A NAMD topology/coordinate system preparation tool

Navigation

Verified details

These details have been verified by PyPI
Project links
GitHub Statistics
Maintainers
Avatar for cameronabrams from gravatar.com cameronabrams

Unverified details

These details have not been verified by PyPI
Project links
Meta
Classifiers
Report project as malware

Project description

Pestifer

NAMD System Preparation Tool

PyPI PyPI Downloads Docs DOI

Pestifer is a fully automated simulation-ready MD system preparation tool, requiring as inputs only biomolecular structures (e.g., PDB IDs, PDB files, mmCIF files, alphafold IDs) and a handful of customization parameters, to generate NAMD-compatible input files (PSF, PDB, and xsc). It is basically a highly functionalized front end for VMD's psfgen utility. It also has a few handy subcommands for working with NAMD output.

Installation

pip install pestifer

Once installed, the user has access to the main pestifer command.

Pestifer also requires access to the following executables:

  1. namd3 and charmrun
  2. vmd and catdcd
  3. packmol

Pestifer includes a copy of the Feb 2026 Charmm36 force field.

Documentation

Please visit readthedocs for full documentation.

Version History

See the CHANGELOG for full details.

Meta

https://github.com/cameronabrams

Pestifer is maintained by Cameron F. Abrams.

Pestifer is distributed under the MIT license. See LICENSE for more information.

Pestifer was developed with support from the National Institutes of Health via grants GM100472, AI154071, and AI178833.

Contributing

  1. Fork it (https://github.com/cameronabrams/pestifer/fork)
  2. Create your feature branch (git checkout -b feature/fooBar)
  3. Commit your changes (git commit -am 'Add some fooBar')
  4. Push to the branch (git push origin feature/fooBar)
  5. Create a new Pull Request

Project details

Verified details

These details have been verified by PyPI
Project links
GitHub Statistics
Maintainers
Avatar for cameronabrams from gravatar.com cameronabrams

Unverified details

These details have not been verified by PyPI
Project links
Meta
Classifiers

Release history Release notifications | RSS feed

2.5.0

2.4.13

2.4.12

2.4.11

2.4.10

2.4.9

2.4.8

2.4.4

2.4.3

2.4.2

2.4.1

2.4.0

2.3.1

2.3.0

2.2.11

2.2.10

2.2.9

2.2.8

2.2.6

This version

2.2.5

2.2.4

2.2.3

2.2.2

2.2.1

2.1.9

2.1.8

2.1.7

2.1.6

2.1.5

2.1.5a0 pre-release

2.1.4

2.1.3

2.1.2

2.1.1

2.1.0

2.0.3

2.0.1

1.21.2

1.21.1

1.21.0

1.20.3

1.20.2

1.20.1

1.20.0

1.19.1

1.19.0

1.18.5

1.18.4

1.18.3

1.18.2

1.18.1

1.17.0

1.16.3

1.16.2

1.16.0

1.15.0

1.14.1

1.14.0

1.13.3

1.13.2

1.13.1

1.13.0

1.12.1

1.11.3

1.11.1

1.11.0

1.10.0

1.9.0

1.8.3

1.8.2

1.8.1

1.8.0

1.7.4

1.7.3

1.7.2

1.7.1

1.7.0a1 pre-release

1.6.5

1.6.4a2 pre-release

1.6.4a1 pre-release

1.6.4a0 pre-release

1.6.2a0 pre-release

1.6.1

1.5.9

1.5.8

1.5.6

1.5.4

1.5.3

1.5.2

1.5.1

1.5.0

1.4.9

1.4.8

1.4.7

1.4.4

1.4.3

1.4.2

1.4.1

1.4.0

1.3.9

1.3.8

1.3.7

1.3.5

1.3.4

1.3.3

1.3.2

1.3.1

1.3.0

1.2.9

1.2.8

1.2.5

1.2.3

1.2.2

1.2.0

1.1.2

1.1.1

1.0.9

1.0.8

1.0.7

1.0.6

1.0.3

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pestifer-2.2.5.tar.gz (60.5 MB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

pestifer-2.2.5-py3-none-any.whl (28.6 MB view details)

Uploaded Python 3

File details

Details for the file pestifer-2.2.5.tar.gz.

File metadata

  • Download URL: pestifer-2.2.5.tar.gz
  • Upload date:
  • Size: 60.5 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for pestifer-2.2.5.tar.gz
Algorithm Hash digest
SHA256 e2f07ed9f56a0c23f555a247b3a94b4e60848ef930d07c569cfabf26f1fd3cdf
MD5 f4d53d5a784ea0089e73aededf8a23f1
BLAKE2b-256 52fc3e7a81f43a3f558efca91c9b2bb75e5152e000af624d4dcfff08e9082b22

See more details on using hashes here.

Provenance

The following attestation bundles were made for pestifer-2.2.5.tar.gz:

Publisher: release.yaml on cameronabrams/pestifer

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file pestifer-2.2.5-py3-none-any.whl.

File metadata

  • Download URL: pestifer-2.2.5-py3-none-any.whl
  • Upload date:
  • Size: 28.6 MB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for pestifer-2.2.5-py3-none-any.whl
Algorithm Hash digest
SHA256 bd714aee72a3a8001f4252d51ac6a2021c8743866967bc97f7c2145067dabc30
MD5 0fa3170c585a9c7b52ae7abf9fece112
BLAKE2b-256 56e0307cbe99ecc395112e38f88238d49ac5515fb3e234cb019470b7c22b48c6

See more details on using hashes here.

Provenance

The following attestation bundles were made for pestifer-2.2.5-py3-none-any.whl:

Publisher: release.yaml on cameronabrams/pestifer

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page