Leela S. Dodda leelasd
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bdrown
/ calc_pbf.py
Created
April 5, 2016 16:12
Script for calculating the PBF score of molecules. Script can be incorporated into Schrodinger's Maestro GUI in order to process structures selected in the Project Table.
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| #Name: Project Table:Plane of Best Fit - PJH Lab | |
| #Command: pythonrun calc_pbf.run | |
| __doc__ = """ | |
| Performs plane of best fit analysis. | |
| Calculates the average distance of all atoms in each molecule to the plane that | |
| fits each structure. Plane fitting is performed by single value decomposition | |
| (SVD) using the Numpy package. | |
| The script can also be run from the command line. | |
| """ |
PatWalters
/ compare_rocs_plec.ipynb
Created
May 30, 2020 19:45
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greglandrum
/ Schmidtke_ReversingReactions.ipynb
Last active
October 27, 2020 22:52
Schmidtke_ReversingReactions.ipynb
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greglandrum
/ iwatobipen_reactions_and_coordinates.ipynb
Created
May 11, 2019 05:41
iwatobipen_reactions_and_coordinates
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greglandrum
/ Show_Ph4_Features_in_PyMOL.ipynb
Created
January 15, 2019 09:52
Show_Ph4_Features_in_PyMOL.ipynb
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greglandrum
/ MCS Pharmacophore.ipynb
Created
July 11, 2017 15:52
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n-yoshikawa
/ schnet_pred_edge.py
Created
November 12, 2019 20:28
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| import torch | |
| import torch.nn as nn | |
| from torch.nn import Softplus | |
| from torch.utils.data import Dataset, DataLoader | |
| import dgl | |
| import dgl.function as fn | |
| from dgl.batched_graph import sum_nodes | |
| from dgl.data.chem.utils import mol_to_complete_graph | |
| import numpy as np | |
| from collections import defaultdict |
wiederm
/ MD_using_ANI1cxx.py
Last active
June 12, 2021 01:16
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| from openmmtools.constants import kB | |
| from simtk import unit | |
| import numpy as np | |
| from tqdm import tqdm | |
| from IPython.core.display import display, HTML | |
| from IPython.display import SVG | |
| from rdkit.Chem.Draw import IPythonConsole | |
| import mdtraj as md | |
| #from utils import * | |
| import nglview |
iwatobipen
/ combination.ipynb
Created
June 6, 2021 12:37
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greglandrum
/ KNIME_from_Jupyter_demo.ipynb
Created
January 14, 2019 13:43
KNIME from Jupyter_demo.ipynb
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