edraizen’s gists

edraizen / calculate_contacts.py

Created September 2, 2022 21:03

Calculated PDB contacts and outputs a similar form to protein contact atlas

	from pathlib import Path

	import click
	import numpy as np
	import pandas as pd
	from biotite.structure.io.pdb import PDBFile
	from sklearn.metrics import pairwise_distances

	@click.command()
	@click.argument('pdb_file', required=1, type=click.Path(exists=True))

edraizen / worker_cachingFileStoreError.out

Created December 29, 2021 22:40

	INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
	INFO:toil:Running Toil version 5.6.0a1-458a26c04268e57ebace072e1d64b6a087e99e51-dirty on host default-toil-c49a786e-6899-4cc4-ae90-f49e2c9cfaaf-0-j5pbg.
	DEBUG:toil:Configuration: {'workflowID': 'be4ac964-d6a0-4efa-84e3-220a4b14a690', 'workflowAttemptNumber': 0, 'jobStore': 's3hsds:us-east-1:/home/ed4bu/hello-world', 'logLevel': 'DEBUG', 'workDir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'kubernetes', 'disableAutoDeployment': False, 'maxLocalJobs': 2, 'manualMemArgs': False, 'coalesceStatusCalls': False, 'statePollingWait': None, 'parasolCommand': 'parasol', 'parasolMaxBatches': 10000, 'scale': 1.0, 'mesos_endpoint': '10.42.0.155:5050', 'allocate_mem': False, 'tes_endpoint': 'http://10.42.0.155:8000', 'tes_user': None, 'tes_password': None, 'tes_bearer_token': None, 'kubernetes_host_path': '/media/smb-rivanna/ed4bu/UrfoldServer/urfold_runs/cath_pipeline/h5_restructure/k8/', 'kubernetes_ow

edraizen / hello_world.out

Created December 22, 2021 20:26

	/usr/local/lib/python3.8/dist-packages/requests/__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.7) or chardet (2.3.0)/charset_normalizer (2.0.6) doesn't match a supported version!
	warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "
	[2021-12-22T20:20:43+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'adal-python', 'botocore', 'kubernetes', 'urllib3', 'docker', 'boto', 'websocket', 'pymesos', 'charset_normalizer', 'bcdocs', 'google', 'oauthlib', 'google_auth_oauthlib', 'dill', 'requests_oauthlib', 'requests', 'boto3'}
	[2021-12-22T20:20:43+0000] [MainThread] [D] [toil.batchSystems.contained_executor] Starting executor
	[2021-12-22T20:20:43+0000] [MainThread] [D] [toil.batchSystems.contained_executor] Adopting environment: dict_keys(['TOIL_S3_HOST', 'TOIL_S3_PORT', 'TOIL_S3_USE_SSL', 'HS_ENDPOINT', 'HS_USERNAME', 'HS_PASSWORD', 'TOIL_RT_LOGGING_ADDRESS', 'TOIL_RT_LOGGING_LEVEL', 'OMP_NUM_THREADS'])
	[2021-12-22T20:20:43+0000]

edraizen / hsds_jobstore.out

Created December 21, 2021 04:49

This file has been truncated, but you can view the full file.

	#env \| grep TOIL
	TOIL_WORKDIR=/var/lib/toil
	TOIL_S3_HOST=minio.minio-tenant-1.svc.cluster.local
	TOIL_AWS_SECRET_NAME=aws-credentials
	TOIL_KUBERNETES_HOST_PATH=/media/smb-rivanna/ed4bu/UrfoldServer/urfold_runs/cath_pipeline/h5_restructure/k8/
	TOIL_DOCKER_NAME=molmimic
	TOIL_S3_USE_SSL=False
	TOIL_KUBERNETES_OWNER=default
	TOIL_APPLIANCE_SELF=edraizen/molmimic:0.0.1
	TOIL_S3_PORT=80

edraizen / fixes_for_masif.sh

Last active October 29, 2021 20:48

	export MASIF_DIR=/change/me/

	sed -i '/pyparsing/d' $MASIF_DIR/masif_env/lib/python3.7/site-packages/packaging-21.2-py3.7.egg/EGG-INFO/requires.txt
	sed -i '/pandas/d' $MASIF_DIR/masif_env/lib/python3.7/site-packages/dask-2021.10.0-py3.7.egg/EGG-INFO/requires.txt
	sed -i '/pandas/d' $MASIF_DIR/masif_env/lib/python3.7/site-packages/StrBioInfo-0.9a0.dev1-py3.7.egg/EGG-INFO/requires.txt

edraizen / grid.html

Created October 5, 2021 16:20

	<!DOCTYPE html>
	<html>
	<head>
	<title>Grid</title>
	<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.0.0/jquery.min.js"></script>
	<script src="https://3Dmol.org/build/3Dmol-min.js"></script>
	<style type="text/css">
	.mol-container {
	width: 100%;
	height: 800px;

edraizen / DistributedDataset.py

Created September 9, 2021 18:11

	from torch.utils.data import Dataset as _Dataset
	from torch.utils.data import Subset

	import h5pyd

	class DistributedDataset(_Dataset):
	"""Read dataset from h5 file. If key specifies a dataset, each row is an
	independent sample. If kay specifies a group, each dataset is an independent
	sample.

edraizen / vae.py

Last active April 1, 2021 21:41

	# Copyright (c) Chris Choy ([email protected]).
	#
	# Permission is hereby granted, free of charge, to any person obtaining a copy of
	# this software and associated documentation files (the "Software"), to deal in
	# the Software without restriction, including without limitation the rights to
	# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
	# of the Software, and to permit persons to whom the Software is furnished to do
	# so, subject to the following conditions:
	#
	# The above copyright notice and this permission notice shall be included in all

edraizen / ME.err

Last active October 15, 2020 18:13

	$sudo /usr/local/bin/singularity build --tmpdir /home/ec2-user/SageMaker/scratch pytorch_1.6.0_ME_0.5_v1.simg Singularity
	....
	+ git clone https://github.com/NVIDIA/MinkowskiEngine.git
	+ cd MinkowskiEngine
	+ git checkout v0.5
	+ make clean
	+ export CXX=/usr/bin/gcc-8
	+ python setup.py install --force_cuda --cuda_home=/usr/local/cuda-10.2
	No CUDA runtime is found, using CUDA_HOME='/usr/local/cuda-10.2'
	WARNING: Skipping MinkowskiEngine as it is not installed.

edraizen / intro-to-jupyter-bme4550.ipynb

Created September 14, 2020 17:44

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Eli Draizen edraizen