From 4412e203b68afc57646aacbe020fd3193f6176fe Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 10 Jul 2018 10:46:58 -0500
Subject: [PATCH] Fixed PDB writer to correctly include system dimensions and
to write the segname to the pdb
---
arbdmodel.py | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/arbdmodel.py b/arbdmodel.py
index 0b0a9a1..b5f1edf 100644
--- a/arbdmodel.py
+++ b/arbdmodel.py
@@ -442,14 +442,17 @@ class PdbModel(Transformable, Parent):
self._updateParticleOrder()
with open(filename,'w') as fh:
## Write header
- fh.write("CRYST1 {:>5f} {:>5f} {:>5f} 90.00 90.00 90.00 P 1 1\n".format( *self.dimensions ))
+ fh.write("CRYST1{:>9.3f}{:>9.3f}{:>9.3f} 90.00 90.00 90.00 P 1 1\n".format( *self.dimensions ))
## Write coordinates
- # formatString = "ATOM {:>5d} {:^4.4s}{:1.1s}{:3.3s} {:1.1s}{:>5.5s} {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}{:2.2s}{:2f}\n"
- formatString = "ATOM {:>6.6s} {:^4.4s}{:1.1s}{:3.3s} {:1.1s}{:>5.5s} {:8.8s}{:8.8s}{:8.8s}{:6.2f}{:6.2f}{:2.2s}{:2f}\n"
+ formatString = "ATOM {:>6.6s} {:^4.4s}{:1.1s}{:3.3s} {:1.1s}{:>5.5s} {:8.8s}{:8.8s}{:8.8s}{:6.2f}{:6.2f}{:2.2s}{:2d}{:>6s}\n"
for p in self.particles:
## http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
idx = p.idx+1
+ try:
+ segname = p.segname
+ except:
+ segname = "A"
try:
resname = p.resname
except:
@@ -484,7 +487,7 @@ class PdbModel(Transformable, Parent):
resid = "{:<4d}".format(resid)
fh.write( formatString.format(
- idx, name, "", resname, chain, resid, x, y, z, occ, beta, "", charge ))
+ idx, name, "", resname, chain, resid, x, y, z, occ, beta, "", charge, segname ))
return
def writePsf(self, filename):
--
GitLab