wolberlab/pyrod

PyRod - Tracing water molecules in molecular dynamics simulations

pyrod's Issues

Other trajectory file formats that can be used in pyrod analysis

Hi!

I want to use pyrod for water pharmacopore modelling towards a multi-targeting drug design. In regards with this I have been running 10ns TIP4Ew simulation with amber14 force field for my targets. My question is will pyrod accept trajectory files generated in .pdb format from these simulation?
If not please. specify the file formats that are preferred for analysis through pyrod?

Unable to perform ROC analysis with helper script

Hi David,

I have used Pyrod to successfully generate a super pharmacophore. Afterwards, I selected potentially important features and generated a combinatorial library, which consists of 404 pharmacophores. I then tried using the Python helper script (library_roc_analysis.py) to perform an ROC analysis of the pharmacophores. Unfortunately, the script is not able to perform the analysis in my case. I am running the script on a Windows 10 computer with Python 3.10 and LigandScout 4.4.3

While the program is running, it continuously outputs the same message (Analyzing pharmacophore 0 of 404.). However, it does not make any progress. Here is the entire output after I interrupted it manually (otherwise it would continue running indefinitely):

The only file that gets created is roc_statistics.txt (with no results):
roc_statistics.txt

I have also tried running it through the command line in Windows, but it is also stuck at the start (Analyzing pharmacophore 0 of 404.). This is the output when cancelling the process:

Analyzing pharmacophore 0 of 404.Traceback (most recent call last):
File "C:\Users\martinl\Dropbox\PC\Desktop\SRC KNASE\PYROD_real\lck_last100frames\PYROD_HELPERSCRIPT\library_roc_analysis_LS_local.py", line 173, in
subprocess.run('{0} -q {1}.pml -d {2}:active -o {1}.sdf -l {1}.log -C {3} -M {4}'.format(
File "C:\Users\martinl\AppData\Local\Programs\Python\Python311\Lib\subprocess.py", line 548, in run
with Popen(*popenargs, **kwargs) as process:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\martinl\AppData\Local\Programs\Python\Python311\Lib\subprocess.py", line 1026, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "C:\Users\martinl\AppData\Local\Programs\Python\Python311\Lib\subprocess.py", line 1538, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
KeyboardInterrupt

Here are the files I used, including the python script:
test_files.zip

I am otherwise able to load the files into Ligandscout and perform an ROC analysis individually on each pharmacophore with no problems. I suspect there might be an issue with program versions, but I have not been able to locate the problem. I would greatly appreciate any help.

Thank you and regards,
Martin

data shape error

Hello developers:
I am trying to use pyrod with trajectory_analysis.cfg file.

The trajectory_analysis.cfg file fellows:
[directory]
directory:

[trajectory analysis parameters]
center: 48, 40, 35
edge lengths: 35, 35, 35
topology: /data/shiyu/tmp_pyrod/protein_UNK_prod.gro
trajectories: /data/shiyu/tmp_pyrod/protein_UNK_prod.xtc
first frame: 100
last frame: 200
step size: 1
metal names:
map formats: cns, xplor, kont
number of processes: 1
dmifs only: false

The error information appears on my screen:
Starting trajectory analysis.
Initializing grid.
Analyzing 101 frames from 1 trajectory.
Process Process-2:
Traceback (most recent call last):
File "/soft/anaconda3/2022.05/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/soft/anaconda3/2022.05/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/soft/AIDD/pyrod/pyrod_lib/trajectory.py", line 68, in trajectory_analysis
hd_atomids, hd_types, hd_hydrogen_atomid_lists = hd_selection(main_atoms)
File "/soft/AIDD/pyrod/pyrod_lib/trajectory_helper.py", line 85, in hd_selection
return np.array(atomids), np.array(types), np.array(hydrogen_atomid_lists)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (354,) + inhomogeneous part.
Processing results.
Traceback (most recent call last):
File "/soft/AIDD/pyrod/pyrod.py", line 130, in
dmif, partners = post_processing(results_list, total_number_of_frames)
File "/soft/AIDD/pyrod/pyrod_lib/grid.py", line 85, in post_processing

I don't know how to make it works.

Why generated 0 features from 5ns protein's trajectory

Dear David,

I recently used pyrod to explore the pharmacophore of the protein. This protein has been made into a 5ns MD using amber16, then the trajectory has been converted into a .nc format trajectory using cpptraj with autoimage parameter. When I performed "pyrod trajectory_pharmacophore_combo.cfg" (using the default parameters), the log shows that 0 features are generated. Due to I am a long-time user of ligandscout. I opened a * .pml file with ligandscout and only displayed Exclusion Volumes balls. Would you help me to solve this problem, many thanks.

Kindest regards

Jiyuan

errot

FileNotFoundError: [Errno 2] No such file or directory: '/hdd1/software/pyrod/pyrod/centroid/frames_0.csv'

Traceback (most recent call last):
File "pyrod.py", line 240, in
ensemble_to_centroid(topology, trajectories, output_name, directory, debugging)
File "/hdd1/software/pyrod/pyrod_lib/trajectory.py", line 578, in ensemble_to_centroid
with open('{}/frames_{}.csv'.format(output_directory, x), 'r') as csv:
FileNotFoundError: [Errno 2] No such file or directory: '/hdd1/software/pyrod/pyrod/centroid/frames_0.csv'

Generating 0 exclusion volumes and features for a 10ns protein

traj_Rv0827c.txt
Hi David,

I have been trying to attain a super pharmacophore for a 10ns simulation run in TIP4Pew water model. After the trajectory analysis, the program is resulting in generation of 0 exclusion volumes and thus, 0 features. Can you please help me out in troubleshooting? Here i am attaching the config file for your perusal.
Please help us out in figuring out the mistake, where we are going wrong.

Thanks and regards
Praveena K

Shift in the density maps

Hi,

I am inputting an AMBER trajectory into pyrod. The issue that I am facing is that the density maps shift a bit when I compare them to the water density that I calculated from the trajectory. I was wondering if you could tell me why this shift is happening and how I can fix it.

Thanks,
Sepehr

Issue encountered while running pyrod - Seeking guidance

Hi David,
I hope this message finds you well. Firstly, I would like to express my gratitude for developing the Pyrod on GitHub. I recently downloaded and attempted to reproduce the project, but encountered an issue that I need assistance with.I use gromacs for dynamics simulations to generate trajectories，

Problem Description:
While executing the project, I encountered the following error:
File "/home/ai/anaconda3/envs/pyrod/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/ai/anaconda3/envs/pyrod/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "trajectory.py", line 68, in trajectory_analysis
hd_atomids, hd_types, hd_hydrogen_atomid_lists = hd_selection(main_atoms)
File "pyrod/pyrod_lib/trajectory_helper.py", line 85, in hd_selection
return np.array(atomids), np.array(types), np.array(hydrogen_atomid_lists)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (294,) + inhomogeneous part.
Processing results.
Traceback (most recent call last):
File "pyrod.py", line 130, in
dmif, partners = post_processing(results_list, total_number_of_frames)
File "grid.py", line 85, in post_processing
dmif = results[0][0]
IndexError: list index out of range
Expected assistance:
I would greatly appreciate any guidance or suggestions you can provide to help me overcome this problem. If there are specific changes I need to make in order to successfully execute the project, please let me know. Additionally, if there is any further information or logs that would be helpful for you in troubleshooting this issue, please advise.

Thank you for your time and support. Your expertise and guidance will be immensely valuable to me. Please feel free to reach out to me if you require any additional information or have any further questions.

Best regards,

centroid.cfg file

Can you share a centroid.cfg file for a specific target

Issue encountered while running pyrod - Seeking guidance

Hi David,
I hope this message finds you well. Firstly, I would like to express my gratitude for developing the Pyrod on GitHub. I recently downloaded and attempted to reproduce the project, but encountered an issue that I need assistance with.I use gromacs for dynamics simulations to generate trajectories，

Problem Description:
While executing the project, I encountered the following error:
File "/home/ai/anaconda3/envs/pyrod/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/ai/anaconda3/envs/pyrod/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "trajectory.py", line 68, in trajectory_analysis
hd_atomids, hd_types, hd_hydrogen_atomid_lists = hd_selection(main_atoms)
File "pyrod/pyrod_lib/trajectory_helper.py", line 85, in hd_selection
return np.array(atomids), np.array(types), np.array(hydrogen_atomid_lists)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (294,) + inhomogeneous part.
Processing results.
Traceback (most recent call last):
File "pyrod.py", line 130, in
dmif, partners = post_processing(results_list, total_number_of_frames)
File "grid.py", line 85, in post_processing
dmif = results[0][0]
IndexError: list index out of range
Expected assistance:
I would greatly appreciate any guidance or suggestions you can provide to help me overcome this problem. If there are specific changes I need to make in order to successfully execute the project, please let me know. Additionally, if there is any further information or logs that would be helpful for you in troubleshooting this issue, please advise.

Thank you for your time and support. Your expertise and guidance will be immensely valuable to me. Please feel free to reach out to me if you require any additional information or have any further questions.

Best regards,

How to determine the features obtained by pyrod could be used for virtual screening

Dear David,

I have obtained the 180 features by pyrod. Would ask you how to determine the features obtained by pyrod could be used for virtual screening. I also attacheed the .pml and the top file in Pyrod_Test.zip
Pyrod_Test.zip
. Many thanks.

Kindest regards

Jiyuan