def from_mdin(cls, mdin_name, engine='sander'):
"""Read an AMBER mdin file and return an AmberMdin object."""
# Separate the namelists as a NamelistCollection and convert to a
# list of AmberNamelists (with assigned defaults). Parse the remaining
# lines for title information and NMR variables (a NoneType
# AmberNamelist).
nls,other_lines = NamelistCollection.separate_nls(mdin_name)
if nls.first_match('cntrl') is not None:
cntrl = nls.first_match('cntrl')
else:
cntrl = {}
if nls.first_match('ewald') is not None:
ewald = nls.first_match('ewald')
else:
ewald = {}
if nls.first_match('qmmm') is not None:
qmmm = nls.first_match('qmmm')
else:
qmmm = {}
if nls.first_match('pb') is not None:
pb = nls.first_match('pb')
else:
pb = {}
wts = [m for m in nls.matches('wt')]
title = ''
nmr_vars = {}
for line in other_lines:
try:
line = line[:line.index('!')]
except ValueError:
pass
tokens = line.split('=')
if len(tokens) > 1:
nmr_vars[tokens[0].strip()] = tokens[1].strip()
else:
title += line.strip() + '\n'
return cls(title,cntrl,ewald,qmmm,pb,wts,nmr_vars,engine)
def from_disang(cls, filename):
"""Create an AmberRestraint from a file with &rst namelists."""
nls,lines = NamelistCollection.separate_nls(filename)
rst = AmberRestraint(title=''.join(lines))
for nl in nls.matches('rst'):
try:
iat = [int(i) for i in nl.pop('iat').split(',')]
except KeyError:
raise KeyError("'iat' is required for nmropt restraints!")
try:
rstwt = [float(w) for w in nl.pop('rstwt').split(',')]
rst.append(GenDistCoordRestraint(iat=iat,rstwt=rstwt,**nl))
except KeyError:
if len(iat) == 2:
rst.append(BondRestraint(iat=iat,**nl))
elif len(iat) == 3:
rst.append(AngleRestraint(iat=iat,**nl))
elif len(iat) == 4:
rst.append(TorsionRestraint(iat=iat,**nl))
else:
raise ValueError("Bad 'iat' specification in %s"%filename)
if len(rst) < 1:
print 'WARNING! No &rst namelists found in %s.'%filename
return rst