[Bug]: error in computing electrostatics

avilella commented 1 month ago

Operating System

Unix (e.g., Ubuntu 20.04)

Version

2.2.0

Python Version (optional)

3.10.7

Python Virtual Environment

Not using a virtual environment

Execution Environment

Encapsulated environment from the SURFMAP Docker image

Bug Description

I expected the successful calculation, it gives an error and no output instead.

Steps to Reproduce

surfmap -pdb /bfx_share1/quick_share/alphafold2/outputs/d6/d6472024a556ae23f7ecd8e0b5390ab7/d6472024a556ae23f7ecd8e0b5390ab7.esm.pdb -tomap electrostatics --docker

Error is:

SURFACE MAPPING OF THE ELECTROSTATICS PROPERTY
Step 1: computing a shell around the protein surface
Step 2: computing electrostatics potential
Traceback (most recent call last):
  File "/surfmap/.env/bin/surfmap", line 33, in <module>
    sys.exit(load_entry_point('surfmap', 'console_scripts', 'surfmap')())
  File "/surfmap/surfmap/bin/surfmap.py", line 63, in main
    surfmap_local(params=params)
  File "/surfmap/surfmap/bin/surfmap.py", line 18, in surfmap_local
    surfmap_from_pdb(params=params)
  File "/surfmap/surfmap/lib/core.py", line 180, in surfmap_from_pdb
    shell = run_compute_electrostatics(pdb_filename=params.pdbarg, csv_filename=csv_coords, force_field=params.force_field, pqr_filename=params.pqr, out_dir=outdir_elec)
  File "/surfmap/surfmap/tools/compute_electrostatics.py", line 130, in run
    edit_inputgen(inputgen_file=outfile_in, pqrfile=outfile_pqr)
  File "/surfmap/surfmap/tools/compute_electrostatics.py", line 58, in edit_inputgen
    with open(inputgen_file, 'r') as _file :
FileNotFoundError: [Errno 2] No such file or directory: '/home/surfmap/output/tmp-elec/d6472024a556ae23f7ecd8e0b5390ab7.esm.in'

Relevant Log Output

No response

Additional context (optional)

No response

Confirmation

[X] I confirm I have searched for duplicates and reviewed the relevant documentation.

nchenche commented 4 weeks ago

Hi avilella,

It sounds like the issue is coming from the double extension in your input file: d6472024a556ae23f7ecd8e0b5390ab7.esm.pdb.

I have just tried renaming an input file to add it a double extension like you have. From the original file (foo.pdb), electrostatics computation was ok, however with the double extension (foo.esm.pdb) i had the same issue you have encountered.

So to resolve your issue, you'll just have to rename you input file in order to remove the '.esm' part : d6472024a556ae23f7ecd8e0b5390ab7.pdb

Sorry for the inconvenience, i am gonna try to fix that bug as soon as possible.

Thank you for using SURFMAP and for highlighting a bug we've never met before.

avilella commented 4 weeks ago

Voila! Problem solved.

i2bc / SURFMAP