Calculate NPR values & Generate Heatmap - Revision history

Khtang: /* Setup Python environment */

2020-11-05T07:49:12Z

Setup Python environment

← Older revision		Revision as of 07:49, 5 November 2020
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	(base)$ conda create -c rdkit --name npr-py3 rdkit		(base)$ conda create -c rdkit --name npr-py3 rdkit
	(base)$ conda activate npr-py3		(base)$ conda activate npr-py3
	~~(npr-py3)$ conda update ipython~~
	~~# Install jupyter notebook~~
	~~(npr-py3)$ conda install -c conda-forge notebook~~
	# Install vaex - dataframe library for huge libraries		# Install vaex - dataframe library for huge libraries
	(npr-py3)$ conda install -c conda-forge vaex		(npr-py3)$ conda install -c conda-forge vaex
			(npr-py3)$ pip install ipython==7.9.0

	=== Run NPR calculation ===		=== Run NPR calculation ===
	Your smiles file should be in this format with no header: <smiles> <cid>		Your smiles file should be in this format with no header: <smiles> <cid>

2020-11-05T07:29:08Z

Calculate NPR

← Older revision		Revision as of 07:29, 5 November 2020
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	(base)$ conda create -c rdkit --name npr-py3 rdkit		(base)$ conda create -c rdkit --name npr-py3 rdkit
	(base)$ conda activate npr-py3		(base)$ conda activate npr-py3
			(npr-py3)$ conda update ipython
	# Install jupyter notebook		# Install jupyter notebook
	(npr-py3)$ conda install -c conda-forge notebook		(npr-py3)$ conda install -c conda-forge notebook

2020-11-05T07:06:11Z

Plot

← Older revision		Revision as of 07:06, 5 November 2020
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	From jupyter-notebook interface		From jupyter-notebook interface

	- Select 'single_plot.ipynb'		- Select 'single_plot.ipynb'

	- Change the path to h5py file and run the kernel		- Change the path to h5py file and run the kernel

2020-11-05T07:06:02Z

Plot

← Older revision		Revision as of 07:06, 5 November 2020
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	(npr-py3)$ jupyter-notebook		(npr-py3)$ jupyter-notebook

	From jupyter-notebook interface,		From jupyter-notebook interface
	- Select 'single_plot.ipynb'		- Select 'single_plot.ipynb'
	- Change the path to h5py file and run the kernel		- Change the path to h5py file and run the kernel

2020-11-05T07:05:29Z

Make Heatmap

← Older revision		Revision as of 07:05, 5 November 2020
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	== Make Heatmap ==		== Make Heatmap ==
			=== Generate h5py binary file ===
			(npr-py3)$ python py_csv2hdf5.py {output_smiles_file}

			This script without output h5py that is then can be read by vaex library (it is useful for read huge library into dataframe)

			=== Plot ===
			# Run Jupyter-Notebook
			(npr-py3)$ jupyter-notebook

			From jupyter-notebook interface,
			- Select 'single_plot.ipynb'
			- Change the path to h5py file and run the kernel

2020-11-05T06:54:07Z

Run NPR calculation

← Older revision		Revision as of 06:54, 5 November 2020
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	(npr-py3)$ python extra_newprops.py {smiles_file}		(npr-py3)$ python extra_newprops.py {smiles_file}
	Notes:		Notes:

	- Failed and success molecules are output from this script.		- Failed and success molecules are output from this script.

2020-11-05T06:53:57Z

Run NPR calculation

← Older revision		Revision as of 06:53, 5 November 2020
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	(npr-py3)$ python extra_newprops.py {smiles_file}		(npr-py3)$ python extra_newprops.py {smiles_file}
	Notes:		Notes:
	- Failed and success molecules are output from this script		- Failed and success molecules are output from this script.

	- The calculation maybe slow. It is recommend that you chunk the file and run it on parallel.		- The calculation maybe slow. It is recommend that you chunk the file and run it on parallel.

	== Make Heatmap ==		== Make Heatmap ==

2020-11-05T06:53:45Z

Run NPR calculation

← Older revision		Revision as of 06:53, 5 November 2020
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	=== Run NPR calculation ===		=== Run NPR calculation ===
	Your smiles file should be format ~~like this~~		Your smiles file should be in this format with no header: <smiles> <cid>

	~~'''~~<smiles> <cid>~~'''~~
	(npr-py3)$ python extra_newprops.py {smiles_file}		(npr-py3)$ python extra_newprops.py {smiles_file}
			Notes:
			- Failed and success molecules are output from this script
			- The calculation maybe slow. It is recommend that you chunk the file and run it on parallel.

	== Make Heatmap ==		== Make Heatmap ==

2020-11-05T06:49:20Z

Run NPR calculation

← Older revision		Revision as of 06:49, 5 November 2020
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	=== Run NPR calculation ===		=== Run NPR calculation ===
	Your smiles file should be format like this		Your smiles file should be format like this
	<smiles> <cid>
			'''<smiles> <cid>'''
	(npr-py3)$ python extra_newprops.py {smiles_file}		(npr-py3)$ python extra_newprops.py {smiles_file}

	== Make Heatmap ==		== Make Heatmap ==

2020-11-05T06:48:23Z

Calculate NPR

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 == Calculate NPR ==
-  Anaconda3 environment
+=== Setup Python environment ===
+- Download Anaconda3 installer and install follow the instruction (https://www.anaconda.com/products/individual)
 == Make Heatmap ==