def includeall_isolate_grouped_reaction(each_grouped_reaction):
'''
Given a grouped reaction, will isolate the atoms based on the 'includeall'
critera (all molecules in this grouped reaction over the entire iteration
range will be kept).
NOTE: This function depends on grouped_reactions and molecule_helper being
global.
'''
molecule_numbers = get_all_unique_molecule_numbers(each_grouped_reaction)
iterations = get_all_iterations(each_grouped_reaction)
#We will find the range of iterations we need to operate over:
start_iteration = iterations[0]
end_iteration = iterations[-1]
#Get all the atom numbers in the molecules involved in this reaction
#pathway.
atom_numbers = get_all_unique_atoms_for_molecule_numbers(
molecule_helper, molecule_numbers
)
atom_numbers = set(atom_numbers) #Make into set so we can do quick lookups
#Now we go through all the iterations in the appended XYZ file (xmolout)
#and isolate these molecules. We do this by getting all the atoms in the
#molecules we want to isolate. Then simply keep those atoms and delete
#all other ones.
xmolout = XYZ()
xmolout.load(appendedxyz_file)
new_xyz = XYZ() #We will use this to write our isolated XYZ structure.
for each_xyz in xmolout:
print '.',
#Check if we are in the range of iterations that are grouped reactions
#are defined for:
if xmolout.iteration < start_iteration or \
xmolout.iteration > end_iteration:
continue #skip this iteration
new_xyz.rows = []
#Compare each atom to our atom numbers.
for i, atom in enumerate(each_xyz):
each_xyz_atom_number = i+1 #Since atom numbers start at 1 not 0.
if each_xyz_atom_number in atom_numbers:
new_xyz.rows.append(atom)
#Now append this new xyz to our output file:
output_xyz_filename = appendedxyz_output_file.replace(
'[grouped_reaction_number]',
str(grouped_reactions.grouped_reaction_number)
)
new_xyz.export(output_xyz_filename, append=True)
def includeall_isolate_grouped_reaction(each_grouped_reaction):
'''
Given a grouped reaction, will isolate the atoms based on the 'includeall'
critera (all molecules in this grouped reaction over the entire iteration
range will be kept).
NOTE: This function depends on grouped_reactions and molecule_helper being
global.
'''
molecule_numbers = get_all_unique_molecule_numbers(each_grouped_reaction)
iterations = get_all_iterations(each_grouped_reaction)
#We will find the range of iterations we need to operate over:
start_iteration = iterations[0]
end_iteration = iterations[-1]
#Get all the atom numbers in the molecules involved in this reaction
#pathway.
atom_numbers = get_all_unique_atoms_for_molecule_numbers(
molecule_helper, molecule_numbers)
atom_numbers = set(atom_numbers) #Make into set so we can do quick lookups
#Now we go through all the iterations in the appended XYZ file (xmolout)
#and isolate these molecules. We do this by getting all the atoms in the
#molecules we want to isolate. Then simply keep those atoms and delete
#all other ones.
xmolout = XYZ()
xmolout.load(appendedxyz_file)
new_xyz = XYZ() #We will use this to write our isolated XYZ structure.
for each_xyz in xmolout:
print '.',
#Check if we are in the range of iterations that are grouped reactions
#are defined for:
if xmolout.iteration < start_iteration or \
xmolout.iteration > end_iteration:
continue #skip this iteration
new_xyz.rows = []
#Compare each atom to our atom numbers.
for i, atom in enumerate(each_xyz):
each_xyz_atom_number = i + 1 #Since atom numbers start at 1 not 0.
if each_xyz_atom_number in atom_numbers:
new_xyz.rows.append(atom)
#Now append this new xyz to our output file:
output_xyz_filename = appendedxyz_output_file.replace(
'[grouped_reaction_number]',
str(grouped_reactions.grouped_reaction_number))
new_xyz.export(output_xyz_filename, append=True)
def exact_isolate_grouped_reaction(each_grouped_reaction):
'''
Given a grouped reaction, will isolate the atoms based on the 'exact'
critera (only specific iterations that are defined will be processed and
only the molecules defined for that iteration will be processed).
NOTE: This function depends on grouped_reactions and molecule_helper being
global.
'''
iterations = get_all_iterations(each_grouped_reaction)
iterations = set(iterations)
#Now we go through all the iterations in the appended XYZ file (xmolout)
xmolout = XYZ()
xmolout.load(appendedxyz_file)
new_xyz = XYZ() #We will use this to write our isolated XYZ structure.
for each_xyz in xmolout:
print '.',
#Check if we are at one of the iterations in our grouped reaction list.
#If not, then we skip:
if xmolout.iteration not in iterations:
continue #skip this iteration
#Otherwise, process this iteration, keeping ONLY the molecules defined
#in this iteration.
new_xyz.rows = []
#Compare each atom to our atom numbers.
for i, atom in enumerate(each_xyz):
each_xyz_atom_number = i+1 #Since atom numbers start at 1 not 0.
if each_xyz_atom_number in atom_numbers:
new_xyz.rows.append(atom)
#Now append this new xyz to our output file:
output_xyz_filename = appendedxyz_output_file.replace(
'[grouped_reaction_number]',
str(grouped_reactions.grouped_reaction_number)
)
new_xyz.export(output_xyz_filename, append=True)
def exact_isolate_grouped_reaction(each_grouped_reaction):
'''
Given a grouped reaction, will isolate the atoms based on the 'exact'
critera (only specific iterations that are defined will be processed and
only the molecules defined for that iteration will be processed).
NOTE: This function depends on grouped_reactions and molecule_helper being
global.
'''
iterations = get_all_iterations(each_grouped_reaction)
iterations = set(iterations)
#Now we go through all the iterations in the appended XYZ file (xmolout)
xmolout = XYZ()
xmolout.load(appendedxyz_file)
new_xyz = XYZ() #We will use this to write our isolated XYZ structure.
for each_xyz in xmolout:
print '.',
#Check if we are at one of the iterations in our grouped reaction list.
#If not, then we skip:
if xmolout.iteration not in iterations:
continue #skip this iteration
#Otherwise, process this iteration, keeping ONLY the molecules defined
#in this iteration.
new_xyz.rows = []
#Compare each atom to our atom numbers.
for i, atom in enumerate(each_xyz):
each_xyz_atom_number = i + 1 #Since atom numbers start at 1 not 0.
if each_xyz_atom_number in atom_numbers:
new_xyz.rows.append(atom)
#Now append this new xyz to our output file:
output_xyz_filename = appendedxyz_output_file.replace(
'[grouped_reaction_number]',
str(grouped_reactions.grouped_reaction_number))
new_xyz.export(output_xyz_filename, append=True)
