Question: Parsing Pdb (Protein Data Bank) Files With Python
2
gravatar for saurabhshelar
2.2 years ago by
saurabhshelar20 wrote:

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 dont know the answer.
I tried found some modules like sequtils, protienparam but it dont do such things.
so I researched first and then posted so kindly do not downvote.

Thanks in advance.

ADD COMMENTlink modified 7 weeks ago by a.polo8880 • written 2.2 years ago by saurabhshelar20
1

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

ADD REPLYlink written 2.2 years ago by Neilfws44k

Did you see pdbsum?

ADD REPLYlink written 2.2 years ago by Pappu1.4k
1
gravatar for Neilfws
2.2 years ago by
Neilfws44k
Sydney, Australia
Neilfws44k wrote:

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.

ADD COMMENTlink written 2.2 years ago by Neilfws44k
0
gravatar for quentin.delettre
2.2 years ago by
France
quentin.delettre390 wrote:

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.

ADD COMMENTlink written 2.2 years ago by quentin.delettre390
0
gravatar for a.polo88
7 weeks ago by
a.polo8880
Italy
a.polo8880 wrote:

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 dont 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.

ADD COMMENTlink written 7 weeks ago by a.polo8880
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