search

paiardin / DockingPie

A Consensus Docking Plugin for PyMOL
GNU General Public License v3.0
63 stars 13 forks source link

generate ligand is seemingly busted for me, please help resolve asap #5

Closed jhh1492 closed 5 months ago

jhh1492 commented 8 months ago

PyMOL>fetch 7roq TITLE Alternative Structure of Human ABCA1 ExecutiveLoad-Detail: Detected mmCIF CmdLoad: "./7roq.cif" loaded as "7roq". CmdLoad: "/home/scientist/Downloads/Conformer3D_COMPOUND_CID_4912-2.sdf" loaded as "Conformer3D_COMPOUND_CID_4912-2". Executive: object "temp_obj" created. Executive: object temp_obj created. Traceback (most recent call last): File "/home/scientist/.pymol/startup/DockingPie1/lib/docking_program_main/docking_program_gui/tabs.py", line 2188, in generate_ligand_func is_receptor = False) File "/home/scientist/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 284, in init self.generate_receptor() File "/home/scientist/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 306, in generate_receptor self.generate_checked_object() File "/home/scientist/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 412, in generate_checked_object os.rename(old_name, new_name) FileNotFoundError: [Errno 2] No such file or directory: 'Conformer3D_COMPOUND_CID_4912-2.pdbqt' -> '01_Conformer3D-COMPOUND-CID-4912-2_Vina.pdbqt' INFO and CONTACTS Copyright (C): 2022 Serena Rosignoli, Alessandro Paiardini Contacts: serena.rosignoli@uniroma1.it, alessandro.paiardini@uniroma1.it For information on DockingPie 1.0 visit: https://github.com/paiardin/DockingPie

DockingPie

PyMOL

Python

Operating system

Python libs

SerenaRosi commented 8 months ago

Please double-check that everything is properly configured in DockingPie. Section 3 in User's guide.

Best, Serena

jhh1492 commented 8 months ago

Traceback (most recent call last): File "/home/scientist/pymol/DockingPie1/lib/docking_program_main/config/prepare_ligand4.py", line 236, in attach_singletons=attach_singletons) File "/home/scientist/pymol/DockingPie1/lib/docking_program_main/config/AutoDockTools/AutoDockTools/MoleculePreparation.py", line 1032, in init detect_bonds_between_cycles=detect_bonds_between_cycles) File "/home/scientist/pymol/DockingPie1/lib/docking_program_main/config/AutoDockTools/AutoDockTools/MoleculePreparation.py", line 803, in init self.aromCs = self.ACM.setAromaticCarbons(molecule) File "/home/scientist/pymol/DockingPie1/lib/docking_program_main/config/AutoDockTools/AutoDockTools/atomTypeTools.py", line 225, in setAromaticCarbons assert len(molecule.allAtoms.bonds[0]) AssertionError Traceback (most recent call last): File "/home/scientist/pymol/DockingPie1/lib/docking_program_main/docking_program_gui/tabs.py", line 2206, in generate_ligand_func is_receptor = False) File "/home/scientist/pymol/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 284, in init self.generate_receptor() File "/home/scientist/pymol/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 306, in generate_receptor self.generate_checked_object() File "/home/scientist/pymol/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 412, in generate_checked_object os.rename(old_name, new_name) FileNotFoundError: [Errno 2] No such file or directory: 'Conformer3D_COMPOUND_CID_4912-2.pdbqt' -> '01_Conformer3D-COMPOUND-CID-4912-2_Smina.pdbqt'

uninstalled plugin and reinstalled it, still issues whenever using generet receptor or genereate ligand??

jhh1492 commented 8 months ago

DockingPie

PyMOL

Python

Operating system

Python libs

jhh1492 commented 8 months ago

Python installed, please wait for the rest of ADFRsuite to be installed ./install.sh: 1: /home/scientist/pymol/DockingPie1/lib/docking_program_main/config/external_tools_linux/ADFRsuite_x86_64Linux_1.0/Tools/archosv: Permission denied Running /home/scientist/pymol/DockingPie1/lib/docking_program_main/config/external_tools_linux/ADFRsuite_x86_64Linux_1.0/bin/python2.7 Tools/install.py
Installing ADSPackages Installing files from CCSBpckgs .tar.gz Installing files from ThirdPartyPacks .tar.gz Creating scripts current directory: /home/scientist/pymol/DockingPie1/lib/docking_program_main/config/external_tools_linux/ADFRsuite_x86_64Linux_1.0

jhh1492 commented 8 months ago

could this be causing all of these issues? why would adfr not installing affect all others? whats best bet for fixing? this occurs every time i uninstall and redownload, can't do a sudo command because it's already installed each time I opened plugin

jhh1492 commented 8 months ago

I downloaded a new conda, installed pymol 3.0, and reinstalled the application and it is still giving this error, the recptor seemingly does fine, the ligan it loads it as "temp object" that is missing many atoms, when i hit generate i get below File "/home/scientist/anaconda3/envs/pymol/lib/python3.11/site-packages/pmg_tk/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 412, in generate_checked_object os.rename(old_name, new_name) FileNotFoundError: [Errno 2] No such file or directory: 'Probucol.pdbqt' -> '02_Probucol_Vina.pdbqt'

again new conda, new pymol, new everything to try and get this plug in to work...

SerenaRosi commented 8 months ago

I believe that you are pointing different type of errors.

More over, DockingPie has not been tested for PyMOL 3.0 yet, keeping downloading and re-installing won't solve any issue.

jhh1492 commented 8 months ago

I am not uninstalling and reinstalling the same thing. I have tried multiple versions and always that same installation error from yalls autoadd button. I have tried open source 2.4,2.5 and incentive 2.4 (multiple versions tried) ,2.5.2 and more, so have tested ones listed as approved/tested by you guys. Every single time I get this error (see below). I am following you instructions to the tee for both incentive and open-source.

(inpymol) scientist@OptiPlex-9020:~$ ./install.sh: 1: /home/scientist/anaconda3/envs/openpie/lib/python3.11/site-packages/pmg_tk/startup/DockingPie1/lib/docking_program_main/config/external_tools_linux/ADFRsuite_x86_64Linux_1.0/Tools/archosv: Permission denied

If you would like, to prove this is not user error, I will download whichever incentive and open source pymol version you prefer, screen record the installation process, and send your way.

SerenaRosi commented 8 months ago

Please, send a screenshot of the CONFIGURATION tab.

jhh1492 commented 8 months ago

Bb.zip

jhh1492 commented 8 months ago

IMG_5408 IMG_5407

jhh1492 commented 8 months ago

That is what happens for all versions, says everything got downloaded fine from the plugin, only in one line of terminal output do you see the perms denied

jhh1492 commented 8 months ago

mabe the channel priority from conda messes it up? or ADFR license is up? no clue just trying to help in anyway possible

SerenaRosi commented 7 months ago

We have recently become aware of unexpected issues reported by multiple users, which we believe may be stemming from recent updates to PyMOL and/or other external libraries. These issues were not encountered previously and are likely a result of incompatibilities introduced by these updates. As a result, we have temporarily placed DockingPie under maintenance mode while we work diligently to resolve these issues. Once these issues are resolved, we will promptly update our GitHub page to inform users of the fixes and any necessary instructions. Thank you for your understanding and cooperation during this period.

Best, Serena

jhh1492 commented 7 months ago

No worries this stuff in tough in general, implementing pymol and conda for our ease only complicates things. If you want an external Beta tester let me know, can test any version of either main dependency. Appreciative of yalls hard work! All the best

paiardin commented 5 months ago

Hi, we have just released an updated version of DockingPie, which should fix this issue. Let us know!