def run(pluginManager):
"""
This is the entry point for the plugin manager.
The plugin manager will pass a reference to itself
to the function.
Use the APD_Printer instance returned by
pluginManager.setup() instead of the 'print'
statement to generate autoformated cmd line output.
:param pluginManager: Reference to the plugin manager
instance.
"""
printer = pluginManager.setup()
printer('Reading database file...')
for molecule in database(pluginManager):
h_atoms = atoms_of_element(molecule, 'H')
if not len(h_atoms) == 0:
average_bond_length = mean([atom - atom.partner[0] for atom in h_atoms])
else:
average_bond_length = 0
printer('\nName: {}\nInvariom Priority: {}'
'\nNumber of H atoms: {}'
'\nAverage H-bond length: {:5.3f}'.format(molecule, molecule.criterion.replace(' ', ''),
len(h_atoms), average_bond_length))
def run(pluginManager):
"""
This is the entry point for the plugin manag
The plugin manager will pass a reference to itself
to the function.
Use the APD_Printer instance returned by
pluginManager.setup() instead of the 'print'
statement to generate autoformated cmd line output.
:param pluginManager: Reference to the plugin manager
instance.
"""
printer = pluginManager.setup()
###--------reading chargeDABA.txt into dictionary chargedict ---------------#
printer('Reading list of molecules which are model compounds for hydrogen invarioms')
global hmodelsdict
global hdistdict
hmodelsdict = {}
hdistdict = {}
path_string = pluginManager.get_databasepath()
f = open(path_string + '/H_MAP.txt', 'r')
for line in f.readlines():
line = line[:-1].split(":")
hmodelsdict[line[0]] = line[1]
f.close()
###----------------------
#printer('\nmodelcompound of H@6c:',hmodelsdict["H@6c"])
#print 'h invariom model compounds in dict as list'
#print hmodelsdict.values()
###----------------------
printer('Reading database file...')
count = 0
altcount = 0
dist = 0.0
#print "\nhydrogen.invarioms.keys()[0] bond hydrogen.name name2 name3 \n"
for molecule in database(pluginManager):
if molecule.name in list(hmodelsdict.values()):
#printer(molecule)
count=count+1
h_atoms = atoms_of_element(molecule, 'H')
for hydrogen in h_atoms:
if molecule.name== hmodelsdict[hydrogen.invarioms.keys()[0]]:
bond = hydrogen - hydrogen.partner[0]
name2=' '
name3=' '
if 1 < len(hydrogen.invarioms.keys()):
if hydrogen.invarioms.keys()[1] not in hdistdict and molecule.name== hmodelsdict[hydrogen.invarioms.keys()[1]]:
altcount= altcount+1
name2= hydrogen.invarioms.keys()[1]
print("alternative invariom name NOT covered jet!!!", hydrogen.invarioms.keys()[1])
hdistdict[hydrogen.invarioms.keys()[1]] = bond
elif molecule.name== hmodelsdict[hydrogen.invarioms.keys()[1]]:
print("invariom already present, need to average")
print(bond, hdistdict[hydrogen.invarioms.keys()[1]], hydrogen.invarioms.keys()[1])
average_bond = mean([bond, hdistdict[hydrogen.invarioms.keys()[1]]])
hdistdict[hydrogen.invarioms.keys()[1]] = average_bond
#else:
#print "alternative name already covered", hydrogen.invarioms.keys()[1]
if 2 < len(hydrogen.invarioms.keys()):
if hydrogen.invarioms.keys()[2] not in hdistdict and molecule.name== hmodelsdict[hydrogen.invarioms.keys()[2]]:
altcount= altcount+1
name3= hydrogen.invarioms.keys()[2]
print("alternative invariom name NOT covered jet!!!", hydrogen.invarioms.keys()[2])
hdistdict[hydrogen.invarioms.keys()[2]] = bond
elif molecule.name== hmodelsdict[hydrogen.invarioms.keys()[2]]:
print("invariom already present, need to average")
print(bond, hdistdict[hydrogen.invarioms.keys()[2]], hydrogen.invarioms.keys()[2])
average_bond = mean([bond, hdistdict[hydrogen.invarioms.keys()[2]]])
hdistdict[hydrogen.invarioms.keys()[2]] = average_bond
#else:
# print "2nd alternative name already covered", hydrogen.invarioms.keys()[2]
#print hydrogen.invarioms.keys()[0], bond, hydrogen.name, name2, name3
if hydrogen.invarioms.keys()[0] not in hdistdict:
hdistdict[hydrogen.invarioms.keys()[0]] = bond
#print "not jet present, but just added:", hydrogen.invarioms.keys()[0], hdistdict[hydrogen.invarioms.keys()[0]]
else:
#print "invariom already present, need to average"
#print bond, hdistdict[hydrogen.invarioms.keys()[0]], hydrogen.invarioms.keys()[0]
average_bond = mean([bond, hdistdict[hydrogen.invarioms.keys()[0]]])
hdistdict[hydrogen.invarioms.keys()[0]] = average_bond
#### For those cases in which invariom comes from an atom whose 1st alternative invariom name it is (and the first invariom name is not an invariom supplier)
elif 1 < len(hydrogen.invarioms.keys()):
if molecule.name== hmodelsdict[hydrogen.invarioms.keys()[1]]:
print("the alternative invariom name appears in the hmodelsdict thereby in H_MAP.txt", hydrogen.invarioms.keys()[1])
bond = hydrogen - hydrogen.partner[0]
name2=' '
name3=' '
if hydrogen.invarioms.keys()[1] not in hdistdict:
altcount= altcount+1
name2= hydrogen.invarioms.keys()[1]
print("alternative invariom name NOT covered jet!!!", hydrogen.invarioms.keys()[1])
#else:
#print "alternative name already covered", hydrogen.invarioms.keys()[1]
if 2 < len(hydrogen.invarioms.keys()):
if hydrogen.invarioms.keys()[2] not in hdistdict and molecule.name== hmodelsdict[hydrogen.invarioms.keys()[2]]:
altcount= altcount+1
name3= hydrogen.invarioms.keys()[2]
print("alternative invariom name NOT covered jet!!!", hydrogen.invarioms.keys()[2])
hdistdict[hydrogen.invarioms.keys()[2]] = bond
elif molecule.name== hmodelsdict[hydrogen.invarioms.keys()[2]]:
print("invariom already present, need to average")
print(bond, hdistdict[hydrogen.invarioms.keys()[2]], hydrogen.invarioms.keys()[2])
average_bond = mean([bond, hdistdict[hydrogen.invarioms.keys()[2]]])
hdistdict[hydrogen.invarioms.keys()[2]] = average_bond
#else:
# print "2nd alternative name already covered", hydrogen.invarioms.keys()[2]
#print hydrogen.invarioms.keys()[0], bond, hydrogen.name, name2, name3
if hydrogen.invarioms.keys()[1] not in hdistdict:
hdistdict[hydrogen.invarioms.keys()[1]] = bond
#print "not jet present, but just added:", hydrogen.invarioms.keys()[0], hdistdict[hydrogen.invarioms.keys()[0]]
else:
print("invariom already present, need to average")
print(bond, hdistdict[hydrogen.invarioms.keys()[1]], hydrogen.invarioms.keys()[1])
average_bond = mean([bond, hdistdict[hydrogen.invarioms.keys()[1]]])
hdistdict[hydrogen.invarioms.keys()[1]] = average_bond
elif 2 < len(hydrogen.invarioms.keys()):
if molecule.name== hmodelsdict[hydrogen.invarioms.keys()[2]]:
print("the 2nd alternative invariom name appears in the hmodelsdict thereby in H_MAP.txt", hydrogen.invarioms.keys()[2])
bond = hydrogen - hydrogen.partner[0]
if hydrogen.invarioms.keys()[2] not in hdistdict:
altcount= altcount+1
print("alternative invariom name NOT covered jet!!!", hydrogen.invarioms.keys()[2])
hdistdict[hydrogen.invarioms.keys()[2]] = bond
elif molecule.name== hmodelsdict[hydrogen.invarioms.keys()[2]]:
print("invariom already present, need to average")
print(bond, hdistdict[hydrogen.invarioms.keys()[2]], hydrogen.invarioms.keys()[2])
average_bond = mean([bond, hdistdict[hydrogen.invarioms.keys()[2]]])
hdistdict[hydrogen.invarioms.keys()[2]] = average_bond
#else:
#print 'other reason to kick oth this hydrogen atom with invariom:', hydrogen.invarioms.keys()[0]
#else:
# printer ('Entry in H_MAP.txt not looked at', molecule.name )
length = 0
length = len (list( hmodelsdict.values() ))
printer('The length of the hmodelsdict', length)
printer('Number of molecules supplying hydrogen invarioms', count)
printer('Number of alternative H invarioms to be considered (should be zero)', altcount)
h_invariom_count = 0
dabafile = open(path_string + '/hdistDABA.txt', 'w')
for i in range(len(hdistdict)):
h_invariom_count = h_invariom_count +1
temp=list(hdistdict.popitem())
dabafile.writelines(temp[0] + ' ' + str(temp[1]) +'\n')
printer('Number of hydrogen invarioms written to hdistDABA.txt', h_invariom_count)