From 62675e6e2b123bbfedef1a50ec904884997e57eb Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 1 Jun 2021 16:57:19 -0400 Subject: [PATCH] Minor fixes in pizza tools --- python/examples/pizza/dump.py | 14 +++++++------- python/examples/pizza/gl.py | 6 +++--- python/examples/pizza/gnu.py | 12 ++++++------ python/examples/pizza/pdbfile.py | 12 ++++++------ python/examples/pizza/vizinfo.py | 10 +++++----- python/examples/pizza/vmd.py | 13 ++++++------- 6 files changed, 33 insertions(+), 34 deletions(-) diff --git a/python/examples/pizza/dump.py b/python/examples/pizza/dump.py index 14645ac1f3..443ced1949 100644 --- a/python/examples/pizza/dump.py +++ b/python/examples/pizza/dump.py @@ -275,7 +275,7 @@ class dump: print("no column assignments made") elif len(self.names): print("assigned columns:",self.names2str()) - elif self.snaps[0].atoms == None: + elif self.snaps[0].atoms is None: print("no column assignments made") elif len(self.snaps[0].atoms[0]) == 5: self.map(1,"id",2,"type",3,"x",4,"y",5,"z") @@ -969,12 +969,12 @@ class dump: xhi = yhi = zhi = None for snap in self.snaps: if not snap.tselect: continue - if xlo == None or snap.xlo < xlo: xlo = snap.xlo - if xhi == None or snap.xhi > xhi: xhi = snap.xhi - if ylo == None or snap.ylo < ylo: ylo = snap.ylo - if yhi == None or snap.yhi > yhi: yhi = snap.yhi - if zlo == None or snap.zlo < zlo: zlo = snap.zlo - if zhi == None or snap.zhi > zhi: zhi = snap.zhi + if xlo is None or snap.xlo < xlo: xlo = snap.xlo + if xhi is None or snap.xhi > xhi: xhi = snap.xhi + if ylo is None or snap.ylo < ylo: ylo = snap.ylo + if yhi is None or snap.yhi > yhi: yhi = snap.yhi + if zlo is None or snap.zlo < zlo: zlo = snap.zlo + if zhi is None or snap.zhi > zhi: zhi = snap.zhi return [xlo,ylo,zlo,xhi,yhi,zhi] # -------------------------------------------------------------------- diff --git a/python/examples/pizza/gl.py b/python/examples/pizza/gl.py index 908db67052..d4b4f313c3 100644 --- a/python/examples/pizza/gl.py +++ b/python/examples/pizza/gl.py @@ -851,7 +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 Exception("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); @@ -909,7 +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 Exception("bond type too big") red,green,blue = self.vizinfo.bcolor[itype] rad = self.vizinfo.brad[itype] glPushMatrix() @@ -941,7 +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 Exception("tri type too big") red,green,blue = self.vizinfo.tcolor[itype] glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION, [red,green,blue,1.0]); diff --git a/python/examples/pizza/gnu.py b/python/examples/pizza/gnu.py index 7d796d5586..1336e180e0 100644 --- a/python/examples/pizza/gnu.py +++ b/python/examples/pizza/gnu.py @@ -87,12 +87,12 @@ g.curve(N,'r') set color of curve N # Imports and external programs -import types, os +import os try: from DEFAULTS import PIZZA_GNUPLOT -except: PIZZA_GNUPLOT = "gnuplot -p" +except ImportError: PIZZA_GNUPLOT = "gnuplot -p" try: from DEFAULTS import PIZZA_GNUTERM -except: PIZZA_GNUTERM = "x11" +except ImportError: PIZZA_GNUTERM = "x11" # Class definition @@ -122,7 +122,7 @@ class gnu: def enter(self): while 1: - command = raw_input("gnuplot> ") + command = input("gnuplot> ") if command == "quit" or command == "exit": return self.__call__(command) @@ -136,7 +136,7 @@ class gnu: self.export(file,linear,vectors[0]) self.figures[self.current-1].ncurves = 1 else: - if len(vectors) % 2: raise StandardError("vectors must come in pairs") + if len(vectors) % 2: raise Exception("vectors must come in pairs") for i in range(0,len(vectors),2): file = self.file + ".%d.%d" % (self.current,i/2+1) self.export(file,vectors[i],vectors[i+1]) @@ -170,7 +170,7 @@ class gnu: def export(self,filename,*vectors): n = len(vectors[0]) for vector in vectors: - if len(vector) != n: raise StandardError("vectors must be same length") + if len(vector) != n: raise Exception("vectors must be same length") f = open(filename,'w') nvec = len(vectors) for i in range(n): diff --git a/python/examples/pizza/pdbfile.py b/python/examples/pizza/pdbfile.py index 51c8860424..64e77db75f 100644 --- a/python/examples/pizza/pdbfile.py +++ b/python/examples/pizza/pdbfile.py @@ -68,7 +68,7 @@ index,time,flag = p.iterator(1) # Imports and external programs -import sys, types, glob, urllib +import sys, glob, urllib PY3 = sys.version_info[0] == 3 if PY3: @@ -93,7 +93,7 @@ class pdbfile: elif len(args) == 2: filestr = args[0] self.data = args[1] - else: raise StandardError("invalid args for pdb()") + else: raise Exception("invalid args for pdb()") # flist = full list of all PDB input file names # append .pdb if needed @@ -104,17 +104,17 @@ class pdbfile: for file in list: if '*' in file: flist += glob.glob(file) else: flist.append(file) - for i in xrange(len(flist)): + for i in range(len(flist)): if flist[i][-4:] != ".pdb": flist[i] += ".pdb" if len(flist) == 0: - raise StandardError("no PDB file specified") + raise Exception("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 Exception("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 Exception("no input PDB file(s)") # grab PDB file from http://rcsb.org if not a local file diff --git a/python/examples/pizza/vizinfo.py b/python/examples/pizza/vizinfo.py index acc421a1a6..ebf490584e 100644 --- a/python/examples/pizza/vizinfo.py +++ b/python/examples/pizza/vizinfo.py @@ -79,7 +79,7 @@ class vizinfo: # if list of types has a 0, increment each type value if 0 in ids: - for i in xrange(len(ids)): ids[i] += 1 + for i in range(len(ids)): ids[i] += 1 # extend storage list if necessary # extend other arrays for same "which" so that gl::make_atom_calllist @@ -109,7 +109,7 @@ class vizinfo: ntypes = len(ids) nrgbs = len(rgbs) - for i in xrange(ntypes): + for i in range(ntypes): id = ids[i] if rgbs[0] == "loop": @@ -157,7 +157,7 @@ class vizinfo: # if list of types has a 0, increment each type value if 0 in ids: - for i in xrange(len(ids)): ids[i] += 1 + for i in range(len(ids)): ids[i] += 1 # extend storage list if necessary # extend other arrays for same "which" so that gl::make_atom_calllist @@ -220,7 +220,7 @@ class vizinfo: # if list of types has a 0, increment each type value if 0 in ids: - for i in xrange(len(ids)): ids[i] += 1 + for i in range(len(ids)): ids[i] += 1 # extend storage list if necessary # extend other arrays for same "which" so that gl::make_atom_calllist @@ -234,7 +234,7 @@ class vizinfo: # if list lengths match, set directly, else set types to 1st fill value if len(fills) == len(ids): - for i in xrange(len(ids)): self.tfill[ids[i]] = int(fills[i]) + for i in range(len(ids)): self.tfill[ids[i]] = int(fills[i]) else: for id in ids: self.tfill[id] = int(fills[0]) diff --git a/python/examples/pizza/vmd.py b/python/examples/pizza/vmd.py index fb5095617a..72da0f1a1d 100644 --- a/python/examples/pizza/vmd.py +++ b/python/examples/pizza/vmd.py @@ -45,17 +45,16 @@ v.debug([True|False]) display generated VMD script commands? # Imports and external programs -import types, os -import numpy +import os try: from DEFAULTS import PIZZA_VMDNAME -except: PIZZA_VMDNAME = "vmd" +except ImportError: PIZZA_VMDNAME = "vmd" try: from DEFAULTS import PIZZA_VMDDIR -except: PIZZA_VMDDIR = "/usr/local/lib/vmd" +except ImportError: PIZZA_VMDDIR = "/usr/local/lib/vmd" try: from DEFAULTS import PIZZA_VMDDEV -except: PIZZA_VMDDEV = "win" +except ImportError: PIZZA_VMDDEV = "win" try: from DEFAULTS import PIZZA_VMDARCH -except: PIZZA_VMDARCH = "LINUXAMD64" +except ImportError: PIZZA_VMDARCH = "LINUXAMD64" # try these settings for a Mac #PIZZA_VMDNAME = "vmd" @@ -64,7 +63,7 @@ except: PIZZA_VMDARCH = "LINUXAMD64" #PIZZA_VMDARCH = "MACOSXX86" try: import pexpect -except: +except ImportError: print("pexpect from http://pypi.python.org/pypi/pexpect", \ "is required for vmd tool") raise