def webData(self):
"""
Returns 2 strings with HTML code
"""
# Show weird bond angles topology
we = self.settings.Engine3D()
b1, b2 = '', ''
# b1:
# 1. use 3D geom
# 2. if not available, make 2D picture,
# 3. if not available, make ASCII pseudographics
# ...
#b2 += 'Version: %s' % (self.NBO_version) + web.brn
if self.options:
b2 += web.tag('NBO options:', 'strong') + web.brn
b2 += self.options + web.brn
if self.comments:
b2 += self.comments + web.brn
if self.OpenShell:
b2 += web.tag('Alpha spin NBO interactions', 'strong') + web.brn
b2 += self.setA.webData()
b2 += web.tag('Beta spin NBO interactions', 'strong') + web.brn
b2 += self.setB.webData()
else:
b2 += web.tag('NBO interactions', 'strong') + web.brn
b2 += self.setAB.webData()
log.debug('webData generated successfully')
return b1, b2
def webData(self):
"""
Returns 2 strings with HTML code
"""
# Show weird bond angles topology
we = self.settings.Engine3D()
b1, b2 = '', ''
# b1:
# 1. use 3D geom
# 2. if not available, make 2D picture,
# 3. if not available, make ASCII pseudographics
# ...
#b2 += 'Version: %s' % (self.NBO_version) + web.brn
if self.options:
b2 += web.tag('NBO options:','strong')+web.brn
b2 += self.options + web.brn
if self.comments:
b2 += self.comments + web.brn
if self.OpenShell:
b2 += web.tag('Alpha spin NBO interactions','strong') + web.brn
b2 += self.setA.webData()
b2 += web.tag('Beta spin NBO interactions','strong') + web.brn
b2 += self.setB.webData()
else:
b2 += web.tag('NBO interactions','strong') + web.brn
b2 += self.setAB.webData()
log.debug('webData generated successfully')
return b1, b2
def webData(self):
"""
Makes HTML row.
If some parameteres were read from comment sections of .xyz files,
graph is plotted
return: b1,b2
"""
we = self.settings.Engine3D()
JmolScript = ''
b2 = web.tag('Comments:', 'strong') + web.brn + self.geoms.comment
if self.scan:
b2 += self.scan.webData()
JmolScript += we.measureGau(self.scan.props)
self.wp = self.scan.write(fname='.xyz', vectors=self.vector)
else:
self.wp = self.geoms.write(fname='.xyz', vectors=self.vector)
b1 = we.JMolApplet(webpath=self.wp, ExtraScript=JmolScript) + web.brn
if len(self.geoms.geoms) > 1:
b1 += we.MultipleGeoms()
elif self.vector:
b1 += we.JMolCheckBox('vibration on', 'vibration off', 'Vibration')
log.debug('webData generated successfully')
return b1, b2
def JMolRadioGroup(self, options):
s = ''
for opt in options:
s2 = ''
for o in opt:
s2 += '"%s", ' % (o)
s += '[%s],' % (s2[:-2])
s = 'jmolRadioGroup([%s])' % (s[:-1])
return web.tag(s,'SCRIPT')
def JMolMenu(self, options,script=True):
s = ''
for opt in options:
s2 = ''
for o in opt: s2 += '"%s", ' % (o)
s += '[%s],' % (s2[:-2])
s = 'jmolMenu([%s])' % (s[:-1])
if script:
s = web.tag(s,'SCRIPT')
return s
def MultipleGeoms(self):
s = """jmolButton("frame 1","<<");
jmolButton("anim direction +1 ; frame prev","<");
jmolButton("anim direction +1 ; frame next",">");
jmolButton("anim direction +1 ;frame last",">>");
jmolButton("anim mode once; frame 1; anim direction +1 ; anim on", "Play once");
jmolButton("anim mode once; frame last ; anim direction -1 ; anim on", "Play back");
jmolButton("anim off", "Stop");
"""
opts = []
for a in (1,5,10,25,50):
opts.append(['set animationFPS %s' % (a), a])
opts[2].append('checked')
s += self.JMolMenu(opts,script=False)
return web.tag(s,'SCRIPT')
def JMolCheckBox(self, on, off, label=''):
s = 'jmolCheckbox("%s", "%s", "%s")' % (on, off, label)
return web.tag(s,'SCRIPT')
def JMolText(self,label,position='top left',color='green',script=True):
s = "set echo %s; color echo %s; echo %s;" % (position,color,label)
if script:
s = web.tag(s,'SCRIPT')
return s
def JMolCommandInput(self):
s = 'jmolCommandInput("Execute")'
return web.tag(s,'SCRIPT')
f.write(self.s)
f.close()
log.debug('Web page %s was created' % (file))
def finalize(self):
d = {
'JSMolPath' : self.settings.JSMolLocation,
'timestamp' : self.settings.timestamp,
'JMolPath' : self.settings.JmolPath,
'pageBody' : self.pageBody,
'JMolWinX' : self.settings.JMolWinX,
'JMolWinY' : self.settings.JMolWinY,
}
self.s = self.s % d
if __name__ == "__main__":
h = HTML()
from Settings import Settings
h.settings = Settings()
tr = web.tag('abcd','tr')
# This code is outdated!
h.makeHeader()
h.makeLine('abc','def')
h.makeTail()
print h
def JMolApplet(self, webpath='', ExtraScript=''):
s = "jmolApplet%s = Jmol.getApplet(\"jmolApplet%s\", Info)" % ((self.settings.counter,)*2)
script = self.JMolLoad(webpath=webpath,ExtraScript=ExtraScript)
s += ';\n' + self.JSMolStyle(script)
return web.tag(s,'SCRIPT')
def addLeftDiv(self, *args):
left_panel = ''
for a in args:
left_panel += web.tag(a, 'div', "class='left_panel'") + '\n'
return left_panel
except IOError:
log.critical('Cannot open %s for writing' % (file))
return
f.write(self.s)
f.close()
log.debug('Web page %s was created' % (file))
def finalize(self):
d = {
'JSMolPath': self.settings.JSMolLocation,
'timestamp': self.settings.timestamp,
'JMolPath': self.settings.JmolPath,
'pageBody': self.pageBody,
'JMolWinX': self.settings.JMolWinX,
'JMolWinY': self.settings.JMolWinY,
}
self.s = self.s % d
if __name__ == "__main__":
h = HTML()
from Settings import Settings
h.settings = Settings()
tr = web.tag('abcd', 'tr')
# This code is outdated!
h.makeHeader()
h.makeLine('abc', 'def')
h.makeTail()
print h
def webData(self,StartApplet=True):
we = self.settings.Engine3D()
io = IO()
color = {'err':'red', 'imag':'blue', 'lot':'green'}
b2, JmolScript = '', ''
comments = []
if self.JobType:
sx = self.JobType.upper()
if 'irc' in self.JobType:
sx += ' ' + self.series.textDirection()
sx = web.br + web.tag(sx,'strong')
if self.OK:
b2 += sx
else:
b2 += web.tag(sx,"SPAN style='color:%s'" % (color['err']))
if self.lot:
if self.basis:
self.lot += '/' + self.basis
b2 += web.br + web.tag(self.lot.upper(),"SPAN style='color:%s'" % (color['lot']))
if self.solvent:
sx = 'Solvation: '
if self.solv_model:
sx += '%s(%s)' % (self.solv_model, self.solvent)
else:
sx += self.solvent
b2 += web.br + web.tag(sx,"SPAN style='color:%s'" % (color['lot']))
if self.sym:
b2 += web.br + "Symmetry: %s\n" % (self.sym)
if self.charge:
b2 += web.br + "Charge: %s; " % (self.charge)
if self.mult:
b2 += "Mult: %s\n" % (self.mult)
if self.lot and not self.lot.find('R')==0:
b2 += web.br + "S2= %s,\n" % (self.s2)
if self.scf_e:
b2 += web.br + "E_SCF= %-11.6f\n" % (self.scf_e)
if self.amplitude:
f_ampl = float(self.amplitude)
s_ampl = '%.3f' % (f_ampl)
if f_ampl >= 0.1:
sx = web.tag(s_ampl,"SPAN style='color:%s'" % (color['err']))
else:
sx = s_ampl
b2 += web.br + "Max Amplitude= %s\n" % (sx)
# Add pics for SP
if 'sp' in self.JobType and not self.OK:
wftype = ''
if not self.ci_cc_done:
wftype = 'ci_cc'
if not self.scf_done:
wftype = 'scf'
if wftype:
b2 += web.br + wftype + ' not converged...'
y = getattr(self,wftype+'_conv')
picpath = io.writePic('-sp-conv.png',xname='Step N',yname='E, '+self.settings.EnergyUnits,y=y)
b2 += web.img(picpath)
# Freq
if 'freq' in self.JobType:
# Give thermochemistry values
for i in range(len(self.freq_temp)):
b2 += web.br + "T=%6.2f: H= %10.6f, E+ZPE= %10.6f, G= %10.6f\n" \
% (self.freq_temp[i],self.freq_ent[i],self.freq_zpe[i],self.freq_G[i])
if self.freqs:
# Show freqs
b2 += web.br + "Freqs: "
# Color i-freqs
i = 0
while self.freqs[i] < 0:
s_freq = "% .1f," % (self.freqs[i])
if i == 0:
col = 'imag'
else:
col = 'err'
b2 += web.tag(s_freq, "SPAN style='color:%s'" % (color[col]))
i += 1
b2 += "%.1f .. %.1f\n" % (self.freqs[i], self.freqs[-1])
if self.nimag > 0:
b2 += web.brn + web.tag('Imaginary Freq(s) found!',"SPAN style='color:%s'" % (color['imag']))
# Frozen
if self.frozen:
frs = self.frozen.values()
self.extra += web.br + 'Frozen parameters detected (highlighted with measurement lines)'
JmolScript += we.measureGau(frs)
if len(frs)>3:
JmolScript += 'set measurementlabels off;'
# Opt
if 'opt' in self.JobType:
b2 += web.br + web.tag('NOpt=%i' % (self.opt_iter),'em')
if not self.opt_ok:
b2 += web.br + "Stationary Point not found!\n"
if (not self.OK) or self.settings.FullGeomInfo:
sg = self.geoms
y = [sg.toBaseLine(), sg.max_force, sg.rms_force, sg.max_displacement, sg.rms_displacement]
ylabel = 'E, %s' % (self.settings.EnergyUnits)
picpath = io.writePic('-opt-conv.png',
xname='Step N',yname=ylabel,
keys=['E','Max Force', 'RMS Force', 'Max Displacement', 'RMS Displacement'],
y=y,ny2=4
)
b2 += web.img(picpath)
#b2 += self.geoms.plot(xlabel='Opt point')
# IRC
if 'irc' in self.JobType:
b2 += self.series.webData()
comments = self.series.comments
# Scan
if 'scan' in self.JobType:
#print self.series.props
b2 += self.series.webData()
JmolScript += we.measureGau(self.series.props)
# TD DFT
if 'td' in self.JobType and self.uv:
b2 += web.brn + web.tag('UV Spectra','em') + web.brn
for w in sorted(self.uv):
#if w > 1000.:
if self.uv[w] > 0.01:
b2 += "%s %s\n" % (w, self.uv[w]) + web.brn
b2 += web.brn
#
# Charges
#
sx = ''
for i in range(len(self.geoms)):
g = self.geoms[i]
if g.atprops:
sx += 'Structure %i: ' % (i+1)
for ap in g.atprops:
sx += getattr(g,ap).webData()
sx += we.JMolButton('label off;color atoms cpk','Off') + web.brn
if self.settings.full and hasattr(g,'nbo_analysis'):
nbo_b1,nbo_b2 = g.nbo_analysis.webData()
sx += nbo_b2
b2 += web.brn + sx
# NBO Topology
nbobonds = ''
bo = ('-','S','D','T','Q')
if self.topologies:
pass
# TODO write this topology to MOL file
#for i in self.nbo_topology:
#for j in self.nbo_topology[i]:
#nbobonds += "%s %s %s " % (bo[self.nbo_topology[i][j]],i,j)
if self.comments:
b2 += web.br + web.tag('Comments','strong') + ":%s\n" % self.comments
if self.warnings:
b2 += web.br + web.tag('Warnings','strong') + ":%s\n" % self.warnings
if self.extra:
b2 += web.br + web.tag(self.extra,'em')
b2 += web.br
#
# ----- b1 -----
#
#if self.nbo_topology and not self.vectors:
wp = self.geoms.write(fname='.xyz', vectors=self.vector)
labeltext = '%s: %s' %(self.JobType,self.lot)
if StartApplet:
JmolScript += '; ' + we.JMolText(label=labeltext.upper(),script=False)
#JmolScript += '; ' + we.JMolText(label='model %{_modelNumber}',position='bottom left', script=False)
JmolScript += '; ' + we.JMolText(label='model _modelNumber',position='bottom left', script=False)
b1 = we.JMolApplet(webpath=wp, ExtraScript = JmolScript)
b1 += web.brn + we.JMolCommandInput()
if len(self.geoms)>1:
b1 += web.brn + we.MultipleGeoms()
else:
b1 = we.JMolLoad(webpath=wp, ExtraScript=JmolScript)
b1 += '; ' + we.JMolText(label=labeltext.upper(),script=False)
#b1 += '; ' + we.JMolText(label='model %{_modelNumber}',position='bottom left', script=False)
b1 += '; ' + we.JMolText(label='model _modelNumber',position='bottom left', script=False)
log.debug('webData for Gaussian step generated successfully')
return b1, b2
def addDivRowWrapper(self,*args):
row = ''
for a in args:
row += a
self.pageBody += web.tag(row,'div',"class='row_wrapper'")
def addRightDiv(self,*args):
right_panel = ''
for a in args:
right_panel += web.tag(a,'div',"class='right_panel'")+'\n'
return right_panel
def addLeftDiv(self,*args):
left_panel = ''
for a in args:
left_panel += web.tag(a,'div',"class='left_panel'")+'\n'
return left_panel
def JMolButton(self, action, label):
s = 'jmolButton("%s","%s")' % (action, label)
return web.tag(s,'SCRIPT')
def addRightDiv(self, *args):
right_panel = ''
for a in args:
right_panel += web.tag(a, 'div', "class='right_panel'") + '\n'
return right_panel
def addDivRowWrapper(self, *args):
row = ''
for a in args:
row += a
self.pageBody += web.tag(row, 'div', "class='row_wrapper'")
def JMolApplet(self, webpath='', ExtraScript=''):
script = self.JMolLoad(webpath=webpath,ExtraScript=ExtraScript)
s = 'jmolApplet([%s,%s],"%s")' % (self.settings.JmolWinX, self.settings.JmolWinY, script)
return web.tag(s,'SCRIPT')
def JSMolScript(self, s, intag=''):
s2 = self.JSMolStyle(s)
return web.tag(s2, 'SCRIPT', intag=intag)
def JSMolScript(self, s, intag=''):
s2 = self.JSMolStyle(s)
return web.tag(s2,'SCRIPT',intag=intag)
def Vibration(self):
s = 'jmolCheckbox("vibration on", "vibration off", "Vibration");'
return web.tag(s,'SCRIPT')
def webData(self):
"""
Returns 2 strings with HTML code
"""
# Show weird bond angles topology
we = self.settings.Engine3D()
Lb1, Lb2 = self.L.webData()
Cb1, Cb2 = self.C.webData()
b1 = Lb1
b2 = web.tag('Gaussian Log File','strong')+web.brn + Lb2
b2 += web.tag('Gaussian Chk File','strong')+web.brn + Cb2
#---
def set_webData(nbo_result):
s = ''
any_shown = False
script_off = 'isosurface off; '
if 't' in self.file:
threshold = float(self.file['t'])
else:
threshold = float(self.settings.inbo_threshold)
cubes_done = {}
for sopta in nbo_result.sopta:
if float(sopta.e2) > threshold:
any_shown = True
s += '%s -> %s: %s kcal/mol' % (sopta.donor.sorb, sopta.acceptor.sorb, sopta.e2)
i_donor = str(sopta.donor.chk_index)
if i_donor in cubes_done:
c_donor = cubes_done[i_donor]
else:
c_donor = self.C.fchk.makeCube('MO='+i_donor, name='mo'+i_donor)
i_acceptor = str(sopta.acceptor.chk_index)
if i_acceptor in cubes_done:
c_acceptor = cubes_done[i_acceptor]
else:
c_acceptor = self.C.fchk.makeCube('MO='+i_acceptor, name='mo'+i_acceptor,colors='phase green yellow')
script = "%s ; %s ; %s" % (script_off, c_donor.s_script, c_acceptor.s_script)
#script += we.JMolIsosurface(webpath = c_donor.wpcube, surftype='MO',name='mo'+i_donor)
#script += "; "
#script += we.JMolIsosurface(webpath = c_acceptor.wpcube, surftype='MO',name='mo'+i_acceptor,colors='phase green yellow')
s += we.JMolButton(action=script,label='Show')
s += web.brn
if any_shown:
s += we.JMolButton(action=script_off,label='Off')
return s
#---
if self.nbo.options:
b2 += web.tag('Options:','strong')+web.brn
b2 += self.nbo.options + web.brn
if self.nbo.comments:
b2 += self.nbo.comments + web.brn
if self.nbo.OpenShell:
b2 += web.tag('Alpha spin NBO interactions','strong') + web.brn
b2 += set_webData(self.nbo.setA)
b2 += web.tag('Beta spin NBO interactions','strong') + web.brn
b2 += set_webData(self.nbo.setB)
else:
b2 += web.tag('NBO interactions','strong') + web.brn
b2 += set_webData(self.nbo.setAB)
log.debug('webData generated successfully')
return b1, b2
def JMolApplet(self, webpath='', ExtraScript=''):
s = "jmolApplet%s = Jmol.getApplet(\"jmolApplet%s\", Info)" % (
(self.settings.counter, ) * 2)
script = self.JMolLoad(webpath=webpath, ExtraScript=ExtraScript)
s += ';\n' + self.JSMolStyle(script)
return web.tag(s, 'SCRIPT')