def parse(self):
if 'c' in self.file:
if not is_readable(self.file['c']):
return
chk = ChkGaussian()
chk.file = self.file['c']
self.surface = chk.formchk()
elif 'f' in self.file:
if not is_readable(self.file['f']):
return
self.surface = FchkGaussian()
self.surface.file = self.file['f']
elif 'cb' in self.file:
if not is_readable(self.file['cb']):
return
self.surface = Cube()
self.surface.file = self.file['cb']
else:
log.error('No Gaussian Checkpoint file name provided')
self.surface.isotype = self.file['type']
if 'iv' in self.file:
self.surface.isovalue = self.file['iv']
self.surface.parse()
def parse(self):
#self.file = self.file[0]
if not 'l' in self.file:
log.error('NBOinteraction requires Gaussian .log file as input')
return
self.fileL = self.file['l']
if not is_readable(self.fileL):
return
self.L.file = self.fileL
if 'c' in self.file:
self.fileC = self.file['c']
else:
log.debug('Gaussian checkpoint file name is not provided in the input; trying to guess...')
self.fileC = self.LookUpChkInLog()
if self.fileC:
log.debug('Checkpoint file found: %s' % (self.fileC))
else:
self.fileC = self.LookUpByBasename()
if not is_readable(self.fileC):
return
self.C.file = self.fileC
self.L.parse()
self.C.parse()
def parse(self,WebPath='',ToBeCopied = True):
# Check if .jvxl is readable
if not 'j' in self.file:
log.error('JVXL file is needed')
return
self.fileJ = self.file['j']
if not is_readable(self.fileJ):
log.warning('JVXL file is not readable')
return
# Parse XYZ File
if 'x' in self.file:
self.fileX = self.file['x']
else:
log.debug('XYZ file name is not provided in the input; trying to guess...')
self.fileX = self.LookUpByBasename()
if is_readable(self.fileX):
log.debug('XYZ file found: %s' % (self.fileX))
else:
log.warning('XYZ file is not readable')
return
self.X.file = self.fileX
self.X.parse()
# Copy JVXL file
rp = self.settings.real_path('.jvxl')
shutil.copy(self.fileJ,rp)
self.wp = self.settings.web_path('.jvxl')
def parse(self):
if 'c' in self.file:
if not is_readable(self.file['c']):
return
chk = ChkGaussian()
chk.file = self.file['c']
self.surface = chk.formchk()
elif 'f' in self.file:
if not is_readable(self.file['f']):
return
self.surface = FchkGaussian()
self.surface.file = self.file['f']
elif 'cb' in self.file:
if not is_readable(self.file['cb']):
return
self.surface = Cube()
self.surface.file = self.file['cb']
else:
log.error('No Gaussian Checkpoint file name provided')
self.surface.isotype = self.file['type']
if 'iv' in self.file:
self.surface.isovalue = self.file['iv']
self.surface.parse()
def parse(self, WebPath='', ToBeCopied=True):
# Check if .jvxl is readable
if not 'j' in self.file:
log.error('JVXL file is needed')
return
self.fileJ = self.file['j']
if not is_readable(self.fileJ):
log.warning('JVXL file is not readable')
return
# Parse XYZ File
if 'x' in self.file:
self.fileX = self.file['x']
else:
log.debug(
'XYZ file name is not provided in the input; trying to guess...'
)
self.fileX = self.LookUpByBasename()
if is_readable(self.fileX):
log.debug('XYZ file found: %s' % (self.fileX))
else:
log.warning('XYZ file is not readable')
return
self.X.file = self.fileX
self.X.parse()
# Copy JVXL file
rp = self.settings.real_path('.jvxl')
shutil.copy(self.fileJ, rp)
self.wp = self.settings.web_path('.jvxl')