Cloudsmith - Repositories - Ultimaker (ultimaker) - debian-backup (debian-backup) - pdb2pqr

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Open-Source — ultimaker (Ultimaker) / debian-backup — Project

A certifiably-awesome open-source package repository curated by Ultimaker, hosted by Cloudsmith.

Note: Packages in this repository are licensed as GNU General Public License v3.0 or later (dependencies may be licensed differently).

pdb2pqr 2.1.1+dfsg-5

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One-liner (summary)

Preparation of protein structures for electrostatics calculations

Description

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations. It thus provides a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include: * Adding a limited number of missing heavy atoms to biomolecular structures * Determining side-chain pKas * Placing missing hydrogens * Optimizing the protein for favorable hydrogen bonding * Assigning charge and radius parameters from a variety of force fields

This package also includes PropKa, a tool to modify the protonation state of protein structures in the Protein Data Bank (PDB) format to match a given pKa value. It can also be used to refine NMR structures, which often yield inaccurate pKa values for some residues.

License

Unknown

Size

367.4 KB

Downloads

Status	Completed
Checksum (MD5)	b2ce5de9c62bd4d247f30fc514c72a9e
Checksum (SHA-1)	e17764c50a68f204f94cca78ded9ab9f0da5c086
Checksum (SHA-256)	382b17c2a63d46693c2f21514475949bbefc04918181dab15f2156a733ecb0b3
Checksum (SHA-512)	6015c8e0d8b49818c2d3510ef770566c61dffb9a6a0728f9b1d4beac2ac7fb22fe…
GPG Signature	Download
GPG Fingerprint	c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution	debian/buster - Debian - 10 (Buster)
Storage Region	Dublin, Ireland
Type	Binary (contains binaries and binary artifacts)
Uploaded At	1 year, 1 month ago
Uploaded By
Slug Id	pdb2pqr_211dfsg-5_arm64deb-sph3
Unique Id	tSezOwBPGckI
Version (Raw)	2.1.1+dfsg-5
Version (Parsed)	Major: 2 Minor: 1 Patch: 1 Type: SemVer (Strict) Metadata: dfsg-5
	extended metadata
Homepage	https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
Installed Size	2.8 MB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

88df9172be9ee9c83e3365fc8523899a

Depends	libc6	>=2.17
Depends	libgcc1	>=1:3.0
Depends	libpython2.7	>=2.7
Depends	libstdc++6	>=5.2
Depends	python-networkx
Depends	python-numpy
Depends	python:any
Suggests	apbs
Enhances	autodocktools
Replaces	propka
Provides	propka

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<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pdb2pqr/2.1.1+dfsg-5/a=arm64;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pdb2pqr/2.1.1+dfsg-5/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'pdb2pqr' @ Cloudsmith" /></a>

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|Latest version of 'pdb2pqr' @ Cloudsmith|
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rendered as:

These instructions assume you have setup the repository first (or read it).

To install/use pdb2pqr @ version 2.1.1+dfsg-5 ...

To install packages, you can quickly setup the repository automatically (recommended):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E bash

If you need to force a specific distribution, release/version, architecture, or component (if supported), you can also do that (e.g. if your system is compatible but not identical):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E distro=debian codename=buster arch=ARCH component=COMPONENT bash

or ... you can manually configure it yourself before installing packages:

apt-get install -y debian-keyring  # debian only
apt-get install -y debian-archive-keyring  # debian only
apt-get install -y apt-transport-https
# For Debian Stretch, Ubuntu 16.04 and later
keyring_location=/usr/share/keyrings/ultimaker-debian-backup-archive-keyring.gpg
# For Debian Jessie, Ubuntu 15.10 and earlier
keyring_location=/etc/apt/trusted.gpg.d/ultimaker-debian-backup.gpg
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/gpg.C334EFCB2C4F9BE3.key' |  gpg --dearmor >> ${keyring_location}
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/config.deb.txt?distro=debian&codename=buster&component=main' > /etc/apt/sources.list.d/ultimaker-debian-backup.list
sudo chmod 644 ${keyring_location}
sudo chmod 644 /etc/apt/sources.list.d/ultimaker-debian-backup.list
apt-get update

sudo apt-get install pdb2pqr=2.1.1+dfsg-5

Warning: Note that this package is for Debian 10 (Buster) / arm64 and may only work for that configuration.

Still stuck? Need help? Don't panic. Just contact us for help (even if you're not a customer).

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