End-to-end AMBER system builder from PDB
Project description
AABY
Automated AMBER System Builder
Installation
git clone https://github.com/AmandaStange/AABY.git
cd AABY
micromamba env create -n AABY -f environment.yml
Usage
Example:
python Scripts/AABY.py -f INPUT.pdb --chains A --ph 7.4 --coby-yaml coby_input.yaml --antechamber True --mol2 UNK --nc 0
For help use
python Scripts/AABY.py -h
Example of input coby file (coby_input.yaml)
- -box
- 15
- 15
- 15
- -membrane
- lipid:POPC:6
- lipid:CHL:4
- -protein
- file:{protein_pdb}
- charge:0
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
aaby-0.1.1.tar.gz
(809.3 kB
view details)
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
aaby-0.1.1-py3-none-any.whl
(881.1 kB
view details)
File details
Details for the file aaby-0.1.1.tar.gz.
File metadata
- Download URL: aaby-0.1.1.tar.gz
- Upload date:
- Size: 809.3 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/6.2.0 CPython/3.12.11
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
687d346d9fc0019f618f5b8a38c409326e6dd56f995ba513b4d0a22490ff2d49
|
|
| MD5 |
30afb93c772cfbba944631ce0b51b27b
|
|
| BLAKE2b-256 |
321a4bd177fe682a56f180450fd02e2a0e29961d39444632df37f52b86d4419f
|
File details
Details for the file aaby-0.1.1-py3-none-any.whl.
File metadata
- Download URL: aaby-0.1.1-py3-none-any.whl
- Upload date:
- Size: 881.1 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/6.2.0 CPython/3.12.11
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
8e90ba5ffdef57f1b560c4b54c194436ca806da2d12946729b0a2ffeddeddfe4
|
|
| MD5 |
f50b4a4a4c033a381e4537b349df3e76
|
|
| BLAKE2b-256 |
942297e7ca649844208c23a3afc32308bc8cf202f924037b1669e7a3b51359f0
|
