Residues
Module for assigning and unifying residue identifiers in PDB file lines to ensure consistent numbering.
assign_resid(line, current_resid, prev_original_resid)
¶
Assigns a consistent residue ID based on the sequence of residues encountered.
This function takes a PDB line, the currently assigned residue ID, and the original
residue ID from the previous line. It determines the residue ID for the current line
based on whether the original residue ID has changed. If it's the first residue
encountered (current_resid is None), it assigns the prev_original_resid. If the
current line's original residue ID is the same as the previous one, it retains the
current_resid. If the original residue ID has changed, it increments the
current_resid.
| PARAMETER | DESCRIPTION |
|---|---|
line
|
The PDB line for which the residue ID is to be determined.
TYPE:
|
current_resid
|
The residue ID that has been assigned to the previous
residues. If this is the first residue, it will be
TYPE:
|
prev_original_resid
|
The original residue ID as parsed from the previous PDB line. This is used to detect changes in the residue sequence.
|
| RETURNS | DESCRIPTION |
|---|---|
tuple[str, str]
|
A tuple containing:
|
Examples:
>>> line1 = "ATOM 1 N MET A 1 10.000 20.000 30.000 1.00 20.00 N"
>>> line2 = "ATOM 2 CA MET A 1 11.000 21.000 31.000 1.00 20.00 C"
>>> line3 = "ATOM 3 C ALA A 2 12.000 22.000 32.000 1.00 20.00 C"
>>> assigned_id1, next_orig1 = assign_resid(line1, None, " 1")
>>> print(f"{assigned_id1=}, {next_orig1=}")
assigned_id1=' 1', next_orig1=' 1'
>>> assigned_id2, next_orig2 = assign_resid(line2, assigned_id1, next_orig1)
>>> print(f"{assigned_id2=}, {next_orig2=}")
assigned_id2=' 1', next_orig2=' 1'
>>> assigned_id3, next_orig3 = assign_resid(line3, assigned_id2, next_orig2)
>>> print(f"{assigned_id3=}, {next_orig3=}")
assigned_id3='2', next_orig3=' 2'
unify_resid(line, current_resid, prev_original_resid)
¶
Unifies the residue ID in a PDB line based on a consistent numbering scheme.
This function takes a PDB line, the currently assigned residue ID, and the original
residue ID from the previous line. It calls the assign_resid function to determine
the unified residue ID for the current line and then replaces the original residue ID
in the PDB line with this new, unified ID.
| PARAMETER | DESCRIPTION |
|---|---|
line
|
The PDB line to be modified.
TYPE:
|
current_resid
|
The residue ID that has been assigned to the previous
residues. If this is the first residue, it will be
TYPE:
|
prev_original_resid
|
The original residue ID as parsed from the previous PDB line.
TYPE:
|
| RETURNS | DESCRIPTION |
|---|---|
tuple[str, str, str]
|
A tuple containing:
- The modified PDB line with the unified residue ID.
- The residue ID that was assigned to this atom.
- The original residue ID parsed from the input |
Examples:
>>> line1 = "ATOM 1 N MET A 1 10.000 20.000 30.000 1.00 20.00 N"
>>> line2 = "ATOM 2 CA MET A 1 11.000 21.000 31.000 1.00 20.00 C"
>>> line3 = "ATOM 3 C ALA A 2 12.000 22.000 32.000 1.00 20.00 C"
>>> unified_line1, assigned_id1, next_orig1 = unify_resid(line1, None, " 1")
>>> print(unified_line1.strip())
ATOM 1 N MET A 1 10.000 20.000 30.000 1.00 20.00 N
>>> unified_line2, assigned_id2, next_orig2 = unify_resid(
... line2, assigned_id1, next_orig1
... )
>>> print(unified_line2.strip())
ATOM 2 CA MET A 1 11.000 21.000 31.000 1.00 20.00 C
>>> unified_line3, assigned_id3, next_orig3 = unify_resid(
... line3, assigned_id2, next_orig2
... )
>>> print(unified_line3.strip())
ATOM 3 C ALA A 2 12.000 22.000 32.000 1.00 20.00 C