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

This version

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

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-2.4.3.tar.gz (64.9 MB view details)

Uploaded Source

Built Distribution

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

pestifer-2.4.3-py3-none-any.whl (32.7 MB view details)

Uploaded Python 3

File details

Details for the file pestifer-2.4.3.tar.gz.

File metadata

  • Download URL: pestifer-2.4.3.tar.gz
  • Upload date:
  • Size: 64.9 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for pestifer-2.4.3.tar.gz
Algorithm Hash digest
SHA256 37563a98187c0c5bc3411b3919f189cfeb6463caa1cec20b8c30276d2ab639d6
MD5 b5f60bbbdbc27497785815b59d35c455
BLAKE2b-256 9b92662e4ac40e2c2f7261e00b4968c26c373cdd6c1c1665871493d5e7e6cde5

See more details on using hashes here.

Provenance

The following attestation bundles were made for pestifer-2.4.3.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-2.4.3-py3-none-any.whl.

File metadata

  • Download URL: pestifer-2.4.3-py3-none-any.whl
  • Upload date:
  • Size: 32.7 MB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for pestifer-2.4.3-py3-none-any.whl
Algorithm Hash digest
SHA256 6924236bef5eabdf32504e339a508990baed10f7ae5c82acf53fbe5e663bb2ad
MD5 3b1c37fc37175024c09443df33752786
BLAKE2b-256 d0682dce20e75c64f567ea1c3336bcfb2b6251841aef4c717572802419072889

See more details on using hashes here.

Provenance

The following attestation bundles were made for pestifer-2.4.3-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