[Biopython] Editing Structure and Replacing Coordinates with new set

[Souparno Adhikary]

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Regards,

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.

On Tue, May 23, 2017 at 4:01 PM, Patrick Kunzmann <padix.kleber at gmail.com>
wrote:

> I am currently working on a subpackage for Biopython (called
> Bio.Structure), that converts a Bio.PDB.Model.Model into a numpy array
> containing coordinates and annotations for doing easily efficient
> calculations (for example calculating average structure). This array can be
> converted back into a Bio.PDB.Model.Model and than saved as PDB file using
> PDBIO(). Currently docstrings and code comments are missing, so I will
> contribute this code only in a few days, but you can check out the source
> code at https://github.com/padix-key/biopython/tree/numpy-structure.
>
> Best regards,
>
> Patrick Kunzmann
>
> Am 23.05.2017 um 12:04 schrieb Souparno Adhikary:
>
> I want to calculate the average structure from multiple frames in a pdb
> file and save it to another pdb file.
>
> I wrote the code to calculate the average co-ordinates successfully like
> below:
>
> #!/usr/bin/python
>
> from Bio.PDB.PDBParser import PDBParser
>
> import numpy as np
>
> parser=PDBParser(PERMISSIVE=1)
>
> structure_id="mode_7"
> filename="mode_7.pdb"
> structure=parser.get_structure(structure_id, filename)
> model1=structure[0]
> s=(124,3)
> newc=np.zeros(s,dtype=np.float32)
> counter=1
> fincoord=[]
> for i in range(0,29):
>     coord=[]
>     model=structure[i]
>     for chain in model.get_list():
>         for residue in chain.get_list():
>             ca=residue["CA"]
>             coord.append(ca.get_coord())
>
>     newc=np.add(newc,coord)
>     counter+=1
>
> fincoord=np.divide(newc,counter)
>
> print fincoord
>
> print "END"
>
> Now I want to write the coordinates in fincoord to a new pdb file i.e.
> everything will be the same like the structure[0] except the coordinates.
> Can you tell me how can I edit the coordinates of a specific model or
> replace it with my array and save it to another file?
>
> Thanks
>
> Souparno Adhikary,
> CHPC Lab,
> University of Calcutta.
>
>
> _______________________________________________
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>
>
>
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