pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'

[jiepan1]

PyRosetta-4 2023 [Rosetta PyRosetta4.conda.linux.cxx11thread.serialization.CentOS.python37.Release 2023.11+release.fe5f8333f1cbc3d246e74df5f7017adc23e83bcb 2023-03-13T07:57:24] retrieved from: http://www.pyrosetta.org (C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team. /home/panjie/projects/tools/RoseTTAFold/RoseTTAFold-main/DAN-msa/models/smTr While processing /home/panjie/projects/tools/RoseTTAFold/RoseTTAFold-main/example/pdb-3track/model0_1_0.25.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute 'mul'

[rmarabini]

I have the same question. Did you find out how to solve this?

[jiepan1]

yes,You uninstall your installation package for pyrosetta and install it with pip instead of conda

[rmarabini]

Uhm, that trick does not work for me :-(. Could you tell me which version of pyrosetta are you using? I will try to install the very same one. Do you install form the wheel packages or from the repository?

Thanks

[jiepan1]

python3.8, I install from the repository ，there are my packages: Package Version

---

biopython 1.78 brotlipy 0.7.0 certifi 2022.12.7 cffi 1.14.5 chardet 4.0.0 cryptography 3.4.7 cutadapt 4.1 decorator 5.1.1 dgl-cu110 0.6.1 dnaio 0.9.0 googledrivedownloader 0.4 idna 2.10 isal 0.11.1 Jinja2 3.0.1 joblib 1.0.1 MarkupSafe 2.0.1 mkl-fft 1.3.0 mkl-random 1.2.1 mkl-service 2.3.0 networkx 2.5 numpy 1.20.2 olefile 0.46 packaging 20.9 pandas 1.2.5 Pillow 8.2.0 pip 21.1.3 pycparser 2.20 pyOpenSSL 20.0.1 pyparsing 2.4.7 PySocks 1.7.1 python-dateutil 2.8.1 python-louvain 0.15 pytz 2021.1 requests 2.25.1 scikit-learn 0.24.2 scipy 1.6.2 setuptools 52.0.0.post20210125 setuptools-scm 7.0.5 six 1.16.0 threadpoolctl 2.1.0 tomli 2.0.1 torch 1.9.0 torch-cluster 1.5.9 torch-geometric 1.7.2 torch-scatter 2.0.7 torch-sparse 0.6.10 torch-spline-conv 1.2.1 torchaudio 0.9.0a0+33b2469 torchvision 0.10.0 tqdm 4.61.1 typing-extensions 3.10.0.0 urllib3 1.26.6 wheel 0.36.2 xopen 1.5.0

[rmarabini]

Hi @jiepan1,

I really appreciate your help with rosettafold ;-). Rosettafold provides two scripts called run_e2e_ver.sh and run_pyrosetta_ver.sh. I have no problem executing the first one but I get the above mentioned error with the second one. The difference between these two scripts is that in the second one pyrosetta is used. I understand that run_pyrosetta_ver.sh requires tensorflow-gpu but this module is not in your package version list. Am I missing something?

cheers

[jiepan1]

sorry But I can run run_pyrosetta_ver.sh normally in cpu
(RoseTTAFold) [panjie@cpu9 RoseTTAFold-main]$ bash run_pyrosetta_ver.sh example/input.fa . Running HHblits Running PSIPRED Running hhsearch Predicting distance and orientations Running parallel RosettaTR.py Running DeepAccNet-msa

[brianush1]

For anyone else having this issue, you can do a hotfix by modifying DAN-msa/pyErrorPred/featurize.py:

Line 81: edge = iru.__mul__() → edge = iru.dereference() Line 102: iru.plus_plus() → iru.pre_increment()