acpype

OFFICIAL: AnteChamber PYthon Parser interfacE

https://github.com/alanwilter/acpype

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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DOI references
Found 15 DOI reference(s) in README
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Academic publication links
Links to: scholar.google
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Committers with academic emails
1 of 12 committers (8.3%) from academic institutions
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Scientific vocabulary similarity
Low similarity (7.7%) to scientific vocabulary

Keywords

ambermd ambertools charmm cns gromacs python3 topologies xplor

Keywords from Contributors

autograd interpretability agents transformation interactive cryptocurrencies serializer tensor stacking benchmarking

Last synced: 6 months ago · JSON representation

Repository

OFFICIAL: AnteChamber PYthon Parser interfacE

Basic Info

Host: GitHub
Owner: alanwilter
License: gpl-3.0
Language: Python
Default Branch: master
Homepage: https://alanwilter.github.io/acpype/
Size: 287 MB

Statistics

Stars: 235
Watchers: 8
Forks: 54
Open Issues: 9
Releases: 19

Topics

ambermd ambertools charmm cns gromacs python3 topologies xplor

Created over 8 years ago · Last pushed 9 months ago

Metadata Files

Readme Contributing Funding License

README.md

ACPYPE

GitHub Workflow Status (with event)

AnteChamber PYthon Parser interfacE

A tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN and ARIA.

acpype is pronounced as ace + pipe

Topologies files to be generated so far: CNS/XPLOR, GROMACS, CHARMM and AMBER.

NB: Topologies generated by acpype/Antechamber are based on General Amber Force Field (GAFF) and should be used only with compatible forcefields like AMBER and its variant.

Several flavours of AMBER FF are ported already for GROMACS (see ffamber) as well as to XPLOR/CNS (see xplor-nih) and CHARMM.

This code is released under GNU General Public Licence V3.

See online documentation for more.

NO WARRANTY AT ALL

It was inspired by:

amb2gmx.pl (Eric Sorin, David Mobley and John Chodera) and depends on Antechamber and OpenBabel
YASARA Autosmiles (Elmar Krieger)
topolbuild (Bruce Ray)
xplo2d (G.J. Kleywegt)

For Non-uniform 1-4 scale factor conversion (e.g. if using GLYCAM06), please cite:

BERNARDI, A., FALLER, R., REITH, D., and KIRSCHNER, K. N. ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS. SoftwareX 10 (2019), 100241. Doi: 10.1016/j.softx.2019.100241

For Antechamber, please cite:

WANG, J., WANG, W., KOLLMAN, P. A., and CASE, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling 25, 2 (2006), 247–260. Doi: 10.1016/j.jmgm.2005.12.005

WANG, J., WOLF, R. M., CALDWELL, J. W., KOLLMAN, P. A., and CASE, D. A. Development and testing of a General Amber Force Field. Journal of Computational Chemistry 25, 9 (2004), 1157–1174. Doi: 10.1002/jcc.20035

If you use this code, I am glad if you cite:

SOUSA DA SILVA, A. W. & VRANKEN, W. F. ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes 5 (2012), 367 Doi: 10.1186/1756-0500-5-367

and (optionally)

BATISTA, P. R.; WILTER, A.; DURHAM, E. H. A. B. & PASCUTTI, P. G. Molecular Dynamics Simulations Applied to the Study of Subtypes of HIV-1 Protease. Cell Biochemistry and Biophysics 44 (2006), 395-404. Doi: 10.1385/CBB:44:3:395

Alan Silva, DSc

alanwilter at gmail dot com

How To Use ACPYPE

Introduction

We now have an up-to-date web service at Bio2Byte (but it does not have the amb2gmx functionality).

To run acpype, locally, with its all functionalities, you need ANTECHAMBER from package AmberTools and Open Babel if your input files are of PDB format.

However, if one wants acpype just to emulate amb2gmx.pl, one needs nothing at all but Python.

There are several ways of obtaining acpype:

Via CONDA:

(It should be wholesome, fully functional, all batteries included)

bash conda install -c conda-forge acpype

Via PyPI:

If you're using Linux with Intel processors then

bash pip install acpype

is enough and you should have a complete solution. Oterwise ...

(Make sure you have AmberTools and, optionally but highly recommended, OpenBabel)

```bash # You can use conda to get the needed 3rd parties for example conda create -n acpype --channel conda-forge ambertools openbabel

# Or for Ubuntu 20: apt-get install -y openbabel python3-openbabel libarpack++2-dev libgfortran5

pip install acpype

# or if you feel daring

pip install git+https://github.com/alanwilter/acpype.git ```

NB: If using OpenBabel python module, it's really CRITICAL to have it installed in the same Python environment of acpype.

By downloading it via git:

(Make sure you have AmberTools and, optionally but highly recommended, OpenBabel)

```bash # You can use conda to get the needed 3rd parties for example conda create -n acpype --channel conda-forge ambertools openbabel

# Or for Ubuntu 20: apt-get install -y openbabel python3-openbabel libarpack++2-dev libgfortran5

git clone https://github.com/alanwilter/acpype.git ```

NB: Using this mode, CHARMM topology files will not be generated.

Via Docker:

(It should be wholesome, fully functional, all batteries included)

If you have Docker installed, you can run acpype_docker.sh by:

NOTE: first time may take some time as it pulls the acpype docker image.

On Linux / macOS:

bash ln -fsv "$PWD/acpype_docker.sh" /usr/local/bin/acpype_docker

On Windows: Using Command Prompt:

In the directory where the acpype_docker.bat file is found:

bash setx /M path "%path%;%cd%"

Commands:

```bash acpype_docker -i CCCC

acpype_docker -i tests/DDD.pdb -c gas ```

NB:

By installing via conda or using via docker you get AmberTools v.21.11 and OpenBabel v3.1.1. Our AmberTools v.21.11 is a stripped version from the original containing only the necessary binaries and libraries and comes with the charmmgen binary from AmberTools17 in order to generate CHARMM topologies.
By installing via pip you get AmberTools (as described above) embedded. However, the included binaries may not work in your system (library dependencies issues) and with only provide binaries for Linux (Ubuntu20) and macOS (Intel).

To Test, if doing via `git`

At folder acpype/, type:

bash ./run_acpype.py -i tests/FFF.pdb

It'll create a folder called FFF.acpype, and inside it one may find topology files for GROMACS and CNS/XPLOR.

Or using a molecule in SMILES notation:

bash ./run_acpype.py -i CCCC # smiles for C4H6 1,3-Butadiene compound

It'll create a folder called smilesmolecule.acpype_.

To get help and more information, type:

bash ./run_acpype.py -h

To Install

At folder acpype/, type:

bash ln -fsv "$PWD/run_acpype.py" /usr/local/bin/acpype

Then re-login or start another shell session.

If via conda or pip, acpype should be in your $PATH.

To Verify with GMX

GROMACS < v.5.0

```bash cd FFF.acpype/ grompp -c FFFGMX.gro -p FFFGMX.top -f em.mdp -o em.tpr mdrun -v -deffnm em

And if you have VMD

vmd em.gro em.trr ```

GROMACS > v.5.0

```bash cd FFF.acpype/ gmx grompp -c FFFGMX.gro -p FFFGMX.top -f em.mdp -o em.tpr gmx mdrun -v -deffnm em

And if you have VMD

vmd em.gro em.trr ```

For MD, do

GROMACS < v.5.0

bash grompp -c em.gro -p FFF_GMX.top -f md.mdp -o md.tpr mdrun -v -deffnm md vmd md.gro md.trr

GROMACS > v.5.0

bash gmx grompp -c em.gro -p FFF_GMX.top -f md.mdp -o md.tpr gmx mdrun -v -deffnm md vmd md.gro md.trr

To Emulate `amb2gmx.pl`

For any given prmtop and inpcrd files (outputs from AMBER LEaP), type:

bash acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd

The output files FFF_GMX.gro and FFF_GMX.top will be generated inside folder FFFGMX.amb2gmx_

To Verify with CNS/XPLOR

At folder FFF.acpype, type:

bash cns < FFF_CNS.inp

To Verify with NAMD

see TutorialNAMD

Owner

Name: Alan Silva
Login: alanwilter
Kind: user
Location: London
Company: MEH

Website: https://readingcentre.org/teams/data_science/#dr-alan-sousa-da-silva
Repositories: 23
Profile: https://github.com/alanwilter

Scientific Programmer & Data Scientist, DSc in Biophysics, Python3 mostly. ACPYPE creator and maintainer.

GitHub Events

Total

Issues event: 3
Watch event: 29
Delete event: 4
Issue comment event: 9
Push event: 3
Pull request event: 11
Fork event: 6
Create event: 3

Last Year

Issues event: 3
Watch event: 29
Delete event: 4
Issue comment event: 9
Push event: 3
Pull request event: 11
Fork event: 6
Create event: 3

Committers

Last synced: 9 months ago

All Time

Total Commits: 620
Total Committers: 12
Avg Commits per committer: 51.667
Development Distribution Score (DDS): 0.437

Past Year

Commits: 10
Committers: 2
Avg Commits per committer: 5.0
Development Distribution Score (DDS): 0.1

Top Committers

Name	Email	Commits
Alan Silva	3****r	349
lkagami	l**i@u**r	240
dependabot[bot]	4****]	18
Alan Silva	a**r@e**k	3
Luciano Porto Kagami	l**i@h**m	2
boneta	b**a@u**s	2
sota.n	s**g@g**m	1
g-vykhodtsev	6****v	1
austenb28	a**8@g**m	1
Ivo	i**1@g**m	1
Alan	y**u@e**m	1
9527567	5****7	1

Committer Domains (Top 20 + Academic)

unizar.es: 1 ebi.ac.uk: 1 ufrgs.br: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 51
Total pull requests: 89
Average time to close issues: 3 months
Average time to close pull requests: 7 days
Total issue authors: 46
Total pull request authors: 12
Average comments per issue: 2.39
Average comments per pull request: 0.28
Merged pull requests: 63
Bot issues: 0
Bot pull requests: 27

Past Year

Issues: 7
Pull requests: 12
Average time to close issues: 2 days
Average time to close pull requests: 4 days
Issue authors: 7
Pull request authors: 2
Average comments per issue: 1.29
Average comments per pull request: 0.08
Merged pull requests: 8
Bot issues: 0
Bot pull requests: 8

View more stats

Top Authors

Issue Authors

mquevill (2)
simonbray (2)
DavidCdeB (2)
UnixJunkie (2)
gundalav (2)
pguillem (1)
dvdvbrn (1)
alanwilter (1)
azbven (1)
qinghualiao (1)
archana433 (1)
Pippetta87 (1)
BerAnton (1)
riquri (1)
darekb94 (1)

Pull Request Authors

dependabot[bot] (38)
alanwilter (27)
lkagami (21)
Mishakolok (4)
boneta (2)
austenb28 (2)
ijpulidos (1)
ivopr (1)
sotanengel (1)
simonbray (1)
g-vykhodtsev (1)
9527567 (1)

Top Labels

Issue Labels

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dependencies (38) python (3)

Packages

Total packages: 2
Total downloads:
- pypi 1,455 last-month
Total docker downloads: 103

Total dependent packages: 2
(may contain duplicates)
Total dependent repositories: 2
(may contain duplicates)
Total versions: 27
Total maintainers: 2

pypi.org: acpype

ACPYPE - AnteChamber PYthon Parser interfacE

Homepage: https://alanwilter.github.io/acpype/
Documentation: https://acpype.readthedocs.io/
License: GPL-3.0-or-later
Latest release: 2023.10.27
published over 2 years ago

Versions: 11
Dependent Packages: 2
Dependent Repositories: 1
Downloads: 1,455 Last month
Docker Downloads: 103

Rankings

Docker downloads count: 3.2%

Dependent packages count: 4.7%

Stargazers count: 5.9%

Forks count: 6.2%

Downloads: 8.0%

Average: 8.3%

Dependent repos count: 21.7%

Maintainers (2)

acpype lkagami

Last synced: 6 months ago

conda-forge.org: acpype

A tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with other python applications like CCPN or ARIA.

Homepage: https://github.com/alanwilter/acpype
License: GPL-3.0-or-later
Latest release: 2022.7.21
published over 3 years ago

Versions: 16
Dependent Packages: 0
Dependent Repositories: 1

Rankings

Dependent repos count: 24.2%

Forks count: 28.4%

Stargazers count: 31.6%

Average: 34.0%

Dependent packages count: 51.6%

Last synced: 6 months ago

Dependencies

poetry.lock pypi

alabaster 0.7.12 develop
appnope 0.1.2 develop
atomicwrites 1.4.0 develop
attrs 21.4.0 develop
babel 2.9.1 develop
backcall 0.2.0 develop
black 21.12b0 develop
bleach 4.1.0 develop
certifi 2021.10.8 develop
cffi 1.15.0 develop
cfgv 3.3.1 develop
charset-normalizer 2.0.10 develop
click 8.0.3 develop
colorama 0.4.4 develop
coverage 6.2 develop
cryptography 36.0.1 develop
dataclasses 0.8 develop
decorator 5.1.1 develop
distlib 0.3.4 develop
docutils 0.17.1 develop
fancycompleter 0.9.1 develop
filelock 3.4.1 develop
flake8 4.0.1 develop
identify 2.4.4 develop
idna 3.3 develop
imagesize 1.3.0 develop
importlib-metadata 4.2.0 develop
importlib-resources 5.2.3 develop
iniconfig 1.1.1 develop
ipdb 0.13.0 develop
ipython 7.16.3 develop
ipython-genutils 0.2.0 develop
isort 5.10.1 develop
jedi 0.17.2 develop
jeepney 0.7.1 develop
jinja2 3.0.3 develop
keyring 23.4.1 develop
markupsafe 2.0.1 develop
mccabe 0.6.1 develop
mypy 0.920 develop
mypy-extensions 0.4.3 develop
nodeenv 1.6.0 develop
packaging 21.3 develop
parso 0.7.1 develop
pathspec 0.9.0 develop
pdbpp 0.10.3 develop
pexpect 4.8.0 develop
pickleshare 0.7.5 develop
pkginfo 1.8.2 develop
platformdirs 2.4.0 develop
pluggy 1.0.0 develop
pre-commit 2.17.0 develop
prompt-toolkit 3.0.24 develop
ptyprocess 0.7.0 develop
py 1.11.0 develop
pycodestyle 2.8.0 develop
pycparser 2.21 develop
pyflakes 2.4.0 develop
pygments 2.11.2 develop
pyparsing 3.0.7 develop
pyreadline 2.1 develop
pyrepl 0.9.0 develop
pytest 6.2.5 develop
pytest-cov 3.0.0 develop
pytest-random-order 1.0.4 develop
pytz 2021.3 develop
pyupgrade 2.31.0 develop
pywin32-ctypes 0.2.0 develop
pyyaml 6.0 develop
readme-renderer 32.0 develop
requests 2.27.1 develop
requests-toolbelt 0.9.1 develop
rfc3986 1.5.0 develop
secretstorage 3.3.1 develop
six 1.16.0 develop
snowballstemmer 2.2.0 develop
sphinx 4.3.2 develop
sphinxcontrib-applehelp 1.0.2 develop
sphinxcontrib-devhelp 1.0.2 develop
sphinxcontrib-htmlhelp 2.0.0 develop
sphinxcontrib-jsmath 1.0.1 develop
sphinxcontrib-qthelp 1.0.3 develop
sphinxcontrib-serializinghtml 1.1.5 develop
tokenize-rt 4.2.1 develop
toml 0.10.2 develop
tomli 1.2.3 develop
tqdm 4.62.3 develop
traitlets 4.3.3 develop
twine 3.7.1 develop
typed-ast 1.5.1 develop
typing-extensions 4.0.1 develop
urllib3 1.26.8 develop
virtualenv 20.13.0 develop
wcwidth 0.2.5 develop
webencodings 0.5.1 develop
wmctrl 0.4 develop
zipp 3.6.0 develop

pyproject.toml pypi

Sphinx ^4.3.2 develop
black ^21.12b0 develop
flake8 ^4.0.1 develop
importlib-metadata ^4.1 develop
ipdb 0.13 develop
isort ^5.10.1 develop
mypy ^0.920 develop
pdbpp ^0.10.3 develop
pre-commit ^2.16.0 develop
pytest-cov ^3.0.0 develop
pytest-random-order ^1.0.4 develop
pyupgrade ^2.31.0 develop
twine ^3.7.1 develop
python >=3.6.2,<4.0

.github/workflows/check_acpype.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/create-release v1 composite
actions/github-script v3 composite
actions/setup-python v2 composite
codecov/codecov-action v2 composite

.github/workflows/codeql-analysis.yml actions

actions/checkout v2 composite
github/codeql-action/analyze v1 composite
github/codeql-action/init v1 composite

Dockerfile docker

ubuntu 20.04 build

docs/requirements.txt pypi

Sphinx ==7.1.2
sphinx-rtd-theme ==1.3.0

acpype

Science Score: 46.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

ACPYPE

AnteChamber PYthon Parser interfacE

NO WARRANTY AT ALL

How To Use ACPYPE

Introduction

To Test, if doing via git

To Install

To Verify with GMX

And if you have VMD

And if you have VMD

For MD, do

To Emulate amb2gmx.pl

To Verify with CNS/XPLOR

To Verify with NAMD

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: acpype

Rankings

Maintainers (2)

conda-forge.org: acpype

Rankings

Dependencies

To Test, if doing via `git`

To Emulate `amb2gmx.pl`