIDS \n\t* Get bioassays for each compound\n\n2. Concatenate bioassays into a bioprofile\n\t* eliminate bioassays based of number of actives\n\t* remove invivo assays\n\t* remove highly correlated assays\n\n3. Find invitro/invivo correlations\n\t* remove assays based on different stats\n\t* use those stats to find bio nearest neighbors \n\t* find the assays that minimize the difference in activity between target cmp and nn\n\n\nA python class for extending [CIIPro](ciipro.rutgers.edu) functionality.\nCIIProMol looks to extend the [Python rdkit API]\n(http://www.rdkit.org/docs/api/index.html).\nCIIProMol requires several packages (e.g., rdkit, Pandas, Numpy). \nThese dependencies are listed in the file `explicit-spec-file.txt` and \ncan be loaded directly into a new [conda](http://conda.pydata.org/docs/) environment.\n\nUse the following code to install the required Python packages into a \nnew conda environment.\n\n```bash\n$ conda create --name ciipromol --file explicit-spec-file.txt\n```\n\nCIIProMol is broken down into three modules:  \n1) `ciipromol.py`  \n2) `ciiprofiler.py`  \n3) `ciipredictor.py`  \n\n### ciipromol\n\nContains `class CIIProMol`.  A `CIIProMol` object can by instantiated \nwith an rdkit `Mol` object.  \n\n```python \nfrom ciipromol import *\nfrom rdkit import Chem\n\nmol = Chem.MolFromSmiles('CC(=O)OC1=CC=CC=C1C(=O)O')\ncpm = CIIProMol(mol, activity=20.0)\n```\n\nIf `cids=None` (default), all PubChem Compound ID's (CIDs) associated with\nthat structure will be retrieved.  Biological assays associated with those CIDs\ncan be retrieved.\n\n```python\ncpm.GetBioAssays()\n```\n\nIf `attribute=True` (default), the BioAssays can be acccessed as a Pandas DataFrame\nusing the attribute, `cpm.BioAssays`\n\n### ciiprofiler \n\nContains `class CIIProfiler`.  A `CIIProfiler` object can be instantiated by passing \na list of `CIIProMol` objects. \n\n ```python\n ciiprofiler = CIIProfiler([cpm1, cpm2, cmp3])\n ```\n \n The function `MakeBioProfiler()` will concatenate the attributes `cpm1.BioAssays`,\n  `cpm2.BioAssays`, etc., into one matrix.",
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