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Fix PolyConf Polymer.copy() to ensure dimensions are retained #56

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Merged
lunamorrow merged 1 commit into from
Feb 5, 2025
Merged

Fix PolyConf Polymer.copy() to ensure dimensions are retained #56

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18 changes: 9 additions & 9 deletions polyconf/polyconf/Polymer.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
#!/usr/bin/env python
from __future__ import annotations
from .Monomer import Monomer

import numpy as np
Expand Down Expand Up @@ -59,18 +60,17 @@ def select_atoms(self, selection) -> mda.AtomGroup:
"""
return self.polymer.select_atoms(selection)

def copy(self) -> mda.Universe:
def copy(self) -> Polymer:
"""
Use MDAnalysis Merge to create a new MDAnalysis Universe that is an
exact copy of this one containing the polymer. Deepcopy is not used as
it can be problematic with open file sockets.
Use MDAnalysis Universe.copy() to create a new MDAnalysis Universe that
is an exact copy of this one containing the polymer. Deepcopy is not
used as it can be problematic with open file sockets.

:return: A new MDAnalysis Universe that is an exact copy of the polymer
:rtype: mda.Universe
:return: A new Polymer that is an exact copy of this polymer
:rtype: Polymer
"""
new_u = mda.Merge(self.polymer.atoms)
return Polymer(Monomer.monomer_from_u(new_u), keep_resids=True)
# return Polymer(Monomer.monomer_from_u(new_u), keep_resids=True)
new = self.polymer.copy()
return Polymer(Monomer.monomer_from_u(new), keep_resids=True)

def renamer(self, resid, namein, nameout='X'):
"""
Expand Down