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wangcui2011金蟲 (小有名氣)
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[求助]
NWChem計算生成的.top文件和 .rst文件各行各列的含義
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各位前輩，Topology 文件和 Restart 文件是NWChem做QMMM運算需要的兩個很重要的文件，想問下，這兩種文件里面各行各列都是表示什么含義。如果哪位蟲友知道，希望可以幫忙解答。先說一聲：謝謝！ 我下面給出一個例子，這個例子是nwchem documentation里面提供的: (1) cloh.top NWChem topology file Generated by the NWChem prepare module 4.60000001/28/09 22:55:38 amber 1 5 4 2 0.833333 1.000000 0.000000 0 1 17 CL Q 35.453000 2 8 OH Q 15.999400 3 1 HO Q 1.008000 4 8 OWS w 15.999400 5 1 HWS w 1.008000 1 1 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 2 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 3 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 4 6.11777E-03 3.05888E-03 1.79398E-05 8.96989E-06 1 5 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2 2 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2 3 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2 4 2.71815E-03 1.35907E-03 2.83540E-06 1.41770E-06 2 5 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 3 3 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 3 4 4.31389E-04 2.15694E-04 1.90177E-07 9.50885E-08 3 5 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 4 4 2.61691E-03 1.30845E-03 2.63324E-06 1.31662E-06 4 5 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 5 5 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.000000 0.00000E+00 2 -0.847600 0.00000E+00 3 0.423800 0.00000E+00 4 0.000000 0.00000E+00 1CLD 1 -2 1 1 1 1 2OH 2 -2 2 2 1 1 3 3 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 spce OW 4 2 2 2 1 spce 2HW 5 3 3 3 2 spce 3HW 5 3 3 3 3 1 2 1 1 0.100000 1.00000E+06 1 3 1 2 0.100000 1.00000E+06 2 3 1 3 0.163333 1.00000E+06 spce HOH 5.220000 CLD Cl 1 1 1 1 1 1 4 4 4 0 0 1 1 OH O1 1 2 2 2 2 2 4 4 4 0 0 1 2 OH H1 1 2 2 2 2 3 4 4 4 0 0 1 3 (2) cloh_rs.rst Restart file 4.20000001/29/09 14:08:50 1 F 01/29/09 14:08:50 cloh_opt00 1 0 0.097665 2.624300 0.000000 0.000000 0.000000 2.624300 0.000000 0.000000 0.000000 2.624300 0.00000E+00 0.000000 0.000000 0.000000 590 3 2 3 590 1 2 0 0 0.08394658 0.18596279 -0.17665358 0.00000000 0.00000000 0.00000000 -0.01256243 0.20438730 -0.15803778 0.00000000 0.00000000 0.00000000 0.09813034 0.08731282 -0.18483929 0.00000000 0.00000000 0.00000000 00 0.00000000 0.00000000 0.00000000 0.06624620 -0.10225782 -0.22140211 0.00000000 0.00000000 0.00000000 0.06556329 -0.10534104 -0.12145195 0.00000000 0.00000000 0.00000000 -0.02771490 -0.09757372 -0.25530455 0.00000000 0.00000000 0.00000000 .. .......... ......... ........... .......... ........... ........... 00 0.00000000 0.00000000 0.00000000 00 -0.15572466 0.02643901 0.02211421 0.00000000 0.00000000 0.00000000 0 00 0.07232217 -0.05744605 0.06064107 0.00000000 0.00000000 0.00000000 0 00 0.10481826 0.03465585 0.05711075 0.00000000 0.00000000 0.00000000 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1 1 restart input 1 1 1 1 0 1 0 0 0 0 0 0 0 1000 500 0.000000 0.001000 1.000000 1.000000 100 0.000001 100 0.000001 0 0.10250E+06 0.500000 0.45300E-09 0 0 298.150000 0.100000 0.100000 298.150000 0.000000 0.000000 0 0 298.150000 12345 10 100 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1000 0 0 0 0.000000 0.000000 0 0 0 0 1 0 0.000000 1 0 0.000000 restart properties 150 0 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 .................. ................... .................. .................... restart space 32 33 2 4 4 2 4 4 32 0.131215000000E+01 0.262430000000E+01 0.656075000000E+00 0.131215000000E+01 0.196822500000E+01 0.262430000000E+01 0.656075000000E+00 0.131215000000E+01 0.196822500000E+01 0.262430000000E+01 0 11 0 0 0 0 2 2 0 243 4 4 0 543 8 8 0 695 10 10 0 1016 12 12 0 1241 16 16 0 1357 18 18 0 1500 20 20 0 1608 26 26 0 1641 28 28 0 1890 1 27 1 1 1 0 0 0 1 228 2 2 1 472 3 3 1 650 4 4 1 931 5 5 1 1040 6 6 1 1169 8 8 1 1361 9 9 1 1542 10 10 1 1886 11 11 1 2018 12 12 1 2209 13 13 1 2315 14 14 1 2430 16 16 1 2566 17 17 1 2675 18 18 1 2813 19 19 1 2915 20 20 1 3023 21 21 1 3056 22 22 1 3089 24 24 1 3192 26 26 1 3378 27 27 1 3527 28 28 1 3740 29 29 1 3844 30 30 1 3957 2 11 2 2 2 0 4 4 2 203 6 6 2 523 10 10 2 646 12 12 2 944 14 14 2 1128 18 18 2 1231 20 20 2 1342 22 22 2 1452 28 28 2 1485 30 30 2 1674 ........................................... |
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wangcui2011
金蟲 (小有名氣)
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2樓2012-09-17 16:55:56
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看看這個有用不 #! /bin/python # This script converts amber rst to nwchem rst format. class NwFmtRst(): def __init__(self): self.overflow_flag = 0 self.filename = "nw.rst" self.topname = "nw.top" self.title = "" self.hist = "" self.atomnum = -1 self.MAXATOM = 100000 self.rst = {} self.rst['coord'] = 1 self.rst['vel'] = 1 self.rst['box'] = 1 self.atom = {} self.atom['coord'] = [] self.atom['vel'] = [] self.atom['box'] = [] self.dim = {} # crystal solvent(c) and not crystal solvent(x) # element key: coord, vel, iwm self.wmc = {} self.wmc['coord'] = [] self.wmc['vel'] = [] self.wmc['iwm'] = [] self.wmx = {} self.wmx['coord'] = [] self.wmx['vel'] = [] self.wmx['iwm'] = [] # solute atom # dic key: coord, vel, isar, ips self.solute = {} self.solute['coord'] = [] self.solute['vel'] = [] self.solute['isar'] = [] self.solute['ips'] = [] # @ Initialize the top related variables. self.top = {} self.top['dim'] = {} print """ ------------------------------------------------------- @Comment: This is amber/nwchem Interface. Just a format Converter. @Address: Come form chem306. @Date: 2010/03/25 ------------------------------------------------------- """ def __rd_rst_atom(self, fin): """ read a section in rst/crd file, i.e. coordinate/vel ... This is a private type func... """ # read amb atom coord and vel (optional) natom = self.atomnum atom = [] i = 0 line = fin.readline() nline = len(line) while line!="" and i < natom: # now, a very strange test: # see ./src/antechamber/rst.c for reference. &_& if line[4] == ".": x = float(line[0:12]) y = float(line[12:24]) z = float(line[24:36]) coord = [x, y, z] atom.append(coord) i = i+1 else: print "format error" break # then, again another three if nline > 48 and line[40] == ".": x = float(line[36:48]) y = float(line[48:60]) z = float(line[60:72]) coord = [x, y, z] atom.append(coord) i = i+1 else: print "Maybe, end of file. [X]" print "current line is :\n" + line break; line = fin.readline() nline = len(line) print "end of this section" print "total number of atom is %d, and current number is %d" % (natom, i) return atom def __rd_rst_dim(self, fin): """ read in dimensional info. """ # @comment: dimensions on the restart file # c # c 1 i10 nwm number of solvent molecules # c 2 i10 nwa number of atoms per solvent molecule # c 3 i10 nsm number of solute molecules # c 4 i10 nsa number of solute atoms # c 5 i10 nwmc number of crystal solvent molecules # c 6 i10 nsf number of solute fractions # c 7 i10 nss number of solute segments # c 8 i5 nprev number of processors used in previous job # c 9 i5 noe number of noe constraints # c # c 6 & 8 may be useless, and rdrst do not read it # c line = fin.readline() dim = {} dim['nwm'] = int(line[0:10]) dim['nwa'] = int(line[10:20]) dim['nsm'] = int(line[20:30]) dim['nsa'] = int(line[30:40]) dim['nwmc'] = int(line[40:50]) dim['nsf'] = int(line[50:60]) dim['nss'] = int(line[60:70]) dim['nprev'] = int(line[70:75]) dim['noe'] = int(line[75:80]) # print dim return dim def __rd_rst_nwm(self, fin, xc): """ read in solvent molecules crystal or not """ nwm = self.dim['nwm'] nwmc = self.dim['nwmc'] nwa = self.dim['nwa'] w = {} w['coord'] = [] w['vel'] = [] w['iwm'] = [] # checking ... if xc == "c": nw = nwmc else: nw = nwm - nwmc if nw <= 0: print xc + " water is zero: Noting Done" # reading... if nwm > 0: for i in range(nw): for j in range(nwa): line = fin.readline() cx = float(line[2:15]) cy = float(line[15:28]) cz = float(line[28:41]) vx = float(line[41:54]) vy = float(line[54:67]) vz = float(line[67:80]) coord = [cx, cy, cz] vel = [vx, vy, vz] w['coord'].append(coord) w['vel'].append(vel) # if lforces, IGNORE # read iwrc line = fin.readline() i = int(line[0:1]) w['iwm'].append(i) return w def __rd_rst_solute(self, fin): """ read in solute molecules """ nsa = self.dim['nsa'] s = {} s['coord'] = [] s['vel'] = [] s['isar'] = [] s['ips'] = [] # checking ... if nsa <= 0: print "Number of solute atom is zero: Noting Done" # reading... if nsa > 0: for i in range(nsa): line = fin.readline() cx = float(line[2:15]) cy = float(line[15:28]) cz = float(line[28:41]) vx = float(line[41:54]) vy = float(line[54:67]) vz = float(line[67:80]) isar = int(line[0:1]) ips = int(line[80:85]) coord = [cx, cy, cz] vel = [vx, vy, vz] # if lforces, IGNORE s['coord'].append(coord) s['vel'].append(vel) s['isar'].append(isar) s['ips'].append(ips) return s def rd_rst(self, filename="nw.rst"  :""" open and read amber rst file. this can be use for nwchem version >=4.6 thanks for pre_rdrst.F#rdrst and pre_wrtrst#wrtrst and for version 3.1, maybe one can refer the sub rrst and wtrst. """ self.filename = filename try: fin = open(filename, "r" except: print "Error: while opening " + filename exit(1) ### read in nw rst file # read nw title; jump three line line=fin.readline() self.title += line line=fin.readline() self.title += line line=fin.readline() self.title += line # print self.title # read some tedious info. # rdummy means useless var. here # copy from pre_rdrst.F in prepar@nwchem line=fin.readline() rdummy = float(line[0:12]) rstdat = line[12:22] rdtim = line[22:32] nhist = int(line[32:37]) lforces = line[41:42] # print rstdat, rdtim, nhist, lforces # U know, i have read nhist, which is the record for previous calc. type # then if nhist > 0, i should read the hist entity. Now checking and reading hist... if nhist > 0: for i in range(nhist): dummy = fin.readline() self.hist += dummy # print self.hist # read in pbc type[period/vacuum], box type, and box dimension # i think argos md code is not in a good code style. Bad bad very bad... # Nwchem argos md module is tedious... pay more attention to understand it, if you want. line = fin.readline() npbtyp = int(line[0:5]) nbxtyp = int(line[5:10]) rsgm = float(line[10:22]) # This variable is not useful in current version. bad # read box dimen. remember to jump the useless zero line = fin.readline() x = float(line[0:12]) line = fin.readline() y = float(line[12:24]) line = fin.readline() z = float(line[24:36]) # print x, y, z # read a dummy line, contain format(e12.5) line = fin.readline() dummy = float(line[0:12]) # print dummy # read another dummy line, contain format(3f12.6) line = fin.readline() # @ read the dimensional info. self.dim = self.__rd_rst_dim(fin) # @ Finally, now, we can read the coordinates. # ... read crystal/not crystal solvent first self.nwc = self.__rd_rst_nwm(fin, "c" self.nwx = self.__rd_rst_nwm(fin, "x" # read solute atom self.solute = self.__rd_rst_solute(fin) # read solute molecule, IGNORE in this verion # read solute seq, IGNORE in this verion fin.close() return def wrt_rst(self, filename="nwout.rst" :""" write out amber rst file. haha """ ### Exception checking... try: fout = open(filename, "w" except: print "Error: while opening " + filename exit(1) fout.close() return rst = NwFmtRst() rst.rd_rst("crown.rst" rst.wrt_rst() |
3樓2012-09-18 19:34:25
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#! /bin/python # This script converts amber rst to nwchem rst format. class NwFmtRst(): def __init__(self, filename='crown.rst'): # file pointer if filename == '': self.filename = "crown.rst" else: self.filename = filename self.fp = {'input': '', 'output': ''} self.fpin = self.fp['input'] self.fpout = self.fp['output'] self.atomnum = -1 self.MAXATOM = 100000 # data structure of rst file format self.rst = {} # title self.rst['title'] = [] self.rst['hist'] = {} self.rst['coord'] = 1 self.rst['vel'] = 1 self.rst['box'] = 1 self.atom = {} self.atom['coord'] = [] self.atom['vel'] = [] self.atom['box'] = [] self.dim = {} # crystal solvent(c) and not crystal solvent(x) # element key: coord, vel, iwm self.wmc = {} self.wmc['coord'] = [] self.wmc['vel'] = [] self.wmc['iwm'] = [] self.wmx = {} self.wmx['coord'] = [] self.wmx['vel'] = [] self.wmx['iwm'] = [] # solute atom # dic key: coord, vel, isar, ips self.solute = {} self.solute['coord'] = [] self.solute['vel'] = [] self.solute['isar'] = [] self.solute['ips'] = [] # @ Initialize the top related variables. self.top = {} self.top['dim'] = {} print """ ------------------------------------------------------- @Comment: This is amber/nwchem Interface. Just a format Converter. @Address: Come form chem306. @Date: 2012/03/25 ------------------------------------------------------- """ def __open_file(self, filename, mode='r'): """ ### Exception checking... """ try: fp = open(filename, mode) except: print "Error: while opening " + filename exit(1) return fp # >S rd/wrt title $ def __rd_rst_title(self): """ first three line about title info. """ fpin = self.fpin # read nw title; jump three line self.rst['title'].append(fpin.readline()[:-1]) self.rst['title'].append(fpin.readline()[:-1]) self.rst['title'].append(fpin.readline()[:-1]) return def __rd_rst_hist(self): """ the history info. about previous calc. """ fpin = self.fpin # read nw version, date, time, nhist, lforces, and hist... # rdummy means useless var. here # line=fpin.readline() self.top['hist']['version'] = float(line[0:12]) self.top['hist']['rstdate'] = line[12:22] self.top['hist']['rdtime'] = line[22:32] self.top['hist']['nhist'] = int(line[32:37]) self.top['hist']['lforces'] = line[41:42] self.top['hist']['content'] = [] # i have read nhist, which is the record for previous calc. type # then if nhist > 0, i should read the hist entity. Now checking and reading hist... if nhist > 0: for i in range(nhist): dummy = fin.readline() self.top['hist']['content'].append(dummy) return def __rd_rst_pbc(self): """ read in pbc type[period/vacuum], box type, and box dimension """ # % pbctype = npbtyp in pre_wrtrst.F # c 1 for periodic, while 0 for vacuum. # c # % boxtype = nbxtyp # c 0 for cube/box/sphere, 2 for troct : [default: 0] # % rsgm # c see manual md section : program control options. # segmentsize # sets the maximum size of a segment. This value is used to # determine which segments at the boundary of the cutoff radius # should be considered in the generation of the pairlists. # This value is also determined by the prepare module and # written to the restart file. # Use of this directive is not needed for simulations that use the current # prepare module to generate the restart file. # % boxsize # box size info. # 2.000000 0.000000 0.000000 # 0.000000 2.000000 0.000000 # 0.000000 0.000000 2.000000 # c # Nwchem argos md module is tedious... # pay more attention to understand it, if you want. # c line = fin.readline() pbctype = int(line[0:5]) boxtype = int(line[5:10]) rsgm = float(line[10:22]) # read box dimen. remember to jump the useless zero x = float(fin.readline()[0:12]) y = float(fin.readline()[12:24]) z = float(fin.readline()[24:36]) self.rst['sys']['pbctype'] = pbctype self.rst['sys']['boxtype'] = boxtype self.rst['sys']['rsgm'] = rsgm self.rst['sys']['box'] = [x, y, z] # print x, y, z return def __rd_rst_atom(self, fin): """ read a section in rst/crd file, i.e. coordinate/vel ... This is a private type func... """ # read amb atom coord and vel (optional) natom = self.atomnum atom = [] i = 0 line = fin.readline() nline = len(line) while line!="" and i < natom: # now, a very strange test: # see ./src/antechamber/rst.c for reference. &_& if line[4] == ".": x = float(line[0:12]) y = float(line[12:24]) z = float(line[24:36]) coord = [x, y, z] atom.append(coord) i = i+1 else: print "format error" break # then, again another three if nline > 48 and line[40] == ".": x = float(line[36:48]) y = float(line[48:60]) z = float(line[60:72]) coord = [x, y, z] atom.append(coord) i = i+1 else: print "Maybe, end of file. [X]" print "current line is :\n" + line break; line = fin.readline() nline = len(line) print "end of this section" print "total number of atom is %d, and current number is %d" % (natom, i) return atom def __rd_rst_dim(self, fin): """ read in dimensional info. """ # @comment: dimensions on the restart file # c # c 1 i10 nwm number of solvent molecules # c 2 i10 nwa number of atoms per solvent molecule # c 3 i10 nsm number of solute molecules # c 4 i10 nsa number of solute atoms # c 5 i10 nwmc number of crystal solvent molecules # c 6 i10 nsf number of solute fractions # c 7 i10 nss number of solute segments # c 8 i5 nprev number of processors used in previous job # c 9 i5 noe number of noe constraints # c # c 6 & 8 may be useless, and rdrst do not read it # c line = fin.readline() dim = {} dim['nwm'] = int(line[0:10]) dim['nwa'] = int(line[10:20]) dim['nsm'] = int(line[20:30]) dim['nsa'] = int(line[30:40]) dim['nwmc'] = int(line[40:50]) dim['nsf'] = int(line[50:60]) dim['nss'] = int(line[60:70]) dim['nprev'] = int(line[70:75]) dim['noe'] = int(line[75:80]) # print dim return dim def __rd_rst_nwm(self, fin, xc): """ read in solvent molecules crystal or not """ nwm = self.dim['nwm'] nwmc = self.dim['nwmc'] nwa = self.dim['nwa'] w = {} w['coord'] = [] w['vel'] = [] w['iwm'] = [] # checking ... if xc == "c": nw = nwmc else: nw = nwm - nwmc if nw <= 0: print xc + " water is zero: Noting Done" # reading... if nwm > 0: for i in range(nw): for j in range(nwa): line = fin.readline() cx = float(line[2:15]) cy = float(line[15:28]) cz = float(line[28:41]) vx = float(line[41:54]) vy = float(line[54:67]) vz = float(line[67:80]) coord = [cx, cy, cz] vel = [vx, vy, vz] w['coord'].append(coord) w['vel'].append(vel) # if lforces, IGNORE # read iwrc line = fin.readline() i = int(line[0:1]) w['iwm'].append(i) return w def __rd_rst_solute(self, fin): """ read in solute molecules """ nsa = self.dim['nsa'] s = {} s['coord'] = [] s['vel'] = [] s['isar'] = [] s['ips'] = [] # checking ... if nsa <= 0: print "Number of solute atom is zero: Noting Done" # reading... if nsa > 0: for i in range(nsa): line = fin.readline() cx = float(line[2:15]) cy = float(line[15:28]) cz = float(line[28:41]) vx = float(line[41:54]) vy = float(line[54:67]) vz = float(line[67:80]) isar = int(line[0:1]) ips = int(line[80:85]) coord = [cx, cy, cz] vel = [vx, vy, vz] # if lforces, IGNORE s['coord'].append(coord) s['vel'].append(vel) s['isar'].append(isar) s['ips'].append(ips) return s def rd_rst(self): """ open and read amber rst file. this can be use for nwchem version >=4.6 thanks for pre_rdrst.F#rdrst and pre_wrtrst#wrtrst and for version 3.1, maybe one can refer the sub rrst and wtrst. """ self.fpin = self.__open_file(self.filename, mode='r') ### read in nw rst file # read nw title; jump three line self.__rd_rst_title() # read version, time .. hist. info. self.__rd_rst_hist() # read in pbc type[period/vacuum], box type, and box dimension # i think argos md code is not in a good code style. Bad bad very bad... # Nwchem argos md module is tedious... pay more attention to understand it, if you want. line = fin.readline() npbtyp = int(line[0:5]) nbxtyp = int(line[5:10]) rsgm = float(line[10:22]) # This variable is not useful in current version. bad # read box dimen. remember to jump the useless zero line = fin.readline() x = float(line[0:12]) line = fin.readline() y = float(line[12:24]) line = fin.readline() z = float(line[24:36]) # print x, y, z # read a dummy line, contain format(e12.5) line = fin.readline() dummy = float(line[0:12]) # print dummy # read another dummy line, contain format(3f12.6) line = fin.readline() # @ read the dimensional info. self.dim = self.__rd_rst_dim(fin) # @ Finally, now, we can read the coordinates. # ... read crystal/not crystal solvent first self.nwc = self.__rd_rst_nwm(fin, "c" self.nwx = self.__rd_rst_nwm(fin, "x" # read solute atom self.solute = self.__rd_rst_solute(fin) # read solute molecule, IGNORE in this verion # read solute seq, IGNORE in this verion fin.close() return def wrt_rst(self, filename="nwout.rst" :""" write out amber rst file. haha """ ### Exception checking... try: fout = open(filename, "w" except: print "Error: while opening " + filename exit(1) fout.close() return rst = NwFmtRst("crown.rst" rst.rd_rst() rst.wrt_rst() |
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wangcui20114樓2012-09-18 19:42:29
wangcui2011
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。 5樓2012-09-19 11:04:15
wangcui2011
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非常感謝！ 6樓2012-09-19 11:11:40
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