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

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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).

concavity 0.1+dfsg.1-4

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One-liner (summary)

predictor of protein ligand binding sites from structure and conservation

Description

ConCavity predicts protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

ConCavity takes as input a PDB format protein structure and optionally files that characterize the evolutionary sequence conservation of the chains in the structure file.

The following result files are produced by default: * Residue ligand binding predictions for each chain (*.scores). * Residue ligand binding predictions in a PDB format file (residue scores placed in the temp. factor field, *_residue.pdb). * Pocket prediction locations in a DX format file (*.dx). * PyMOL script to visualize the predictions (*.pml).

License

Unknown

Size

265.7 KB

Downloads

Status	Completed
Checksum (MD5)	4862d4b8ba4ca8a5fe2e6ef88f5e2649
Checksum (SHA-1)	d3bc129fb26a011f859ae26c824b3833798c0dba
Checksum (SHA-256)	20d060c71d04360dab062a4afb65570684a8896405039995baeec69162d88c00
Checksum (SHA-512)	44e1793e903c4b799814d65fb21259fc11733424d85a477a9daa34a778c4794a53…
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	8 months, 2 weeks ago
Uploaded By
Slug Id	concavity_01dfsg1-4_armhfdeb-kvpe
Unique Id	nMe0i6L7UN0f
Version (Raw)	0.1+dfsg.1-4
Version (Parsed)	Major: 0 Minor: 1 Type: SemVer (Compat) Metadata: dfsg.1-4
	extended metadata
Homepage	http://compbio.cs.princeton.edu/concavity/
Installed Size	422.0 KB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

ef206cefa2570909329dacda4b727366

Depends	libc6	>=2.4
Depends	libgcc1	>=1:3.5
Depends	libstdc++6	>=5
Suggests	conservation-code
Suggests	pymol

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[![This version of 'concavity' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/concavity/0.1+dfsg.1-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/concavity/0.1+dfsg.1-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)

|This version of 'concavity' @ Cloudsmith|
.. |This version of 'concavity' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/concavity/0.1+dfsg.1-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/concavity/0.1+dfsg.1-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/concavity/0.1+dfsg.1-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/concavity/0.1+dfsg.1-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'concavity' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/concavity/0.1+dfsg.1-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/concavity/0.1+dfsg.1-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'concavity' @ Cloudsmith" /></a>

rendered as:

To embed the badge for the latest package version, use the following:

[![Latest version of 'concavity' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/concavity/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/concavity/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)

|Latest version of 'concavity' @ Cloudsmith|
.. |Latest version of 'concavity' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/concavity/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/concavity/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/concavity/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/concavity/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="Latest version of 'concavity' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/concavity/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/concavity/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true" alt="Latest version of 'concavity' @ Cloudsmith" /></a>

rendered as:

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

To install/use concavity @ version 0.1+dfsg.1-4 ...

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 concavity=0.1+dfsg.1-4

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

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