Parsing Pdb (Protein Data Bank) Files With Python

Question

[saurabhshelar]

Hi,

I am working on bio project. I have .pdb (protein data bank) file which contains information about the molecule.

I want to find out:

1. molecular weight.
2. H bond donor.
3. H bond acceptor.
4. LogP.
5. Refractivity.

Is there any module in python which can deal with .pdb file in finding this? If not then can anyone please let me know how can I do the same?

Please do not downvote if you don't know the answer. I tried found some modules like sequtils, protienparam but they don't do such things. So I researched first and then posted so kindly do not downvote.

Thanks in advance

[Neilfws]

Don't worry, we're not allowed to downvote ;)

[Pappu]

Did you see pdbsum?

Answer 1

[Neilfws]

There's Bio.PDB in BioPython and some good documentation (PDF).

I'm unsure what you mean by LogP and I don't recall ever seeing a property called "refractivity" in a PDB file.

Answer 2

[quentin.delettre]

If you are considering small molecules in PDB format, just convert them to an adapted format like sdf or mol2. From here you will be able to use some tools like chemaxon marvin/calcx in a bash script or openbabel in python.

Answer 3

[a.polo88]

I think that all this information are present in the information content on pdb. A out the H-bonds you can use HBPLUS for the other ones I don't know but a think that also a graphical program is useful! Pymol or insightII! About python I don't know any packages. Perhaps other persons can help you.