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fix docstring #62

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recombinatrix merged 1 commit into from
Feb 17, 2025
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fix docstring #62

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31 changes: 19 additions & 12 deletions polyconf/polyconf/Polymer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,7 @@ def extend(self, monomer, n, nn, names, joins, ortho=[1,1,1],
:type beta: int, optional

For example:
{'P1':'CA','Q1':'C','P2':'CMA','Q2':'CN'}, with n=1 and
{'P':'CMA','Q':'CA','R':'CN','S':'C'}, with n=1 and
nn=2 and joins=[('C','CA')] would produce a polymer of
'...-CA1-C1-CA2-C2-...'

Expand Down Expand Up @@ -291,13 +291,20 @@ def rotate(self,J,J_resid,K,K_resid,mult=3,step=1):
"""
Given a pair of bonded atoms J and K within some torsion, uses _split_pol() to identify all atoms connected to J, then rotates them around vector JK by (step * int(360/mult)) degrees, rotating the dihedral centered over J-K by one step.

Args:
J (atom name): the name of the first atom in the bond
J_resid: the resid of the first atom in the bond
K (atom name): the name of the second atom in the bond
K_resid: the resid of the second atom in the bond
mult: the multiplicity of the dihedral centered over J-K
step: how many steps around the dihedral to rotate
:param J: the name of the first atom in the torsion
:type J: str
:param J_resid: the resid of the first atom in the torsion
:type J_resid: int
:param K: the name of the second atom in the torsion
:type K: str
:param K_resid: the resid of the second atom in the torsion
:type K_resid: int
:param mult: the multiplicity of the dihedral centered over J-K,
defaults to 3
:type mult: int, optional
:param step: how many steps to rotate around the torsion, where one step = 320/mult degrees,
defaults to 3
:type step: int, optional
"""

fore,_=self._split_pol(J,J_resid,K,K_resid)
Expand Down Expand Up @@ -353,13 +360,13 @@ def shuffle(self,J,J_resid,K,K_resid,dummies='X*',mult=3,cutoff=0.5,clashcheck=F
resulting structure has overlapping atoms, and will undo the rotation
if so.

:param J: the name of the first atom in the bond
:param J: the name of the first atom in the torsion
:type J: str
:param J_resid: the resid of the first atom in the bond
:param J_resid: the resid of the first atom in the torsion
:type J_resid: int
:param K: the name of the second atom in the bond
:param K: the name of the second atom in the torsion
:type K: str
:param K_resid: the resid of the second atom in the bond
:param K_resid: the resid of the second atom in the torsion
:type K_resid: int
:param dummies: the names of dummy atoms, to be excluded from the
distance calculation. Passed to :func:`dist`, defaults to 'X*'
Expand Down