def __init__(self, chainlines, parent):
Polymer.__init__(self, chainlines, parent)
# store a list element for each nucleotide in chainlines
last_line = None
current_residue = []
atoms = []
atom_cnt = 0
for line in chainlines:
current_line = line[25:29]
if current_line == last_line:
# just append to the previously created one
current_residue.append(line)
atoms.append(self.atoms[atom_cnt])
else:
# make a new amino acid and append it to residues list
if len(current_residue) > 0:
new_residue = Nucleotide(current_residue, self, atoms)
self.add_residue(new_residue)
# reset the current list and append the new line to it
current_residue = []
current_residue.append(line)
atoms = []
atoms.append(self.atoms[atom_cnt])
last_line = current_line
atom_cnt = atom_cnt + 1
# append the last one created
new_residue = Nucleotide(current_residue, self, atoms)
self.add_residue(new_residue)
self.locate_termini()
self.residues_dict = {}
for res in self.residues:
self.residues_dict['%s' % (res.res_number)] = res
def __init__(self, chainlines, parent):
Polymer.__init__(self,chainlines, parent)
# store a list element for each nucleotide in chainlines
last_line = None
current_residue = []
atoms = []
atom_cnt = 0
for line in chainlines:
current_line = line[25:29]
if current_line == last_line:
# just append to the previously created one
current_residue.append(line)
atoms.append(self.atoms[atom_cnt])
else:
# make a new amino acid and append it to residues list
if len(current_residue)>0:
new_residue = Nucleotide(current_residue, self, atoms)
self.add_residue(new_residue)
# reset the current list and append the new line to it
current_residue = []
current_residue.append(line)
atoms = []
atoms.append(self.atoms[atom_cnt])
last_line = current_line
atom_cnt = atom_cnt + 1
# append the last one created
new_residue = Nucleotide(current_residue, self, atoms)
self.add_residue(new_residue)
self.locate_termini()
self.residues_dict = {}
for res in self.residues:
self.residues_dict['%s'%(res.res_number)] = res
def __init__(self, PDBlines, parent):
self.atomsHydList=[]
Polymer.__init__(self,PDBlines, parent)
# store a list element for each amino acid in PDBlines
last_line = None
current_residue = []
atoms = []
atom_cnt = 0
offset = 0
min_lengths = {'ALA':5, 'CYS':6, 'ASP':8, 'GLU':9, 'PHE':11, 'GLY':4, 'HIS':10,
'ILE':8, 'LYS':9, 'LEU':8, 'MET':8, 'ASN':8, 'PRO':7, 'GLN':9,
'ARG':11, 'SER':6, 'THR':7, 'VAL':7, 'TRP':14, 'TYR':12}
for line in PDBlines:
current_line = line[25:29]
if current_line == last_line:
# handle duplicate atom records
atomname = line[12:16]
splitname = string.split(string.strip(atomname))
if len(splitname) == 2: # have a 'CA A' or some such thing
if splitname[1] != 'A': # dismiss B or C duplicates
last_line = current_line
atom_cnt += 1
continue
else:
line = line[:15] + ' ' + line[16:] # just get rid of the 'A'
self.atoms[atom_cnt].atom_type = string.split(self.atoms[atom_cnt].atom_type)[0]
else:
# if the line has a number, followed by a letter, it must be duplicate
if line[14] in ['1','2','3','4'] and line[15] in ['A','B','C','D']:
if line[15] in ['B','C','D']: # get rid of the Bs Cs and Ds
last_line = current_line
atom_cnt += 1
continue
else:
line = line[:15] + ' ' + line[16:]
self.atoms[atom_cnt].atom_type = self.atoms[atom_cnt].atom_type[:-1]
# just append to the previously created one
current_residue.append(line)
atoms.append(self.atoms[atom_cnt])
else:
# make a new amino acid and append it to residues list
if len(current_residue)>0:
if len(current_residue) >= min_lengths[current_residue[0][17:20]]:
new_residue = AminoAcid(self, current_residue, atoms)
self.add_residue(new_residue)
# reset the current list and append the new line to it
current_residue = []
atoms = []
current_residue.append(line)
atoms.append(self.atoms[atom_cnt])
last_line = current_line
atom_cnt += 1
# append the last one created
if len(current_residue) >= min_lengths[current_residue[0][17:20]]:
new_residue = AminoAcid(self, current_residue, atoms)
self.add_residue(new_residue)
# this initializes proteolysis type, so that the chain knows if a calculation has been done
self.proteolysis_type = 'none'
self.locate_termini()
self.residues_dict = {}
for res in self.residues:
self.residues_dict['%s'%(res.res_number)] = res
def __init__(self, PDBlines, parent):
self.atomsHydList=[]
Polymer.__init__(self,PDBlines, parent)
# store a list element for each amino acid in PDBlines
last_line = None
current_residue = []
atoms = []
atom_cnt = 0
offset = 0
min_lengths = {'ALA':5, 'CYS':6, 'ASP':8, 'GLU':9, 'PHE':11, 'GLY':4, 'HIS':10,
'ILE':8, 'LYS':9, 'LEU':8, 'MET':8, 'ASN':8, 'PRO':7, 'GLN':9,
'ARG':11, 'SER':6, 'THR':7, 'VAL':7, 'TRP':14, 'TYR':12}
for line in PDBlines:
current_line = line[25:29]
if current_line == last_line:
# handle duplicate atom records
atomname = line[12:16]
splitname = string.split(string.strip(atomname))
if len(splitname) == 2: # have a 'CA A' or some such thing
if splitname[1] != 'A': # dismiss B or C duplicates
last_line = current_line
atom_cnt += 1
continue
else:
line = line[:15] + ' ' + line[16:] # just get rid of the 'A'
self.atoms[atom_cnt].atom_type = string.split(self.atoms[atom_cnt].atom_type)[0]
else:
# if the line has a number, followed by a letter, it must be duplicate
if line[14] in ['1','2','3','4'] and line[15] in ['A','B','C','D']:
if line[15] in ['B','C','D']: # get rid of the Bs Cs and Ds
last_line = current_line
atom_cnt += 1
continue
else:
line = line[:15] + ' ' + line[16:]
self.atoms[atom_cnt].atom_type = self.atoms[atom_cnt].atom_type[:-1]
# just append to the previously created one
current_residue.append(line)
atoms.append(self.atoms[atom_cnt])
else:
# make a new amino acid and append it to residues list
if len(current_residue)>0:
if len(current_residue) >= min_lengths[current_residue[0][17:20]]:
new_residue = AminoAcid(self, current_residue, atoms)
self.add_residue(new_residue)
# reset the current list and append the new line to it
current_residue = []
atoms = []
current_residue.append(line)
atoms.append(self.atoms[atom_cnt])
last_line = current_line
atom_cnt += 1
# append the last one created
if len(current_residue) >= min_lengths[current_residue[0][17:20]]:
new_residue = AminoAcid(self, current_residue, atoms)
self.add_residue(new_residue)
# this initializes proteolysis type, so that the chain knows if a calculation has been done
self.proteolysis_type = 'none'
self.locate_termini()
self.residues_dict = {}
for res in self.residues:
self.residues_dict['%s'%(res.res_number)] = res