def get_s(self, pdb_file=None):
if self._pdb_file is not None:
pdb = self._pdb_file
else:
pdb = iotbx.pdb.input(file_name=pdb_file)
s = 0
tot = 0
for a in pdb.atoms_with_labels():
if a.resname in ['DOD', 'HOH']:
if a.name.strip() == 'O':
s += a.occ
tot += a.occ
return s/tot
def get_rmm(self, pdb_file=None):
if self._pdb_file is not None:
pdb = self._pdb_file
else:
pdb = iotbx.pdb.input(file_name=file)
rmm = 0
for a in pdb.atoms_with_labels():
if a.resname in ['ASP', 'ALA', 'HIS', 'ARG', 'LYS', 'GLN', 'GLU',
'TYR', 'PRO', 'LEU', 'ILE', 'MET', 'VAL', 'SER',
'ASN', 'CYS', 'GLY', 'TRP', 'PHE', 'THR', 'LYS']:
rmm += self._weights[a.name.strip()[0]] * a.occ
return rmm
def get_chains(self, pdb_file):
residues = []
pdb = iotbx.pdb.input(file_name=pdb_file)
for a in pdb.atoms_with_labels():
rid = int(a.resid())
if rid not in residues:
residues.append(rid)
cid = 'A'
res_lookup = {}
_last = 0
for r in sorted(residues):
if r - _last > 21:
cid = chr(ord(cid)+1)
res_lookup[r] = cid
_last = r
return res_lookup
def get_bond_lengths(self, pdb_file):
self._omitted = {'asp': [], 'glu': [], 'his': [], 'arg': []}
self._residues = {'asp': {}, 'glu': {}, 'his': {}, 'arg': {}}
b_avg_array = [[],[],[]]
rlist = {'asp': {}, 'glu': {}, 'his': {}, 'arg': {}}
t = {'ASP': [' CG ', ' OD1', ' OD2'], 'GLU': [' CD ', ' OE1', ' OE2']}
pdb = iotbx.pdb.input(file_name=pdb_file)
for a in pdb.atoms_with_labels():
b_avg_array[2].append(a.b)
if a.resname in ['HOH', 'DOD']:
b_avg_array[1].append(a.b)
if a.resname in ['ASP', 'ALA', 'HIS', 'ARG', 'LYS', 'GLN', 'GLU',
'TYR', 'PRO', 'LEU', 'ILE', 'MET', 'VAL', 'SER',
'ASN', 'CYS', 'GLY', 'TRP', 'PHE', 'THR', 'LYS']:
b_avg_array[0].append(a.b)
rid = int(a.resid())
if a.resname in t.keys():
n = t[a.resname]
rn = a.resname.lower()
if a.occ < 1:
if rid not in self._omitted[rn]:
self._omitted[rn].append(rid)
else:
if a.name in n:
id = n.index(a.name)
if rid in rlist[rn].keys():
rlist[rn][rid][id] = a
else:
rlist[rn][rid] = {id:a}
# his CG CD2 NE2, ND1 CE1 NE2
elif a.resname == 'HIS':
if a.occ < 1:
if rid not in self._omitted['his']:
self._omitted['his'].append(rid)
else:
atoms = [' CG ', ' CD2', ' NE2', ' ND1', ' CE1']
if a.name in atoms:
id = atoms.index(a.name)
if rid in rlist['his'].keys():
rlist['his'][rid][id] = a
else:
rlist['his'][rid] = {id:a}
# arg CZ NH2, CZ NE, CZ NH1, CD NE?
elif a.resname == 'ARG':
if a.occ < 1:
if rid not in self._omitted['arg']:
self._omitted['arg'].append(rid)
else:
atoms = [' CZ ', ' NH2', ' NE ', ' NH1']
if a.name in atoms:
id = atoms.index(a.name)
if rid in rlist['arg'].keys():
rlist['arg'][rid][id] = a
else:
rlist['arg'][rid] = {id:a}
for t in rlist.keys():
for rid,res in rlist[t].iteritems():
if t == 'asp' or t == 'glu':
if len(res) == 3:
self._residues[t][rid] = {1: [res[0].distance(res[1]), res[1].occ, res[1].b], 2: [res[0].distance(res[2]), res[2].occ, res[2].b]}
elif t == 'his':
if len(res) == 5:
#for i,a in res.iteritems():
# print i,a.name
self._residues[t][rid] = { 1: [res[1].angle(res[0], res[2], True), res[1].occ, res[1].b],
2: [res[4].angle(res[3], res[2], True), res[4].occ, res[4].b],
3: [res[2].angle(res[1], res[4], True), res[2].occ, res[2].b],
4: [res[3].angle(res[0], res[4], True), res[3].occ, res[3].b],
5: [res[0].angle(res[3], res[1], True), res[0].occ, res[0].b],
}
elif t == 'arg':
if len(res) == 4:
self._residues[t][rid] = {1: [res[0].distance(res[1]), res[1].occ, res[1].b], 2: [res[0].distance(res[2]), res[2].occ, res[2].b], 3: [res[0].distance(res[3]), res[3].occ, res[3].b]}
self._residues['avg'] = {}
for i,k in enumerate(['pro', 'sol', 'all']):
if len(b_avg_array[i]) > 0:
val = sum(b_avg_array[i])/len(b_avg_array[i])
else:
val = 0;
self._residues['avg'][k] = val
#self._residues['avg'] = {'b': (sum(b_avg_array)/len(b_avg_array))}
return self._omitted, self._residues
def analyse(self):
self._omitted = {'asp': [], 'glu': [], 'his': [], 'arg': []}
self._residues = {'asp': {}, 'glu': {}, 'his': {}, 'arg': {}}
self._highlight = -1
b_avg_array = []
rlist = {'asp': {}, 'glu': {}, 'his': {}, 'arg': {}}
t = {'ASP': [' CG ', ' OD1', ' OD2'], 'GLU': [' CD ', ' OE1', ' OE2']}
pdb = iotbx.pdb.input(file_name=self._bond_lengths)
for a in pdb.atoms_with_labels():
if a.resname in ['ASP', 'ALA', 'HIS', 'ARG', 'LYS', 'GLN', 'GLU',
'TYR', 'PRO', 'LEU', 'ILE', 'MET', 'VAL', 'SER',
'ASN', 'CYS', 'GLY', 'TRP', 'PHE', 'THR', 'LYS']:
b_avg_array.append(a.b)
rid = int(a.resid())
if a.resname in t.keys():
n = t[a.resname]
rn = a.resname.lower()
if a.occ < 1:
if rid not in self._omitted[rn]:
self._omitted[rn].append(rid)
else:
if a.name in n:
id = n.index(a.name)
if rid in rlist[rn].keys():
rlist[rn][rid][id] = a
else:
rlist[rn][rid] = {id:a}
# his CG CD2 NE2, ND1 CE1 NE2
elif a.resname == 'HIS':
if a.occ < 1:
if rid not in self._omitted['his']:
self._omitted['his'].append(rid)
else:
atoms = [' CG ', ' CD2', ' NE2', ' ND1', ' CE1']
if a.name in atoms:
id = atoms.index(a.name)
if rid in rlist['his'].keys():
rlist['his'][rid][id] = a
else:
rlist['his'][rid] = {id:a}
# arg CZ NH2, CZ NE, CZ NH1, CD NE?
elif a.resname == 'ARG':
if a.occ < 1:
if rid not in self._omitted['arg']:
self._omitted['arg'].append(rid)
else:
atoms = [' CZ ', ' NH2', ' NE ', ' NH1']
if a.name in atoms:
id = atoms.index(a.name)
if rid in rlist['arg'].keys():
rlist['arg'][rid][id] = a
else:
rlist['arg'][rid] = {id:a}
for t in rlist.keys():
for rid,res in rlist[t].iteritems():
if t == 'asp' or t == 'glu':
if len(res) == 3:
self._residues[t][rid] = {1: [res[0].distance(res[1]), res[1].occ, res[1].b], 2: [res[0].distance(res[2]), res[2].occ, res[2].b]}
elif t == 'his':
if len(res) == 5:
self._residues[t][rid] = {1: [res[1].angle(res[0], res[2], True), res[0].occ, res[0].b], 2: [res[4].angle(res[3], res[2], True), res[3].occ, res[3].b]}
elif t == 'arg':
if len(res) == 4:
self._residues[t][rid] = {1: [res[0].distance(res[1]), res[1].occ, res[1].b], 2: [res[0].distance(res[2]), res[2].occ, res[2].b], 3: [res[0].distance(res[3]), res[3].occ, res[3].b]}
self._residues['avg'] = {'b': (sum(b_avg_array)/len(b_avg_array))}
if os.path.exists(self._std_devs):
devs = open(self._std_devs)
asp_re = re.compile(r'CG_(\d+) OD(1|2)_\1 (\d+\.\d+)\((\d+)\)')
glu_re = re.compile(r'CD_(\d+) OE(1|2)_\1 (\d+\.\d+)\((\d+)\)')
his_re = [re.compile(r'CG_(\d+) CD2_\1 NE2_\1 (\d+)\((\d+)\)'),
re.compile(r'ND1_(\d+) CE1_\1 NE2_\1 (\d+)\((\d+)\)'),
re.compile(r'NE2_(\d+) CD2_\1 CG_\1 (\d+)\((\d+)\)'),
re.compile(r'NE2_(\d+) CE1_\1 ND1_\1 (\d+)\((\d+)\)'),
]
arg_re = [re.compile(r'CZ_(\d+) NH2_\1 (\d+\.\d+)\((\d+)\)'),
re.compile(r'CZ_(\d+) NE_\1 (\d+\.\d+)\((\d+)\)'),
re.compile(r'CZ_(\d+) NH1_\1 (\d+\.\d+)\((\d+)\)'),
re.compile(r'NH2_(\d+) CZ_\1 (\d+\.\d+)\((\d+)\)'),
re.compile(r'NE_(\d+) CZ_\1 (\d+\.\d+)\((\d+)\)'),
re.compile(r'NH1_(\d+) CZ_\1 (\d+\.\d+)\((\d+)\)')
]
for s in devs:
for t,rex in {'asp': asp_re, 'glu': glu_re}.items():
a = rex.match(s)
if a:
if int(a.group(1)) in self._residues[t]:
if len(self._residues[t][int(a.group(1))][int(a.group(2))]) < 4:
d = pow(10, len((a.group(3).split('.'))[1]))
self._residues[t][int(a.group(1))][int(a.group(2))].append(float(a.group(4))/d)
for id,rex in enumerate(his_re):
a = rex.match(s)
if a:
if int(a.group(1)) in self._residues['his']:
self._residues['his'][int(a.group(1))][(id%2)+1].append(float(a.group(3)))
for id,rex in enumerate(arg_re):
a = rex.match(s)
if a:
if int(a.group(1)) in self._residues['arg']:
d = pow(10, len((a.group(2).split('.'))[1]))
self._residues['arg'][int(a.group(1))][(id%3)+1].append(float(a.group(3))/d)
devs.close()
for type in self._residues.keys():
std_arr = []
for res in self._residues[type]:
if type == 'asp'or type == 'glu' or type == 'his':
r = self._residues[type][res]
if len(r[1]) == 4 and len(r[2]) == 4:
std_arr.append(r[1][3])
std_arr.append(r[2][3])
delta = abs(r[1][0] - r[2][0])
sigdel = math.sqrt(pow(r[1][3],2)+pow(r[2][3],2))
siglev = delta/sigdel
bavg = (r[1][2]+r[2][2])/2
self._residues[type][res]['r'] = [delta, sigdel, siglev, r[1][1], bavg]
if len(std_arr) > 0:
self._residues['avg'][type] = sum(std_arr)/len(std_arr)
self._update_lists()
self._show_residue()