AttributeError: 'XTCReader' object has no attribute '_xdr' #73
Description
Hi,
Im trying to compare and cluster 2 replicates with PENSa.
The code that I am using is the following one
import os
from pensa.preprocessing import load_selection, \
extract_coordinates, extract_coordinates_combined, \
extract_aligned_coordinates, extract_combined_grid
# Define root directory
root_dir = '/scratch_shared/MOR/'
# Simulation A
ref_file_a = root_dir+'prod5/structure.psf'
pdb_file_a = root_dir+'prod5/structure.pdb'
trj_file_a = [root_dir+'prod5/output.xtc']
# Simulation B
ref_file_b = root_dir+'prod4/structure.psf'
pdb_file_b = root_dir+'prod4/structure.pdb'
trj_file_b = [root_dir+'prod4/output4.xtc']
# Output directories
for subdir in ['traj', 'features', 'plots', 'vispdb', 'pca', 'clusters', 'results']:
os.makedirs(subdir, exist_ok=True)
# Define selection
resnums = "59:61 96:130 137:172 181:207 229:274 292:329 335:367"
sel_string_a = f"segid R and resnum {resnums}"
sel_string_b = f"segid R and resnum {resnums}"
print(f'Selection A:\n{sel_string_a}\n')
print(f'Selection B:\n{sel_string_b}\n')
# Extract coordinates
out_name_a = "traj/condition-a"
out_name_b = "traj/condition-b"
extract_coordinates(ref_file_a, pdb_file_a, trj_file_a, out_name_a+"_tm", sel_string_a)
extract_coordinates(ref_file_b, pdb_file_b, trj_file_b, out_name_b+"_tm", sel_string_b)
# Load structures
sim_a_tmr = read_structure_features(
out_name_a+"_tm.gro",
out_name_a+"_tm.xtc",
cossin=True
)
sim_b_tmr = read_structure_features(
out_name_b+"_tm.gro",
out_name_b+"_tm.xtc",
cossin=True
)
sim_a_tmr_feat, sim_a_tmr_data = sim_a_tmr
sim_b_tmr_feat, sim_b_tmr_data = sim_b_tmr
# Concatenate torsions
combined_data_tors = np.concatenate((sim_a_tmr_data['bb-torsions'], sim_b_tmr_data['bb-torsions']),
axis=0)
# Perform PCA
pca_combined = calculate_pca(combined_data_tors)
# Plot eigenvalues
idx, ev = pca_eigenvalues_plot(
pca_combined, num=12,
plot_file='plots/combined_tmr_eigenvalues.pdf'
)
# Compare projections
_ = compare_projections(
sim_a_tmr_data['bb-torsions'],
sim_b_tmr_data['bb-torsions'],
pca_combined,
label_a='A', label_b='B'
)
# Sort trajectories along principal components
_ = sort_trajs_along_common_pc(
sim_a_tmr_data['bb-torsions'], sim_b_tmr_data['bb-torsions'],
out_name_a+"_tm.gro", out_name_b+"_tm.gro",
out_name_a+"_tm.xtc", out_name_b+"_tm.xtc",
"pca/receptor_by_tmr", num_pc=3, start_frame=0
)
# PCA feature correlation
_ = pca_feature_correlation(
sim_a_tmr_feat['bb-torsions'], sim_a_tmr_data['bb-torsions'],
pca=pca_combined, num=3, threshold=0.4
)
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/Bio/Application/__init__.py:39: BiopythonD
eprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.
We instead now recommend building your command line and invoking it directly
with the subprocess module.
warnings.warn(
Selection A:
segid R and resnum 59:61 96:130 137:172 181:207 229:274 292:329 335:367
Selection B:
segid R and resnum 59:61 96:130 137:172 181:207 229:274 292:329 335:367
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/PDB.py:777: UserWar
ning: Unit cell dimensions not found. CRYST1 record set to unitary values.
warnings.warn("Unit cell dimensions not found. "
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/PDB.py:1154: UserWa
rning: Found no information for attr: 'altLocs' Using default value of ' '
warnings.warn("Found no information for attr: '{}'"
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/PDB.py:1154: UserWa
rning: Found no information for attr: 'icodes' Using default value of ' '
warnings.warn("Found no information for attr: '{}'"
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/PDB.py:1154: UserWa
rning: Found no information for attr: 'chainIDs' Using default value of ''
warnings.warn("Found no information for attr: '{}'"
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/PDB.py:1154: UserWa
rning: Found no information for attr: 'occupancies' Using default value of '1.0'
warnings.warn("Found no information for attr: '{}'"
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/PDB.py:1154: UserWa
rning: Found no information for attr: 'tempfactors' Using default value of '0.0'
warnings.warn("Found no information for attr: '{}'"
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/PDB.py:1154: UserWa
rning: Found no information for attr: 'elements' Using default value of ' '
warnings.warn("Found no information for attr: '{}'"
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/PDB.py:1154: UserWa
rning: Found no information for attr: 'record_types' Using default value of 'ATOM'
warnings.warn("Found no information for attr: '{}'"
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/PDB.py:1154: UserWa
rning: Found no information for attr: 'formalcharges' Using default value of '0'
warnings.warn("Found no information for attr: '{}'"
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/PDB.py:1201: UserWa
rning: Found missing chainIDs. Corresponding atoms will use value of 'X'
warnings.warn("Found missing chainIDs."
/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/GRO.py:479: UserWar
ning: missing dimension - setting unit cell to zeroed box [0., 0., 0.]
warnings.warn(wmsg)
Traceback (most recent call last):
File "/scratch_shared/MOR/clustering1.py", line 37, in <module>
extract_coordinates(ref_file_b, pdb_file_b, trj_file_b, out_name_b+"_tm", sel_string_b)
File "/home/***/.conda/envs/pensa/lib/python3.10/site-packages/pensa/preprocessing/coordinates.py
", line 48, in extract_coordinates
u = mda.Universe(top, trj)
File "/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/core/universe.py", line
436, in __init__
self.load_new(coordinates, format=format, in_memory=in_memory,
File "/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/core/universe.py", line
665, in load_new
self.trajectory = reader(filename, format=format, **kwargs)
File "/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/lib/util.py", line 2562
, in wrapper
return func(self, *args, **kwargs)
File "/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/XDR.py", li
ne 148, in __init__
self._xdr = self._file(self.filename)
File "MDAnalysis/lib/formats/libmdaxdr.pyx", line 135, in MDAnalysis.lib.formats.libmdaxdr._XDRFi
le.__cinit__
File "MDAnalysis/lib/formats/libmdaxdr.pyx", line 194, in MDAnalysis.lib.formats.libmdaxdr._XDRFi
le.open
OSError: File does not exist: b'/scratch_shared/MOR/prod4/output4.xtc'
Exception ignored in: <function ReaderBase.__del__ at 0x7f0d78c93e20>
Traceback (most recent call last):
File "/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/base.py", l
ine 1531, in __del__
self.close()
File "/home/***/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/coordinates/XDR.py", li
ne 186, in close
self._xdr.close()
AttributeError: 'XTCReader' object has no attribute '_xdr'
In the past I had this issue too using MDAnalysis AttributeError: 'XTCReader' object has no attribute '_xdr' but I was able to fix it doing this
u = mda.Universe(data.TPR, data.XTC, refresh_offsets=True)
Is there a way to fix this in PENSA? Or I messed up somehting for clustering the MD?
Im using the following environment
conda list -n pensa
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.13 hb9d3cd8_0 conda-forge
biopython 1.85 py310ha75aee5_1 conda-forge
biotite 1.1.0 py310hf71b8c6_1 conda-forge
biotraj 1.2.2 py310hf71b8c6_0 conda-forge
blosc 1.21.6 he440d0b_1 conda-forge
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py310hf71b8c6_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.4 hb9d3cd8_0 conda-forge
ca-certificates 2025.1.31 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.18.2 h3394656_1 conda-forge
certifi 2024.12.14 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py310h8deb56e_0 conda-forge
cftime 1.6.4 py310hf462985_1 conda-forge
charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge
click 8.1.8 pypi_0 pypi
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.1 py310h3788b33_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
cyrus-sasl 2.1.27 h54b06d7_7 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
deeptime 0.4.4 py310h5eaa309_3 conda-forge
double-conversion 3.3.0 h59595ed_0 conda-forge
expat 2.6.4 h5888daf_0 conda-forge
fasteners 0.19 pyhd8ed1ab_1 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 0 conda-forge
fonttools 4.55.8 py310h89163eb_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
gpcrmining 0.2.0 pypi_0 pypi
graphite2 1.3.13 h59595ed_1003 conda-forge
griddataformats 1.0.2 pyhd8ed1ab_1 conda-forge
gsd 3.4.2 py310ha75aee5_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
h5py 3.12.1 nompi_py310hacc6608_103 conda-forge
harfbuzz 10.2.0 h4bba637_0 conda-forge
hatch-cython 0.5.1 pypi_0 pypi
hdf4 4.2.15 h2a13503_7 conda-forge
hdf5 1.14.4 nompi_h2d575fe_105 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
joblib 1.4.2 pyhd8ed1ab_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.7 py310h3788b33_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_2 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libblas 3.9.0 28_h59b9bed_openblas 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 28_he106b2a_openblas conda-forge
libclang-cpp19.1 19.1.7 default_hb5137d0_1 conda-forge
libclang13 19.1.7 default_h9c6a7e4_1 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.11.1 h332b0f4_0 conda-forge
libdeflate 1.23 h4ddbbb0_0 conda-forge
libdrm 2.4.124 hb9d3cd8_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libegl 1.7.0 ha4b6fd6_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.6.4 h5888daf_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 14.2.0 h77fa898_1 conda-forge
libgcc-ng 14.2.0 h69a702a_1 conda-forge
libgfortran 14.2.0 h69a702a_1 conda-forge
libgfortran5 14.2.0 hd5240d6_1 conda-forge
libgl 1.7.0 ha4b6fd6_2 conda-forge
libglib 2.82.2 h2ff4ddf_1 conda-forge
libglvnd 1.7.0 ha4b6fd6_2 conda-forge
libglx 1.7.0 ha4b6fd6_2 conda-forge
libgomp 14.2.0 h77fa898_1 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 28_h7ac8fdf_openblas conda-forge
libllvm19 19.1.7 ha7bfdaf_1 conda-forge
liblzma 5.6.4 hb9d3cd8_0 conda-forge
liblzma-devel 5.6.4 hb9d3cd8_0 conda-forge
libnetcdf 4.9.2 nompi_h5ddbaa4_116 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libntlm 1.8 hb9d3cd8_0 conda-forge
libopenblas 0.3.28 pthreads_h94d23a6_1 conda-forge
libopengl 1.7.0 ha4b6fd6_2 conda-forge
libpciaccess 0.18 hd590300_0 conda-forge
libpng 1.6.46 h943b412_0 conda-forge
libpq 17.2 h3b95a9b_1 conda-forge
libsqlite 3.48.0 hee588c1_1 conda-forge
libssh2 1.11.1 hf672d98_0 conda-forge
libstdcxx 14.2.0 hc0a3c3a_1 conda-forge
libstdcxx-ng 14.2.0 h4852527_1 conda-forge
libtiff 4.7.0 hd9ff511_3 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.5.0 h851e524_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxkbcommon 1.8.0 hc4a0caf_0 conda-forge
libxml2 2.13.5 h8d12d68_1 conda-forge
libxslt 1.1.39 h76b75d6_0 conda-forge
libzip 1.11.2 h6991a6a_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
matplotlib 3.10.0 py310hff52083_0 conda-forge
matplotlib-base 3.10.0 py310h68603db_0 conda-forge
mda-xdrlib 0.2.0 pyhd8ed1ab_1 conda-forge
mdahole2-base 0.5.0 pyhd8ed1ab_1 conda-forge
mdanalysis 2.8.0 py310h5eaa309_0 conda-forge
mmtf-python 1.1.3 pyhd8ed1ab_0 conda-forge
mrcfile 1.5.4 pyhd8ed1ab_0 conda-forge
msgpack-python 1.1.0 py310h3788b33_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 9.0.1 h266115a_4 conda-forge
mysql-libs 9.0.1 he0572af_4 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
netcdf4 1.7.2 nompi_py310h5146f0f_101 conda-forge
networkx 3.4.2 pyh267e887_2 conda-forge
numpy 2.2.2 py310hefbff90_0 conda-forge
openjpeg 2.5.3 h5fbd93e_0 conda-forge
openldap 2.6.9 he970967_0 conda-forge
openssl 3.4.0 h7b32b05_1 conda-forge
packaging 24.2 pyhd8ed1ab_2 conda-forge
pandas 2.2.3 py310h5eaa309_1 conda-forge
pathsimanalysis 1.2.0 pyhd8ed1ab_1 conda-forge
patsy 1.0.1 pyhd8ed1ab_1 conda-forge
pcre2 10.44 hba22ea6_2 conda-forge
pensa 0.6.0 pypi_0 pypi
pillow 11.1.0 py310h7e6dc6c_0 conda-forge
pip 25.0 pyh8b19718_0 conda-forge
pixman 0.44.2 h29eaf8c_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pyedr 0.8.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.2.1 pyhd8ed1ab_0 conda-forge
pyside6 6.8.2 py310hfd10a26_0 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.10.0 h543edf9_3_cpython conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_1 conda-forge
python-tzdata 2025.1 pyhd8ed1ab_0 conda-forge
python_abi 3.10 5_cp310 conda-forge
pytng 0.3.3 py310he95d665_1 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
qhull 2020.2 h434a139_5 conda-forge
qt6-main 6.8.2 h588cce1_0 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
scikit-learn 1.6.1 py310h27f47ee_0 conda-forge
scipy 1.15.1 py310hfa6ec8c_0 conda-forge
seaborn 0.13.2 hd8ed1ab_3 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_3 conda-forge
setuptools 75.8.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
snappy 1.2.1 h8bd8927_1 conda-forge
sqlite 3.48.0 h9eae976_1 conda-forge
statsmodels 0.14.4 py310hf462985_0 conda-forge
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tidynamics 1.1.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tornado 6.4.2 py310ha75aee5_0 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
tzdata 2025a h78e105d_0 conda-forge
unicodedata2 16.0.0 py310ha75aee5_0 conda-forge
urllib3 2.3.0 pyhd8ed1ab_0 conda-forge
waterdynamics 1.2.0 pyhd8ed1ab_1 conda-forge
wayland 1.23.1 h3e06ad9_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xcb-util 0.4.1 hb711507_2 conda-forge
xcb-util-cursor 0.1.5 hb9d3cd8_0 conda-forge
xcb-util-image 0.4.0 hb711507_2 conda-forge
xcb-util-keysyms 0.4.1 hb711507_0 conda-forge
xcb-util-renderutil 0.3.10 hb711507_0 conda-forge
xcb-util-wm 0.4.2 hb711507_0 conda-forge
xkeyboard-config 2.43 hb9d3cd8_0 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.5 he73a12e_0 conda-forge
xorg-libx11 1.8.11 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxcomposite 0.4.6 hb9d3cd8_2 conda-forge
xorg-libxcursor 1.2.3 hb9d3cd8_0 conda-forge
xorg-libxdamage 1.1.6 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.1 hb9d3cd8_0 conda-forge
xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge
xorg-libxrandr 1.5.4 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge
xorg-libxxf86vm 1.1.6 hb9d3cd8_0 conda-forge
xz 5.6.4 hbcc6ac9_0 conda-forge
xz-gpl-tools 5.6.4 hbcc6ac9_0 conda-forge
xz-tools 5.6.4 hb9d3cd8_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 py310ha39cb0e_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
Thanks in advacne!