def setAtomsDictionary(self, atoms=None, pdbfile=None):
"""
set reference to the atoms dictionary
atoms = dictionary with atom objects to make the protein from, i.e. atoms[chainID][resName]
"""
if atoms != None:
self.atoms = atoms
elif pdbfile != None:
self.atoms = pdb.readPDB(filename=pdbfile)
else:
print("need either an atoms dictionary or pdbfile to create a protein")
sys.exit(9)
return
def makeCompositeAtomsDictionary(protein=None, pdbfiles=None, options=None):
"""
This routine creates a composite 'atoms' dictionary.
"""
if options.mutations == None:
# not making mutations, we don't need 'atoms-dictionary'
return None
elif options.mutator.label in ["alignment", "overlap"]:
atoms = {protein.name: protein.atoms}
if options.thermophiles == None:
# read the pdbcode from mutations and get the pdb atoms
for mutation in options.mutations:
if isinstance(mutation, str):
# keeping string notation of mutation
pdbcode = mutation[:4]
if pdbcode not in atoms:
atoms[pdbcode] = pdb.readPDB(filename=pdbcode)
else:
# extracting pdbcode if mutation is in dictionary format
for key in mutation.keys():
pdbcode = mutation[key]['pdb']
if pdbcode not in atoms:
atoms[pdbcode] = pdb.readPDB(filename=pdbcode)
else:
# Match thermophile pdb files to the mutation code
if len(options.thermophiles) != 0:
import re
for pdbname in options.thermophiles:
for mutation in options.mutations:
code, rest = splitStringMutationInTwo(mutation)
print(mutation, code, rest)
if re.search(code, pdbname):
atoms[code] = pdb.readPDB(filename=pdbname)
return atoms
else:
# not using alignment or overlap mutator, we don't need 'atoms dictionary'
return None
% (element, d))
a = a.rescale(d)
return a
if __name__ == '__main__':
import protein, pdb, sys, os
arguments = sys.argv
if len(arguments) != 2:
print('Usage: protonate.py <pdb_file>')
sys.exit(0)
filename = arguments[1]
if not os.path.isfile(filename):
print('Error: Could not find \"%s\"' % filename)
sys.exit(1)
p = Protonate()
pdblist = pdb.readPDB(filename)
my_protein = protein.Protein(pdblist, 'test.pdb')
p.remove_all_hydrogen_atoms_from_protein(my_protein)
my_protein.writePDB('before_protonation.pdb')
p.protonate_protein(my_protein)
## write out protonated file
my_protein.writePDB('protonated.pdb')
a = a.rescale(d)
return a
if __name__ == '__main__':
import protein, pdb, sys,os
arguments = sys.argv
if len(arguments) != 2:
print('Usage: protonate.py <pdb_file>')
sys.exit(0)
filename = arguments[1]
if not os.path.isfile(filename):
print('Error: Could not find \"%s\"'%filename)
sys.exit(1)
p = Protonate()
pdblist = pdb.readPDB(filename)
my_protein = protein.Protein(pdblist,'test.pdb')
p.remove_all_hydrogen_atoms_from_protein(my_protein)
my_protein.writePDB('before_protonation.pdb')
p.protonate_protein(my_protein)
## write out protonated file
my_protein.writePDB('protonated.pdb')
