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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15358 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-07-22 22:57:54 +00:00
parent 2f936d5e56
commit 778f4d338c
22 changed files with 694 additions and 246 deletions
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33
python/examples/pizza/pdbfile.py
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@ -6,6 +6,9 @@
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# for python3 compatibility
from __future__ import print_function
# pdb tool
oneline = "Read, write PDB files in combo with LAMMPS snapshots"
@ -83,7 +86,7 @@ class pdbfile:
elif len(args) == 2:
filestr = args[0]
self.data = args[1]
else: raise StandardError, "invalid args for pdb()"
else: raise StandardError("invalid args for pdb()")
# flist = full list of all PDB input file names
# append .pdb if needed
@ -97,14 +100,14 @@ class pdbfile:
for i in xrange(len(flist)):
if flist[i][-4:] != ".pdb": flist[i] += ".pdb"
if len(flist) == 0:
raise StandardError,"no PDB file specified"
raise StandardError("no PDB file specified")
self.files = flist
else: self.files = []
if len(self.files) > 1 and self.data:
raise StandardError, "cannot use multiple PDB files with data object"
raise StandardError("cannot use multiple PDB files with data object")
if len(self.files) == 0 and not self.data:
raise StandardError, "no input PDB file(s)"
raise StandardError("no input PDB file(s)")
# grab PDB file from http://rcsb.org if not a local file
@ -112,7 +115,7 @@ class pdbfile:
try:
open(self.files[0],'r').close()
except:
print "downloading %s from http://rcsb.org" % self.files[0]
print("downloading %s from http://rcsb.org" % self.files[0])
fetchstr = "http://www.rcsb.org/pdb/cgi/export.cgi/%s?format=PDB&pdbId=2cpk&compression=None" % self.files[0]
urllib.urlretrieve(fetchstr,self.files[0])
@ -142,20 +145,20 @@ class pdbfile:
which,time,flag = self.data.iterator(flag)
if flag == -1: break
self.convert(f,which)
print >>f,"END"
print time,
print("END",file=f)
print(time,end='')
sys.stdout.flush()
n += 1
else:
for file in self.files:
f.write(open(file,'r').read())
print >>f,"END"
print file,
print("END",file=f)
print(file,end='')
sys.stdout.flush()
f.close()
print "\nwrote %d datasets to %s in PDB format" % (n,file)
print("\nwrote %d datasets to %s in PDB format" % (n,file))
# --------------------------------------------------------------------
# write series of numbered PDB files
@ -190,7 +193,7 @@ class pdbfile:
self.convert(f,which)
f.close()
print time,
print(time,end='')
sys.stdout.flush()
n += 1
@ -210,12 +213,12 @@ class pdbfile:
f = open(file,'w')
f.write(open(infile,'r').read())
f.close()
print file,
print(file,end='')
sys.stdout.flush()
n += 1
print "\nwrote %d datasets to %s*.pdb in PDB format" % (n,root)
print("\nwrote %d datasets to %s*.pdb in PDB format" % (n,root))
# --------------------------------------------------------------------
# write a single PDB file
@ -280,10 +283,10 @@ class pdbfile:
if self.atomlines.has_key(id):
(begin,end) = self.atomlines[id]
line = "%s%8.3f%8.3f%8.3f%s" % (begin,atom[2],atom[3],atom[4],end)
print >>f,line,
print(line,file=f,end='')
else:
for atom in atoms:
begin = "ATOM %6d %2d R00 1 " % (atom[0],atom[1])
middle = "%8.3f%8.3f%8.3f" % (atom[2],atom[3],atom[4])
end = " 1.00 0.00 NONE"
print >>f,begin+middle+end
print(begin+middle+end,file=f)