Updated pdb writers so resid is left justified, system dimensions are 1000 AA

atomicModel.py

@@ -914,7 +914,7 @@ class atomicModel():
              open("%s.psf" % prefix,'w') as psf:
 
             ## Write headers
-            pdb.write("CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1\n")
+            pdb.write("CRYST1    1000.    1000.    1000.  90.00  90.00  90.00 P 1           1\n")
             psf.write("PSF NAMD\n\n") # create NAMD formatted psf
             psf.write("{:>8d} !NTITLE\n\n".format(0))
 

beadModel.py

@@ -858,10 +858,10 @@ class beadModel():
     def writePdb(self, filename):
         with open(filename,'w') as fh:
             ## Write header
-            fh.write("CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1\n")
+            fh.write("CRYST1    1000.    1000.    1000.  90.00  90.00  90.00 P 1           1\n")
 
             ## Write coordinates
-            formatString = "ATOM  {:>5d} {:^4s}{:1s}{:3s} {:1s}  {:>5s}{:1s}{:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}{:2s}{:2f}\n"
+            formatString = "ATOM  {:>5d} {:^4s}{:1s}{:3s} {:1s}{:>5s}   {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}{:2s}{:2f}\n"
             for n,hid,zid in self.particles:
                 ## http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
                 idx = n.idx
@@ -873,11 +873,11 @@ class beadModel():
                 beta = zid
                 x,y,z = [x for x in n.position]
                 
-                assert(idx < 100000)
+                assert(idx < 1e5)
                 resid = "{:<4d}".format(idx)
 
                 fh.write( formatString.format(
-                    idx, name[:1], "", resname, chain, resid, "", x, y, z, occ, beta, "", charge ))
+                    idx, name[:1], "", resname, chain, resid, x, y, z, occ, beta, "", charge ))
         return
         
     def writePsf(self, filename):

beadModelTwist.py

@@ -952,10 +952,10 @@ class beadModelTwist():
     def writePdb(self, filename):
         with open(filename,'w') as fh:
             ## Write header
-            fh.write("CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1\n")
+            fh.write("CRYST1    1000.    1000.    1000.  90.00  90.00  90.00 P 1           1\n")
 
             ## Write coordinates
-            formatString = "ATOM  {:>5d} {:^4s}{:1s}{:3s} {:1s}  {:>5s}{:1s}{:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}{:2s}{:2f}\n"
+            formatString = "ATOM  {:>5d} {:^4s}{:1s}{:3s} {:1s}{:>5s}   {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}{:2s}{:2f}\n"
             for n,hid,zid in self.particles:
                 ## http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
                 idx = n.idx
@@ -967,11 +967,11 @@ class beadModelTwist():
                 beta = zid
                 x,y,z = [x for x in n.position]
                 
-                assert(idx < 100000)
+                assert(idx < 1e5)
                 resid = "{:<4d}".format(idx)
 
                 fh.write( formatString.format(
-                    idx, name[:1], "", resname, chain, resid, "", x, y, z, occ, beta, "", charge ))
+                    idx, name[:1], "", resname, chain, resid, x, y, z, occ, beta, "", charge ))
         return
         
     def writePsf(self, filename):