def optimize(self, shot=0, method="newton", crit=1e-4):
""" Optimize the geometry and align the optimized geometry to the starting geometry. """
logger.error(
'Geometry optimizations are not yet implemented in AMBER interface'
)
raise NotImplementedError
# Code from tinkerio.py
if os.path.exists('%s.xyz_2' % self.name):
os.unlink('%s.xyz_2' % self.name)
self.mol[shot].write('%s.xyz' % self.name, ftype="tinker")
if method == "newton":
if self.rigid: optprog = "optrigid"
else: optprog = "optimize"
elif method == "bfgs":
if self.rigid: optprog = "minrigid"
else: optprog = "minimize"
o = self.calltinker("%s %s.xyz %f" % (optprog, self.name, crit))
# Silently align the optimized geometry.
M12 = Molecule("%s.xyz" % self.name, ftype="tinker") + Molecule(
"%s.xyz_2" % self.name, ftype="tinker")
if not self.pbc:
M12.align(center=False)
M12[1].write("%s.xyz_2" % self.name, ftype="tinker")
rmsd = M12.ref_rmsd(0)[1]
cnvgd = 0
mode = 0
for line in o:
s = line.split()
if len(s) == 0: continue
if "Optimally Conditioned Variable Metric Optimization" in line:
mode = 1
if "Limited Memory BFGS Quasi-Newton Optimization" in line:
mode = 1
if mode == 1 and isint(s[0]): mode = 2
if mode == 2:
if isint(s[0]): E = float(s[1])
else: mode = 0
if "Normal Termination" in line:
cnvgd = 1
if not cnvgd:
for line in o:
logger.info(str(line) + '\n')
logger.info(
"The minimization did not converge in the geometry optimization - printout is above.\n"
)
return E, rmsd
def parse_atomtype_line(line):
""" Parses the 'atomtype' line.
Parses lines like this:\n
<tt> opls_135 CT 6 12.0107 0.0000 A 3.5000e-01 2.7614e-01\n
C 12.0107 0.0000 A 3.7500e-01 4.3932e-01\n
Na 11 22.9897 0.0000 A 6.068128070229e+03 2.662662556402e+01 0.0000e+00 ; PARM 5 6\n </tt>
Look at all the variety!
@param[in] line Input line.
@return answer Dictionary containing:\n
atom type\n
bonded atom type (if any)\n
atomic number (if any)\n
atomic mass\n
charge\n
particle type\n
force field parameters\n
number of optional fields
"""
# First split the line up to the comment. We don't care about the comment at this time
sline = line.split(';')[0].split()
# The line must contain at least six fields to be considered data.
if len(sline) < 6:
return
# Using variable "wrd" because the line has a variable number of fields
# Can you think of a better way?
wrd = 0
bonus = 0
atomtype = sline[wrd]
batomtype = sline[wrd]
wrd += 1
# The bonded atom type, a pecularity of OPLS-AA
# Test if it begins with a letter. Seems to work. :)
if re.match('[A-Za-z]',sline[wrd]):
batomtype = sline[wrd]
wrd += 1
bonus += 1
# Now to test if the next line is an atomic number or a mass.
# Atomic numbers never have decimals...
atomicnum = -1
if isint(sline[wrd]):
atomicnum = int(sline[wrd])
wrd += 1
bonus += 1
# The mass can be overridden in the 'atoms' section.
mass = float(sline[wrd])
wrd += 1
# Atom types have a default charge though this is almost always overridden
chg = float(sline[wrd])
wrd += 1
# Particle type. Actual atom or virtual site?
ptp = sline[wrd]
wrd += 1
param = [float(i) for i in sline[wrd:]]
answer = {'atomtype':atomtype, 'batomtype':batomtype, 'atomicnum':atomicnum, 'mass':mass, 'chg':chg, 'ptp':ptp, 'param':param, 'bonus':bonus}
return answer
def optimize(self, shot=0, method="newton", crit=1e-4):
""" Optimize the geometry and align the optimized geometry to the starting geometry. """
logger.error('Geometry optimizations are not yet implemented in AMBER interface')
raise NotImplementedError
# Code from tinkerio.py
if os.path.exists('%s.xyz_2' % self.name):
os.unlink('%s.xyz_2' % self.name)
self.mol[shot].write('%s.xyz' % self.name, ftype="tinker")
if method == "newton":
if self.rigid: optprog = "optrigid"
else: optprog = "optimize"
elif method == "bfgs":
if self.rigid: optprog = "minrigid"
else: optprog = "minimize"
o = self.calltinker("%s %s.xyz %f" % (optprog, self.name, crit))
# Silently align the optimized geometry.
M12 = Molecule("%s.xyz" % self.name, ftype="tinker") + Molecule("%s.xyz_2" % self.name, ftype="tinker")
if not self.pbc:
M12.align(center=False)
M12[1].write("%s.xyz_2" % self.name, ftype="tinker")
rmsd = M12.ref_rmsd(0)[1]
cnvgd = 0
mode = 0
for line in o:
s = line.split()
if len(s) == 0: continue
if "Optimally Conditioned Variable Metric Optimization" in line: mode = 1
if "Limited Memory BFGS Quasi-Newton Optimization" in line: mode = 1
if mode == 1 and isint(s[0]): mode = 2
if mode == 2:
if isint(s[0]): E = float(s[1])
else: mode = 0
if "Normal Termination" in line:
cnvgd = 1
if not cnvgd:
for line in o:
logger.info(str(line) + '\n')
logger.info("The minimization did not converge in the geometry optimization - printout is above.\n")
return E, rmsd
def is_mol2_atom(line):
s = line.split()
if len(s) < 9:
return False
return all([
isint(s[0]),
isfloat(s[2]),
isfloat(s[3]),
isfloat(s[4]),
isfloat(s[8])
])
def normal_modes(self, shot=0, optimize=True):
logger.error('Normal modes are not yet implemented in AMBER interface')
raise NotImplementedError
# Copied from tinkerio.py
if optimize:
self.optimize(shot, crit=1e-6)
o = self.calltinker("vibrate %s.xyz_2 a" % (self.name))
else:
warn_once("Asking for normal modes without geometry optimization?")
self.mol[shot].write('%s.xyz' % self.name, ftype="tinker")
o = self.calltinker("vibrate %s.xyz a" % (self.name))
# Read the TINKER output. The vibrational frequencies are ordered.
# The six modes with frequencies closest to zero are ignored
readev = False
calc_eigvals = []
calc_eigvecs = []
for line in o:
s = line.split()
if "Vibrational Normal Mode" in line:
freq = float(s[-2])
readev = False
calc_eigvals.append(freq)
calc_eigvecs.append([])
elif "Atom" in line and "Delta X" in line:
readev = True
elif readev and len(s) == 4 and all(
[isint(s[0]),
isfloat(s[1]),
isfloat(s[2]),
isfloat(s[3])]):
calc_eigvecs[-1].append([float(i) for i in s[1:]])
calc_eigvals = np.array(calc_eigvals)
calc_eigvecs = np.array(calc_eigvecs)
# Sort by frequency absolute value and discard the six that are closest to zero
calc_eigvecs = calc_eigvecs[np.argsort(np.abs(calc_eigvals))][6:]
calc_eigvals = calc_eigvals[np.argsort(np.abs(calc_eigvals))][6:]
# Sort again by frequency
calc_eigvecs = calc_eigvecs[np.argsort(calc_eigvals)]
calc_eigvals = calc_eigvals[np.argsort(calc_eigvals)]
os.system("rm -rf *.xyz_* *.[0-9][0-9][0-9]")
return calc_eigvals, calc_eigvecs
def feed(self, line, linindep=False):
""" Feed in a line.
@param[in] line The line of data
"""
if linindep:
if match('^ *!', line):
self.destroy = True
else:
self.destroy = False
line = sub('^ *!', '', line)
line = line.split('!')[0].strip()
s = line.split()
self.ln += 1
# No sense in doing anything for an empty line or a comment line.
if len(s) == 0 or match('^ *!', line): return None, None
# Now go through all the cases.
if match('^[A-Za-z][A-Za-z]? +[0-9]$', line):
# This is supposed to match the element line. For example 'Li 0'
self.element = s[0].capitalize()
self.isdata = False
self.destroy = False
elif len(s) == 3 and match('[SPDFGH]+', s[0]) and isint(
s[1]) and isfloat(s[2]):
self.amom = s[0]
if self.amom == self.last_amom:
self.basis_number[self.element] += 1
else:
self.basis_number[self.element] = 0
self.last_amom = self.amom
self.contraction_number = -1
self.isdata = True
# This is supposed to match a line like 'P 1 1.00'
elif len(s) == 2 and isfloat(s[0]) and isfloat(s[1]):
self.contraction_number += 1
self.isdata = True
else:
self.isdata = False
self.destroy = False
def feed(self, line, linindep=False):
""" Feed in a line.
@param[in] line The line of data
"""
if linindep:
if match('^ *!',line):
self.destroy = True
else:
self.destroy = False
line = sub('^ *!','',line)
line = line.split('!')[0].strip()
s = line.split()
self.ln += 1
# No sense in doing anything for an empty line or a comment line.
if len(s) == 0 or match('^ *!',line): return None, None
# Now go through all the cases.
if match('^[A-Za-z][A-Za-z]? +[0-9]$',line):
# This is supposed to match the element line. For example 'Li 0'
self.element = capitalize(s[0])
self.isdata = False
self.destroy = False
elif len(s) == 3 and match('[SPDFGH]+',s[0]) and isint(s[1]) and isfloat(s[2]):
self.amom = s[0]
if self.amom == self.last_amom:
self.basis_number[self.element] += 1
else:
self.basis_number[self.element] = 0
self.last_amom = self.amom
self.contraction_number = -1
self.isdata = True
# This is supposed to match a line like 'P 1 1.00'
elif len(s) == 2 and isfloat(s[0]) and isfloat(s[1]):
self.contraction_number += 1
self.isdata = True
else:
self.isdata = False
self.destroy = False
def normal_modes(self, shot=0, optimize=True):
logger.error('Normal modes are not yet implemented in AMBER interface')
raise NotImplementedError
# Copied from tinkerio.py
if optimize:
self.optimize(shot, crit=1e-6)
o = self.calltinker("vibrate %s.xyz_2 a" % (self.name))
else:
warn_once("Asking for normal modes without geometry optimization?")
self.mol[shot].write('%s.xyz' % self.name, ftype="tinker")
o = self.calltinker("vibrate %s.xyz a" % (self.name))
# Read the TINKER output. The vibrational frequencies are ordered.
# The six modes with frequencies closest to zero are ignored
readev = False
calc_eigvals = []
calc_eigvecs = []
for line in o:
s = line.split()
if "Vibrational Normal Mode" in line:
freq = float(s[-2])
readev = False
calc_eigvals.append(freq)
calc_eigvecs.append([])
elif "Atom" in line and "Delta X" in line:
readev = True
elif readev and len(s) == 4 and all([isint(s[0]), isfloat(s[1]), isfloat(s[2]), isfloat(s[3])]):
calc_eigvecs[-1].append([float(i) for i in s[1:]])
calc_eigvals = np.array(calc_eigvals)
calc_eigvecs = np.array(calc_eigvecs)
# Sort by frequency absolute value and discard the six that are closest to zero
calc_eigvecs = calc_eigvecs[np.argsort(np.abs(calc_eigvals))][6:]
calc_eigvals = calc_eigvals[np.argsort(np.abs(calc_eigvals))][6:]
# Sort again by frequency
calc_eigvecs = calc_eigvecs[np.argsort(calc_eigvals)]
calc_eigvals = calc_eigvals[np.argsort(calc_eigvals)]
os.system("rm -rf *.xyz_* *.[0-9][0-9][0-9]")
return calc_eigvals, calc_eigvecs
def feed(self, line, linindep=False):
""" Feed in a line.
@param[in] line The line of data
"""
line = line.split('!')[0].strip()
s = line.split()
self.ln += 1
# No sense in doing anything for an empty line or a comment line.
if len(s) == 0 or match('^ *!',line): return None, None
# Now go through all the cases.
if match('^[A-Za-z][A-Za-z]? +[0-9]$',line):
# This is supposed to match the element line. For example 'Li 0'
self.element = capitalize(s[0])
self.radii[self.element] = float(s[1])
self.isdata = False
self.point = 0
elif len(s) >= 2 and isint(s[0]) and isfloat(s[1]):
self.point += 1
self.isdata = True
else:
self.isdata = False
def feed(self, line, linindep=False):
""" Feed in a line.
@param[in] line The line of data
"""
line = line.split('!')[0].strip()
s = line.split()
self.ln += 1
# No sense in doing anything for an empty line or a comment line.
if len(s) == 0 or match('^ *!', line): return None, None
# Now go through all the cases.
if match('^[A-Za-z][A-Za-z]? +[0-9]$', line):
# This is supposed to match the element line. For example 'Li 0'
self.element = s[0].capitalize()
self.radii[self.element] = float(s[1])
self.isdata = False
self.point = 0
elif len(s) >= 2 and isint(s[0]) and isfloat(s[1]):
self.point += 1
self.isdata = True
else:
self.isdata = False
QDict[i] = float("%.4f" % Q)
# Try to zero out the atomic charge.
print(
"The following code aims to get an integer-charge molecule using precision 4 floating points."
)
TQ = sum([QDict[T[i]] for i in range(na)])
print("All atom types have been selected; molecule has a net charge of %.4f" %
TQ)
Corr1 = (float("%.4f" % (-1 * TQ / na)))
choice = input(
"Create overall integer charge (enter integer), enter your own (enter float), or skip this step (hit Enter)? --> "
) + " "
#if 'y' == choice[0] or 'Y' == choice[0]:
if isint(choice.strip()):
WantQ = int(choice)
Corr1 = (float("%.4f" % ((WantQ - 1 * TQ) / na)))
for i in QDict:
QDict[i] += Corr1
TQ = sum([QDict[T[i]] for i in range(na)])
print("Adding a charge of %.4f to each atom" % Corr1)
print(
"Now all atom types have been selected; molecule has a net charge of %.4f"
% TQ)
else:
try:
Corr1 = float(choice)
for i in QDict:
QDict[i] += Corr1
TQ = sum([QDict[T[i]] for i in range(na)])
def is_mol2_atom(line):
s = line.split()
if len(s) < 9:
return False
return all([isint(s[0]), isfloat(s[2]), isfloat(s[3]), isfloat(s[4]), isfloat(s[8])])
COM = "OPLS " + OPLSExplanations[sline[0]]
BAT[i] = i
OPLSNicks[BAT[i]] = SelectedLine.split()[1]
TEDict[BAT[i]] = Element
M[i] = [ANum,PeriodicTable[Element],SIG,EPS,COM]
QDict[i] = float("%.4f" % Q)
# Try to zero out the atomic charge.
print "The following code aims to get an integer-charge molecule using precision 4 floating points."
TQ = sum([QDict[T[i]] for i in range(na)])
print "All atom types have been selected; molecule has a net charge of %.4f" % TQ
Corr1 = (float("%.4f" % (-1*TQ/na)))
choice = raw_input("Create overall integer charge (enter integer), enter your own (enter float), or skip this step (hit Enter)? --> ") + " "
#if 'y' == choice[0] or 'Y' == choice[0]:
if isint(choice.strip()):
WantQ = int(choice)
Corr1 = (float("%.4f" % ((WantQ - 1*TQ)/na)))
for i in QDict:
QDict[i] += Corr1
TQ = sum([QDict[T[i]] for i in range(na)])
print "Adding a charge of %.4f to each atom" % Corr1
print "Now all atom types have been selected; molecule has a net charge of %.4f" % TQ
else:
try:
Corr1 = float(choice)
for i in QDict:
QDict[i] += Corr1
TQ = sum([QDict[T[i]] for i in range(na)])
print "Now all atom types have been selected; molecule has a net charge of %.4f" % TQ
except: print "You didn't enter a number, exiting this section"
