def __init__(self, atom1=0, atom2=0):
self.vectors = []
self.keys = []
# store vectors for all configurations of atoms
if atom1 != 0:
self.keys = lib.get_sorted_configurations(
atom1.configurations.keys())
if atom2 != 0:
keys2 = lib.get_sorted_configurations(
atom2.configurations.keys())
if self.keys != keys2:
pka_print(
"ERROR: Inequivalent configurations for atoms, please correct your pdbfile to single configuration"
)
pka_print("%s\n%s" % (atom1, atom2))
sys.exit(8)
#raise 'Cannot make multi vector: Atomic configurations mismatch for\n %s\n %s\n'%(atom1,atom2)
for key in self.keys:
atom1.setConfiguration(key)
if atom2 != 0:
atom2.setConfiguration(key)
v = vector(atom1=atom1, atom2=atom2)
self.vectors.append(v)
#pka_print(key,v)
return
def writePDB(self,
file=None,
filename=None,
all_configuration=False,
hydrogens=False,
options=None):
"""
Writes a new pdbfile based on what is in the protein
"""
configurations = lib.get_sorted_configurations(self.configurations)
if len(configurations) == 1 or all_configuration == False:
output.writePDB(self, filename=filename, hydrogens=hydrogens)
else:
# file is opened here
if file == None:
if filename == None:
filename = "%s.pdb" % (protein.name)
file = open(filename, 'w')
# write configurations
for configuration in configurations:
self.setConfiguration(configuration)
file.write("MODEL%9d\n" % (int(configuration[1])))
output.writePDB(self, file=file, hydrogens=hydrogens)
file.write('ENDMDL\n')
# file is closed here
if file == None:
file.close()
def __init__(self, atom1=0, atom2=0):
self.vectors = []
self.keys = []
# store vectors for all configurations of atoms
if atom1!=0:
self.keys = lib.get_sorted_configurations(atom1.configurations.keys())
if atom2!=0:
keys2 = lib.get_sorted_configurations(atom2.configurations.keys())
if self.keys != keys2:
pka_print("ERROR: Inequivalent configurations for atoms, please correct your pdbfile to single configuration")
pka_print("%s\n%s" % (atom1, atom2))
sys.exit(8)
#raise 'Cannot make multi vector: Atomic configurations mismatch for\n %s\n %s\n'%(atom1,atom2)
for key in self.keys:
atom1.setConfiguration(key)
if atom2!=0:
atom2.setConfiguration(key)
v = vector(atom1=atom1, atom2=atom2)
self.vectors.append(v)
#pka_print(key,v)
return
def writePDB(self, pdbname):
print("writing pdbfile %s" % (pdbname))
file = open(pdbname, 'w')
configurations = lib.get_sorted_configurations(self.configuration_keys)
if len(configurations)==1:
self.write_atoms(file)
else:
for configuration in configurations:
self.setConfiguration(configuration)
file.write('MODEL%9d\n'%int(configuration[1]))
self.write_atoms(file)
file.write('ENDMDL\n')
file.close()
return
def writePDB(self, pdbname):
pka_print("writing pdbfile %s" % (pdbname))
file = open(pdbname, 'w')
configurations = lib.get_sorted_configurations(self.configuration_keys)
if len(configurations) == 1:
self.write_atoms(file)
else:
for configuration in configurations:
self.setConfiguration(configuration)
file.write('MODEL%9d\n' % int(configuration[1]))
self.write_atoms(file)
file.write('ENDMDL\n')
file.close()
return
def writePDB(self, file=None, filename=None, all_configuration=False, hydrogens=False, options=None):
"""
Writes a new pdbfile based on what is in the protein
"""
configurations = lib.get_sorted_configurations(self.configurations)
if len(configurations) == 1 or all_configuration == False:
output.writePDB(self, filename=filename, hydrogens=hydrogens)
else:
# file is opened here
if file == None:
if filename == None:
filename = "%s.pdb" % (protein.name)
file = open(filename, 'w')
# write configurations
for configuration in configurations:
self.setConfiguration(configuration)
file.write("MODEL%9d\n" % (int(configuration[1])))
output.writePDB(self, file=file, hydrogens=hydrogens)
file.write('ENDMDL\n')
# file is closed here
if file == None:
file.close()