rnaimehaom / parallel_descriptors.py

Created November 21, 2022 20:01 — forked from PatWalters/parallel_descriptors.py

Calculate RDKit descriptors with Dask

	#!/usr/bin/env python

	import sys
	import pandas as pd
	import dask.dataframe as dd
	from rdkit import Chem
	from rdkit.Chem import Descriptors
	import numpy as np
	import time
	import multiprocessing

rnaimehaom / howto-forward-x11-to-win10-via-putty-vcxsrv.md

Created September 29, 2022 15:02 — forked from vietlq/howto-forward-x11-to-win10-via-putty-vcxsrv.md

Code2Pro: How to Forward X11 to Windows 10 via PuTTY & vcxsrv

Scope

Tested on Windows 10 & Ubuntu 16.

Steps

rnaimehaom / drugBank_tree_structure.txt

Created August 19, 2022 18:46 — forked from rosherbal/drugBank_tree_structure.txt

Extract information from DrugBank xml file

rnaimehaom / read_bam.R

Created March 15, 2022 20:49 — forked from davetang/read_bam.R

Read in BAM file and store as a data frame using Bioconductor's Rsamtools

	#install if necessary
	source("http://bioconductor.org/biocLite.R")
	biocLite("Rsamtools")

	#load library
	library(Rsamtools)

	#read in entire BAM file
	bam <- scanBam("wgEncodeRikenCageHchCellPapAlnRep1.bam")

rnaimehaom / data.table-joins.R

Created February 6, 2022 23:57 — forked from nacnudus/data.table-joins.R

How to do joins with data.table

	library(data.table)

	?`[.data.table`

	DT <- data.table(x=rep(c("b","a","c"),each=3), y=c(1,3,6), v=1:9)
	X <- data.table(x=c("c","b"), v=8:7, foo=c(4,2))

	colnames(DT)
	# [1] "x" "y" "v"

rnaimehaom / SoftEther VPN for Ubuntu 16.04 & 18.04

Created February 5, 2022 21:27 — forked from amanjuman/SoftEther VPN for Ubuntu 16.04 & 18.04

SoftEther VPN for Ubuntu 16.04 & 18.04

	sudo apt-get update && sudo apt-get upgrade -y && sudo apt-get autoremove -y
	apt-get -y install build-essential wget curl gcc make wget tzdata git libreadline-dev libncurses-dev libssl-dev zlib1g-dev

	wget https://github.com/SoftEtherVPN/SoftEtherVPN_Stable/releases/download/v4.38-9760-rtm/softether-vpnserver-v4.38-9760-rtm-2021.08.17-linux-x64-64bit.tar.gz
	tar xzf softether-vpnserver-v4.38-9760-rtm-2021.08.17-linux-x64-64bit.tar.gz && rm softether-vpnserver-v4.38-9760-rtm-2021.08.17-linux-x64-64bit.tar.gz

	cd vpnserver && sudo make
	cd ..
	sudo mv vpnserver /usr/local && cd /usr/local/vpnserver/
	sudo chmod 600 *

rnaimehaom / conf_gen.py

Created December 25, 2021 01:09 — forked from tdudgeon/conf_gen.py

Conformer generation using RDKit

	import sys
	from rdkit import Chem
	from rdkit.Chem import AllChem, TorsionFingerprints
	from rdkit.ML.Cluster import Butina


	def gen_conformers(mol, numConfs=100, maxAttempts=1000, pruneRmsThresh=0.1, useExpTorsionAnglePrefs=True, useBasicKnowledge=True, enforceChirality=True):
	ids = AllChem.EmbedMultipleConfs(mol, numConfs=numConfs, maxAttempts=maxAttempts, pruneRmsThresh=pruneRmsThresh, useExpTorsionAnglePrefs=useExpTorsionAnglePrefs, useBasicKnowledge=useBasicKnowledge, enforceChirality=enforceChirality, numThreads=0)
	return list(ids)

rnaimehaom / convert_molecules.py

Created December 17, 2021 20:36 — forked from leelasd/convert_molecules.py

Convert Smiles code to 3D and save to SDF

	import pandas as pd
	from rdkit import Chem
	from rdkit.Chem import AllChem
	df = pd.read_csv('SMILES.csv')
	mols = [Chem.MolFromSmiles(smi) for smi in df.SMILES]
	hmols = [Chem.AddHs(m) for m in mols]
	for mol in hmols:
	AllChem.EmbedMolecule(mol,AllChem.ETKDG())
	print(AllChem.UFFOptimizeMolecule(mol,1000))
	smiles = list(df.SMILES)