Hi, nice tool!
I installed the gaCaretta and tried to test the tool using the test data you provided, but an error appeared. Could you help with this?
Thanks!
The output for caretta-cli --help is ok.

the log is here:

(gaCaretta) liuhongbin@slurm-master:~/soft/Pockets/gamaps/gaCaretta$ caretta-cli test_data/ --ga=True
Traceback (most recent call last):
File "/home/liuhongbin/anaconda3/envs/shogun/bin/caretta-cli", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/home/liuhongbin/soft/Pockets/gamaps/gaCaretta/bin/caretta-cli", line 90, in
fire.Fire(align)
File "/home/liuhongbin/anaconda3/envs/shogun/lib/python3.7/site-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/home/liuhongbin/anaconda3/envs/shogun/lib/python3.7/site-packages/fire/core.py", line 480, in _Fire
target=component.name)
File "/home/liuhongbin/anaconda3/envs/shogun/lib/python3.7/site-packages/fire/core.py", line 691, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/home/liuhongbin/soft/Pockets/gamaps/gaCaretta/bin/caretta-cli", line 86, in align
overwrite_dssp, ga, ga_lim_time, ga_lim_iter, ga_lim_same, ga_pop_size)
File "/home/liuhongbin/soft/Pockets/gamaps/gaCaretta/caretta/msa_numba.py", line 445, in align_from_pdb_files
overwrite_dssp)
File "/home/liuhongbin/soft/Pockets/gamaps/gaCaretta/caretta/msa_numba.py", line 290, in from_pdb_files
pdb_files = parse_pdb_files(input_pdb, cleaned_pdb_folder)
File "/home/liuhongbin/soft/Pockets/gamaps/gaCaretta/caretta/msa_numba.py", line 229, in parse_pdb_files
pdb = pd.parsePDB(pdb_file).select("protein")
File "/home/liuhongbin/anaconda3/envs/shogun/lib/python3.7/site-packages/prody/proteins/pdbfile.py", line 124, in parsePDB
return _parsePDB(pdb[0], **kwargs)
File "/home/liuhongbin/anaconda3/envs/shogun/lib/python3.7/site-packages/prody/proteins/pdbfile.py", line 231, in _parsePDB
if pdb.endswith('.pdb') or pdb.endswith('.pdb.gz'):
AttributeError: 'PosixPath' object has no attribute 'endswith'

packages that have been installed:

(gaCaretta) liuhongbin@slurm-master:~/soft/Pockets/gamaps/gaCaretta$ conda list

packages in environment at /home/liuhongbin/anaconda3/envs/gaCaretta:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
binutils_impl_linux-64 2.39 he00db2b_1 conda-forge
binutils_linux-64 2.39 h5fc0e48_11 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
dssp 3.0.0 hf484d3e_3 salilab
gcc_impl_linux-64 12.2.0 hcc96c02_19 conda-forge
gcc_linux-64 12.2.0 h4798a0e_11 conda-forge
gxx_impl_linux-64 12.2.0 hcc96c02_19 conda-forge
gxx_linux-64 12.2.0 hb41e900_11 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
libboost 1.67.0 h46d08c1_4 anaconda
libgcc-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libsanitizer 12.2.0 h46fd767_19 conda-forge
libstdcxx-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
msms 2.6.1 h516909a_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.11 h36c2ea0_1011 conda-forge