rkakamilan rkakamilan

## making-the-most-of-local-llms.ipynb

      
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              88 stars
            
          
                kyo-takano
                / making-the-most-of-local-llms.ipynb
            
            
              Last active
              November 7, 2025 04:00
            
              
                 ローカルLLMはこーやって使うの💢
              
          
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## highlight_atoms_3d.py
import py3Dmol
from rdkit import Chem

def draw_mol_with_highlights(mol, hit_ats, style=None):
    """Draw molecule in 3D with highlighted atoms.

    Parameters
    ----------
    mol : RDKit molecule
    hit_ats : tuple of tuples

## NOTES.md

      
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                biochem-fan
                / NOTES.md
            
            
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              March 13, 2024 07:29
            
              
                AlphaFold2 without Docker
              
          
    Warning: this is my personal messy ad-hoc note. Not intended for production installation.
Instruction by @kalinialab is probably better.
My environment


Cent OS 7.0
CUDA 11.2
Without root accoumt

Directories


## Tetherheavy.ipynb

      
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                ptosco
                / Tetherheavy.ipynb
            
            
              Created
              August 21, 2020 21:47
            
              
                TetherHeavy
              
          
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## twittermute.txt
Mute these words in your settings here: https://twitter.com/settings/muted_keywords

ActivityTweet
generic_activity_highlights
generic_activity_momentsbreaking
RankedOrganicTweet
suggest_activity
suggest_activity_feed
suggest_activity_highlights
suggest_activity_tweet

## rdkit_installer.py
import sys
import os
import requests
import subprocess
import shutil
from logging import getLogger, StreamHandler, INFO


logger = getLogger(__name__)
logger.addHandler(StreamHandler())

## OE_toandfrom_RDK.ipynb

      
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                bannanc
                / OE_toandfrom_RDK.ipynb
            
            
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              February 5, 2025 21:18
            
              
                This is a jupyter notebook explaining how to convert molecules in OpenEye toolkits to the equivalent molecule in RDKit going both directions between toolkits.
              
          
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## ffmpeg.md

      
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              1470 stars
            
          
                steven2358
                / ffmpeg.md
            
            
              Last active
              December 11, 2025 18:19
            
              
                FFmpeg cheat sheet
              
          
    FFmpeg cheat sheet

A list of useful commands for the FFmpeg command line tool.
Download FFmpeg: https://www.ffmpeg.org/download.html
Full documentation: https://www.ffmpeg.org/ffmpeg.html
Basic conversion


## PLINK-JP.markdown

      
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                kokitsuyuzaki
                / PLINK-JP.markdown
            
            
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              October 4, 2023 07:30
            
              
                GWAS研究で利用されるソフトウェア"PLINK"のチュートリアルを大雑把に要約したもの
              
          
    Hapmapに登録された89のアジア人(中国人45人、日本人44人)における83534SNPsの解析


PLINK Web site : http://pngu.mgh.harvard.edu/~purcell/plink/
PLINK Tutorial : http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml

=======
あらかじめ準備しておく事


コンソール画面でRとlinuxコマンドが使える環境(more、sort、headとか)
PLINKのダウンロード、インストール（PLINK Web siteから)
hapmap1.zipのダウンロード（PLINK Tutorialから)
	import py3Dmol
	from rdkit import Chem

	def draw_mol_with_highlights(mol, hit_ats, style=None):
	"""Draw molecule in 3D with highlighted atoms.

	Parameters
	----------
	mol : RDKit molecule
	hit_ats : tuple of tuples
	Mute these words in your settings here: https://twitter.com/settings/muted_keywords

	ActivityTweet
	generic_activity_highlights
	generic_activity_momentsbreaking
	RankedOrganicTweet
	suggest_activity
	suggest_activity_feed
	suggest_activity_highlights
	suggest_activity_tweet
	import sys
	import os
	import requests
	import subprocess
	import shutil
	from logging import getLogger, StreamHandler, INFO


	logger = getLogger(__name__)
	logger.addHandler(StreamHandler())