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#Attracting Cavities 3.0
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#License
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Licensed Work: Attracting Cavities version 3
Licensor: Molecular Modelling Group of the Swiss Institute of BioinformaticsChange Date: 2030-01-01
Change License: GPL v3

Additional Use GrantPermitted Uses:
- Personal research use
- Academic research use
- Educational use
- Internal business use

Restrictions:
1. Redistribution Prohibited
The Licensed Work, in original or modified form, may not be redistributed, sublicensed, or shared with third parties without prior written permission from the Licensor.

2. Commercial Use Prohibited
The Licensed Work may not be sold or licensed for a fee.
    
3. Competing Services Prohibited
The Licensed Work may not be used to create, operate, support, or provide any web service, server, platform, or software system competing with SwissDock, whether commercial or non-commercial.
    
4. Publication Citation Requirement
Any publication, presentation, report, or public disclosure containing results generated using the Licensed Work must appropriately cite the following publications:

    (a) Röhrig UF, Mathieu-Bugnon M, Zoete V. Attracting Cavities 3.0: Faster and More Versatile Molecular Docking for the SwissDock Webserver. Bioinformatics, 2026, ASAP

    (b) Röhrig UF, Goullieux M, Bugnon M, Zoete V. Attracting Cavities 2.0: improving the flexibility and robustness for small-molecule docking. J. Chem. Inf. Model., 2023, 63 (12), 3925–3940, DOI: 10.1021/acs.jcim.3c00054

    (c) Zoete V, Schuepbach T, Bovigny C, Chaskar P, Daina A, Röhrig UF, Michielin O. Attracting Cavities for Docking. Replacing the Rough Energy Landscape of the Protein by a Smooth Attracting Landscape. J. Comput. Chem., 2016, 37 (4), 437–447. DOI: 10.1002/jcc.24249

5. Modification
Users may modify the Licensed Work for their own permitted internal use, but modified versions remain subject to all terms of this License.

Effective on the Change Date, this license will convert to GPL v3.

This program uses the external program CHARMM (https://www.academiccharmm.org/), subject to its own license terms.

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#Installation 
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1. Install Python3.12

/!\ You will also need several packages. To install them, we would recommand to create an environment:
1.1 create environment
python3 -m venv /path-to-ac/ac-env

1.2. activate the env
source /path-to-ac/ac-env/bin/activate

1.3. Install packages:
pip install pdbecif==1.5
pip install gemmi==0.7.5
pip install python-textops3==3.2.1
pip install densitypeakclustering==1.0.1
pip install psutil==7.2.2
pip install pyarrow==23.0.1
pip install spyrmsd==0.9.0
pip install Jinja2
pip install biopandas==0.5.1
pip install requests==2.32.5
pip install rdkit=2025.3.3


2. Install and compile CHARMM **

3. Run: $ which <charmm_executable> 
Will give you the location of your CHARMM executable (let's call it charmm_loc)

4. Run: $ type env 
Will give you your env path.

5. Run: $ ./config.sh <charmm_loc> <path_env>
example:
$ ./config.sh /home/username/bin/c48b1 /usr/bin/env


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#Note for maintainers 
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Please run the following command before pushing on git :)
./change-path-back.sh <charmm_loc> <env>

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### Run
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To run the program:
$ python /path-to-your-program-installation/start-ac-charmm.py ac.inp

If you need help, plase run:
$ python /path-to-your-program-installation/start-ac-charmm.py -h
or 
$ python /path-to-your-program-installation/start-ac-charmm.py --help

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# ** Install CHARMM
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To be able to use all options of AC, including QM/MM options,
install CHARMM with the following flags:

./configure --without-qchem --with-g09
This will disable qchem and install the g09 option.

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# *** Install Gaussian
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