def main():
"""
Reads a structure from a Gaussian Log file and other parameters from a
Gaussian Com file and creates a new Gaussian Com.
"""
args = get_args()
gaulog = GaussianLog(args.log)
gaucom = GaussianCom(args.template_com)
atoms_log_coords = gaulog.read_geometry(args.opt_step, args.scan_step)
for no, atom in enumerate(gaucom.atoms_list):
atom.SetVector(atoms_log_coords[no].GetVector())
gaucom.write_to_file(args.new_com)
def main():
import os
import getopt, sys
from omg.gaussian.gaussian import GaussianLog as GL
from omg import misc, asciiplot, geom
try:
opts, args = getopt.gnu_getopt(sys.argv[1:], 'e:w:h')
except getopt.GetoptError as err:
sys.stderr.write(err + '\n')
usage()
sys.exit(2)
# defaults
scan_pts = 0
energytype = 'default'
maxwidth = 80
multiline = True
explain_symbols = False
# provided input
for o, a in opts:
if o == '-s': scan_pts = int(a)
elif o == '-e': energytype = a.lower()
elif o == '-w': maxwidth = int(a)
elif o == '-m': multiline = True
elif o == '-h': explain_symbols = True
if len(args) < 1 and explain_symbols:
print(symbol_legend())
sys.exit(0)
if len(args) < 1:
usage()
print('missing:')
print(' inputname.log')
sys.exit(2)
elif len(args) > 1:
usage()
print('too many args:')
print(' %s' % (','.join(args)))
filein = args[0]
basename, input_extension = os.path.splitext(filein)
if input_extension not in ['.log']:
print('WARNING:')
print(' inputname suffix is: %s' % input_extension)
# read gaussian.log
gl = GL(filein)
converged = []
for byte in gl.bytedict['Converged?'][-1]:
# labels and thresh are constant for every byte, keep only last iter
(labels, values, thresh) = gl.read_converged(byte)
converged.append(values)
converged = misc.transpose_list_of_lists(converged)
# print!
pretty = print_convergence_symbols(thresh, converged,
labels, maxwidth, multiline)
print(pretty)
# scan info
scan_info = False
now_scan_point = len(gl.bytedict['Converged?'])
total_scan_num_pts = 1 # default for opt
if gl.modreds: # not None
for modred in gl.modreds:
if modred.action == 'S':
scan_info = ['', '']
total_scan_num_pts = modred.scan_num_pts + 1
#measure_func = {'S': geom.distance,
# 'A': geom.angle,
# 'D': geom.dihedral
# }
#measure_func = measure_func[modred.coordtype]
a = gl.atoms_list[modred.atomids[0]-1]
b = gl.atoms_list[modred.atomids[1]-1]
if modred.coordtype == 'B':
scan_info[0] = 'distance'
start_measure = a.GetDistance(b)
elif modred.coordtype == 'A':
scan_info[0] = 'angle'
c = gl.atoms_list[modred.atomids[2]-1]
start_measure = a.GetAngle(b, c) # b in the middle!
elif modred.coordtype == 'D':
scan_info[0] = 'dihedral'
c = gl.atoms_list[modred.atomids[2]-1]
d = gl.atoms_list[modred.atomids[3]-1]
start_measure = a.GetDihedral(b,c,d)
# x axis for asciiplot
x_axis = [start_measure + modred.scan_step_sz*i
for i in range(now_scan_point)]
for atomid in modred.atomids:
scan_info[1] += '%d %s, %s\n' % (
gl.atoms_list[atomid-1].resinfo.resnum,
gl.atoms_list[atomid-1].resinfo.resname,
gl.atoms_list[atomid-1].resinfo.name)
scan_info[1] += '%s %s %s %d %f\n' % (
modred.coordtype,
' '.join([str(at) for at in modred.atomids]),
modred.action,
modred.scan_num_pts,
modred.scan_step_sz)
print ('Opt #: %3d out of %3d\n' % (
now_scan_point, total_scan_num_pts))
if explain_symbols:
print(symbol_legend())
# get key for gl.energies dict
energykey = energytype_convert(gl, energytype)
# ENERGIES: if scan: last opt in each step; if opt: last scan_pt
if len(gl.bytedict['Converged?']) > 1:
energies = [e[-1] for e in gl.energies[energykey]]
oneopt = False
else:
energies = gl.energies[energykey][-1]
x_axis = [i+1 for i in range(len(energies))]
oneopt = True
HARTREE2KCAL = 627.509
minene = min(energies)
y = [HARTREE2KCAL*(i - minene) for i in energies]
p = asciiplot.AFigure()
_ = p.plot(x_axis, y, marker='_s')
p.xlim(min(x_axis), max(x_axis) )
print(p.draw().encode('utf-8'))
if oneopt:
print('Energy along optimization point.')
else:
print('Energy for optimized (or not) steps. (this is a scan)')
if scan_info:
print('X axis matches %s between:' % scan_info[0])
print(scan_info[1])
def main():
import os
import getopt, sys
from omg.gaussian.gaussian import GaussianLog as GL
from omg import misc, asciiplot, geom
try:
opts, args = getopt.gnu_getopt(sys.argv[1:], 'e:w:h')
except getopt.GetoptError as err:
sys.stderr.write(err + '\n')
usage()
sys.exit(2)
# defaults
scan_pts = 0
energytype = 'default'
maxwidth = 80
multiline = True
explain_symbols = False
# provided input
for o, a in opts:
if o == '-s': scan_pts = int(a)
elif o == '-e': energytype = a.lower()
elif o == '-w': maxwidth = int(a)
elif o == '-m': multiline = True
elif o == '-h': explain_symbols = True
if len(args) < 1 and explain_symbols:
print(symbol_legend())
sys.exit(0)
if len(args) < 1:
usage()
print('missing:')
print(' inputname.log')
sys.exit(2)
elif len(args) > 1:
usage()
print('too many args:')
print(' %s' % (','.join(args)))
filein = args[0]
basename, input_extension = os.path.splitext(filein)
if input_extension not in ['.log']:
print('WARNING:')
print(' inputname suffix is: %s' % input_extension)
# read gaussian.log
gl = GL(filein)
converged = []
for byte in gl.bytedict['Converged?'][-1]:
# labels and thresh are constant for every byte, keep only last iter
(labels, values, thresh) = gl.read_converged(byte)
converged.append(values)
converged = misc.transpose_list_of_lists(converged)
# print!
pretty = print_convergence_symbols(thresh, converged, labels, maxwidth,
multiline)
print(pretty)
# scan info
scan_info = False
now_scan_point = len(gl.bytedict['Converged?'])
total_scan_num_pts = 1 # default for opt
if gl.modreds: # not None
for modred in gl.modreds:
if modred.action == 'S':
scan_info = ['', '']
total_scan_num_pts = modred.scan_num_pts + 1
#measure_func = {'S': geom.distance,
# 'A': geom.angle,
# 'D': geom.dihedral
# }
#measure_func = measure_func[modred.coordtype]
a = gl.atoms_list[modred.atomids[0] - 1]
b = gl.atoms_list[modred.atomids[1] - 1]
if modred.coordtype == 'B':
scan_info[0] = 'distance'
start_measure = a.GetDistance(b)
elif modred.coordtype == 'A':
scan_info[0] = 'angle'
c = gl.atoms_list[modred.atomids[2] - 1]
start_measure = a.GetAngle(b, c) # b in the middle!
elif modred.coordtype == 'D':
scan_info[0] = 'dihedral'
c = gl.atoms_list[modred.atomids[2] - 1]
d = gl.atoms_list[modred.atomids[3] - 1]
start_measure = a.GetDihedral(b, c, d)
# x axis for asciiplot
x_axis = [
start_measure + modred.scan_step_sz * i
for i in range(now_scan_point)
]
for atomid in modred.atomids:
scan_info[1] += '%d %s, %s\n' % (
gl.atoms_list[atomid - 1].resinfo.resnum,
gl.atoms_list[atomid - 1].resinfo.resname,
gl.atoms_list[atomid - 1].resinfo.name)
scan_info[1] += '%s %s %s %d %f\n' % (
modred.coordtype, ' '.join(
[str(at) for at in modred.atomids]), modred.action,
modred.scan_num_pts, modred.scan_step_sz)
print('Opt #: %3d out of %3d\n' % (now_scan_point, total_scan_num_pts))
if explain_symbols:
print(symbol_legend())
# get key for gl.energies dict
energykey = energytype_convert(gl, energytype)
# ENERGIES: if scan: last opt in each step; if opt: last scan_pt
if len(gl.bytedict['Converged?']) > 1:
energies = [e[-1] for e in gl.energies[energykey]]
oneopt = False
else:
energies = gl.energies[energykey][-1]
x_axis = [i + 1 for i in range(len(energies))]
oneopt = True
HARTREE2KCAL = 627.509
minene = min(energies)
y = [HARTREE2KCAL * (i - minene) for i in energies]
p = asciiplot.AFigure()
_ = p.plot(x_axis, y, marker='_s')
p.xlim(min(x_axis), max(x_axis))
print(p.draw().encode('utf-8'))
if oneopt:
print('Energy along optimization point.')
else:
print('Energy for optimized (or not) steps. (this is a scan)')
if scan_info:
print('X axis matches %s between:' % scan_info[0])
print(scan_info[1])
if len(sys.argv) == 1 or sys.argv[1] in ["-h", "--help"]:
print("Como usar: {0} file.log ").format(sys.argv[0])
sys.exit()
#ficheiro entrada (output do gaussian)
global filein
filein = sys.argv[1]
#transformar o ficheiro log aberto numa variavel global (ler com o GaussianLog)
############## INICIO ##############
main()
#ler os bytes de todo o ficheiro e fazer todos os atributos d
gaussianlog = GaussianLog(filein)
for i, scan_step in enumerate( gaussianlog.grep_bytes['Step number'] ):
print( "Scan", i, ": ", len(gaussianlog.grep_bytes['Step number'][i]), "opt steps" )
scan_step = input('Type "scan_step" that you which to extract. Options: scan_step="all": ')
opt_step = input('Type "opt_step" that you which to extract. Options: opt_step="all": ')
#verificar se existe o ficheiro
output = input('Type the name of the output file: ')
if path.exists(str(output) + '.pdb'):
raise RuntimeError('%s already exists' %(str(output)+".pdb"))
open_output = open(str(output) + ".pdb", "w")
#casos em que extraio todos os scans
if str(scan_step) == 'all':
print(len(gaussianlog.grep_bytes['orientation:']))
