Irfan Alibay IAlibay

## AnalyzingMultistateFiles.ipynb

      
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                IAlibay
                / AnalyzingMultistateFiles.ipynb
            
            
              Created
              August 23, 2023 23:52
            
              
                AnalyzingMultistateFiles
              
          
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## cinnabar_plotting.ipynb

      
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                / cinnabar_plotting.ipynb
            
            
              Created
              May 30, 2023 09:17
            
          
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## alchemical_gather.ipynb

      
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                / alchemical_gather.ipynb
            
            
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              May 30, 2023 07:52
            
          
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## simulate_with_systemgenerator.py
# imports
from openmm import app, unit, MonteCarloBarostat, LangevinMiddleIntegrator, XmlSerializer
from openmm.app import PDBFile, Modeller
from openmmforcefields.generators import SystemGenerator
from openfe import SmallMoleculeComponent
from openff.units.openmm import ensure_quantity

# system_generator
forcefield_kwargs = {
    'constraints': app.HBonds,

## tyk2_viz_alchemiscale.ipynb

      
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                IAlibay
                / tyk2_viz_alchemiscale.ipynb
            
            
              Last active
              May 4, 2023 03:27
            
              
                Build, visualize, and submit a tyk2 perturbation network using openfe and alchemiscale
              
          
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## alchemiscale_restart_errors.py
import os
from alchemiscale import AlchemiscaleClient, Scope, ScopedKey

user_id = os.environ['ALCHEMISCALE_ID']
user_key = os.environ['ALCHEMISCALE_KEY']
asc =  AlchemiscaleClient('https://api.alchemiscale.org', user_id, user_key)
scope = Scope('openfe', 'v0_7_3', 'tyk2_off2_0')
with open('scoped-key.dat', 'r') as f:
    network = asc.get_network(f.read())

## alchemiscale_print_errors.py
import os
from pprint import pprint
from alchemiscale import AlchemiscaleClient, Scope, ScopedKey

user_id = os.environ['ALCHEMISCALE_ID']
user_key = os.environ['ALCHEMISCALE_KEY']
asc =  AlchemiscaleClient('https://api.alchemiscale.org', user_id, user_key)
scope = Scope('openfe', 'v0_7_3', 'tyk2_off2_0')
with open('scoped-key.dat', 'r') as f:
    network = asc.get_network(f.read())

## alchemiscale_status.py
import os
from alchemiscale import AlchemiscaleClient, Scope, ScopedKey

user_id = os.environ['ALCHEMISCALE_ID']
user_key = os.environ['ALCHEMISCALE_KEY']
asc =  AlchemiscaleClient('https://api.alchemiscale.org', user_id, user_key)
scope = Scope('openfe', 'v0_7_3', 'tyk2_off2_0')
with open('scoped-key.dat', 'r') as f:
    network = asc.get_network(f.read())

## alchemiscale_gen_tyk2_network.py
import os
import copy
import json
import openfe
from openfe import ChemicalSystem
from openfe.protocols.openmm_rfe import RelativeHybridTopologyProtocol as RHTP
from gufe import AlchemicalNetwork, tokenization
from openff.units import unit
from rdkit import Chem
from openfe_benchmarks import tyk2

## gen_networks.py
import yaml
import json
import argparse
from typing import List

import numpy as np
from rdkit import Chem

from openfe import SmallMoleculeComponent
from openfe.setup import LomapAtomMapper, lomap_scorers, LigandNetwork
	# imports
	from openmm import app, unit, MonteCarloBarostat, LangevinMiddleIntegrator, XmlSerializer
	from openmm.app import PDBFile, Modeller
	from openmmforcefields.generators import SystemGenerator
	from openfe import SmallMoleculeComponent
	from openff.units.openmm import ensure_quantity

	# system_generator
	forcefield_kwargs = {
	'constraints': app.HBonds,
	import os
	from alchemiscale import AlchemiscaleClient, Scope, ScopedKey

	user_id = os.environ['ALCHEMISCALE_ID']
	user_key = os.environ['ALCHEMISCALE_KEY']
	asc = AlchemiscaleClient('https://api.alchemiscale.org', user_id, user_key)
	scope = Scope('openfe', 'v0_7_3', 'tyk2_off2_0')
	with open('scoped-key.dat', 'r') as f:
	network = asc.get_network(f.read())
	import os
	from pprint import pprint
	from alchemiscale import AlchemiscaleClient, Scope, ScopedKey

	user_id = os.environ['ALCHEMISCALE_ID']
	user_key = os.environ['ALCHEMISCALE_KEY']
	asc = AlchemiscaleClient('https://api.alchemiscale.org', user_id, user_key)
	scope = Scope('openfe', 'v0_7_3', 'tyk2_off2_0')
	with open('scoped-key.dat', 'r') as f:
	network = asc.get_network(f.read())
	import os
	import copy
	import json
	import openfe
	from openfe import ChemicalSystem
	from openfe.protocols.openmm_rfe import RelativeHybridTopologyProtocol as RHTP
	from gufe import AlchemicalNetwork, tokenization
	from openff.units import unit
	from rdkit import Chem
	from openfe_benchmarks import tyk2
	import yaml
	import json
	import argparse
	from typing import List

	import numpy as np
	from rdkit import Chem

	from openfe import SmallMoleculeComponent
	from openfe.setup import LomapAtomMapper, lomap_scorers, LigandNetwork