CSM installation issue

[Megha Parashar]

Dear Prof. Inbal Tuvi-Arad

I am facing some issues while installing CSM via github code.

This is the error I am getting:
cc1plus: fatal error: csm/CPP_wrapper/fast.cpp: No such file or directory
compilation terminated.

And I noticed indeed there is no file that goes by name fast.cpp in csm/CPP_wrapper directory.

Can you please help me with this?

Thank you for your assistance.

Best Regards,

Megha

[Inbal Tuvi-Arad]

 

Dear Megha,

Thank you for reaching out.

Unfortunately, direct installation of the CSM is very tricky.

Please try to install the code using docker. There is a link on the github website.

 

All the best,

Inbal

 

 

___________________________

Prof. Inbal Tuvi-Arad

Department of Natural Sciences

The Open University of Israel

1 University Road., POB 808

Raanana 4353701

ISRAEL

Tel: 09-7781773

Fax: 09-7780661

Email: inb...@openu.ac.il

http://www.openu.ac.il/en/personalsites/InbalTuviArad.aspx

https://telem.openu.ac.il/symmetry/

http://csm.ouproj.org.il/

___________________________

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[Megha Parashar]

Dear Prof. Inbal Tuvi-Arad

Thanks for your reply, I was able to install it using pip and it is running fine with one frame coordinate file. However, I could not figure out how to supply entire trajectory to it and get the values per frame. I tried following using MDAnalysis:

u = mda.Universe('../aromatic_core.pdb','../aromatic_core.trr', in_memory=True)
#u = mda.Universe('resid5_core.mol2', in_memory=True)
#sel = u.select_atoms("resid 5 and name C1 C2 C3 C4 C5 C6 C7 C8 C9 N1 N2 N3 O1 O2 O3")
#sel = u.select_atoms("name C1 C2 C3 C4 C5 C6 C7 O8 N9 C10 O11 N12 C13 O14 N15")
for ts in u.trajectory:
    sel = u.select_atoms("name C1 C2 C3 C4 C5 C6 C7 O8 N9 C10 O11 N12 C13 O14 N15")
    coords = sel.positions
    if np.isnan(coords).any():
        continue  # skip frame if invalid

    symbols = [a.name[0] for a in sel.atoms]
    print(symbols)
    print(coords)
    atoms = [csm.molecule.atom.Atom(index=i, symbol=s, pos=p) for i, (s, p) in enumerate(zip(symbols, coords))]
    print(atoms)
    for atom in atoms:
        print(f"  Index: {atom.index}, Sym: {atom.symbol}, Pos: {atom.pos}")
    mol = csm.molecule.molecule.Molecule(atoms=atoms)
    #print(csm.molecule.atom.Atom(index=i, symbol=s, pos=p) for i, (s, p) in enumerate(zip(symbols, coords)))
    #print(mol)
    op = Operation("C3")  # Symmetry group C3
    calculation = Exact(op, mol)
    print(f"Frame {ts.frame}: CSM = {calculation.calculate()}")

However, I am getting this error: raise CSMValueError("Failed to calculate a csm value for %s %d" % (op_type, op_order), best_csm)
csm.calculations.exact_calculations.CSMValueError: Failed to calculate a csm value for CN 3

I could not figure out how to get the values per frame, can you please help me with it?

Thank you for your time.

Best regards,

Megha

[Megha Parashar]

Dear Prof. Inbal Tuvi-Arad

I was able to install it using pip after some failures.

It is working fine for one frame, but I could not figure out how to provide the inputs for a trajectory and get the results for each frame, can you please help me with it.

Thank you so much for your time.

Best Regards,

Megha

On Sunday, 4 May 2025 at 22:45:20 UTC+5:30 Inbal Tuvi-Arad wrote:

[Megha Parashar]

Dear Prof. Inbal Tuvi-Arad

Thanks for your reply.

I was able to install using pip, faced some issues, but it is running.

However, I have one new issue, how can I use it on a trajectory?

I tried supplying separately the elements and their coordinates information but unable to successfully do it.

Can you please help me here?

Once again thank you for your time

Best Regards,

Megha

On Sunday, 4 May 2025 at 22:45:20 UTC+5:30 Inbal Tuvi-Arad wrote:

[Continuous Symmetry Measures (CSM)]

Dear Megha,
I'm glad you managed with the installation. If there are additional instructions you would recommend us to add to the Github website - please let me know.
To run the CSM for a trajectory, you need to have both the coordinates of each molecule along the path, and the connectivity between them. This could be a separate file, in a format similar tot he CONECT section in  pdb files.
alternatively, use the babel-bond flag to let Openbabel decide how to connect the atoms.

All the best,
Inbal