[BUG] OF3 return just irregular cloud of aminoacids #120
Description
After the January library update, OF3 no longer returns a structure representing a cloud of unconnected amino acids. I ran OpenFold3 in Docker container, used Dockerfile from project. OpenFold3 itself works without errors in container, but the Docker image build freezes on line with COPY environments/production.yml /opt/openfold3/environment.yml
RUN mamba env update -n base --file /opt/openfold3/environment.yml \
&& mamba clean --all --yes \
&& conda clean --all --yes.
However, when downgrading conda on 24.9.2-0, mamba starts working. I tried pip3 install (as in the manual) and downloading the zip archive (0.3.1). All the same. All unit tests are passed
I ran OpenFold3 on GPU NVIDIA GeForce RTX 3090, 24Gb, CUDA ver 12.4
Conda Packages:
# packages in environment at /opt/conda:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 7_kmp_llvm conda-forge
absl-py 2.4.0 pyhd8ed1ab_0 conda-forge
amply 0.1.6 pyhd8ed1ab_1 conda-forge
annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge
appdirs 1.4.4 pyhd8ed1ab_1 conda-forge
archspec 0.2.3 pyhd8ed1ab_0 conda-forge
argparse-dataclass 2.0.0 pyhd8ed1ab_1 conda-forge
aria2 1.37.0 hbc8128a_2 conda-forge
attrs 25.4.0 pyhcf101f3_1 conda-forge
aws-c-auth 0.9.1 hef928c7_8 conda-forge
aws-c-cal 0.9.13 h2c9d079_1 conda-forge
aws-c-common 0.12.6 hb03c661_0 conda-forge
aws-c-compression 0.3.1 h8b1a151_9 conda-forge
aws-c-event-stream 0.5.7 h28f887f_1 conda-forge
aws-c-http 0.10.7 ha8fc4e3_5 conda-forge
aws-c-io 0.23.3 had5c4f5_4 conda-forge
aws-c-mqtt 0.13.3 hc63082f_11 conda-forge
aws-c-s3 0.11.2 h0019752_1 conda-forge
aws-c-sdkutils 0.2.4 h8b1a151_4 conda-forge
aws-checksums 0.2.7 h8b1a151_5 conda-forge
awscli 2.33.8 py312h20c3967_0 conda-forge
awscrt 0.29.1 py312he7d6d80_1 conda-forge
biopython 1.86 py312h4c3975b_1 conda-forge
biotite 1.2.0 py312h2ec8cdc_0 conda-forge
biotraj 1.2.2 py312h8285ef7_2 conda-forge
blas 1.0 mkl conda-forge
boltons 24.0.0 pyhd8ed1ab_0 conda-forge
boto3 1.42.44 pyhd8ed1ab_0 conda-forge
botocore 1.42.44 pyhd8ed1ab_0 conda-forge
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.32.3 h4bc722e_0 conda-forge
ca-certificates 2026.1.4 hbd8a1cb_0 conda-forge
cairo 1.18.4 h3394656_0 conda-forge
certifi 2026.1.4 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py312h06ac9bb_0 conda-forge
charset-normalizer 3.4.0 pyhd8ed1ab_0 conda-forge
click 8.3.1 pyh8f84b5b_1 conda-forge
coin-or-cbc 2.10.12 h4d16d09_5 conda-forge
coin-or-cgl 0.60.9 hc46dffc_7 conda-forge
coin-or-clp 1.17.10 hc03379b_4 conda-forge
coin-or-osi 0.108.11 hf4fecb4_8 conda-forge
coin-or-utils 2.11.12 hc93afbd_7 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
coloredlogs 15.0.1 pyhd8ed1ab_4 conda-forge
conda 24.9.2 py312h7900ff3_0 conda-forge
conda-inject 1.3.2 pyhd8ed1ab_0 conda-forge
conda-libmamba-solver 24.9.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.4.0 pyh7900ff3_0 conda-forge
conda-package-streaming 0.11.0 pyhd8ed1ab_0 conda-forge
configargparse 1.7.1 pyhe01879c_0 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
contourpy 1.3.3 py312h0a2e395_4 conda-forge
cpython 3.12.12 py312hd8ed1ab_2 conda-forge
cuda-bindings 13.1.1 pypi_0 pypi
cuda-cudart 12.4.127 he02047a_2 conda-forge
cuda-cudart_linux-64 12.4.127 h85509e4_2 conda-forge
cuda-cupti 12.4.127 he02047a_2 conda-forge
cuda-libraries 12.4.1 ha770c72_1 conda-forge
cuda-nvrtc 12.4.127 he02047a_2 conda-forge
cuda-nvtx 12.4.127 he02047a_2 conda-forge
cuda-opencl 12.4.127 he02047a_1 conda-forge
cuda-pathfinder 1.3.3 pypi_0 pypi
cuda-python 13.1.1 pypi_0 pypi
cuda-runtime 12.4.1 ha804496_0 conda-forge
cuda-version 12.4 h3060b56_3 conda-forge
cycler 0.12.1 pyhcf101f3_2 conda-forge
cyrus-sasl 2.1.28 hd9c7081_0 conda-forge
deepspeed 0.18.5 pypi_0 pypi
distro 1.8.0 pyhd8ed1ab_0 conda-forge
docker-pycreds 0.4.0 py_0 conda-forge
docutils 0.18.1 py312h7900ff3_1 conda-forge
dpath 2.2.0 pyha770c72_1 conda-forge
eido 0.2.5 pyhd8ed1ab_0 conda-forge
einops 0.8.2 pypi_0 pypi
eval_type_backport 0.3.1 pyha770c72_0 conda-forge
exceptiongroup 1.3.1 pyhd8ed1ab_0 conda-forge
filelock 3.20.3 pyhd8ed1ab_0 conda-forge
fmt 10.2.1 h00ab1b0_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 hc364b38_1 conda-forge
fonttools 4.61.1 py312h8a5da7c_0 conda-forge
freetype 2.14.1 ha770c72_0 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
frozendict 2.4.6 py312h66e93f0_0 conda-forge
fsspec 2026.2.0 pyhd8ed1ab_0 conda-forge
func_timeout 4.3.5 pyhd8ed1ab_1 conda-forge
gawk 5.3.1 hcd3d067_0 conda-forge
gemmi 0.7.4 pypi_0 pypi
gitdb 4.0.12 pyhd8ed1ab_0 conda-forge
gitpython 3.1.46 pyhd8ed1ab_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
gmpy2 2.2.1 py312hcaba1f9_2 conda-forge
greenlet 3.3.1 py312h8285ef7_1 conda-forge
gsl 2.7 he838d99_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
hatch-cython 0.5.1 pypi_0 pypi
hhsuite 3.3.0 h503566f_15 bioconda
hjson 3.1.0 pypi_0 pypi
hmmer 3.4 hb6cb901_4 bioconda
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
humanfriendly 10.0 pyh707e725_8 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_0 conda-forge
ihm 2.9 py312h4c3975b_0 conda-forge
ijson 3.4.0.post0 pyhd8ed1ab_0 conda-forge
immutables 0.21 py312h4c3975b_2 conda-forge
iniconfig 2.3.0 pyhd8ed1ab_0 conda-forge
jinja2 3.1.6 pyhcf101f3_1 conda-forge
jmespath 1.0.1 pyhd8ed1ab_1 conda-forge
jsonpatch 1.33 pyhd8ed1ab_0 conda-forge
jsonpointer 3.0.0 py312h7900ff3_1 conda-forge
jsonschema 4.26.0 pyhcf101f3_0 conda-forge
jsonschema-specifications 2025.9.1 pyhcf101f3_0 conda-forge
jupyter_core 5.9.1 pyhc90fa1f_0 conda-forge
kalign2 2.04 h7b50bb2_8 bioconda
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.9 py312h0a2e395_2 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_2 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libabseil 20260107.0 cxx17_h7b12aa8_0 conda-forge
libarchive 3.7.4 hfca40fe_0 conda-forge
libasprintf 0.25.1 h3f43e3d_1 conda-forge
libblas 3.9.0 20_linux64_mkl conda-forge
libboost 1.86.0 h6c02f8c_3 conda-forge
libboost-python 1.86.0 py312hf890105_5 conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge
libcblas 3.9.0 20_linux64_mkl conda-forge
libcublas 12.4.5.8 he02047a_2 conda-forge
libcufft 11.2.1.3 he02047a_2 conda-forge
libcufile 1.9.1.3 he02047a_2 conda-forge
libcurand 10.3.5.147 he02047a_2 conda-forge
libcurl 8.10.1 hbbe4b11_0 conda-forge
libcusolver 11.6.1.9 he02047a_2 conda-forge
libcusparse 12.3.1.170 he02047a_2 conda-forge
libdeflate 1.23 h86f0d12_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.3 hecca717_0 conda-forge
libffi 3.5.2 h3435931_0 conda-forge
libfreetype 2.14.1 ha770c72_0 conda-forge
libfreetype6 2.14.1 h73754d4_0 conda-forge
libgcc 15.2.0 he0feb66_17 conda-forge
libgcc-ng 15.2.0 h69a702a_17 conda-forge
libgettextpo 0.25.1 h5888daf_0 conda-forge
libgfortran 15.2.0 h69a702a_17 conda-forge
libgfortran-ng 15.2.0 h69a702a_17 conda-forge
libgfortran5 15.2.0 h68bc16d_17 conda-forge
libglib 2.82.2 h2ff4ddf_1 conda-forge
libgomp 15.2.0 he0feb66_17 conda-forge
libhwloc 2.11.2 default_h0d58e46_1001 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.1.2 hb03c661_0 conda-forge
liblapack 3.9.0 20_linux64_mkl conda-forge
liblapacke 3.9.0 20_linux64_mkl conda-forge
liblzma 5.8.2 hb03c661_0 conda-forge
liblzma-devel 5.8.2 hb03c661_0 conda-forge
libmamba 1.5.9 h4cc3d14_0 conda-forge
libmambapy 1.5.9 py312h7fb9e8e_0 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnpp 12.2.5.30 he02047a_2 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libntlm 1.8 hb9d3cd8_0 conda-forge
libnvfatbin 12.4.127 he02047a_2 conda-forge
libnvjitlink 12.4.127 he02047a_2 conda-forge
libnvjpeg 12.3.1.117 he02047a_2 conda-forge
libpng 1.6.54 h421ea60_0 conda-forge
libpq 18.1 h5c52fec_2 conda-forge
librdkit 2025.09.5 h3c5c181_0 conda-forge
libsolv 0.7.30 h3509ff9_0 conda-forge
libsqlite 3.51.2 h0c1763c_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 15.2.0 h934c35e_17 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_17 conda-forge
libtiff 4.7.0 hd9ff511_3 conda-forge
libuuid 2.41.3 h5347b49_0 conda-forge
libwebp-base 1.6.0 hd42ef1d_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.13.5 h8d12d68_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lightning-utilities 0.15.2 pyhd8ed1ab_0 conda-forge
llvm-openmp 15.0.7 h0cdce71_0 conda-forge
logmuse 0.2.8 pyhd8ed1ab_1 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 hd590300_1001 conda-forge
mamba 1.5.9 py312h9460a1c_0 conda-forge
markdown-it-py 4.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 3.0.3 py312h8a5da7c_0 conda-forge
matplotlib-base 3.10.8 py312he3d6523_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_1 conda-forge
memory_profiler 0.61.0 pyhcf101f3_1 conda-forge
menuinst 2.2.0 py312h7900ff3_0 conda-forge
mkl 2023.2.0 ha770c72_50498 conda-forge
ml-collections 1.0.0 pyh29332c3_0 conda-forge
mmseqs2 18.8cc5c hd6d6fdc_0 bioconda
modelcif 1.6 pyhd8ed1ab_0 conda-forge
mpc 1.3.1 h24ddda3_1 conda-forge
mpfr 4.2.1 h90cbb55_3 conda-forge
mpi 1.0 openmpi conda-forge
mpmath 1.3.0 pyhd8ed1ab_1 conda-forge
msgpack-python 1.1.2 py312hd9148b4_1 conda-forge
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 he02047a_1 conda-forge
networkx 3.6.1 pyhcf101f3_0 conda-forge
ninja 1.13.0 pypi_0 pypi
numpy 2.4.2 py312h33ff503_1 conda-forge
nvidia-cutlass 3.8.0.0 pypi_0 pypi
ocl-icd 2.3.3 hb9d3cd8_0 conda-forge
opencl-headers 2025.06.13 h5888daf_0 conda-forge
openfold3 0.3.1 pypi_0 pypi
openjpeg 2.5.3 h55fea9a_1 conda-forge
openldap 2.6.10 he970967_0 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssl 3.6.1 h35e630c_1 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.3.3 py312hf79963d_1 conda-forge
pcre2 10.44 hc749103_2 conda-forge
pdbeccdutils 1.0.0 pypi_0 pypi
pephubclient 0.4.4 pyhd8ed1ab_1 conda-forge
peppy 0.40.8 pyhd8ed1ab_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pillow 11.3.0 py312h7b42cdd_3 conda-forge
pip 26.0.1 pyh8b19718_0 conda-forge
pixman 0.46.4 h54a6638_1 conda-forge
platformdirs 4.3.6 pyhd8ed1ab_0 conda-forge
pluggy 1.5.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.51 pyha770c72_0 conda-forge
protobuf 6.33.5 py312ha7b3241_0 conda-forge
psutil 7.2.2 py312h5253ce2_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pulp 2.8.0 py312hd0750ca_3 conda-forge
py-cpuinfo 9.0.0 pypi_0 pypi
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycairo 1.29.0 py312h2596900_0 conda-forge
pycosat 0.6.6 py312h98912ed_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pydantic 2.12.5 pyhcf101f3_1 conda-forge
pydantic-core 2.41.5 py312h868fb18_1 conda-forge
pydot 4.0.1 pypi_0 pypi
pygments 2.19.2 pyhd8ed1ab_0 conda-forge
pyparsing 3.3.2 pyhcf101f3_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytest 9.0.2 pyhcf101f3_0 conda-forge
python 3.12.12 hd63d673_2_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.21.2 pyhe01879c_0 conda-forge
python-lmdb 1.6.2 py312h8fd8f52_0 conda-forge
python-tzdata 2025.3 pyhd8ed1ab_0 conda-forge
python_abi 3.12 5_cp312 conda-forge
pytorch 2.5.1 py3.12_cuda12.4_cudnn9.1.0_0 pytorch
pytorch-cuda 12.4 hc786d27_7 pytorch
pytorch-lightning 2.6.1 pyhcf101f3_0 conda-forge
pytorch-mutex 1.0 cuda pytorch
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.3 py312h8a5da7c_1 conda-forge
qhull 2020.2 h434a139_5 conda-forge
rdkit 2025.09.5 py312h3ecb6ed_0 conda-forge
readline 8.3 h853b02a_0 conda-forge
referencing 0.37.0 pyhcf101f3_0 conda-forge
reportlab 4.4.9 py312h4c3975b_0 conda-forge
reproc 14.2.4.post0 hd590300_1 conda-forge
reproc-cpp 14.2.4.post0 h59595ed_1 conda-forge
requests 2.32.5 pyhcf101f3_1 conda-forge
reretry 0.11.8 pyhd8ed1ab_1 conda-forge
rich 14.3.2 pyhcf101f3_0 conda-forge
rlpycairo 0.4.0 pyh6c17108_0 conda-forge
rpds-py 0.30.0 py312h868fb18_0 conda-forge
ruamel.yaml 0.17.17 py312h4c3975b_4 conda-forge
ruamel.yaml.clib 0.2.8 py312h66e93f0_1 conda-forge
s2n 1.6.1 h23ded05_1 conda-forge
s3transfer 0.16.0 pyhd8ed1ab_0 conda-forge
scipy 1.17.0 py312h54fa4ab_1 conda-forge
sentry-sdk 2.52.0 pyhd8ed1ab_0 conda-forge
setproctitle 1.3.7 py312h5253ce2_0 conda-forge
setuptools 82.0.0 pyh332efcf_0 conda-forge
shellingham 1.5.4 pyhd8ed1ab_2 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
slack-sdk 3.39.0 pyhd8ed1ab_0 conda-forge
slack_sdk 3.39.0 hd8ed1ab_0 conda-forge
smart_open 7.5.0 pyhcf101f3_0 conda-forge
smmap 5.0.2 pyhd8ed1ab_0 conda-forge
snakemake 9.16.3 hdfd78af_0 bioconda
snakemake-interface-common 1.22.0 pyhd4c3c12_0 bioconda
snakemake-interface-executor-plugins 9.3.9 pyhdfd78af_0 bioconda
snakemake-interface-logger-plugins 2.0.0 pyhd4c3c12_0 bioconda
snakemake-interface-report-plugins 1.3.0 pyhd4c3c12_0 bioconda
snakemake-interface-scheduler-plugins 2.0.2 pyhd4c3c12_0 bioconda
snakemake-interface-storage-plugins 4.3.2 pyhd4c3c12_0 bioconda
snakemake-minimal 9.16.3 pyhdfd78af_0 bioconda
sqlalchemy 2.0.46 py312h5253ce2_1 conda-forge
sympy 1.13.1 pypi_0 pypi
tabulate 0.9.0 pyhcf101f3_3 conda-forge
tbb 2021.13.0 hceb3a55_1 conda-forge
throttler 1.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.4.0 pyhcf101f3_0 conda-forge
torchmetrics 1.8.2 pyhd8ed1ab_0 conda-forge
torchtriton 3.1.0 py312 pytorch
tqdm 4.67.3 pyh8f84b5b_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
treelib 1.8.0 pypi_0 pypi
truststore 0.10.0 pyhd8ed1ab_0 conda-forge
typer 0.21.1 pyhf8876ea_0 conda-forge
typer-slim 0.21.1 pyhcf101f3_0 conda-forge
typer-slim-standard 0.21.1 h378290b_0 conda-forge
typing 3.10.0.0 pyhd8ed1ab_2 conda-forge
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing-inspection 0.4.2 pyhd8ed1ab_1 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
tzdata 2024b hc8b5060_0 conda-forge
ubiquerg 0.8.0 pyhd8ed1ab_0 conda-forge
unicodedata2 17.0.0 py312h4c3975b_1 conda-forge
urllib3 2.2.3 pyhd8ed1ab_0 conda-forge
veracitools 0.1.3 py_0 conda-forge
wandb 0.24.2 py312h0ccc70a_0 conda-forge
wcwidth 0.2.14 pyhd8ed1ab_0 conda-forge
wheel 0.45.0 pyhd8ed1ab_0 conda-forge
wrapt 1.17.3 py312h4c3975b_1 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb03c661_1 conda-forge
xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge
xorg-libxext 1.3.7 hb03c661_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xz 5.8.2 ha02ee65_0 conda-forge
xz-gpl-tools 5.8.2 ha02ee65_0 conda-forge
xz-tools 5.8.2 hb03c661_0 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
yaml-cpp 0.8.0 h59595ed_0 conda-forge
yte 1.9.4 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 py312hef9b889_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
pip3 packages:
absl-py @ file:///home/conda/feedstock_root/build_artifacts/absl-py_1769637056219/work
amply @ file:///home/conda/feedstock_root/build_artifacts/amply_1734602966974/work
annotated-types @ file:///home/conda/feedstock_root/build_artifacts/annotated-types_1733247046149/work
appdirs @ file:///home/conda/feedstock_root/build_artifacts/appdirs_1733753955715/work
archspec @ file:///home/conda/feedstock_root/build_artifacts/archspec_1708969572489/work
argparse_dataclass @ file:///home/conda/feedstock_root/build_artifacts/argparse-dataclass_1764079528156/work
attrs @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_attrs_1764875182/work
awscli @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_awscli_1769638686/work
awscrt @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_awscrt_1764860005/work
biopython @ file:///home/conda/feedstock_root/build_artifacts/biopython_1768646495278/work
biotite @ file:///home/conda/feedstock_root/build_artifacts/biotite_1742162519687/work
biotraj @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_biotraj_1767272628/work
boltons @ file:///home/conda/feedstock_root/build_artifacts/boltons_1711936407380/work
boto3 @ file:///home/conda/feedstock_root/build_artifacts/boto3_1770452703895/work
botocore @ file:///home/conda/feedstock_root/build_artifacts/botocore_1770422989225/work
Brotli @ file:///home/conda/feedstock_root/build_artifacts/brotli-split_1725267488082/work
certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1767500808759/work/certifi
cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1725560558132/work
charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1728479282467/work
click @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_click_1764518652/work
colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work
coloredlogs @ file:///home/conda/feedstock_root/build_artifacts/coloredlogs_1733927977068/work
conda @ file:///home/conda/feedstock_root/build_artifacts/conda_1729155160285/work
conda-inject @ file:///home/conda/feedstock_root/build_artifacts/conda-inject_1717043556818/work
conda-libmamba-solver @ file:///home/conda/feedstock_root/build_artifacts/conda-libmamba-solver_1727359833193/work/src
conda-package-handling @ file:///home/conda/feedstock_root/build_artifacts/conda-package-handling_1729006966809/work
conda_package_streaming @ file:///home/conda/feedstock_root/build_artifacts/conda-package-streaming_1729004031731/work
ConfigArgParse @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_configargparse_1748302135/work
connection-pool @ file:///home/conda/feedstock_root/build_artifacts/connection_pool_1608581887050/work
contourpy @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_contourpy_1769155979/work
cuda-bindings==13.1.1
cuda-pathfinder==1.3.3
cuda-python==13.1.1
cycler @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_cycler_1764466758/work
deepspeed==0.18.5
distro @ file:///home/conda/feedstock_root/build_artifacts/distro_1675116244235/work
docker-pycreds==0.4.0
docutils @ file:///home/conda/feedstock_root/build_artifacts/docutils_1755942543230/work
dpath @ file:///home/conda/feedstock_root/build_artifacts/dpath_1762165291153/work
eido @ file:///home/conda/feedstock_root/build_artifacts/eido_1770170656035/work
einops==0.8.2
eval_type_backport @ file:///home/conda/feedstock_root/build_artifacts/eval_type_backport_1764679206270/work
exceptiongroup @ file:///home/conda/feedstock_root/build_artifacts/exceptiongroup_1763918002538/work
fastjsonschema @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_python-fastjsonschema_1755304154/work/dist
filelock @ file:///home/conda/feedstock_root/build_artifacts/filelock_1768022204021/work
fonttools @ file:///home/conda/feedstock_root/build_artifacts/fonttools_1765632549069/work
freetype-py @ file:///home/conda/feedstock_root/build_artifacts/freetype-py_1650983368720/work
frozendict @ file:///home/conda/feedstock_root/build_artifacts/frozendict_1728841327252/work
fsspec @ file:///home/conda/feedstock_root/build_artifacts/fsspec_1770387778895/work
func_timeout @ file:///home/conda/feedstock_root/build_artifacts/func_timeout_1735326823389/work
gemmi==0.7.4
gitdb @ file:///home/conda/feedstock_root/build_artifacts/gitdb_1735887193964/work
GitPython @ file:///home/conda/feedstock_root/build_artifacts/gitpython_1767358723114/work
gmpy2 @ file:///home/conda/feedstock_root/build_artifacts/gmpy2_1762946764387/work
greenlet @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_greenlet_1770077497/work
h2 @ file:///home/conda/feedstock_root/build_artifacts/h2_1634280454336/work
hatch-cython @ git+https://github.com/joshua-auchincloss/hatch-cython.git@eb543af9299a662f9388d46bca2928aea928c8e9
hjson==3.1.0
hpack==4.0.0
humanfriendly @ file:///home/conda/feedstock_root/build_artifacts/humanfriendly_1733927922002/work
hyperframe @ file:///home/conda/feedstock_root/build_artifacts/hyperframe_1619110129307/work
idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1726459485162/work
ihm @ file:///home/conda/feedstock_root/build_artifacts/ihm_1769115713110/work
ijson @ file:///home/conda/feedstock_root/build_artifacts/ijson_1760081689203/work
immutables @ file:///home/conda/feedstock_root/build_artifacts/immutables_1757685311337/work
iniconfig @ file:///home/conda/feedstock_root/build_artifacts/iniconfig_1760831328738/work
Jinja2 @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_jinja2_1764517220/work
jmespath @ file:///home/conda/feedstock_root/build_artifacts/jmespath_1733229141657/work
jsonpatch @ file:///home/conda/feedstock_root/build_artifacts/jsonpatch_1695536281965/work
jsonpointer @ file:///home/conda/feedstock_root/build_artifacts/jsonpointer_1725302935093/work
jsonschema @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_jsonschema_1767839954/work
jsonschema-specifications @ file:///tmp/tmptzik3dqa/src
jupyter_core @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_jupyter_core_1760643864/work
kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_kiwisolver_1762488738/work
libmambapy @ file:///home/conda/feedstock_root/build_artifacts/mamba-split_1725066159413/work/libmambapy
lightning-utilities @ file:///home/conda/feedstock_root/build_artifacts/lightning-utilities_1754515506335/work
lmdb @ file:///home/conda/feedstock_root/build_artifacts/python-lmdb_1736585063846/work
logmuse @ file:///home/conda/feedstock_root/build_artifacts/logmuse_1735078170018/work
mamba @ file:///home/conda/feedstock_root/build_artifacts/mamba-split_1725066159413/work/mamba
markdown-it-py @ file:///home/conda/feedstock_root/build_artifacts/markdown-it-py_1754951200865/work
MarkupSafe @ file:///home/conda/feedstock_root/build_artifacts/markupsafe_1759055168201/work
matplotlib==3.10.8
mdurl @ file:///home/conda/feedstock_root/build_artifacts/mdurl_1733255585584/work
memory_profiler @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_memory_profiler_1764885507/work
menuinst @ file:///home/conda/feedstock_root/build_artifacts/menuinst_1731146972698/work
ml_collections @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_ml-collections_1731417481/work
modelcif @ file:///home/conda/feedstock_root/build_artifacts/modelcif_1765578803631/work
mpmath @ file:///home/conda/feedstock_root/build_artifacts/mpmath_1733302684489/work
msgpack @ file:///home/conda/feedstock_root/build_artifacts/msgpack-python_1762503974934/work
munkres==1.1.4
nbformat @ file:///home/conda/feedstock_root/build_artifacts/nbformat_1733402752141/work
networkx @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_networkx_1765215107/work
ninja==1.13.0
numpy @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_numpy_1770098484/work/dist/numpy-2.4.2-cp312-cp312-linux_x86_64.whl#sha256=b7bef5ec2cd1cc474384a65c015869d8df9b26ffcb0de8674705011d77d42046
nvidia-cutlass==3.8.0.0
openfold3==0.3.1
packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1718189413536/work
pandas @ file:///home/conda/feedstock_root/build_artifacts/pandas_1759265541279/work
pdbeccdutils==1.0.0
pephubclient @ file:///home/conda/feedstock_root/build_artifacts/pephubclient_1735078162946/work
peppy @ file:///home/conda/feedstock_root/build_artifacts/peppy_1760990634896/work
pillow @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pillow_1758208668/work
platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1726613481435/work
pluggy @ file:///home/conda/feedstock_root/build_artifacts/pluggy_1713667077545/work
prompt_toolkit @ file:///home/conda/feedstock_root/build_artifacts/prompt-toolkit_1744724089886/work
protobuf @ file:///home/conda/feedstock_root/build_artifacts/protobuf_1769754629255/work/bazel-bin/python/dist/protobuf-6.33.5-cp312-abi3-linux_x86_64.whl#sha256=b79249ebd4a1b0ac379bf50f3a7fa48c814c703c83283af5e5b198775a3b4f93
psutil @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_psutil_1769678155/work
PuLP @ file:///home/conda/feedstock_root/build_artifacts/pulp_1757853199946/work
py-cpuinfo==9.0.0
pycairo==1.29.0
pycosat @ file:///home/conda/feedstock_root/build_artifacts/pycosat_1696355774225/work
pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1711811537435/work
pydantic @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pydantic_1764434463/work
pydantic_core @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pydantic-core_1762989004/work
pydot==4.0.1
Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1750615794071/work
pyparsing @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pyparsing_1769003998/work
PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1661604839144/work
pytest @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pytest_1765062031/work
python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1709299778482/work
pytorch-lightning @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pytorch-lightning_1769802510/work
pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1742920838005/work
PyYAML @ file:///home/conda/feedstock_root/build_artifacts/pyyaml_1770223234623/work
rdkit @ file:///home/conda/feedstock_root/build_artifacts/rdkit-meta_1770016749455/work
referencing @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_referencing_1760379115/work
reportlab @ file:///home/conda/feedstock_root/build_artifacts/reportlab_1768558311601/work
requests @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_requests_1766926974/work
reretry @ file:///home/conda/feedstock_root/build_artifacts/reretry_1735477434309/work
rich @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_rich_1769971520/work/dist
rlPyCairo @ file:///home/conda/feedstock_root/build_artifacts/rlpycairo_1756864152814/work
rpds-py @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_rpds-py_1764543174/work
ruamel.yaml @ file:///home/conda/feedstock_root/build_artifacts/ruamel.yaml_1757164408556/work
ruamel.yaml.clib @ file:///home/conda/feedstock_root/build_artifacts/ruamel.yaml.clib_1728724466132/work
s3transfer @ file:///home/conda/feedstock_root/build_artifacts/s3transfer_1764589692484/work
scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy-split_1768799527240/work/dist/scipy-1.17.0-cp312-cp312-linux_x86_64.whl#sha256=8b499fab1921b5531f77c66246d6a64569714eeb749de15e7f3ceeb2a749a3b0
sentry-sdk @ file:///home/conda/feedstock_root/build_artifacts/sentry-sdk_1770230820515/work
setproctitle @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_setproctitle_1766684430/work
setuptools==82.0.0
shellingham @ file:///home/conda/feedstock_root/build_artifacts/shellingham_1762858192781/work
six @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_six_1753199211/work
slack_sdk @ file:///home/conda/feedstock_root/build_artifacts/slack-sdk_1763658153295/work
smart_open @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_smart_open_1762641207/work/dist
smmap @ file:///home/conda/feedstock_root/build_artifacts/smmap_1739781697784/work
snakemake @ file:///opt/conda/conda-bld/snakemake_1770308750344/work
snakemake-interface-common @ file:///opt/conda/conda-bld/snakemake-interface-common_1759253090937/work
snakemake-interface-executor-plugins @ file:///opt/conda/conda-bld/snakemake-interface-executor-plugins_1753822061496/work
snakemake-interface-logger-plugins @ file:///opt/conda/conda-bld/snakemake-interface-logger-plugins_1759090722025/work
snakemake-interface-report-plugins @ file:///opt/conda/conda-bld/snakemake-interface-report-plugins_1761910435031/work
snakemake-interface-scheduler-plugins @ file:///opt/conda/conda-bld/snakemake-interface-scheduler-plugins_1760984069577/work
snakemake-interface-storage-plugins @ file:///opt/conda/conda-bld/snakemake-interface-storage-plugins_1764856019233/work
SQLAlchemy @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_sqlalchemy_1769087054/work
sympy==1.13.1
tabulate @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_tabulate_1765140047/work
throttler @ file:///home/conda/feedstock_root/build_artifacts/throttler_1691135466785/work
tomli @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_tomli_1768146676/work
torch==2.5.1
torchmetrics @ file:///home/conda/feedstock_root/build_artifacts/torchmetrics_1756932631856/work
tqdm @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_tqdm_1770153424/work
traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1733367359838/work
treelib==1.8.0
triton==3.1.0
truststore @ file:///home/conda/feedstock_root/build_artifacts/truststore_1729762363021/work
typer==0.21.1
typer-slim==0.21.1
typing-inspection @ file:///home/conda/feedstock_root/build_artifacts/typing-inspection_1764158251755/work
typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_typing_extensions_1756220668/work
tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1765719872007/work
ubiquerg @ file:///home/conda/feedstock_root/build_artifacts/ubiquerg_1719492656897/work
unicodedata2 @ file:///home/conda/feedstock_root/build_artifacts/unicodedata2_1763054767730/work
urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1726496430923/work
veracitools==0.1.3
wandb @ file:///home/conda/feedstock_root/build_artifacts/wandb_1770406990694/work
wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1758622279606/work
wheel==0.45.0
wrapt @ file:///home/conda/feedstock_root/build_artifacts/wrapt_1756851611084/work
yte @ file:///home/conda/feedstock_root/build_artifacts/yte_1764250624582/work
zstandard==0.23.0
Input JSON
{
"queries": {
"task": {
"chains": [
{
"molecule_type": "protein",
"chain_ids": "A",
"sequence": "GLAGLAGLAGLALALALA"
},
{
"molecule_type": "protein",
"chain_ids": "B",
"sequence": "MAYMAYMAYMAYMAYAMA"
}
]
}
}
}
Output CIF
In attachment (test.txt)