def __init__(self, file_name, file_type='xyz'):
self.struc = struc_linalg.structure(name=file_name[:4])
self.struc.read_file(file_path=file_name, file_type=file_type)
self.num_at = self.struc.ret_num_at()
print
print "%s read in" % file_name
print "Number of atoms: %i" % self.num_at
def __init__(self, file_name, file_type='xyz', vib=False):
self.struc = struc_linalg.structure(name=file_name[:4])
self.struc.read_file(file_path=file_name, file_type=file_type)
self.num_at = self.struc.ret_num_at()
self.file_name = file_name
self.file_type = file_type
self.vib = vib
if self.vib:
self.freqs = numpy.zeros([3 * self.num_at])
self.vib_mat = numpy.zeros([3 * self.num_at, 3 * self.num_at])
self.curr_vib = 0
print
print "Template %s read in" % file_name
print "Number of atoms: %i" % self.num_at
raise
try:
from matilda import file_handler, struc_linalg, superposition
except:
print "Error in importing module of this distribution"
print "check the PYTHONPATH environment variable"
raise
if __name__ == '__main__':
ref_file = file_handler.def_input("Template structure file")
ins_file = file_handler.def_input("File name of the molecule to insert")
file_type = file_handler.def_input("File type", "xyz")
ins = struc_linalg.structure(name=ins_file[:4])
ins.read_file(file_path=ins_file, file_type=file_type)
num_at = ins.ret_num_at()
ref = struc_linalg.structure(name=ref_file[:4])
ref.read_file(file_path=ref_file, file_type=file_type)
print
print "Number of atoms to insert: %i" % num_at
print """
Enter indices of the atoms in the template structure corresponding to the
indices of the molecule inserted
"""
at_list_ref = []
for iat in xrange(1, num_at + 1):
start_file = sys.argv[1]
end_file = sys.argv[2]
out_dir = sys.argv[3]
steps_nr = eval(sys.argv[4])
file_type = sys.argv[5]
try:
os.makedirs(out_dir)
except OSError:
print 'Output directory could not be created. It either already exists or you have no writing access.'
# for calculations an instance of this class with a default molecule has to be defined
mc = struc_linalg.mol_calc(def_file_path=start_file, file_type=file_type)
# load the structures
st = struc_linalg.structure(name='st') # optional name for output
st.read_file(file_path=start_file, file_type=file_type)
en_temp = struc_linalg.structure(name='en_t')
en_temp.read_file(file_path=end_file, file_type=file_type)
# superimpose the structures
en = en_temp.ret_superimposed_structure(struc=st, mass_wt_pw=1, name='en')
# define the vector for the linear interpolation
diff_vect = mc.subtract(en, st)
# create <steps_nr> structures and put them into separate folders
for i in xrange(1, steps_nr + 1):
x = i * 1. / (steps_nr + 1)
plus_struc = mc.scalar_mult(x, diff_vect)
elif arg == '-h':
print 'Usage example: int_coor.py dist 4 5 struc.xyz'
print 'Supported internal coordinates: dist, bend, tors'
print 'Arguments: -type (xyz, tmol, mol ...)'
print ' -dig (number of digits in print out)'
sys.exit()
elif arg[0] == '-':
print 'Unsupported option: ' + arg
print 'int_coor.py -h for more information'
sys.exit()
else:
files += [arg]
#print coors, files
struc = struc_linalg.structure()
tm = file_handler.table_maker(col_widths=[20] + len(coors) * [5 + digits])
tm.write_line(['File'] + [coor[0] for coor in coors])
for file in files:
struc.read_file(file_path=file, file_type=file_type)
out_line = [file]
for coor in coors:
if coor[0] == 'dist':
dist = struc.ret_bond_length(*coor[1:])
out_line += [locale.format("%.*f", (digits, dist))]
elif coor[0] == 'bend':
bend = struc.ret_bend(*coor[1:])
out_line += [locale.format("%.*f", (digits, bend))]
elif coor[0] == 'tors':
tors = struc.ret_tors(*coor[1:])
out_line += [locale.format("%.*f", (digits, tors))]
ref_file = sys.argv[1]
super_files = [] # list with filenames to be superimposed onto ref_struc
for arg in sys.argv[2:]:
if arg[:4] == '-mwp':
mass_wt_pw = eval(arg[4:])
elif arg[:2] == '-t':
file_type = arg[2:]
else:
super_files += [arg]
# for calculations an instance of this class with a default molecule has to be defined
# from it the numbering of the atoms and their masses are taken
mc = struc_linalg.mol_calc(def_file_path=ref_file, file_type=file_type)
# load the structures (DK and MK are random names used for identification)
ref = struc_linalg.structure(name=ref_file[:9])
ref.read_file(file_path=ref_file, file_type=file_type)
strucs = [] #initial structures and superimposed structures
for i, super_file in enumerate(super_files):
strucs += [struc_linalg.structure(name=super_file[:9])]
strucs[-1].read_file(file_path=super_file, file_type=file_type)
# superimpose the structures
strucs += [
strucs[-1].ret_superimposed_structure(struc=ref,
mass_wt_pw=mass_wt_pw,
name=super_file[:2] + '_X')
]
strucs[-1].make_coord_file('SI_' + super_file, file_type=file_type)
# to follow the effect of the superposition, a matrix with the distances can be printed out
digits = 4
files = []
for arg in sys.argv[1:]:
if arg[:4] == '-mwp':
mass_wt_pw = eval(arg[4:])
elif arg[:2] == '-t':
file_type = arg[2:]
elif arg[:4] == '-fit':
fitting = arg[4:]
elif arg[:4] == '-dig':
digits = int(arg[4:])
else:
files += [arg]
struc0 = struc_linalg.structure(name=files[0][:4])
struc0.read_file(file_path=files[0], file_type=file_type)
out_strucs = [struc0]
for i, file in enumerate(files[1:]):
struc = struc_linalg.structure(name=file[:digits + 3])
struc.read_file(file_path=file, file_type=file_type)
# superimpose the structures
if fitting == 1:
print '- Superimposing the structures'
out_strucs += [
struc.ret_superimposed_structure(struc0, mass_wt_pw=mass_wt_pw)
]
else:
out_strucs += [struc]
print 'At least 5 arguments required.'
print 'Syntax: python add_normal_mode.py <in_struc> <out_struc> <vib_file> <nm_ind> <disp> [<type>]'
sys.exit()
# read in data
in_file = sys.argv[1]
out_file = sys.argv[2]
vib_file = sys.argv[3]
nm_ind = eval(sys.argv[4])
disp = eval(sys.argv[5]) # displacement
try:
file_type = sys.argv[6]
except IndexError:
file_type = 'xyz'
in_struc = struc_linalg.structure()
in_struc.read_file(file_path=in_file, file_type=file_type)
vmol = vib_molden.vib_molden()
vmol.read_molden_file(vib_file)
#print in_struc.ret_vector()
#print disp
#print vmol.vibs[nm_ind - 1].ret_joined_vector()
# it is not -ttmol !
new_vec = in_struc.ret_vector() + disp * vmol.vibs[nm_ind -
1].ret_joined_vector()
out_struc = struc_linalg.structure()
out_struc.read_file_vector(def_file_path=in_file,
file_type=file_type,