Posts published by: Matt Geballe

Bayesian Query Comparison


  • Generate some example Virtual Screening data.
  • Construct a bayesian model for predicting probability of activity given a certain similarity score.
  • Use this to compare to different queries.
In [3]:
import numpy as np
import pandas as pd
import scipy as sp
from matplotlib import pyplot as plt

from scipy ...

Clustering Molecules with Fingerprints and DBSCAN


  • Calculate Molecule Similarities
  • Use DBSCAN method to cluster
  • Examine data
In [13]:
import matplotlib.pyplot as plt
import mpld3
%matplotlib inline
import seaborn as sns
colors = sns.color_palette()
# sns.palplot(colors)
do_tooltips = True

import warnings
In [14]:
# import OE tools and data
import ...

Finding Correlations in Molecule Data

The Pandas DataFrame we use within OENotebook makes it very easy to calculate correlations for molecule data. In this example we'll load some molecules, generate and store some associated data for each molecule, and then explore some built-in functions to calculate and visualize correlations in this data.

In [2 ...

Visualizing Molecule Data


  • Generate some molecule data
  • Plot histograms of data
  • Explore dealing with categorical grouping
In [16]:
from __future__ import print_function

# import OE tools and data
import oenotebook as oenb
# oenb.capture_errors()
import warnings

from openeye.oechem import OECalculateMolecularWeight
from openeye.oemolprop import OEGetXLogP, OEGet2dPSA, OEGetFractionCsp3, OEGetAromaticRingCount

from ...

Embedding Molecules in 2D-space

Embedding Molecules in a 2D Space

by Matt Geballe

Many times in computational chemistry we want to think about molecules in relationship to each other based on some definition of similarity. Example uses could be evaluating whether a set of molecules is "diverse" or not (for some definition of diversity ...

Getting Started

The best way to get started with a scientific python stack is to install Anaconda . See the installation instructions for additional assistance.

Once you have installed and activated your anaconda environment, OpenEye Toolkits can be installed through the following command

pip install -i OpenEye-toolkits ...