angelruizmoreno / jupyter_dock Goto Github PK

Dear, Angel Ruiz Moreno

Thank you for your nice tutorial notebook. It really helped me a lot

If you are okay with it, can you add molecular dynamic simulation tutorial in this repository?

It will help many researchers

Thank you again.

Sincerely,

Ingoo Lee

I try to run the script of 6.- Covalent_Docking.ipynb, but I got the following error:

the file S_atom.sdf doesn't exist in the dir of test/Covalent_Docking/

Thx!

Dear AngelRuizMoreno,
Excited to see docking in jupyter notebook. Thanks for the wonderful tutorial notebooks. Had issues when running prolif
error as follows:
module 'prolif' has no attribute 'Molecule'

unable to resolve this
If possible can you help it out

regards
Aparna

Hi, Can the Autodock-GPU be supported?

Hello! and thank you for very nice work.
I am facing issue in creating the environment from the Jupyter_Dock.yml file
as here :

ResolvePackageNotFound: 
  - pyqt5-sip==4.19.18=py37hcd2ae1e_7
  - python-utils==2.5.6=py37h06a4308_0
  - mpeg_encode==1=h14c3975_1
  - - argon2-cffi==20.1.0=py37h27cfd23_1
  - libopus==1.3.1=h7f98852_1
  - curl==7.78.0=h1ccaba5_0
  - xorg-libx11==1.6.9=h516909a_0
  - _openmp_mutex==4.5=1_llvm
  - pytables==3.6.1=py37h71ec239_0
  - icu==68.1=h58526e2_0
  - reportlab==3.5.68=py37h69800bb_0
  - cairo==1.16.0=h6cf1ce9_1008
  - glib-tools==2.68.4=h9c3ff4c_0
  - importlib-metadata==3.10.0=py37h06a4308_0
  - xorg-renderproto==0.11.1=h14c3975_1002
  - xorg-kbproto==1.0.7=h14c3975_1002
  - mysql-common==8.0.25=ha770c72_0
  - lz4-c==1.9.3=h295c915_1
  - cffi==1.14.6=py37hc58025e_0
  - _libgcc_mutex==0.1=conda_forge
  - ipython==7.26.0=py37hb070fc8_0
  - mistune==0.8.4=py37h14c3975_1001
  - pandocfilters==1.4.3=py37h06a4308_1
  - gsd==2.1.1=py37h03ebfcd_0
  - notebook==6.4.3=py37h06a4308_0
  - xz==5.2.5=h7b6447c_0
  - zeromq==4.3.4=h2531618_0
  - pixman==0.40.0=h36c2ea0_0
  - dbus==1.13.18=hb2f20db_0
  - libglu==9.0.0=hf484d3e_1
  - llvm-openmp==12.0.1=h4bd325d_1
  - jpeg==9d=h36c2ea0_0
  - expat==2.4.1=h2531618_2
  - numpy==1.19.1=py37hbc911f0_0
  - krb5==1.19.2=hac12032_0
  - libnetcdf==4.7.3=hb80b6cc_0
  - ncurses==6.2=he6710b0_1
  - lcms2==2.12=h3be6417_0
  - pytest==6.2.4=py37h06a4308_2
  - certifi==2021.5.30=py37h89c1867_0
  - scipy==1.5.0=py37h0b6359f_0
  - cftime==1.5.0=py37h6323ea4_0
  - libssh2==1.9.0=h1ba5d50_1
  - intel-openmp==2021.3.0=h06a4308_3350
  - nspr==4.30=h9c3ff4c_0
  - h5py==2.10.0=py37h7918eee_0
  - pyqt==5.12.3=py37h89c1867_7
  - pillow==8.3.1=py37h2c7a002_0
  - autodock-vina==1.1.2=h9ee0642_3
  - cython==0.29.24=py37h295c915_0
  - pip==21.0.1=py37h06a4308_0
  - lxml==4.6.3=py37h77fd288_0
  - xorg-libice==1.0.10=h516909a_0
  - tornado==6.1=py37h27cfd23_0
  - mengine==1=h14c3975_1
  - xorg-xproto==7.0.31=h27cfd23_1007
  - markupsafe==2.0.1=py37h27cfd23_0
  - xorg-xextproto==7.3.0=h14c3975_1002
  - libxkbcommon==1.0.3=he3ba5ed_0
  - numpy-base==1.19.1=py37hfa32c7d_0
  - libxcb==1.14=h7b6447c_0
  - sqlalchemy==1.4.23=py37h5e8e339_0
  - typed-ast==1.4.3=py37h7f8727e_1
  - libstdcxx-ng==11.1.0=h56837e0_8
  - mkl_fft==1.3.0=py37h54f3939_0
  - gettext==0.19.8.1=h0b5b191_1005
  - prody==1.10.8=py37h04863e7_0
  - zstd==1.4.9=haebb681_0
  - pysocks==1.7.1=py37_1
  - xorg-libxext==1.3.4=h516909a_0
  - psutil==5.8.0=py37h27cfd23_1
  - libogg==1.3.4=h7f98852_1
  - libcurl==7.78.0=h0b77cf5_0
  - gstreamer==1.18.5=h76c114f_0
  - pycairo==1.20.1=py37hfff247e_0
  - libllvm11==11.1.0=hf817b99_2
  - libsodium==1.0.18=h7b6447c_0
  - xorg-libsm==1.2.3=h84519dc_1000
  - libclang==11.1.0=default_ha53f305_1
  - mtz2ccp4_px==1.0=h9ac9557_3
  - brotlipy==0.7.0=py37h27cfd23_1003
  - cryptography==3.4.7=py37hd23ed53_0
  - libglib==2.68.4=h3e27bee_0
  - libuuid==2.32.1=h14c3975_1000
  - libev==4.33=h7b6447c_0
  - lzo==2.10=h7b6447c_2
  - pandas==1.0.3=py37h0da4684_1
  - greenlet==1.1.1=py37hcd2ae1e_0
  - numexpr==2.7.3=py37hb2eb853_0
  - libiconv==1.16=h516909a_0
  - libffi==3.3=h58526e2_2
  - hdf4==4.2.13=h3ca952b_2
  - pyrsistent==0.17.3=py37h7b6447c_0
  - nss==3.69=hb5efdd6_0
  - jedi==0.18.0=py37h06a4308_1
  - biopython==1.76=py37h516909a_0
  - libholoplaycore==0.1.0_rc4=1
  - libxml2==2.9.12=h72842e0_0
  - xorg-libxrender==0.9.10=h516909a_1002
  - blosc==1.21.0=h8c45485_0
  - pyqt-impl==5.12.3=py37he336c9b_7
  - libpng==1.6.37=hbc83047_0
  - openjpeg==2.4.0=h3ad879b_0
  - regex==2021.8.3=py37h7f8727e_0
  - libtiff==4.2.0=h85742a9_0
  - mysql-libs==8.0.25=h935591d_0
  - bzip2==1.0.8=h7b6447c_0
  - sqlite==3.36.0=hc218d9a_0
  - pyzmq==22.2.1=py37h295c915_1
  - readline==8.1=h27cfd23_0
  - libgcc-ng==11.1.0=hc902ee8_8
  - matplotlib-base==3.4.3=py37h1058ff1_0
  - statsmodels==0.12.2=py37h27cfd23_0
  - scikit-learn==0.24.2=py37ha9443f7_0
  - nbconvert==6.1.0=py37h06a4308_0
  - boost==1.74.0=py37h6dcda5c_3
  - jupyter_core==4.7.1=py37h06a4308_0
  - libxslt==1.1.33=h15afd5d_2
  - sip==4.19.8=py37hf484d3e_0
  - zlib==1.2.11=h7b6447c_3
  - freetype==2.10.4=h5ab3b9f_0
  - c-ares==1.17.1=h27cfd23_0
  - matplotlib==3.4.3=py37h89c1867_0
  - tk==8.6.10=hbc83047_0
  - libwebp-base==1.2.0=h27cfd23_0
  - mdtraj==1.9.3=py37h1c801a5_1
  - libedit==3.1.20210714=h7f8727e_0
  - rdkit==2021.03.5=py37h13c2175_0
  - pymol==2.4.0=py37h913975d_0
  - msgpack-python==1.0.2=py37hff7bd54_1
  - alsa-lib==1.2.3=h516909a_0
  - gst-plugins-base==1.18.5=hf529b03_0
  - hdf5==1.10.4=hb1b8bf9_0
  - apbs==1.5=h14c3975_3
  - ld_impl_linux-64==2.35.1=h7274673_9
  - boost-cpp==1.74.0=hc6e9bd1_3
  - libgfortran4==7.5.0=ha8ba4b0_17
  - openbabel==3.1.1=py37h6aa62a1_1
  - pcre==8.45=h295c915_0
  - et_xmlfile==1.1.0=py37h06a4308_0
  - glib==2.68.4=h9c3ff4c_0
  - pluggy==0.13.1=py37h06a4308_0
  - fontconfig==2.13.1=hba837de_1005
  - mkl==2020.2=256
  - libvorbis==1.3.7=h9c3ff4c_0
  - libpq==13.3=hd57d9b9_0
  - pyqtchart==5.12=py37he336c9b_7
  - pyqtwebengine==5.12.1=py37he336c9b_7
  - setuptools==52.0.0=py37h06a4308_0
  - libopenblas==0.3.13=h4367d64_0
  - kiwisolver==1.3.1=py37h2531618_0
  - libnghttp2==1.41.0=hf8bcb03_2
  - netcdf4==1.5.3=py37hbf33ddf_0
  - ca-certificates==2021.5.30=ha878542_0
  - terminado==0.9.4=py37h06a4308_0
  - libevent==2.1.10=hcdb4288_3
  - libgfortran-ng==7.5.0=ha8ba4b0_17
  - python==3.7.10=hffdb5ce_100_cpython
  - mkl-service==2.3.0=py37he8ac12f_0
  - mkl_random==1.1.1=py37h0573a6f_0
  - qt==5.12.9=hda022c4_4
  - openssl==1.1.1l=h7f98852_0

and the rest of all the libraries needed.
am using macOS Big sur 11.5.2

Is there anyway to workaround this?
thanks

`Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Collecting vina
Using cached https://pypi.tuna.tsinghua.edu.cn/packages/75/b2/1dad979aea28fcca8aa06832744aa1b62ab80cad08980115a580a4861b8d/vina-1.2.5.tar.gz (89 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [56 lines of output]
Version found 1.2.5 (from init.py)
running egg_info
creating vina.egg-info
writing vina.egg-info\PKG-INFO
writing dependency_links to vina.egg-info\dependency_links.txt
writing requirements to vina.egg-info\requires.txt
writing top-level names to vina.egg-info\top_level.txt
writing manifest file 'vina.egg-info\SOURCES.txt'
Boost library is not installed in this conda environment.
Traceback (most recent call last):
File "C:\Users\zhaol.conda\envs\jupyter_dock\lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 353, in
main()
File "C:\Users\zhaol.conda\envs\jupyter_dock\lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "C:\Users\zhaol.conda\envs\jupyter_dock\lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools\build_meta.py", line 325, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools\build_meta.py", line 295, in get_build_requires
self.run_setup()
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools\build_meta.py", line 311, in run_setup
exec(code, locals())
File "", line 346, in
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools_init.py", line 103, in setup
return distutils.core.setup(**attrs)
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools_distutils\core.py", line 185, in setup
return run_commands(dist)
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools_distutils\core.py", line 201, in run_commands
dist.run_commands()
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools_distutils\dist.py", line 969, in run_commands
self.run_command(cmd)
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools\dist.py", line 963, in run_command
super().run_command(command)
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command
cmd_obj.run()
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 321, in run
self.find_sources()
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 329, in find_sources
mm.run()
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 551, in run
self.add_defaults()
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 589, in add_defaults
sdist.add_defaults(self)
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools\command\sdist.py", line 112, in add_defaults
super().add_defaults()
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools_distutils\command\sdist.py", line 251, in add_defaults
self._add_defaults_ext()
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools_distutils\command\sdist.py", line 335, in _add_defaults_ext
build_ext = self.get_finalized_command('build_ext')
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools_distutils\cmd.py", line 305, in get_finalized_command
cmd_obj.ensure_finalized()
File "C:\Users\zhaol\AppData\Local\Temp\pip-build-env-dkc_93fy\overlay\Lib\site-packages\setuptools_distutils\cmd.py", line 111, in ensure_finalized
self.finalize_options()
File "", line 247, in finalize_options
ValueError: Boost library location was not found!
Directories searched: conda env, /usr/local/include and /usr/include.
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.`

When I run prepare-receptor in notebook 1 i got error:

So I open this file and see this path:
## Set some environment variables. ADS_ROOT="/mnt/d/Projects/Jupyter_Dock_devel/bin/ADFRsuite" export ADS_ROOT

I don't know what is it mean. Can you help me to fix it?

After reading your documentation I didn't find a script that will tell the docking software to bind a ligand in a specific area/residues desired. Can you help me in that?

Hi Angel,

First, I'd like to thank you for the wonderful work of setting this up. I'm a newcomer to the field of molecular docking, and I'm currently supervising a student in a molecular docking project. It'll make both our lives much easier!

The notebook for docking analysis is empty. Is it on purpose? Could you kindly provide a copy of a working notebook for docking analysis?

Best,

Marcos

Marcos Verissimo Alves
Departamento de Fisica - ICEx - Universidade Federal Fluminense
Volta Redonda, RJ - Brazil