AttributeError: 'Residue' object has no attribute 'sort'

[raoufkeskes]

Code

I am reporting a problem with Biopython version, Python version, and operating
system as follows:

from Bio.PDB import PDBParser
p = PDBParser()
structure = p.get_structure("/home/raouf-ks/Downloads/7nd4_HL.pdb",
                            "/home/raouf-ks/Downloads/7nd4_HL.pdb")
for model in structure:
    for chain in model:
        for residue in chain:
            residue.sort()

Output

Traceback (most recent call last):
  File "test.py", line 19, in <module>
    residue.sort()
AttributeError: 'Residue' object has no attribute 'sort'

the methode sort according to the documentation should sort child atoms, where N, CA, C, O always come first, thereafter alphabetically by name, with any alternative location specifier for disordered atoms (altloc) as a tie-breaker.
but it is not working !

[peterjc]

You are looking at the (old) documentation for Biopython 1.75. This method was deprecated (not sure when) and removed in Biopython 1.79, quoting DEPRECATED.rst

The sort and get_atom methods of the Residue class were removed in Release 1.79.

That method therefore isn't listed in the current documentation:

https://biopython.org/docs/latest/api/Bio.PDB.Residue.html
https://biopython.org/docs/1.79/api/Bio.PDB.Residue.html#Bio.PDB.Residue.Residue.sort

[raoufkeskes]

Ok I got you !

so do you have an alternative way to sort atoms after removing it in the new version ?

[peterjc]

The deprecation message was: The custom sort() method will be removed in the future in favour of rich comparison methods. Use the built-in sorted() function instead.

See also #1360.

[raoufkeskes]

I used the built-in sorted() methods but it does not solve the problem

I hope that they will bring back the sort method, it was perfect !

[JoaoRodrigues]

Can you paste your code and what the error is when you use sorted ()? A quinta, 8/09/2022, 08:26, raoufks ***@***.***> escreveu:

…

I used the built-in sorted() methods but it does not solve the problem I hope that they will bring back the sort method, it was perfect ! — Reply to this email directly, view it on GitHub <#4075 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABZ6ECAAJJIKYVECHV2N23V5HLQHANCNFSM6AAAAAAQHPRMSQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[raoufkeskes]

@JoaoRodrigues

It works BUT my goal is to sort atoms in a PDB, ..., my problem is therefore in this case after sorting with built-in sorted method, I want to save them in the residue, something that was doable with only residue.sort()

PDB

ATOM      1  C   ALA A  27     110.972 180.723 157.553  1.00 81.55           C  
ATOM      2  O   ALA A  27     111.891 180.818 158.365  1.00 81.55           O  
ATOM      3  CB  ALA A  27     109.037 182.248 157.980  1.00 81.55           C
ATOM      4  N   ALA A  27     109.355 180.240 159.340  1.00 81.55           N
ATOM      5  CA  ALA A  27     109.519 180.807 158.006  1.00 81.55           C      
ATOM      6  N   TYR A  28     111.174 180.539 156.250  1.00 83.54           N  
ATOM      7  CA  TYR A  28     112.503 180.472 155.666  1.00 83.54           C  
ATOM      8  C   TYR A  28     112.548 181.334 154.414  1.00 83.54           C  
ATOM      9  O   TYR A  28     111.532 181.534 153.744  1.00 83.54           O  
ATOM     10  CB  TYR A  28     112.891 179.030 155.316  1.00 83.54           C  
ATOM     11  CG  TYR A  28     113.043 178.122 156.516  1.00 83.54           C  
ATOM     12  CD1 TYR A  28     111.936 177.531 157.109  1.00 83.54           C  
ATOM     13  CD2 TYR A  28     114.294 177.851 157.052  1.00 83.54           C  
ATOM     14  CE1 TYR A  28     112.069 176.701 158.205  1.00 83.54           C  
ATOM     15  CE2 TYR A  28     114.437 177.020 158.147  1.00 83.54           C  
ATOM     16  CZ  TYR A  28     113.322 176.449 158.720  1.00 83.54           C  
ATOM     17  OH  TYR A  28     113.461 175.620 159.809  1.00 83.54           O 

python code

in_pdb_file = "/home/raouf-ks/Downloads/7nd4_custom.pdb"
out_pdb_file="/home/raouf-ks/Downloads/7nd4_custom_sorted.pdb"

p = PDBParser()
structure = p.get_structure(in_pdb_file, in_pdb_file)
for model in structure:
    for chain in model:
        for residue in chain:
            print("before : ", [a for a in residue.get_atoms()])
            print("after : ", [a for a in sorted(residue.get_atoms())])
            # HOW TO SAVE THE SORTED ATOMS
            break
        break
    break

# save 
io = PDBIO()
io.set_structure(structure)
io.save(out_pdb_file)

output

before :  [<Atom C>, <Atom O>, <Atom CB>, <Atom N>, <Atom CA>]
after :  [<Atom N>, <Atom CA>, <Atom C>, <Atom O>, <Atom CB>]

[JoaoRodrigues]

That's an entirely different (and valid!) problem :) Will look into it. A quinta, 8/09/2022, 09:31, raoufks ***@***.***> escreveu:

…

It works BUT my goal is to sort atoms in a PDB, ..., my problem is therefore in this case after sorting with built-in sorted method, I want to save them in the residue, something that was doable with only residue.sort() *PDB* ATOM 1 C ALA A 27 110.972 180.723 157.553 1.00 81.55 C ATOM 2 O ALA A 27 111.891 180.818 158.365 1.00 81.55 O ATOM 3 CB ALA A 27 109.037 182.248 157.980 1.00 81.55 C ATOM 4 N ALA A 27 109.355 180.240 159.340 1.00 81.55 N ATOM 5 CA ALA A 27 109.519 180.807 158.006 1.00 81.55 C ATOM 6 N TYR A 28 111.174 180.539 156.250 1.00 83.54 N ATOM 7 CA TYR A 28 112.503 180.472 155.666 1.00 83.54 C ATOM 8 C TYR A 28 112.548 181.334 154.414 1.00 83.54 C ATOM 9 O TYR A 28 111.532 181.534 153.744 1.00 83.54 O ATOM 10 CB TYR A 28 112.891 179.030 155.316 1.00 83.54 C ATOM 11 CG TYR A 28 113.043 178.122 156.516 1.00 83.54 C ATOM 12 CD1 TYR A 28 111.936 177.531 157.109 1.00 83.54 C ATOM 13 CD2 TYR A 28 114.294 177.851 157.052 1.00 83.54 C ATOM 14 CE1 TYR A 28 112.069 176.701 158.205 1.00 83.54 C ATOM 15 CE2 TYR A 28 114.437 177.020 158.147 1.00 83.54 C ATOM 16 CZ TYR A 28 113.322 176.449 158.720 1.00 83.54 C ATOM 17 OH TYR A 28 113.461 175.620 159.809 1.00 83.54 O *python code* in_pdb_file = "/home/raouf-ks/Downloads/7nd4_custom.pdb"p = PDBParser()structure = p.get_structure(in_pdb_file, in_pdb_file)for model in structure: for chain in model: for residue in chain: print("before : ", [a for a in residue.get_atoms()]) print("after : ", [a for a in sorted(residue.get_atoms())]) # HOW TO SAVE THE SORTED ATOMS break break break # save the new structureif not out_pdb_file: out_pdb_file = in_pdb_file io = PDBIO()io.set_structure(structure)io.save(out_pdb_file) *output* before : [<Atom C>, <Atom O>, <Atom CB>, <Atom N>, <Atom CA>] after : [<Atom N>, <Atom CA>, <Atom C>, <Atom O>, <Atom CB>] — Reply to this email directly, view it on GitHub <#4075 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABZ6EDLM6UHWVO66FNTMFTV5HTE5ANCNFSM6AAAAAAQHPRMSQ> . You are receiving this because you commented.Message ID: ***@***.***>

[raoufkeskes]

@JoaoRodrigues
since I checked previous versions code, I fixed it with a tricky line of code but I hope it will be back

residue.child_list.sort()