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<p>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
<a class="moz-txt-link-freetext" href="https://github.com/padix-key/biopython/tree/numpy-structure">https://github.com/padix-key/biopython/tree/numpy-structure</a>.</p>
<p>Best regards,</p>
<p>Patrick Kunzmann<br>
</p>
<br>
<div class="moz-cite-prefix">Am 23.05.2017 um 12:04 schrieb Souparno
Adhikary:<br>
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<div>I want to calculate the average structure from multiple
frames in a pdb file and save it to another pdb file.<br>
<br>
</div>
I wrote the code to calculate the average co-ordinates
successfully like below:<br>
<br>
#!/usr/bin/python<br>
<br>
from Bio.PDB.PDBParser import PDBParser<br>
<br>
import numpy as np<br>
<br>
parser=PDBParser(PERMISSIVE=1)<br>
<br>
structure_id="mode_7"<br>
filename="mode_7.pdb"<br>
structure=parser.get_structure(structure_id, filename)<br>
model1=structure[0]<br>
s=(124,3)<br>
newc=np.zeros(s,dtype=np.float32)<br>
counter=1<br>
fincoord=[]<br>
for i in range(0,29):<br>
coord=[] <br>
model=structure[i]<br>
for chain in model.get_list():<br>
for residue in chain.get_list():<br>
ca=residue["CA"]<br>
coord.append(ca.get_coord())<br>
<br>
newc=np.add(newc,coord)<br>
counter+=1<br>
<br>
fincoord=np.divide(newc,counter)<br>
<br>
print fincoord<br>
<br>
print "END"<br>
<br>
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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?<br>
<br>
</div>
Thanks<br clear="all">
<div>
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<div>Souparno Adhikary,<br>
</div>
<div>CHPC Lab,<br>
</div>
<div>University of Calcutta.<br>
</div>
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