Sync copies of pizza
This commit is contained in:
Richard Berger
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@ -6,6 +6,9 @@
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# certain rights in this software. This software is distributed under
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# the GNU General Public License.
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# for python3 compatibility
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from __future__ import print_function
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# gnu tool
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oneline = "Create plots via GnuPlot plotting program"
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@ -84,12 +87,13 @@ g.curve(N,'r') set color of curve N
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# Imports and external programs
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import types, os
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import os
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import sys
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try: from DEFAULTS import PIZZA_GNUPLOT
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except: PIZZA_GNUPLOT = "gnuplot"
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except ImportError: PIZZA_GNUPLOT = "gnuplot -p"
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try: from DEFAULTS import PIZZA_GNUTERM
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except: PIZZA_GNUTERM = "x11"
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except ImportError: PIZZA_GNUTERM = "x11"
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# Class definition
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@ -119,6 +123,9 @@ class gnu:
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def enter(self):
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while 1:
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if sys.version_info[0] == 3:
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command = input("gnuplot> ")
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else:
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command = raw_input("gnuplot> ")
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if command == "quit" or command == "exit": return
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self.__call__(command)
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@ -133,7 +140,7 @@ class gnu:
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self.export(file,linear,vectors[0])
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self.figures[self.current-1].ncurves = 1
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else:
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if len(vectors) % 2: raise StandardError,"vectors must come in pairs"
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if len(vectors) % 2: raise Exception("vectors must come in pairs")
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for i in range(0,len(vectors),2):
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file = self.file + ".%d.%d" % (self.current,i/2+1)
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self.export(file,vectors[i],vectors[i+1])
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@ -167,13 +174,13 @@ class gnu:
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def export(self,filename,*vectors):
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n = len(vectors[0])
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for vector in vectors:
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if len(vector) != n: raise StandardError,"vectors must be same length"
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if len(vector) != n: raise Exception("vectors must be same length")
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f = open(filename,'w')
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nvec = len(vectors)
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for i in xrange(n):
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for j in xrange(nvec):
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print >>f,vectors[j][i],
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print >>f
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for i in range(n):
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for j in range(nvec):
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print(str(vectors[j][i])+" ",file=f,end='')
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print ("",file=f)
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f.close()
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# --------------------------------------------------------------------
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@ -350,7 +357,7 @@ class gnu:
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self.__call__("set key off")
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cmd = 'plot '
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for i in range(fig.ncurves):
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for i in range(int(fig.ncurves)):
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file = self.file + ".%d.%d" % (self.current,i+1)
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if len(fig.colors) > i and fig.colors[i]:
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cmd += "'" + file + "' using 1:2 with line %d, " % fig.colors[i]
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@ -6,6 +6,9 @@
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# certain rights in this software. This software is distributed under
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# the GNU General Public License.
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# for python3 compatibility
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from __future__ import print_function
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# pdb tool
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oneline = "Read, write PDB files in combo with LAMMPS snapshots"
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@ -51,6 +54,7 @@ index,time,flag = p.iterator(1)
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# History
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# 8/05, Steve Plimpton (SNL): original version
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# 3/17, Richard Berger (Temple U): improve Python 3 compatibility
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# ToDo list
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# for generic PDB file (no template) from a LJ unit system,
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@ -64,7 +68,13 @@ index,time,flag = p.iterator(1)
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# Imports and external programs
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import sys, types, glob, urllib
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import sys, glob, urllib
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PY3 = sys.version_info[0] == 3
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if PY3:
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string_types = str,
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else:
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string_types = basestring
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# Class definition
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@ -74,7 +84,7 @@ class pdbfile:
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def __init__(self,*args):
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if len(args) == 1:
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if type(args[0]) is types.StringType:
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if type(args[0]) is string_types:
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filestr = args[0]
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self.data = None
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else:
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@ -83,7 +93,7 @@ class pdbfile:
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elif len(args) == 2:
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filestr = args[0]
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self.data = args[1]
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else: raise StandardError, "invalid args for pdb()"
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else: raise Exception("invalid args for pdb()")
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# flist = full list of all PDB input file names
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# append .pdb if needed
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@ -94,17 +104,17 @@ class pdbfile:
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for file in list:
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if '*' in file: flist += glob.glob(file)
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else: flist.append(file)
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for i in xrange(len(flist)):
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for i in range(len(flist)):
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if flist[i][-4:] != ".pdb": flist[i] += ".pdb"
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if len(flist) == 0:
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raise StandardError,"no PDB file specified"
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raise Exception("no PDB file specified")
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self.files = flist
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else: self.files = []
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if len(self.files) > 1 and self.data:
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raise StandardError, "cannot use multiple PDB files with data object"
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raise Exception("cannot use multiple PDB files with data object")
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if len(self.files) == 0 and not self.data:
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raise StandardError, "no input PDB file(s)"
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raise Exception("no input PDB file(s)")
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# grab PDB file from http://rcsb.org if not a local file
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@ -112,7 +122,7 @@ class pdbfile:
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try:
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open(self.files[0],'r').close()
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except:
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print "downloading %s from http://rcsb.org" % self.files[0]
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print("downloading %s from http://rcsb.org" % self.files[0])
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fetchstr = "http://www.rcsb.org/pdb/cgi/export.cgi/%s?format=PDB&pdbId=2cpk&compression=None" % self.files[0]
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urllib.urlretrieve(fetchstr,self.files[0])
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@ -142,20 +152,20 @@ class pdbfile:
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which,time,flag = self.data.iterator(flag)
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if flag == -1: break
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self.convert(f,which)
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print >>f,"END"
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print time,
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print("END",file=f)
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print(time,end='')
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sys.stdout.flush()
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n += 1
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else:
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for file in self.files:
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f.write(open(file,'r').read())
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print >>f,"END"
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print file,
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print("END",file=f)
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print(file,end='')
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sys.stdout.flush()
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f.close()
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print "\nwrote %d datasets to %s in PDB format" % (n,file)
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print("\nwrote %d datasets to %s in PDB format" % (n,file))
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# --------------------------------------------------------------------
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# write series of numbered PDB files
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@ -190,7 +200,7 @@ class pdbfile:
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self.convert(f,which)
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f.close()
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print time,
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print(time,end='')
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sys.stdout.flush()
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n += 1
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@ -210,12 +220,12 @@ class pdbfile:
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f = open(file,'w')
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f.write(open(infile,'r').read())
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f.close()
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print file,
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print(file,end='')
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sys.stdout.flush()
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n += 1
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print "\nwrote %d datasets to %s*.pdb in PDB format" % (n,root)
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print("\nwrote %d datasets to %s*.pdb in PDB format" % (n,root))
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# --------------------------------------------------------------------
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# write a single PDB file
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@ -280,10 +290,10 @@ class pdbfile:
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if self.atomlines.has_key(id):
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(begin,end) = self.atomlines[id]
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line = "%s%8.3f%8.3f%8.3f%s" % (begin,atom[2],atom[3],atom[4],end)
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print >>f,line,
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print(line,file=f,end='')
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else:
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for atom in atoms:
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begin = "ATOM %6d %2d R00 1 " % (atom[0],atom[1])
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middle = "%8.3f%8.3f%8.3f" % (atom[2],atom[3],atom[4])
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end = " 1.00 0.00 NONE"
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print >>f,begin+middle+end
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print(begin+middle+end,file=f)
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