From 5d01a8a5abf449a5288107052ef15954f6943a11 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Thu, 25 Jun 2020 07:50:54 -0500
Subject: [PATCH] Updated bondAngle to be two angles, one bond
---
mrdna/arbdmodel/__init__.py | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/mrdna/arbdmodel/__init__.py b/mrdna/arbdmodel/__init__.py
index 51c26bd..0f97148 100644
--- a/mrdna/arbdmodel/__init__.py
+++ b/mrdna/arbdmodel/__init__.py
@@ -149,12 +149,12 @@ class Parent():
# for b in (i,j): assert(b in beads)
self.exclusions.append( (i,j) )
- def add_bond_angle(self, i,j,k, bond_angle, exclude=False):
- assert( len(set((i,j,k))) == 3 )
+ def add_bond_angle(self, i,j,k,l, bond_angle, exclude=False):
+ assert( len(set((i,j,k,l))) == 4 )
## TODO: how to handle duplicating and cloning bonds
# beads = [b for b in self]
# for b in (i,j): assert(b in beads)
- self.bond_angles.append( (i,j,k, bond_angle) )
+ self.bond_angles.append( (i,j,k,l, bond_angle) )
def get_restraints(self):
ret = []
@@ -219,14 +219,14 @@ class Parent():
def _get_bond_potentials(self):
bonds = [b for i,j,b,ex in self.get_bonds()]
- bondangles1 = [b[1] for i,j,k,b in self.get_bond_angles()]
- bondangles2 = [b[2] for i,j,k,b in self.get_bond_angles()]
- return list(set( bonds+bondangles1+bondangles2 ))
+ bondangles1 = [b[1] for i,j,k,l,b in self.get_bond_angles()]
+ return list(set( bonds+bondangles1 ))
def _get_angle_potentials(self):
angles = [b for i,j,k,b in self.get_angles()]
- bondangles = [b[0] for i,j,k,b in self.get_bond_angles()]
- return list(set( angles+bondangles ))
+ bondangles1 = [b[0] for i,j,k,l,b in self.get_bond_angles()]
+ bondangles2 = [b[2] for i,j,k,l,b in self.get_bond_angles()]
+ return list(set( angles+bondangles1+bondangles2 ))
## Removed because prohibitively slow
@@ -1240,7 +1240,7 @@ component "data" value 3
with open(self._bond_angle_filename,'w') as fh:
for b in self.get_bond_angles():
item = tuple([p.idx for p in b[:-1]] + [str(p) for p in b[-1]])
- fh.write("BONDANGLE %d %d %d %s %s %s\n" % item)
+ fh.write("BONDANGLE %d %d %d %d %s %s %s\n" % item)
def dimensions_from_structure( self, padding_factor=1.5, isotropic=False ):
## TODO: cache coordinates using numpy arrays for quick min/max
--
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