Resolve runtime issues with cts_pkasolver

[popenc]

Pkasolver is throwing a conversion error at execution after upgrading the requirements to resolve security vulnerabilities, specifically torch-geometric from the pinned 2.0.1 to 2.6.1.

root@1042ba171021:/src# conda run -n pka_prediction cts_pkasolver.py
/tmp/tmpcot6rt3k: line 3: cts_pkasolver.py: command not found

ERROR conda.cli.main_run:execute(125): `conda run cts_pkasolver.py` failed. (See above for error)
root@1042ba171021:/src# conda run -n pka_prediction python cts_pkasolver.py
Traceback (most recent call last):
  File "/src/cts_pkasolver.py", line 404, in <module>
    chart_data, species, pka_list = cts_pkasolver.main(test_smiles)
                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/src/cts_pkasolver.py", line 348, in main
    for n, p, ps, ds, i in data:
                           ^^^^
  File "/src/cts_pkasolver.py", line 62, in run_pka_solver
    protonation_states = calculate_microstate_pka_values(mol) # performs internal calculations and st
ores as object
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/mamba/envs/pka_prediction/lib/python3.12/site-packages/pkasolver/query.py", line 243, in
 calculate_microstate_pka_values
    query_model = QueryModel()
                  ^^^^^^^^^^^^
  File "/opt/mamba/envs/pka_prediction/lib/python3.12/site-packages/pkasolver/query.py", line 84, in
__init__
    model.load_state_dict(checkpoint["model_state_dict"])
  File "/opt/mamba/envs/pka_prediction/lib/python3.12/site-packages/torch/nn/modules/module.py", line
 2593, in load_state_dict
    raise RuntimeError(
RuntimeError: Error(s) in loading state_dict for GINPairV1:
        Missing key(s) in state_dict: "GIN_p.convs.0.nn.lins.0.weight", "GIN_p.convs.0.nn.lins.0.bias
", "GIN_p.convs.0.nn.lins.1.weight", "GIN_p.convs.0.nn.lins.1.bias", "GIN_p.convs.1.nn.lins.0.weight"
, "GIN_p.convs.1.nn.lins.0.bias", "GIN_p.convs.1.nn.lins.1.weight", "GIN_p.convs.1.nn.lins.1.bias", "
GIN_p.convs.2.nn.lins.0.weight", "GIN_p.convs.2.nn.lins.0.bias", "GIN_p.convs.2.nn.lins.1.weight", "G
IN_p.convs.2.nn.lins.1.bias", "GIN_p.convs.3.nn.lins.0.weight", "GIN_p.convs.3.nn.lins.0.bias", "GIN_
p.convs.3.nn.lins.1.weight", "GIN_p.convs.3.nn.lins.1.bias", "GIN_d.convs.0.nn.lins.0.weight", "GIN_d
.convs.0.nn.lins.0.bias", "GIN_d.convs.0.nn.lins.1.weight", "GIN_d.convs.0.nn.lins.1.bias", "GIN_d.co
nvs.1.nn.lins.0.weight", "GIN_d.convs.1.nn.lins.0.bias", "GIN_d.convs.1.nn.lins.1.weight", "GIN_d.con
vs.1.nn.lins.1.bias", "GIN_d.convs.2.nn.lins.0.weight", "GIN_d.convs.2.nn.lins.0.bias", "GIN_d.convs.
2.nn.lins.1.weight", "GIN_d.convs.2.nn.lins.1.bias", "GIN_d.convs.3.nn.lins.0.weight", "GIN_d.convs.3
.nn.lins.0.bias", "GIN_d.convs.3.nn.lins.1.weight", "GIN_d.convs.3.nn.lins.1.bias".
        Unexpected key(s) in state_dict: "GIN_p.lin.weight", "GIN_p.lin.bias", "GIN_p.convs.0.nn.0.we
ight", "GIN_p.convs.0.nn.0.bias", "GIN_p.convs.0.nn.1.weight", "GIN_p.convs.0.nn.1.bias", "GIN_p.conv
s.0.nn.1.running_mean", "GIN_p.convs.0.nn.1.running_var", "GIN_p.convs.0.nn.1.num_batches_tracked", "
GIN_p.convs.0.nn.3.weight", "GIN_p.convs.0.nn.3.bias", "GIN_p.convs.1.nn.0.weight", "GIN_p.convs.1.nn
.0.bias", "GIN_p.convs.1.nn.1.weight", "GIN_p.convs.1.nn.1.bias", "GIN_p.convs.1.nn.1.running_mean",
"GIN_p.convs.1.nn.1.running_var", "GIN_p.convs.1.nn.1.num_batches_tracked", "GIN_p.convs.1.nn.3.weigh
t", "GIN_p.convs.1.nn.3.bias", "GIN_p.convs.2.nn.0.weight", "GIN_p.convs.2.nn.0.bias", "GIN_p.convs.2
.nn.1.weight", "GIN_p.convs.2.nn.1.bias", "GIN_p.convs.2.nn.1.running_mean", "GIN_p.convs.2.nn.1.runn
ing_var", "GIN_p.convs.2.nn.1.num_batches_tracked", "GIN_p.convs.2.nn.3.weight", "GIN_p.convs.2.nn.3.
bias", "GIN_p.convs.3.nn.0.weight", "GIN_p.convs.3.nn.0.bias", "GIN_p.convs.3.nn.1.weight", "GIN_p.co
nvs.3.nn.1.bias", "GIN_p.convs.3.nn.1.running_mean", "GIN_p.convs.3.nn.1.running_var", "GIN_p.convs.3
.nn.1.num_batches_tracked", "GIN_p.convs.3.nn.3.weight", "GIN_p.convs.3.nn.3.bias", "GIN_d.lin.weight
", "GIN_d.lin.bias", "GIN_d.convs.0.nn.0.weight", "GIN_d.convs.0.nn.0.bias", "GIN_d.convs.0.nn.1.weig
ht", "GIN_d.convs.0.nn.1.bias", "GIN_d.convs.0.nn.1.running_mean", "GIN_d.convs.0.nn.1.running_var",
"GIN_d.convs.0.nn.1.num_batches_tracked", "GIN_d.convs.0.nn.3.weight", "GIN_d.convs.0.nn.3.bias", "GI
N_d.convs.1.nn.0.weight", "GIN_d.convs.1.nn.0.bias", "GIN_d.convs.1.nn.1.weight", "GIN_d.convs.1.nn.1
.bias", "GIN_d.convs.1.nn.1.running_mean", "GIN_d.convs.1.nn.1.running_var", "GIN_d.convs.1.nn.1.num_
batches_tracked", "GIN_d.convs.1.nn.3.weight", "GIN_d.convs.1.nn.3.bias", "GIN_d.convs.2.nn.0.weight"
, "GIN_d.convs.2.nn.0.bias", "GIN_d.convs.2.nn.1.weight", "GIN_d.convs.2.nn.1.bias", "GIN_d.convs.2.n
n.1.running_mean", "GIN_d.convs.2.nn.1.running_var", "GIN_d.convs.2.nn.1.num_batches_tracked", "GIN_d
.convs.2.nn.3.weight", "GIN_d.convs.2.nn.3.bias", "GIN_d.convs.3.nn.0.weight", "GIN_d.convs.3.nn.0.bi
as", "GIN_d.convs.3.nn.1.weight", "GIN_d.convs.3.nn.1.bias", "GIN_d.convs.3.nn.1.running_mean", "GIN_
d.convs.3.nn.1.running_var", "GIN_d.convs.3.nn.1.num_batches_tracked", "GIN_d.convs.3.nn.3.weight", "
GIN_d.convs.3.nn.3.bias".

ERROR conda.cli.main_run:execute(125): `conda run python cts_pkasolver.py` failed. (See above for err
or)