From dc623af9e2cb1b456fd2f3a916f7d67d4dc67b1a Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Wed, 13 Jun 2018 15:58:13 -0500
Subject: [PATCH] Fixed bugs in psf bond writing
---
CanonicalNucleotideAtoms.py | 4 ++--
arbdmodel.py | 8 ++++++++
2 files changed, 10 insertions(+), 2 deletions(-)
diff --git a/CanonicalNucleotideAtoms.py b/CanonicalNucleotideAtoms.py
index 9f9c541..e8403c0 100644
--- a/CanonicalNucleotideAtoms.py
+++ b/CanonicalNucleotideAtoms.py
@@ -72,14 +72,14 @@ class CanonicalNucleotideFactory(Group):
b = self.bonds
a = self.angles
d = self.dihedrals
- i = self.impropers
+ imp = self.impropers
for i,j in zip(b[::2],b[1::2]):
nt.add_bond( atoms[i], atoms[j], None )
for i,j,k in zip(a[::3],a[1::3],a[2::3]):
nt.add_angle( atoms[i], atoms[j], atoms[k], None )
for i,j,k,l in zip(d[::4],d[1::4],d[2::4],d[3::4]):
nt.add_dihedral( atoms[i], atoms[j], atoms[k], atoms[l], None )
- for i,j,k,l in zip(d[::4],d[1::4],d[2::4],d[3::4]):
+ for i,j,k,l in zip(imp[::4],imp[1::4],imp[2::4],imp[3::4]):
nt.add_improper( atoms[i], atoms[j], atoms[k], atoms[l], None )
return nt
diff --git a/arbdmodel.py b/arbdmodel.py
index d92f235..61e3d86 100644
--- a/arbdmodel.py
+++ b/arbdmodel.py
@@ -506,6 +506,8 @@ class PdbModel(Transformable, Parent):
if counter == 4:
fh.write("\n")
counter = 0
+ else:
+ fh.write(" ")
fh.write("\n")
## Write out angles
@@ -518,6 +520,8 @@ class PdbModel(Transformable, Parent):
if counter == 3:
fh.write("\n")
counter = 0
+ else:
+ fh.write(" ")
fh.write("\n")
## Write out dihedrals
@@ -530,6 +534,8 @@ class PdbModel(Transformable, Parent):
if counter == 2:
fh.write("\n")
counter = 0
+ else:
+ fh.write(" ")
fh.write("\n")
## Write out impropers
@@ -542,6 +548,8 @@ class PdbModel(Transformable, Parent):
if counter == 2:
fh.write("\n")
counter = 0
+ else:
+ fh.write(" ")
fh.write("\n")
--
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