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biopython | Bio/motifs/pfm.py | .py | # Copyright 2015 by Gert Hulselmans. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Parse various positio... | 424 | 17,229 |
biopython | Bio/motifs/matrix.py | .py | # Copyright 2013 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Support for various... | 624 | 24,049 |
biopython | Bio/motifs/meme.py | .py | # Copyright 2008 by Bartek Wilczynski.
# Revisions copyright 2019 by Victor Lin.
# Adapted from Bio.MEME.Parser by Jason A. Hackney. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this packa... | 188 | 6,397 |
biopython | Bio/motifs/minimal.py | .py | # Copyright 2018 by Ariel Aptekmann.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Module for the supp... | 222 | 7,161 |
biopython | Bio/motifs/thresholds.py | .py | # Copyright 2008 by Norbert Dojer. All rights reserved.
# Adapted by Bartek Wilczynski.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Approximate calculation of appropriate thresholds for motif ... | 110 | 4,530 |
biopython | Bio/motifs/clusterbuster.py | .py | # Copyright 2015 by Gert Hulselmans. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Parse Cluster Buster ... | 118 | 3,852 |
biopython | Bio/motifs/transfac.py | .py | # Copyright 2003 by Bartek Wilczynski. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Parsing TRANSFAC ... | 332 | 12,127 |
biopython | Bio/motifs/jaspar/__init__.py | .py | # Copyright 2013 by Anthony Mathelier and David Arenillas. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
""... | 375 | 11,388 |
biopython | Bio/motifs/jaspar/db.py | .py | # Copyright 2013 by David Arenillas and Anthony Mathelier. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
""... | 785 | 27,976 |
biopython | Bio/KEGG/__init__.py | .py | # Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code to work with ... | 97 | 3,038 |
biopython | Bio/KEGG/REST.py | .py | # Copyright 2014 by Kevin Wu.
# Revisions copyright 2014 by Peter Cock.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of thi... | 331 | 11,302 |
biopython | Bio/KEGG/Enzyme/__init__.py | .py | # Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Copyright 2007 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code to work with the KEGG En... | 340 | 11,185 |
biopython | Bio/KEGG/Gene/__init__.py | .py | # Copyright 2017 by Kozo Nishida. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code to work with the ... | 143 | 4,288 |
biopython | Bio/KEGG/Map/__init__.py | .py | # Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Copyright 2007 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been i... | 50 | 1,642 |
biopython | Bio/KEGG/KGML/KGML_pathway.py | .py | # Copyright 2013 by Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Classes to repre... | 858 | 27,600 |
biopython | Bio/KEGG/KGML/__init__.py | .py | # Copyright 2013 by Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code to work wit... | 17 | 516 |
biopython | Bio/KEGG/KGML/KGML_parser.py | .py | # Copyright 2013 by Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Classes and func... | 194 | 6,347 |
biopython | Bio/KEGG/Compound/__init__.py | .py | # Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Copyright 2007 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been... | 181 | 5,470 |
biopython | Bio/Align/emboss.py | .py | # Copyright 2008-2016 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 247 | 10,387 |
biopython | Bio/Align/msf.py | .py | # Copyright 2019, National Marrow Donor Program (NMPD). All rights reserved.
# Written by Peter Cock, The James Hutton Institute, under contract to NMDP.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see th... | 245 | 9,481 |
biopython | Bio/Align/a2m.py | .py | # Copyright 2022 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 122 | 4,523 |
biopython | Bio/Align/exonerate.py | .py | # Copyright 2022 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 656 | 26,538 |
biopython | Bio/Align/bed.py | .py | # Copyright 2022 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 260 | 9,932 |
biopython | Bio/Align/mauve.py | .py | # Copyright 2015-2015 by Eric Rasche. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support f... | 254 | 10,056 |
biopython | Bio/Align/hhr.py | .py | # Copyright 2022 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 237 | 9,503 |
biopython | Bio/Align/analysis.py | .py | # Copyright 2013 by Zheng Ruan (zruan1991@gmail.com). All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code... | 1,300 | 46,214 |
biopython | Bio/Align/fasta.py | .py | # Copyright 2022 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 87 | 3,141 |
biopython | Bio/Align/sam.py | .py | # Copyright 2022 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 766 | 30,547 |
biopython | Bio/Align/chain.py | .py | # Copyright 2023 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 268 | 9,448 |
biopython | Bio/Align/__init__.py | .py | # Copyright 2000, 2004 by Brad Chapman.
# Revisions copyright 2010-2013, 2015-2018 by Peter Cock.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have be... | 4,967 | 196,489 |
biopython | Bio/Align/psl.py | .py | # Copyright 2022 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 542 | 22,119 |
biopython | Bio/Align/stockholm.py | .py | # Copyright 2006-2016 by Peter Cock. All rights reserved.
# Copyright 2021 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been ... | 625 | 26,134 |
biopython | Bio/Align/clustal.py | .py | # Copyright 2006-2016 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 251 | 9,298 |
biopython | Bio/Align/nexus.py | .py | # Copyright 2006-2016 by Peter Cock. All rights reserved.
# Revisions copyright 2021 by Michiel de Hoon.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as ... | 195 | 7,330 |
biopython | Bio/Align/bigmaf.py | .py | # Copyright 2022 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 354 | 13,702 |
biopython | Bio/Align/maf.py | .py | # Copyright 2011, 2012 by Andrew Sczesnak. All rights reserved.
# Revisions Copyright 2011, 2017 by Peter Cock. All rights reserved.
# Revisions Copyright 2014, 2015 by Adam Novak. All rights reserved.
# Revisions Copyright 2015, 2017 by Blaise Li. All rights reserved.
#
# This file is part of the Biopython distrib... | 458 | 18,139 |
biopython | Bio/Align/bigpsl.py | .py | # Copyright 2022 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 614 | 23,410 |
biopython | Bio/Align/interfaces.py | .py | # Copyright 2006-2021 by Peter Cock.
# Copyright 2022 by Michiel de Hoon.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of t... | 350 | 12,461 |
biopython | Bio/Align/AlignInfo.py | .py | # Copyright 2000 Brad Chapman. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Extract information from a... | 55 | 1,713 |
biopython | Bio/Align/bigbed.py | .py | # Copyright 2022 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 2,242 | 81,893 |
biopython | Bio/Align/tabular.py | .py | # Copyright 2021 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 409 | 16,525 |
biopython | Bio/Align/phylip.py | .py | # Copyright 2006-2016 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support fo... | 182 | 6,401 |
biopython | Bio/Align/substitution_matrices/__init__.py | .py | # Copyright 2019 by Michiel de Hoon.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Substitution matrices."""
import os
impo... | 509 | 17,563 |
biopython | Bio/Sequencing/Ace.py | .py | # Copyright 2004 by Frank Kauff and Cymon J. Cox. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Parser ... | 606 | 20,432 |
biopython | Bio/Sequencing/__init__.py | .py | # Copyright 2004 Frank Kauff. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code to deal with various pr... | 13 | 530 |
biopython | Bio/Sequencing/Phd.py | .py | # Copyright 2004 by Cymon J. Cox and Frank Kauff. All rights reserved.
# Copyright 2008 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2009 by Cymon J. Cox. All rights reserved.
# Revisions copyright 2009 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and gov... | 205 | 5,684 |
biopython | Bio/PDB/ic_rebuild.py | .py | # Copyright 2019-2022 by Robert T. Miller. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Convert XYZ Str... | 506 | 18,341 |
biopython | Bio/PDB/Superimposer.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Superimpose two s... | 57 | 1,943 |
biopython | Bio/PDB/vectors.py | .py | # Copyright (C) 2004, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Vector class, inc... | 730 | 20,140 |
biopython | Bio/PDB/HSExposure.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Half-sphere expos... | 328 | 11,337 |
biopython | Bio/PDB/Entity.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Base class for Res... | 591 | 18,506 |
biopython | Bio/PDB/NeighborSearch.py | .py | # Copyright (C) 2002, 2004 Thomas Hamelryck (thamelry@binf.ku.dk)
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# pa... | 132 | 4,490 |
biopython | Bio/PDB/PDBList.py | .py | #!/usr/bin/env python
# Copyright 2003, by Kristian Rother. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#... | 806 | 31,347 |
biopython | Bio/PDB/internal_coords.py | .py | # Copyright 2019-22 by Robert T. Miller. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Classes to suppor... | 4,942 | 188,706 |
biopython | Bio/PDB/PDBParser.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Parser for PDB files."""
import warnings
import numpy as np
from Bio.File import as_... | 413 | 17,185 |
biopython | Bio/PDB/ic_data.py | .py | # Copyright 2019-22 by Robert T. Miller. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Per residue backb... | 1,790 | 59,270 |
biopython | Bio/PDB/ResidueDepth.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# Copyright (C) 2017, Joao Rodrigues (j.p.g.l.m.rodrigues@gmail.com)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that shoul... | 618 | 22,252 |
biopython | Bio/PDB/DSSP.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
r"""Use the DSSP pro... | 573 | 20,210 |
biopython | Bio/PDB/MMCIF2Dict.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Turn an mmCIF fil... | 132 | 5,063 |
biopython | Bio/PDB/Model.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Model class, used in Structure objects."""
from typing import TYPE_CHECKING
from Bio.... | 81 | 2,358 |
biopython | Bio/PDB/StructureBuilder.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Consumer class that builds a Structure object.
This is used by the PDBParser and MMCIF... | 322 | 12,137 |
biopython | Bio/PDB/SCADIO.py | .py | # Copyright 2019-21 by Robert T. Miller. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""SCADIO: write Ope... | 907 | 35,847 |
biopython | Bio/PDB/Dice.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code for chopping... | 79 | 2,315 |
biopython | Bio/PDB/PDBIO.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Output of PDB files."""
import os
import warnings
from Bio.Data.IUPACData import atom... | 486 | 16,441 |
biopython | Bio/PDB/Structure.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""The structure cla... | 71 | 2,147 |
biopython | Bio/PDB/alphafold_db.py | .py | """A module for interacting with the AlphaFold Protein Structure Database.
See the `database website <https://alphafold.com/>`_ and the `API docs <https://alphafold.com/api-docs/>`_.
"""
import json
import os
from os import PathLike
from collections.abc import Iterator
from typing import Optional
from typing import U... | 117 | 3,991 |
biopython | Bio/PDB/Chain.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Chain class, used... | 227 | 7,101 |
biopython | Bio/PDB/PSEA.py | .py | # Copyright (C) 2006, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Wrappers for PSEA... | 121 | 3,141 |
biopython | Bio/PDB/Polypeptide.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Polypeptide-relat... | 460 | 14,220 |
biopython | Bio/PDB/mmcifio.py | .py | # Copyright 2017 Joe Greener. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Write an mmCIF file.
See h... | 380 | 15,454 |
biopython | Bio/PDB/SASA.py | .py | # Copyright (C) 2020, Joao Rodrigues (j.p.g.l.m.rodrigues@gmail.com)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Calculati... | 252 | 8,505 |
biopython | Bio/PDB/FragmentMapper.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Classify protein ... | 324 | 9,621 |
biopython | Bio/PDB/NACCESS.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
# NACCESS interface ... | 212 | 7,219 |
biopython | Bio/PDB/Selection.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Selection of atom... | 86 | 2,589 |
biopython | Bio/PDB/cealign.py | .py | # Copyright (C) 2022, Joao Rodrigues (j.p.g.l.m.rodrigues@gmail.com)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Protein S... | 194 | 7,535 |
biopython | Bio/PDB/Residue.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Residue class, us... | 196 | 6,395 |
biopython | Bio/PDB/PICIO.py | .py | # Copyright 2019-2022 by Robert T. Miller. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""PICIO: read and... | 1,120 | 41,280 |
biopython | Bio/PDB/qcprot.py | .py | # Copyright (C) 2022, Joao Rodrigues (j.p.g.l.m.rodrigues@gmail.com
# Anuj Sharma (anuj.sharma80@gmail.com)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should ... | 364 | 12,295 |
biopython | Bio/PDB/PDBExceptions.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Some Bio.PDB-spec... | 35 | 934 |
biopython | Bio/PDB/AbstractPropertyMap.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Class that maps (... | 131 | 4,080 |
biopython | Bio/PDB/MMCIFParser.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""mmCIF parsers."""
import warnings
import numpy as np
from Bio.File import as_handle
... | 636 | 25,471 |
biopython | Bio/PDB/binary_cif.py | .py | """
A module to interact with BinaryCIF-formatted files.
"""
import gzip
from collections import deque
from typing import Optional
import numpy as np
try:
import msgpack
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install msgpack to use B... | 306 | 10,229 |
biopython | Bio/PDB/StructureAlignment.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Map residues of t... | 185 | 7,021 |
biopython | Bio/PDB/Atom.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Atom class, used ... | 603 | 20,481 |
biopython | Bio/PDB/parse_pdb_header.py | .py | #!/usr/bin/env python
# Copyright 2004 Kristian Rother.
# Revisions copyright 2004 Thomas Hamelryck.
# Revisions copyright 2024 James Krieger.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE fi... | 373 | 13,618 |
biopython | Bio/PDB/PDBMLParser.py | .py | # This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""This module contains a parser for PDBML (PDB XML) files.
PDBML is a representation of PDB data in XML format.
See https://pdbml.wwpdb.org/.
"""
f... | 170 | 6,858 |
biopython | Bio/PDB/mmtf/DefaultParser.py | .py | # Copyright 2016 Anthony Bradley. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code handle loading mmt... | 232 | 8,888 |
biopython | Bio/PDB/mmtf/mmtfio.py | .py | # Copyright 2019 Joe Greener. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Write a MMTF file."""
impo... | 280 | 11,174 |
biopython | Bio/PDB/mmtf/__init__.py | .py | # Copyright 2016 Anthony Bradley. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Support for loading 3D ... | 54 | 1,568 |
biopython | Bio/Alphabet/__init__.py | .py | # Copyright 2000-2002 by Andrew Dalke.
# Revisions copyright 2007-2010 by Peter Cock.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included ... | 23 | 1,201 |
biopython | Bio/AlignIO/MauveIO.py | .py | # Copyright 2015-2015 by Eric Rasche. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.AlignIO support... | 344 | 13,300 |
biopython | Bio/AlignIO/EmbossIO.py | .py | # Copyright 2008-2016 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.AlignIO support ... | 221 | 8,749 |
biopython | Bio/AlignIO/__init__.py | .py | # Copyright 2008-2018 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Multiple sequence al... | 475 | 18,499 |
biopython | Bio/AlignIO/StockholmIO.py | .py | # Copyright 2006-2016 by Peter Cock. All rights reserved.
# Revisions copyright 2015 by Ben Woodcroft. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should ha... | 621 | 26,397 |
biopython | Bio/AlignIO/FastaIO.py | .py | # Copyright 2008-2016 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.AlignIO support ... | 347 | 13,355 |
biopython | Bio/AlignIO/PhylipIO.py | .py | # Copyright 2006-2016 by Peter Cock. All rights reserved.
# Revisions copyright 2011 Brandon Invergo. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have... | 455 | 17,138 |
biopython | Bio/AlignIO/MsfIO.py | .py | # Copyright 2019, National Marrow Donor Program (NMPD). All rights reserved.
# Written by Peter Cock, The James Hutton Institute, under contract to NMDP.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see th... | 334 | 14,209 |
biopython | Bio/AlignIO/MafIO.py | .py | # Copyright 2011, 2012 by Andrew Sczesnak. All rights reserved.
# Revisions Copyright 2011, 2017 by Peter Cock. All rights reserved.
# Revisions Copyright 2014, 2015 by Adam Novak. All rights reserved.
# Revisions Copyright 2015, 2017 by Blaise Li. All rights reserved.
#
# This file is part of the Biopython distrib... | 870 | 35,258 |
biopython | Bio/AlignIO/NexusIO.py | .py | # Copyright 2008-2010, 2012-2014, 2016-2017 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"... | 174 | 6,226 |
biopython | Bio/AlignIO/Interfaces.py | .py | # Copyright 2008-2018 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""AlignIO support modu... | 159 | 5,598 |
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