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This is not an issue but a question. I just need the alpha shape, how can I extract it? Thank you in advance.

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Dear maintainer, i encounter a problem using PACKMAN

Client Used : PACKMAN GUI provided through pip installation

Error encountered with PDB :

Error encountered with CIF :


In both case, i don't obtain any result

Parameters used on the GUI : default

At first i thought it was the PDB or CIF file i was providing that was with a wrong formatting, so i tried various mean for saving my original file using different software (pdb_tools, pdb2cif, pymol, vmd..).
I also tried to split my structure and kept one monomer, but it doesn't work either.

I tried to use a similar structure (size wise) in CIF, it seemed to work.

So i come in your direction seeking help

Kind Regards

Insert this before the line to make the rotation code work.

self.__AllAtoms_inverse = { self.__AllAtoms[i]:i for i in self.__AllAtoms }

When predicting hinges on the backbone, it sometimes fails due to infinite lengths. Is this caused by unconnected nodes? Can it be fixed by changing the alpha value? Should there be something in the code that handles this issue instead of crashing?

Migrate to pytest using https://pypi.org/project/nose2pytest

============================= test session starts ==============================
platform linux -- Python 3.9.16, pytest-7.2.2, pluggy-1.0.0
rootdir: /home/runner/work/PACKMAN/PACKMAN
collected 15 items

packman/tests/anm/test_anm.py ..                                         [ 13%]
packman/tests/dci/test_dci.py .                                          [ 20%]
packman/tests/entropy/test_entropy.py .                                  [ 26%]
packman/tests/geometry/test_geometry.py ..                               [ 40%]
packman/tests/gnm/test_gnm.py .                                          [ 46%]
packman/tests/molecule/test_molecule.py ........                         [100%]

=============================== warnings summary ===============================
packman/tests/geometry/test_geometry.py::TestGeometry::test_AlphaShape
  /home/runner/work/PACKMAN/PACKMAN/packman/tests/geometry/test_geometry.py:22: DeprecationWarning: Delaunay attribute 'vertices' is deprecated in favour of 'simplices' and will be removed in Scipy 1.11.0.
    self.assertIsInstance( geometry.AlphaShape( [j for i in self.mol[0].get_backbone() for j in i], 4 )[0][0], molecule.Atom )

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================== 15 passed, 1 warning in 6.09s =========================

packman.molecule.load_structure() can not figure out if the file is cif or pdb while working with the biological assemblies.

Assign 'x' instead of 'X'

Will be fixed in the next major release.

FAILED packman/tests/utilities/test_utilities.py::Test_Utilities::test_superimpose - AttributeError: np.mat was removed in the NumPy 2.0 release. Use np.asmatrix instead.

Title says it all

When the path in your .hng file contains any whitespace, the line=i.strip().split() in utilities.load_hinge splits the line into a list that is longer than 3. Afterwards, the HNGinfo[ line[0]+'_'+line[1] ]=[float(j) for j in line[2].split(':')] becomes irrelevant because the first, second, and third elements of line are not as intended

Hello,

I am trying to calculate the entropy of a pdb structure. I uploaded it to the Packing Entropy server, and it said

Job Status: SUCCESS
ERROR:root:Please check the parameters.

I opened the log.txt which said the same thing, and the output.txt did not contain anything. I did not change any of the default parameters, and did not use any chains in the entropy calculation. Considering the error message says to check the parameters, which are all the default parameters, do you know what may be wrong? I have attached my pdb file as a zip file. Thanks!

Best,
Christian
subset.zip

• When we rotate the C or N terminal based on the size, we do achieve good computational efficiency but the axis of rotation ($\vec{e_a}$) changes and the calculations are not right if the angles calculated are from N to C terminal.
• The rotational component should depend on the first neighbor (neighbor of first atoms parsed as an argument for the bond) being on the rotating side.