diff --git a/polyconf/polyconf/Polymer.py b/polyconf/polyconf/Polymer.py index 1f07340..1eb0454 100644 --- a/polyconf/polyconf/Polymer.py +++ b/polyconf/polyconf/Polymer.py @@ -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-...' @@ -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) @@ -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*'