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 Open-Source ultimaker 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).

Debian logo python3-freecontact  1.1-4

One-liner (summary)

fast protein contact predictor - binding for Python3

Description

FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains the Python3 binding.

License

Unknown

Size

29.9 KB

Downloads

0

Status  Completed
Checksum (MD5) bbb7396abb6809c281a47e32a8fa13ce
Checksum (SHA-1) c9038190bdad86e8a269d416d1ea3daf725c8b13
Checksum (SHA-256) 44e1d2e336e7c49f8a04f432a0af84faa5c036356d49d2b0d3fb757a1b9ac374
Checksum (SHA-512) 4ce1152c394eb113de4f534033fb9978bbd15885794df55367dbb56ee9a570d2b9…
GPG Signature
GPG Fingerprint c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution debian/buster - Debian - 10 (Buster)
Storage Region  Dublin, Ireland
Type  Binary (contains binaries and binary artifacts)
Uploaded At 6 months, 3 weeks ago
Uploaded By alex-borro
Slug Id python3-freecontact_11-4_arm64deb-50kp
Unique Id zo8udhKDXAZy
Version (Raw) 1.1-4
Version (Parsed)
  • Major: 1
  • Minor: 1
  • Pre (Str): (empty)
  • Pre (Num Array): 4
  • Type: SemVer (Compat)
  extended metadata
Homepage https://rostlab.org/owiki/index.php/FreeContact
Installed Size 236.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section python
Source python-freecontact
pkg python3-freecontact_1.1-4_arm64… 0
29.9 KB
md5 sha1 sha256 sha512
Package Contents (python3-freecontact_1.1-4_arm64.deb)
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This package has 14 files/directories.

Dependencies

7

Checksum (md5)

bebabe602d87e32b520ccab6d6d99c12

Depends
libboost-python1.67.0
Depends
libc6 >=2.17
Depends
libfreecontact0v5
Depends
libgcc1 >=1:3.0
Depends
libstdc++6 >=5
Depends
python3 >=3.6~
Depends
python3 <<3.8
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|Latest version of 'python3-freecontact' @ Cloudsmith|
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These instructions assume you have setup the repository first (or read it).

To install/use python3-freecontact @ version 1.1-4 ...

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 python3-freecontact=1.1-4
Warning: Note that this package is for Debian 10 (Buster) / arm64 and may only work for that configuration.
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