sulcgroup / oxdna_analysis_tools Goto Github PK

Greetings all,

I had a general query, is there a way to calculate hydrogen bond energy for my system? I'd be very grateful if anyone could point me to a helpful resource.

Thanks!
Prateek

I run oat output_bonds inputMD trajectory_trap.dat > energy2.txt.
And I find each term of energy seems no change when I increase temperature. It is strange. Then I change the Temperature in input file to 100C and run it again. And I found there is also no difference, meaning the code does not read the Temperature.
And if I change the salt concentration, the energy can change reasonably.

Thanks a lot for the help with this script！！！

but when the running structure is very large, this error occurs, how to fix it?

The error is as follows：
python generate_force.py -o external_forces.txt input 1.dat
Traceback (most recent call last):
File "generate_force.py", line 41, in
mysystem = r._get_system()
File "/home/wangyue/Software/oxdna_analysis_tools_old/UTILS/readers.py", line 177, in _get_system
return self._read(only_strand_ends=only_strand_ends, skip=False)
File "/home/wangyue/Software/oxdna_analysis_tools_old/UTILS/readers.py", line 123, in _read
bb = b
UnboundLocalError: local variable 'b' referenced before assignment

Greetings!

When I try to invoke output_bonds I get: ModuleNotFoundError: No module named 'UTILS'. Please help me in this matter. I have attached a picture of one such call I made.

I have added the DNAnalysis path to the config.py file and many other scripts (though not all) are working fine. For eg. compute_mean, duplex_angle_finder, & backbone_flexibility.

Thanking you,
Prateek

when i am trieng to import from oxDNA_analysis_tools i get this error: ModuleNotFoundError: No module named 'oxDNA_analysis_tools.UTILS.get_confs' Note: oxdna kernal is activated, i tried to pip install oxDNA_analysis_tools but it was already there, Also, i compiled file "get_confs" again and appended its path to code but the problem persists. "oat config" output: (oxdna) [sutei081@nesh-fe3 medhi_gen_algo]$ oat config
INFO: oxDNA_analysis_tools version: 2.2.1
INFO: running config.py installed at: /gxfs_home/cau/sutei081/miniconda3/envs/oxdna/lib/python3.9/site-packages/oxDNA_analysis_tools/config.py
INFO: Python version: 3.9.17
INFO: Package Numpy found. Version: 1.25.2
INFO: Package MatPlotLib found. Version: 3.7.2
INFO: Package SciKit-Learn found. Version: 1.3.0
INFO: Package oxpy found. Version: 3.3
INFO: No dependency issues found.

INFO: Analyses will be computed in chunks of 20 configurations at a time
INFO: You can modify this number by running oat config -n , which will be persistent between analyses.
(oxdna) [sutei081@nesh-fe3 medhi_gen_algo]$

Hello!

How do we update the tools? By re-running the pip install oxDNA-analysis-tools command? When I do that I get the following error:

error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\VC\\BIN\\x86_amd64\\cl.exe' failed with exit code 3221225595
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for oxDNA-analysis-tools
Failed to build oxDNA-analysis-tools
ERROR: Could not build wheels for oxDNA-analysis-tools, which is required to install pyproject.toml-based projects

I couldn't find any results for this particular exit code. Please help me out with this. Thanks for your time and for the excellent tools!

Warm Regards
Prateek

Greetings,

When I try to invoke forces2pairs script it shows UnboundLocalError. I have attached the screenshot; please have a look. Thank you for your time and consideration.

Warm Regards
Prateek

When we use 'distance.py' to calculate the distance between two particles, we are actually calculating the distance between the backbone particles (sugares) or alternating nucleotides?

Hi all,
thank you in advance for considering this request. I think it is a real trivial issue, but I wasn't able to solve it yet. I successfully installed the oxdna_analysis_tools via pip. As described in https://github.com/lorenzo-rovigatti/oxDNA, I installed the oxpy package via:

git clone https://github.com/lorenzo-rovigatti/oxDNA.git
cd oxDNA
git checkout oxpy --
pip install .

oxDNA was already working well, but I had troubles in using the incorporated UTILS, which gave me syntax errors by calling the python interpret. Now I'm obtaining errors if I try to execute some tools, and they seem to be linked to the oxpy package. As an example, executing oat generate_force some_input last_conf.dat gives me:

INFO: No outfile name provided, defaulting to "forces.txt"
WARNING: Overwriting key `trajectory_file' (`trajectory.dat' to `last_conf.dat')
Traceback (most recent call last):
  File "/home/simone/anaconda3/bin/oat", line 10, in <module>
    sys.exit(main())
  File "/home/simone/anaconda3/lib/python3.7/site-packages/oxDNA_analysis_tools/entry.py", line 24, in main
    to_call.main()
  File "/home/simone/anaconda3/lib/python3.7/site-packages/oxDNA_analysis_tools/generate_force.py", line 46, in main
    if (not inp["use_average_seq"] or inp.get_bool("use_average_seq")) and "RNA" in inp["interaction_type"]:
AttributeError: 'oxpy.core.InputFile' object has no attribute 'get_bool'

These errors do not occur in other tools such as mean, align, backbone_flexibility or plot_energy. Are these errors due to missing dependencies?

Thank you in advance,
best regards,

Simone

Good day, all!

Regarding the output of the output_bonds script, I wanted to know on what basis two particles are chosen to display their various interacting parameters (such as Hydrogen Bonding energy).

I ask this because, in certain cases, I don't see records of a particular pair of particles' in all the given frames of a simulation even though they are closely spaced and look to me to be bonded throughout.

And even if, at certain instances they are not bonded, I'd expect a record stating HB = 0 like it happens in some cases.

So, how does the script decide which pairs of particle interactions to include in the record for each frame/configuration?

Thanks a lot for your time and consideration and for these excellent tools!

Warm Regards
Prateek

Hi!

These tools are great!

I tried them with a small system and got a crash here, it should probably be 0 by default.

Cheers

Erik

Hi Guys,

Great tools,

I try to run the mean structure on a windows machine but get issues with "from os import O_NONBLOCK" , I dont really understand what it does but it seems to be unix only :/

Is there some alternative solution to this ?

Cheers

Erik B

Hello!

I am running the output bonds script and it shows the following error:
All spawned, waiting for results

WARNING: Overwriting key `trajectory_file' (`MDJohnofTweezer_Salt1_trajectory.dat' to `MDJohnofTweezer_Salt1_trajectory.dat')
WARNING: Overwriting key `trajectory_file' (`MDJohnofTweezer_Salt1_trajectory.dat' to `MDJohnofTweezer_Salt1_trajectory.dat')
WARNING: Overwriting key `trajectory_file' (`MDJohnofTweezer_Salt1_trajectory.dat' to `MDJohnofTweezer_Salt1_trajectory.dat')
WARNING: Overwriting key `trajectory_file' (`MDJohnofTweezer_Salt1_trajectory.dat' to `MDJohnofTweezer_Salt1_trajectory.dat')
WARNING: Overwriting key `trajectory_file' (`MDJohnofTweezer_Salt1_trajectory.dat' to `MDJohnofTweezer_Salt1_trajectory.dat')
WARNING: Overwriting key `trajectory_file' (`MDJohnofTweezer_Salt1_trajectory.dat' to `MDJohnofTweezer_Salt1_trajectory.dat')
WARNING: Overwriting key `trajectory_file' (`MDJohnofTweezer_Salt1_trajectory.dat' to `MDJohnofTweezer_Salt1_trajectory.dat')
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/usr/lib/python3.8/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/home/prateek/.local/lib/python3.8/site-packages/oxDNA_analysis_tools/output_bonds.py", line 26, in compute
    if (not inp["use_average_seq"] or inp.get_bool("use_average_seq")) and "RNA" in inp["interaction_type"]:
oxpy.core.OxDNAError: Key `use_average_seq' not found
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/prateek/.local/bin/oat", line 8, in <module>
    sys.exit(main())
  File "/home/prateek/.local/lib/python3.8/site-packages/oxDNA_analysis_tools/entry.py", line 24, in main
    to_call.main()
  File "/home/prateek/.local/lib/python3.8/site-packages/oxDNA_analysis_tools/output_bonds.py", line 153, in main
    energies = output_bonds(traj_info, top_info, inputfile, visualize, conversion_factor, ncpus)
  File "/home/prateek/.local/lib/python3.8/site-packages/oxDNA_analysis_tools/output_bonds.py", line 97, in output_bonds
    oat_multiprocesser(traj_info.nconfs, ncpus, compute, callback, ctx)
  File "/home/prateek/.local/lib/python3.8/site-packages/oxDNA_analysis_tools/UTILS/oat_multiprocesser.py", line 29, in oat_multiprocesser
    callback(i, r.get())
  File "/usr/lib/python3.8/multiprocessing/pool.py", line 771, in get
    raise self._value
oxpy.core.OxDNAError: Key `use_average_seq' not found

I added the use_average_seq = 0 parameter to my input file and then reran it. This gave a different error. (Also, what are those warnings? Should I be worried about those? )

Traceback (most recent call last):
  File "/usr/lib/python3.8/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/home/prateek/.local/lib/python3.8/site-packages/oxDNA_analysis_tools/output_bonds.py", line 26, in compute
    if (not inp["use_average_seq"] or inp.get_bool("use_average_seq")) and "RNA" in inp["interaction_type"]:
AttributeError: 'oxpy.core.InputFile' object has no attribute 'get_bool'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/prateek/.local/bin/oat", line 8, in <module>
    sys.exit(main())
  File "/home/prateek/.local/lib/python3.8/site-packages/oxDNA_analysis_tools/entry.py", line 24, in main
    to_call.main()
  File "/home/prateek/.local/lib/python3.8/site-packages/oxDNA_analysis_tools/output_bonds.py", line 153, in main
    energies = output_bonds(traj_info, top_info, inputfile, visualize, conversion_factor, ncpus)
  File "/home/prateek/.local/lib/python3.8/site-packages/oxDNA_analysis_tools/output_bonds.py", line 97, in output_bonds
    oat_multiprocesser(traj_info.nconfs, ncpus, compute, callback, ctx)
  File "/home/prateek/.local/lib/python3.8/site-packages/oxDNA_analysis_tools/UTILS/oat_multiprocesser.py", line 29, in oat_multiprocesser
    callback(i, r.get())
  File "/usr/lib/python3.8/multiprocessing/pool.py", line 771, in get
    raise self._value
AttributeError: 'oxpy.core.InputFile' object has no attribute 'get_bool'

Many thanks for looking into this.

Warm Regards
Prateek

INFO: No outfile name provided, defaulting to "forces.txt"
INFO: Analyze the output...
Traceback (most recent call last):
File "generate_force.py", line 49, in
if i[0] == '#':
IndexError: string index out of range

How to solve!!!!
thankkkkkkks!!!!!!