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gndy / dockedpose.py
Created August 6, 2018 05:44 — forked from baoilleach/dockedpose.py
Using Open Babel to calculate the symmetry-corrected RMSD of a docked pose from a crystal structure
import math
import pybel
def squared_distance(coordsA, coordsB):
"""Find the squared distance between two 3-tuples"""
sqrdist = sum( (a-b)**2 for a, b in zip(coordsA, coordsB) )
return sqrdist
def rmsd(allcoordsA, allcoordsB):
"""Find the RMSD between two lists of 3-tuples"""
@gndy
gndy / conf_gen.py
Created June 28, 2018 06:48 — 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)
@gndy
gndy / apple-bluetooth-kb-f20.md
Created May 23, 2017 05:43 — forked from jiphex/apple-bluetooth-kb-f20.md
Pairing an Apple Bluetooth keyboard with Fedora 20

For some reason, this didn't work with the standard GUI bluetooth tools, so I did the following

  1. Run the command-line bluetoothctl tool
  2. type "agent on"
  3. type "scan on"
  4. press the button on your keyboard, the light should flash if it's not paired with anything else
  5. type "devices" (this shows the list of devices)
  6. type "trust xxxx" where xxxx is the keyboard MAC
  7. type "connect xxxx" where xxxx is the keyboard MAC
  8. type "pair xxxx" where xxxx is the keyboard MAC