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JoaoRodrigues / get_rcsb_release_dates.py
Created December 19, 2024 21:40
Example of combining RCSB Search and Data APIs to retrieve entry release dates.
"""Retrieve RCSB entry release dates using the API.
Example of combining Search and Data APIs
"""
import csv
import itertools
import json
import urllib3
from datetime import datetime
@JoaoRodrigues
JoaoRodrigues / frange.py
Last active October 6, 2020 23:13
Python 3.x range-like function with decimal step
import decimal
def frange(start, stop, step, include_stop=True):
"""Range-like function that accepts decimal step values."""
# To avoid rounding issues
# We cast the floats to string and then to decimals
# see: docs on Decimal(0.1) != Decimal('0.1')
dstep = decimal.Decimal(str(step))
@JoaoRodrigues
JoaoRodrigues / benchmark_PDBParser.py
Created August 22, 2020 22:40
Script to test PDBParser (biopython)
#!/usr/bin/env python
"""
Script to benchmark Bio.PDB PDBParser on a collection
of PDB files.
"""
import argparse
import gzip
import pathlib
@JoaoRodrigues
JoaoRodrigues / intermediate_py_links.md
Last active July 6, 2021 13:32
Intermediate Python Links
@JoaoRodrigues
JoaoRodrigues / anton2_reimage.py
Last active October 25, 2019 01:45
Script to reimage Anton2 trajectories
#!/usr/bin/env python
"""
Python script to reimage/unwrap an MD simulation trajectory
ran on the Anton2 supercomputer.
Expects a topology file in .dms format and the trajectory
folder '.dtr'.
Requires:
@JoaoRodrigues
JoaoRodrigues / mdpretty.py
Created October 18, 2019 23:17
Assorted Python function for plotting molecular properties
# Copyright 2019 João Pedro Rodrigues
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
@JoaoRodrigues
JoaoRodrigues / mda_PDBxParser.py
Last active October 16, 2019 06:41
PDBxParser to use with MDAnalysis to load PDBx/mmCIF files as Topologies
#!/usr/bin/env python
from __future__ import absolute_import, print_function
import collections
import re
import numpy as np
import warnings
@JoaoRodrigues
JoaoRodrigues / uniprot_rest_example.py
Created June 7, 2019 22:54
Example of Uniprot REST API (Python)
#!/usr/bin/env python
"""
Queries Uniprot database and retrieves (canonical) sequences.
"""
import argparse
import sys
import urllib.request
@JoaoRodrigues
JoaoRodrigues / fetch_sequences.py
Created June 5, 2019 19:43
Using Biopython (Bio.Entrez) to fetch sequences from NCBI
from Bio import Entrez
Entrez.email = None # change this!
assert Entrez.email is not None
# Read ids from file to a list
id_list = [ ... ]
results = {}
handle = Entrez.efetch(db="protein", id=id_list, retmode="xml")
@JoaoRodrigues
JoaoRodrigues / peptide_wt_pymol_cap_CONECT.pdb
Created April 16, 2018 22:26
REMARK 200 Generated with PyMOL and psico
ATOM 1 CY MET A 1 -57.588 1.993 21.439 1.00 0.00 C
ATOM 2 OY MET A 1 -58.412 1.073 21.529 1.00 0.00 O
ATOM 3 CAY MET A 1 -57.792 3.297 22.180 1.00 0.00 C
ATOM 4 N MET A 1 -56.540 1.838 20.704 1.00 0.00 N
ATOM 5 CA MET A 1 -56.332 0.585 19.985 1.00 0.00 C
ATOM 6 C MET A 1 -54.885 0.158 20.046 1.00 0.00 C
ATOM 7 O MET A 1 -54.053 0.864 20.614 1.00 0.00 O
ATOM 8 CB MET A 1 -56.802 0.738 18.512 1.00 0.00 C
ATOM 9 CG MET A 1 -58.316 0.961 18.308 1.00 0.00 C