some python3 porting of pizza.py code
This commit is contained in:
Axel Kohlmeyer
@ -6,6 +6,10 @@
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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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# dump tool
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oneline = "Read, write, manipulate dump files and particle attributes"
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@ -179,9 +183,7 @@ d.extra(data) extract bond/tri/line list from data
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# Imports and external programs
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from __future__ import print_function
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import sys, commands, re, glob, types
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import sys, re, glob, types
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from os import popen
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from math import * # any function could be used by set()
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@ -222,7 +224,7 @@ class dump:
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self.flist = []
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for word in words: self.flist += glob.glob(word)
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if len(self.flist) == 0 and len(list) == 1:
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raise StandardError,"no dump file specified"
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raise StandardError("no dump file specified")
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if len(list) == 1:
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self.increment = 0
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@ -247,19 +249,19 @@ class dump:
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snap = self.read_snapshot(f)
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while snap:
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self.snaps.append(snap)
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print snap.time,
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print(snap.time,end='')
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sys.stdout.flush()
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snap = self.read_snapshot(f)
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f.close()
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print
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print()
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# sort entries by timestep, cull duplicates
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self.snaps.sort(self.compare_time)
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self.cull()
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self.nsnaps = len(self.snaps)
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print "read %d snapshots" % self.nsnaps
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print("read %d snapshots" % self.nsnaps)
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# select all timesteps and atoms
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@ -268,36 +270,36 @@ class dump:
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# set default names for atom columns if file wasn't self-describing
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if len(self.snaps) == 0:
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print "no column assignments made"
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print("no column assignments made")
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elif len(self.names):
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print "assigned columns:",self.names2str()
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print("assigned columns:",self.names2str())
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elif self.snaps[0].atoms == None:
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print "no column assignments made"
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print("no column assignments made")
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elif len(self.snaps[0].atoms[0]) == 5:
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self.map(1,"id",2,"type",3,"x",4,"y",5,"z")
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print "assigned columns:",self.names2str()
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print("assigned columns:",self.names2str())
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elif len(self.snaps[0].atoms[0]) == 8:
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self.map(1,"id",2,"type",3,"x",4,"y",5,"z",6,"ix",7,"iy",8,"iz")
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print "assigned columns:",self.names2str()
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print("assigned columns:",self.names2str())
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else:
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print "no column assignments made"
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print("no column assignments made")
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# if snapshots are scaled, unscale them
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if (not self.names.has_key("x")) or \
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(not self.names.has_key("y")) or \
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(not self.names.has_key("z")):
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print "no unscaling could be performed"
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print("no unscaling could be performed")
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elif self.nsnaps > 0:
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if self.scaled(self.nsnaps-1): self.unscale()
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else: print "dump is already unscaled"
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else: print("dump is already unscaled")
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# --------------------------------------------------------------------
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# read next snapshot from list of files
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def next(self):
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if not self.increment: raise StandardError,"cannot read incrementally"
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if not self.increment: raise StandardError("cannot read incrementally")
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# read next snapshot in current file using eof as pointer
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# if fail, try next file
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@ -309,15 +311,15 @@ class dump:
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snap = self.read_snapshot(f)
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if not snap:
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self.nextfile += 1
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if self.nextfile == len(self.flist): return -1
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if self.nextfile == len(self.flist): return -1
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f.close()
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self.eof = 0
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continue
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self.eof = 0
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continue
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self.eof = f.tell()
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f.close()
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try:
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self.findtime(snap.time)
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continue
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continue
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except: break
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# select the new snapshot with all its atoms
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@ -415,7 +417,7 @@ class dump:
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def map(self,*pairs):
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if len(pairs) % 2 != 0:
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raise StandardError, "dump map() requires pairs of mappings"
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raise StandardError("dump map() requires pairs of mappings")
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for i in range(0,len(pairs),2):
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j = i + 1
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self.names[pairs[j]] = pairs[i]-1
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@ -432,15 +434,15 @@ class dump:
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self.nsnaps -= 1
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ndel += 1
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else: i += 1
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print "%d snapshots deleted" % ndel
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print "%d snapshots remaining" % self.nsnaps
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print("%d snapshots deleted" % ndel)
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print("%d snapshots remaining" % self.nsnaps)
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# --------------------------------------------------------------------
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# scale coords to 0-1 for all snapshots or just one
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def scale(self,*list):
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if len(list) == 0:
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print "Scaling dump ..."
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print("Scaling dump ...")
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x = self.names["x"]
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y = self.names["y"]
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z = self.names["z"]
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@ -468,7 +470,7 @@ class dump:
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def unscale(self,*list):
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if len(list) == 0:
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print "Unscaling dump ..."
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print("Unscaling dump ...")
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x = self.names["x"]
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y = self.names["y"]
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z = self.names["z"]
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@ -495,7 +497,7 @@ class dump:
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# wrap coords from outside box to inside
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def wrap(self):
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print "Wrapping dump ..."
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print("Wrapping dump ...")
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x = self.names["x"]
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y = self.names["y"]
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@ -517,7 +519,7 @@ class dump:
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# unwrap coords from inside box to outside
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def unwrap(self):
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print "Unwrapping dump ..."
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print("Unwrapping dump ...")
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x = self.names["x"]
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y = self.names["y"]
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@ -539,7 +541,7 @@ class dump:
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# wrap coords to same image as atom ID stored in "other" column
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def owrap(self,other):
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print "Wrapping to other ..."
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print("Wrapping to other ...")
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id = self.names["id"]
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x = self.names["x"]
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@ -583,12 +585,12 @@ class dump:
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def sort(self,*list):
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if len(list) == 0:
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print "Sorting selected snapshots ..."
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print("Sorting selected snapshots ...")
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id = self.names["id"]
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for snap in self.snaps:
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if snap.tselect: self.sort_one(snap,id)
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elif type(list[0]) is types.StringType:
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print "Sorting selected snapshots by %s ..." % list[0]
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print("Sorting selected snapshots by %s ..." % list[0])
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id = self.names[list[0]]
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for snap in self.snaps:
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if snap.tselect: self.sort_one(snap,id)
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@ -616,19 +618,19 @@ class dump:
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else: f = open(file,"a")
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for snap in self.snaps:
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if not snap.tselect: continue
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print snap.time,
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print(snap.time,end='')
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sys.stdout.flush()
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if header:
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print >>f,"ITEM: TIMESTEP"
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print >>f,snap.time
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print >>f,"ITEM: NUMBER OF ATOMS"
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print >>f,snap.nselect
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print >>f,"ITEM: BOX BOUNDS"
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print >>f,snap.xlo,snap.xhi
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print >>f,snap.ylo,snap.yhi
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print >>f,snap.zlo,snap.zhi
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print >>f,"ITEM: ATOMS",namestr
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print("ITEM: TIMESTEP",file=f)
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print(snap.time,file=f)
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print("ITEM: NUMBER OF ATOMS",file=f)
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print(snap.nselect,file=f)
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print("ITEM: BOX BOUNDS",file=f)
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print(snap.xlo,snap.xhi,file=f)
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print(snap.ylo,snap.yhi,file=f)
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print(snap.zlo,snap.zhi,file=f)
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print("ITEM: ATOMS",namestr,file=f)
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atoms = snap.atoms
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nvalues = len(atoms[0])
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@ -640,9 +642,9 @@ class dump:
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line += str(int(atoms[i][j])) + " "
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else:
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line += str(atoms[i][j]) + " "
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print >>f,line
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print(line,file=f)
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f.close()
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print "\n%d snapshots" % self.nselect
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print("\n%d snapshots" % self.nselect)
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# --------------------------------------------------------------------
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# write one dump file per snapshot from current selection
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@ -651,20 +653,20 @@ class dump:
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if len(self.snaps): namestr = self.names2str()
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for snap in self.snaps:
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if not snap.tselect: continue
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print snap.time,
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print(snap.time,end='')
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sys.stdout.flush()
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file = root + "." + str(snap.time)
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f = open(file,"w")
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print >>f,"ITEM: TIMESTEP"
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print >>f,snap.time
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print >>f,"ITEM: NUMBER OF ATOMS"
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print >>f,snap.nselect
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print >>f,"ITEM: BOX BOUNDS"
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print >>f,snap.xlo,snap.xhi
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print >>f,snap.ylo,snap.yhi
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print >>f,snap.zlo,snap.zhi
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print >>f,"ITEM: ATOMS",namestr
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print("ITEM: TIMESTEP",file=f)
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print(snap.time,file=f)
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print("ITEM: NUMBER OF ATOMS",file=f)
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print(snap.nselect,file=f)
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print("ITEM: BOX BOUNDS",file=f)
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print(snap.xlo,snap.xhi,file=f)
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print(snap.ylo,snap.yhi,file=f)
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print(snap.zlo,snap.zhi,file=f)
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print("ITEM: ATOMS",namestr,file=f)
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atoms = snap.atoms
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nvalues = len(atoms[0])
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@ -676,9 +678,9 @@ class dump:
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line += str(int(atoms[i][j])) + " "
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else:
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line += str(atoms[i][j]) + " "
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print >>f,line
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print(line,file=f)
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f.close()
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print "\n%d snapshots" % self.nselect
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print("\n%d snapshots" % self.nselect)
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# --------------------------------------------------------------------
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# find min/max across all selected snapshots/atoms for a particular column
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@ -700,7 +702,7 @@ class dump:
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# set a column value via an equation for all selected snapshots
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def set(self,eq):
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print "Setting ..."
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print("Setting ...")
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pattern = "\$\w*"
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list = re.findall(pattern,eq)
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@ -718,13 +720,13 @@ class dump:
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for snap in self.snaps:
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if not snap.tselect: continue
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for i in range(snap.natoms):
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if snap.aselect[i]: exec ceq
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if snap.aselect[i]: exec(ceq)
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# --------------------------------------------------------------------
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# set a column value via an input vec for all selected snapshots/atoms
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def setv(self,colname,vec):
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print "Setting ..."
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print("Setting ...")
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if not self.names.has_key(colname):
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self.newcolumn(colname)
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icol = self.names[colname]
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@ -732,7 +734,7 @@ class dump:
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for snap in self.snaps:
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if not snap.tselect: continue
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if snap.nselect != len(vec):
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raise StandardError,"vec length does not match # of selected atoms"
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raise StandardError("vec length does not match # of selected atoms")
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atoms = snap.atoms
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m = 0
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for i in range(snap.natoms):
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@ -767,7 +769,7 @@ class dump:
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inew = self.names[new]
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min,max = self.minmax(old)
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print "min/max = ",min,max
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print("min/max = ",min,max)
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gap = max - min
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invdelta = n/gap
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@ -798,7 +800,7 @@ class dump:
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def atom(self,n,*list):
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if len(list) == 0:
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raise StandardError, "no columns specified"
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raise StandardError("no columns specified")
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columns = []
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values = []
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for name in list:
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@ -814,7 +816,7 @@ class dump:
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for i in range(snap.natoms):
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if atoms[i][id] == n: break
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if atoms[i][id] != n:
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raise StandardError, "could not find atom ID in snapshot"
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raise StandardError("could not find atom ID in snapshot")
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for j in range(ncol):
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values[j][m] = atoms[i][columns[j]]
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m += 1
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@ -829,7 +831,7 @@ class dump:
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snap = self.snaps[self.findtime(n)]
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if len(list) == 0:
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raise StandardError, "no columns specified"
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raise StandardError("no columns specified")
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columns = []
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values = []
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for name in list:
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@ -957,7 +959,7 @@ class dump:
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def findtime(self,n):
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for i in range(self.nsnaps):
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if self.snaps[i].time == n: return i
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raise StandardError, "no step %d exists" % n
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raise StandardError("no step %d exists" % n)
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# --------------------------------------------------------------------
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# return maximum box size across all selected snapshots
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@ -1006,7 +1008,7 @@ class dump:
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nbonds = int(f.readline())
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item = f.readline()
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if not re.search("BONDS",item):
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raise StandardError, "could not read bonds from dump file"
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raise StandardError("could not read bonds from dump file")
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words = f.readline().split()
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ncol = len(words)
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@ -1029,7 +1031,7 @@ class dump:
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self.bondflag = 1
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self.bondlist = bondlist
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except:
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raise StandardError,"could not read from bond dump file"
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raise StandardError("could not read from bond dump file")
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# request bonds from data object
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@ -1045,7 +1047,7 @@ class dump:
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self.bondflag = 1
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self.bondlist = bondlist
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except:
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raise StandardError,"could not extract bonds from data object"
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raise StandardError("could not extract bonds from data object")
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# request tris/lines from cdata object
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@ -1059,7 +1061,7 @@ class dump:
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self.lineflag = 1
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self.linelist = lines
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except:
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raise StandardError,"could not extract tris/lines from cdata object"
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raise StandardError("could not extract tris/lines from cdata object")
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# request tris from mdump object
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@ -1068,10 +1070,10 @@ class dump:
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self.triflag = 2
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self.triobj = arg
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except:
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raise StandardError,"could not extract tris from mdump object"
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raise StandardError("could not extract tris from mdump object")
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else:
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raise StandardError,"unrecognized argument to dump.extra()"
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raise StandardError("unrecognized argument to dump.extra()")
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# --------------------------------------------------------------------
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@ -1105,7 +1107,7 @@ class tselect:
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snap.tselect = 1
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data.nselect = len(data.snaps)
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data.aselect.all()
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print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
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print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
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# --------------------------------------------------------------------
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@ -1117,7 +1119,7 @@ class tselect:
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data.snaps[i].tselect = 1
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data.nselect = 1
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data.aselect.all()
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print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
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print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
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# --------------------------------------------------------------------
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@ -1126,7 +1128,7 @@ class tselect:
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for snap in data.snaps:
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snap.tselect = 0
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data.nselect = 0
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print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
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print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
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# --------------------------------------------------------------------
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@ -1142,7 +1144,7 @@ class tselect:
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snap.tselect = 0
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data.nselect -= 1
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data.aselect.all()
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print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
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print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
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# --------------------------------------------------------------------
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@ -1153,12 +1155,12 @@ class tselect:
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ccmd = compile(cmd,'','single')
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for i in range(data.nsnaps):
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if not snaps[i].tselect: continue
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exec ccmd
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exec(ccmd)
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if not flag:
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snaps[i].tselect = 0
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data.nselect -= 1
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data.aselect.all()
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print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
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print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
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# --------------------------------------------------------------------
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# atom selection class
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@ -1205,19 +1207,19 @@ class aselect:
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if not snap.tselect: continue
|
||||
for i in range(snap.natoms):
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if not snap.aselect[i]: continue
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exec ccmd
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exec(ccmd)
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if not flag:
|
||||
snap.aselect[i] = 0
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snap.nselect -= 1
|
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for i in range(data.nsnaps):
|
||||
if data.snaps[i].tselect:
|
||||
print "%d atoms of %d selected in first step %d" % \
|
||||
(data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time)
|
||||
print("%d atoms of %d selected in first step %d" % \
|
||||
(data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time))
|
||||
break
|
||||
for i in range(data.nsnaps-1,-1,-1):
|
||||
if data.snaps[i].tselect:
|
||||
print "%d atoms of %d selected in last step %d" % \
|
||||
(data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time)
|
||||
print("%d atoms of %d selected in last step %d" % \
|
||||
(data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time))
|
||||
break
|
||||
|
||||
else: # one timestep
|
||||
@ -1225,7 +1227,7 @@ class aselect:
|
||||
snap = data.snaps[n]
|
||||
for i in range(snap.natoms):
|
||||
if not snap.aselect[i]: continue
|
||||
exec ccmd
|
||||
exec(ccmd)
|
||||
if not flag:
|
||||
snap.aselect[i] = 0
|
||||
snap.nselect -= 1
|
||||
|
||||
@ -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
|
||||
|
||||
# gl tool
|
||||
|
||||
oneline = "3d interactive visualization via OpenGL"
|
||||
@ -73,7 +76,7 @@ g.ldef() default = 0 fill
|
||||
if atom/bond/tri/line has type > # defined properties, is an error
|
||||
|
||||
from vizinfo import colors access color list
|
||||
print colors list defined color names and RGB values
|
||||
print(colors) list defined color names and RGB values
|
||||
colors["nickname"] = [R,G,B] set new RGB values from 0 to 255
|
||||
|
||||
140 pre-defined colors: red, green, blue, purple, yellow, black, white, etc
|
||||
@ -499,7 +502,7 @@ class gl:
|
||||
# add GL-specific info to each bond
|
||||
|
||||
def reload(self):
|
||||
print "Loading data into gl tool ..."
|
||||
print("Loading data into gl tool ...")
|
||||
data = self.data
|
||||
|
||||
self.timeframes = []
|
||||
@ -527,9 +530,9 @@ class gl:
|
||||
self.triframes.append(tris)
|
||||
self.lineframes.append(lines)
|
||||
|
||||
print time,
|
||||
print(time,end='')
|
||||
sys.stdout.flush()
|
||||
print
|
||||
print()
|
||||
|
||||
self.nframes = len(self.timeframes)
|
||||
self.distance = compute_distance(self.boxframes[0])
|
||||
@ -651,7 +654,7 @@ class gl:
|
||||
self.w.tkRedraw()
|
||||
self.save(file)
|
||||
|
||||
print time,
|
||||
print(time,end='')
|
||||
sys.stdout.flush()
|
||||
i += 1
|
||||
n += 1
|
||||
@ -690,7 +693,7 @@ class gl:
|
||||
fraction*(self.scale_stop - self.scale_start)
|
||||
self.viewupright()
|
||||
|
||||
if n == nstart or self.panflag: self.center = compute_center(box)
|
||||
if n == nstart or self.panflag: self.center = compute_center(box)
|
||||
|
||||
if bonds: self.bonds_augment(bonds)
|
||||
|
||||
@ -706,11 +709,11 @@ class gl:
|
||||
self.w.tkRedraw()
|
||||
self.save(file)
|
||||
|
||||
print n,
|
||||
print(n,end='')
|
||||
sys.stdout.flush()
|
||||
n += 1
|
||||
|
||||
print "\n%d images" % ncount
|
||||
print("\n%d images" % ncount)
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
@ -776,11 +779,11 @@ class gl:
|
||||
ncolor = self.vizinfo.nlcolor
|
||||
for line in self.linedraw:
|
||||
itype = int(line[1])
|
||||
if itype > ncolor: raise StandardError,"line type too big"
|
||||
if itype > ncolor: raise StandardError("line type too big")
|
||||
red,green,blue = self.vizinfo.lcolor[itype]
|
||||
glColor3f(red,green,blue)
|
||||
thick = self.vizinfo.lrad[itype]
|
||||
glLineWidth(thick)
|
||||
glLineWidth(thick)
|
||||
glBegin(GL_LINES)
|
||||
glVertex3f(line[2],line[3],line[4])
|
||||
glVertex3f(line[5],line[6],line[7])
|
||||
@ -825,7 +828,7 @@ class gl:
|
||||
for bond in self.bonddraw:
|
||||
if bond[10] > bound: continue
|
||||
itype = int(bond[1])
|
||||
if itype > ncolor: raise StandardError,"bond type too big"
|
||||
if itype > ncolor: raise StandardError("bond type too big")
|
||||
red,green,blue = self.vizinfo.bcolor[itype]
|
||||
rad = self.vizinfo.brad[itype]
|
||||
glPushMatrix()
|
||||
@ -848,7 +851,7 @@ class gl:
|
||||
ncolor = self.vizinfo.ntcolor
|
||||
for tri in self.tridraw:
|
||||
itype = int(tri[1])
|
||||
if itype > ncolor: raise StandardError,"tri type too big"
|
||||
if itype > ncolor: raise StandardError("tri type too big")
|
||||
red,green,blue = self.vizinfo.tcolor[itype]
|
||||
glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION,[red,green,blue,1.0]);
|
||||
glMaterialf(GL_FRONT_AND_BACK,GL_SHININESS,self.shiny);
|
||||
@ -906,7 +909,7 @@ class gl:
|
||||
ymin >= ylo and ymax <= yhi and zmin >= zlo and zmax <= zhi:
|
||||
if bond[10] > bound: continue
|
||||
itype = int(bond[1])
|
||||
if itype > ncolor: raise StandardError,"bond type too big"
|
||||
if itype > ncolor: raise StandardError("bond type too big")
|
||||
red,green,blue = self.vizinfo.bcolor[itype]
|
||||
rad = self.vizinfo.brad[itype]
|
||||
glPushMatrix()
|
||||
@ -938,7 +941,7 @@ class gl:
|
||||
ymin >= ylo and ymax <= yhi and \
|
||||
zmin >= zlo and zmax <= zhi:
|
||||
itype = int(tri[1])
|
||||
if itype > ncolor: raise StandardError,"tri type too big"
|
||||
if itype > ncolor: raise StandardError("tri type too big")
|
||||
red,green,blue = self.vizinfo.tcolor[itype]
|
||||
glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION,
|
||||
[red,green,blue,1.0]);
|
||||
|
||||
@ -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
|
||||
|
||||
# gnu tool
|
||||
|
||||
oneline = "Create plots via GnuPlot plotting program"
|
||||
@ -172,8 +175,8 @@ class gnu:
|
||||
nvec = len(vectors)
|
||||
for i in range(n):
|
||||
for j in range(nvec):
|
||||
print >>f,vectors[j][i],
|
||||
print >>f
|
||||
print(str(vectors[j][i])+" ",file=f,end='')
|
||||
print ("",file=f)
|
||||
f.close()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
@ -350,7 +353,7 @@ class gnu:
|
||||
|
||||
self.__call__("set key off")
|
||||
cmd = 'plot '
|
||||
for i in range(fig.ncurves):
|
||||
for i in range(int(fig.ncurves)):
|
||||
file = self.file + ".%d.%d" % (self.current,i+1)
|
||||
if len(fig.colors) > i and fig.colors[i]:
|
||||
cmd += "'" + file + "' using 1:2 with line %d, " % fig.colors[i]
|
||||
|
||||
@ -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)
|
||||
|
||||
@ -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
|
||||
|
||||
# vmd tool
|
||||
|
||||
# Minimalistic VMD embedding for Pizza.py
|
||||
@ -52,7 +55,7 @@ except: PIZZA_VMDDIR = "/usr/local/lib/vmd"
|
||||
try: from DEFAULTS import PIZZA_VMDDEV
|
||||
except: PIZZA_VMDDEV = "win"
|
||||
try: from DEFAULTS import PIZZA_VMDARCH
|
||||
except: PIZZA_VMDARCH = "LINUX"
|
||||
except: PIZZA_VMDARCH = "LINUXAMD64"
|
||||
|
||||
# try these settings for a Mac
|
||||
#PIZZA_VMDNAME = "vmd"
|
||||
@ -62,8 +65,8 @@ except: PIZZA_VMDARCH = "LINUX"
|
||||
|
||||
try: import pexpect
|
||||
except:
|
||||
print "pexpect from http://pypi.python.org/pypi/pexpect", \
|
||||
"is required for vmd tool"
|
||||
print("pexpect from http://pypi.python.org/pypi/pexpect", \
|
||||
"is required for vmd tool")
|
||||
raise
|
||||
|
||||
# Class definition
|
||||
@ -109,7 +112,7 @@ class vmd:
|
||||
self.VMD.sendline(command)
|
||||
self.VMD.expect('vmd >')
|
||||
if self.debugme:
|
||||
print "call+result:"+self.VMD.before
|
||||
print("call+result:"+self.VMD.before)
|
||||
return
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
@ -127,9 +130,9 @@ class vmd:
|
||||
# turn on debugging info
|
||||
def debug(self,status=True):
|
||||
if status and not self.debugme:
|
||||
print 'Turning vmd.py debugging ON.'
|
||||
print('Turning vmd.py debugging ON.')
|
||||
if not status and self.debugme:
|
||||
print 'Turning vmd.py debugging OFF.'
|
||||
print('Turning vmd.py debugging OFF.')
|
||||
self.debugme = status
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
@ -141,14 +144,14 @@ class vmd:
|
||||
try:
|
||||
command = raw_input("vmd > ")
|
||||
except EOFError:
|
||||
print "(EOF)"
|
||||
print("(EOF)")
|
||||
self.__call__('menu main off')
|
||||
return
|
||||
if command == "quit" or command == "exit":
|
||||
self.__call__('menu main off')
|
||||
return
|
||||
if command == "gopython":
|
||||
print "gopython not supported here"
|
||||
print("gopython not supported here")
|
||||
continue
|
||||
self.__call__(command)
|
||||
|
||||
|
||||
Reference in New Issue
Block a user