def __init__(self, atoms, resInfo=None, options=None):
"""
Constructer of chain object
"""
self.chainID = atoms[ atoms["keys"][0] ][0].chainID
self.alignment = None
self.residues = []
self.configurations = []
self.last_residue = None
if options.verbose == True:
print("constructing chain %c (atoms: configurations)" % (self.chainID))
# creating the 'residues'
for key in atoms["keys"]:
myResidue = Residue(atoms[key], resInfo=resInfo)
if myResidue.checked():
self.last_residue = myResidue
self.residues.append(myResidue)
# setting up list of configuration keys in this chain
for residue in self.residues:
for key in residue.configurations:
if key not in self.configurations:
self.configurations.append(key)
# checking and correcting C-terminus and N-terminus
self.addNTerminus(resInfo=resInfo)
self.addCTerminus(resInfo=resInfo)
def __init__(self, atoms, resInfo=None, options=None):
"""
Constructer of chain object
"""
self.chainID = atoms[atoms["keys"][0]][0].chainID
self.alignment = None
self.residues = []
self.configurations = []
self.last_residue = None
if options.verbose == True:
pka_print("constructing chain %c (atoms: configurations)" %
(self.chainID))
# creating the 'residues'
for key in atoms["keys"]:
myResidue = Residue(atoms[key], resInfo=resInfo)
if myResidue.checked():
self.last_residue = myResidue
self.residues.append(myResidue)
# setting up list of configuration keys in this chain
for residue in self.residues:
for key in residue.configurations:
if key not in self.configurations:
self.configurations.append(key)
# checking and correcting C-terminus and N-terminus
self.addNTerminus(resInfo=resInfo)
self.addCTerminus(resInfo=resInfo)
def __init__(self, file_name):
'''
Protein class constructor
Receives the file from which it is to be read. It needs to be in pdb or gro formats.
Proteins must be ungapped (all resiude numbers must be consecutive).
Only standard residues are considered.
'''
super(Protein, self).__init__()
ext = file_name.split('.')[-1].lower()
if ext == 'pdb':
with open(fileName, 'r') as f:
fileContent = f.read().split('\n')
for line in fileContent:
if line[0:6] in ['TER ', 'END ']:
return None
elif line[0:6] == 'ATOM ':
index = int(line[6:11])
name = line[12:16].strip()
resName = line[17:20].strip()
if res_name in ['HIP', 'HIE', 'HID']:
res_name = 'HIS'
assert res_name in AMINO_ACID_NAMES, \
"Only standard residues are considered."
resId = int(line[22:26])
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
if resId > 0:
try:
self.addResidue(Residue(resId, resName))
except AssertionError:
pass
self.addAtom(Atom(index, name, x, y, z), resId)
q = [x for x in self if x != None]
assert None not in self[self.index(q[0]):self.index(q[-1])+1], \
"Protein contains gaps."
elif ext == 'gro':
with open(file_name, 'r') as read_file:
file_content = read_file.read().split('\n')
number_of_atoms = int(file_content[1])
for index in range(number_of_atoms):
line = file_content[2 + index].split()
index = int(line[2])
name = line[1]
res_name = line[0][-3:]
res_id = int(line[0][:-3])
pos_x = float(line[3]) * 10
pos_y = float(line[4]) * 10
pos_z = float(line[5]) * 10
try:
self.add_residue(Residue(res_id, res_name))
except AssertionError:
pass
self.add_atom(Atom(index, name, (pos_x, pos_y, pos_z)), res_id)
else:
raise NameError('Unknown file extension')
return None
def generate_residue_sounds(self):
# settings for the residue
d = 0.2
df = 50.
g = 200.
m = 0.9
ns = [9, 10, 11]
dfs = np.arange(-6 + 1, 6) * df
for n in ns:
for df in dfs:
sound = Residue(n, df, m, g)
print str(sound)
sound.save_to_wav(self.fs, d)
def find_common_residues(structures, save_file):
if 1 == 2:
with open(safe_file, "rb") as f:
common_residues = pickle.load(f)
return common_residues
else:
all_residues = []
for structure in structures:
structure_residues = set()
top = md.load(structure).topology
for residue in top.residues:
if residue.is_protein:
res = Residue(resSeq=residue.resSeq,
chain_id=residue.chain.id,
res_name="%s%d" %
(residue.name, residue.resSeq))
#res = Residue(resSeq = residue.resSeq)
structure_residues.add(res)
all_residues.append(structure_residues)
common_residues = list(set.intersection(*all_residues))
print((sorted([r.resSeq for r in common_residues])))
print(("There are %d common residues between input structures" %
len(common_residues)))
import pickle
with open(save_file, "wb") as f:
pickle.dump(common_residues, f)
return common_residues
def __init__(self):
""" Takes a filename and initializes the self.residue_table list
with the contents of a residue table file
"""
self.residue_table = {}
residue_list = data.aminoacids.buildTable()
for r in residue_list:
res = Residue(r[0], r[1], r[2], r[3], r[4], r[5], r[6], r[7])
self.residue_table[res.letterCode3] = res
def addCTerminus(self, resInfo=None):
"""
Creating a C-terminus residue for this chain and adding it to 'residues' list
"""
last_residue = None
for residue in self.residues:
if residue.type == "amino-acid":
last_residue = residue
if last_residue != None:
atoms = last_residue.checkOXT()
Cterminus = Residue(atoms, resName="C- ", resInfo=resInfo)
self.residues.append(Cterminus)
def addNTerminus(self, resInfo=None):
"""
Creating a N-terminus residue for this chain and adding it to 'residues' list
"""
atom = None
for residue in self.residues:
if residue.type == "amino-acid":
atom = residue.getAtom(name="N")
break
if atom != None:
Nterminus = Residue([atom], resName="N+ ", resInfo=resInfo)
self.residues.append(Nterminus)
def LoadFromFile(fname):
from residue import Residue
from atom import Atom
def parse_pdb_line(s):
# atname, resname, resid, xyz
return s[12:16].strip(), \
s[17:21].strip(), \
int(s[22:26]), \
np.array([s[i:i+8] for i in (30,38,46)], dtype=float)
rindex = 0
pivot = None
atoms = [None]
is_head = True
molecule = Molecule('mol')
with open(fname, 'r') as fin:
for line in fin:
if line.startswith('TITLE'):
molecule.name = line[5:].strip()
elif line.startswith('ATOM'):
atname,resname,resid,xyz = parse_pdb_line(line)
if is_head or (resid != rindex):
residue = Residue(resname)
molecule.append_residue(residue, is_head)
is_head = False
rindex = resid
atom = Atom(atname, xyz)
atoms.append(atom)
residue.append_atom(atom)
elif line.startswith('TER'):
is_head = True
elif line.startswith('CONECT'):
idxs = map(int, line[6:].split())
pivot = atoms[idxs[0]]
for i in idxs[1:]:
pivot.connect_to(atoms[i])
auto_setup = pivot is None
molecule.compile(auto_setup=auto_setup)
return molecule
def __init__(self, sequence):
## a. parse the sequence.
match_pattern = re.compile(r'([A-Z])(?:\((\w+)\))?') # Use non-capturing group
seq_list = match_pattern.findall(sequence)
self.mass = 0.0
self.seq = []
for item in seq_list:
res = Residue()
res.bySymbol(item[0])
if item[1] != '':
mod = Modification(item[1])
# Update!!! The mod mass should not be integrated into residue mass.
#res.mass += mod.mass
self.seq.append([res, [mod]])
# Update!!! The mod mass is appended to the precursor directly.
self.mass += mod.mass
else:
self.seq.append([res, []])
self.mass += res.mass
self.length = len(self.seq)
self.mass += Composition("H2O").mass
def load_fragments():
from residue import Residue
import os
ref = Residue('REF')
ref.append_atom(Atom( 'N', [0.000, 0.300, 0.000]))
ref.append_atom(Atom('CA', [1.181, -0.540, 0.000]))
ref.append_atom(Atom( 'C', [2.440, 0.300, 0.000]))
# load all residues
this_dir, this_filename = os.path.split(__file__)
DATA_PATH = os.path.join(this_dir, "static", "residues.pdb")
residue_container = Molecule.LoadFromFile(DATA_PATH)
for fragment in residue_container.iter_residues():
fit(ref, ('N','CA','C'), fragment, ('N','CA','C'))
FragmentProvider.FRAGMENTS[fragment.name] = fragment
def convert_list_to_resobject_list(contact_residues):
resobject_list = []
for residue in contact_residues:
new_residue = Residue(resSeq=residue[1], chain_id=residue[0])
resobject_list.append(new_residue)
return (resobject_list)
def update(self, **kwargs):
"""Rebuild hierarchical view of atoms. This method is called at
instantiation, but can be used to rebuild the hierarchical view
when attributes of atoms change."""
array = np.array
atoms = self._atoms
if isinstance(atoms, AtomGroup):
ag = atoms
_indices = np.arange(ag._n_atoms)
selstr = False
else:
ag = atoms.getAtomGroup()
_indices = atoms._indices
selstr = atoms.getSelstr()
acsi = self._atoms.getACSIndex()
n_atoms = len(ag)
self._dict = _dict = dict()
self._chains = _chains = list()
self._residues = _residues = list()
self._segments = _segments = list()
segindex = -1
segindices = np.zeros(n_atoms, int)
chindex = -1
chindices = np.zeros(n_atoms, int)
resindex = -1
resindices = np.zeros(n_atoms, int)
sgnms = ag._getSegnames()
if sgnms is None:
_segments = None
else:
if selstr:
sgnms = sgnms[_indices]
unique = np.unique(sgnms)
s = sgnms[0]
if len(unique) == 1:
if s != '':
segment = Segment(ag, _indices, acsi=acsi, unique=True,
selstr=selstr)
_dict[s] = segment
_segments.append(segment)
LOGGER.info('Hierarchical view contains segments.')
else:
_segments = None
else:
ps = None
for i, s in enumerate(sgnms):
if s == ps or s in _dict:
continue
ps = s
segindex += 1
idx = _indices[i:][sgnms[i:] == s]
segment = Segment(ag, idx, acsi=acsi, unique=True,
selstr=selstr)
segindices[idx] = segindex
_dict[s] = segment
_segments.append(segment)
LOGGER.info('Hierarchical view contains segments.')
chids = ag._getChids()
if chids is None:
_chains = None
else:
if selstr:
chids = chids[_indices]
if _segments is None:
if len(np.unique(chids)) == 1:
chain = Chain(ag, _indices, acsi=acsi, unique=True)
_dict[(None, chids[0] or None)] = chain
_chains.append(chain)
else:
pc = None
for i, c in enumerate(chids):
if c == pc or (None, c) in _dict:
continue
pc = c
chindex += 1
idx = _indices[i:][chids[i:] == c]
chain = Chain(ag, idx, acsi=acsi, unique=True)
chindices[idx] = chindex
_dict[(None, c)] = chain
_chains.append(chain)
else:
pc = chids[0]
ps = sgnms[0]
_i = 0
for i, c in enumerate(chids):
s = sgnms[i]
if c == pc and s == ps:
continue
s_c = (ps, pc or None)
chain = _dict.get(s_c)
if chain is None:
segment = _dict[ps]
chindex += 1
idx = _indices[_i:i]
chain = Chain(ag, idx, acsi=acsi, segment=segment,
unique=True)
chindices[idx] = chindex
_dict[s_c] = chain
segment._dict[pc] = len(segment._list)
segment._list.append(chain)
_chains.append(chain)
else:
idx = _indices[_i:i]
chindices[idx] = chain._indices[0]
chain._indices = np.concatenate((chain._indices, idx))
pc = c
ps = s
_i = i
s_c = (ps, pc or None)
chain = _dict.get(s_c)
idx = _indices[_i:]
if chain is None:
segment = _dict[ps]
chindex += 1
chindices[idx] = chindex
chain = Chain(ag, idx, acsi=acsi, segment=segment,
unique=True)
_dict[s_c] = chain
segment._dict[pc] = len(segment._list)
segment._list.append(chain)
_chains.append(chain)
else:
chindices[idx] = chain._indices[0]
chain._indices = np.concatenate((chain._indices, idx))
if kwargs.get('chain') == True:
return
rnums = ag._getResnums()
if rnums is None:
raise ValueError('resnums are not set')
if selstr:
rnums = rnums[_indices]
nones = None
if _segments is None:
if nones is None:
nones = [None] * len(rnums)
sgnms = nones
if _chains is None:
if nones is None:
nones = [None] * len(rnums)
chids = nones
icods = ag._getIcodes()
if icods is None:
if nones is None:
nones = [None] * len(rnums)
icods = nones
elif selstr:
icods = icods[_indices]
pr = rnums[0]
pi = icods[0] or None
pc = chids[0]
ps = sgnms[0] or None
_j = 0
for j, r in enumerate(rnums):
i = icods[j] or None
c = chids[j] or None
s = sgnms[j]
if r != pr or i != pi or c != pc or s != ps:
s_c_r_i = (ps, pc, pr, pi)
res = _dict.get(s_c_r_i)
if res is None:
chain = _dict.get((ps, pc))
resindex += 1
idx = _indices[_j:j]
res = Residue(ag, idx, acsi=acsi, chain=chain,
unique=True, selstr=selstr)
resindices[idx] = resindex
if chain is not None:
chain._dict[(pr, pi)] = len(chain._list)
chain._list.append(res)
_residues.append(res)
_dict[s_c_r_i] = res
else:
res._indices = np.concatenate((res._indices,
_indices[_j:j]))
ps = s
pc = c
pr = r
pi = i
_j = j
s_c_r_i = (ps, pc, pr, pi)
res = _dict.get(s_c_r_i)
idx = _indices[_j:]
if res is None:
chain = _dict.get((ps, pc))
resindex += 1
res = Residue(ag, idx, acsi=acsi, chain=chain, unique=True,
selstr=selstr)
resindices[idx] = resindex
if chain is not None:
chain._dict[(pr, pi)] = len(chain._list)
chain._list.append(res)
_residues.append(res)
_dict[s_c_r_i] = res
else:
resindices[idx] = res._indices[0]
res._indices = np.concatenate((res._indices, idx))
ag._data['segindices'] = segindices
ag._data['chindices'] = chindices
ag._data['resindices'] = resindices
def update(self, **kwargs):
"""Update (or build) hierarchical view of atoms. This method is called
at instantiation, but can be used to rebuild the hierarchical view when
attributes of atoms change."""
atoms = self._atoms
if isinstance(atoms, AtomGroup):
ag = atoms
selstr = False
_indices = arange(atoms._n_atoms)
else:
ag = atoms.getAtomGroup()
_indices = atoms._getIndices()
selstr = atoms.getSelstr()
set_indices = False
if atoms == ag:
set_indices = True
_dict = dict()
_residues = list()
_segments = list()
_chains = list()
# also set the attributes, so that when no segments or chains
# are available, num/iter methods won't raise exceptions
self._dict = _dict
self._residues = _residues
self._segments = _segments
self._chains = _chains
acsi = atoms.getACSIndex()
n_atoms = len(ag)
# identify segments
if set_indices:
segindex = -1
segindices = zeros(n_atoms, int)
sgnms = ag._getSegnames()
if sgnms is None:
_segments = None
else:
if selstr:
sgnms = sgnms[_indices]
s = sgnms[0]
if len(unique(sgnms)) == 1:
if s != '':
segment = Segment(ag, _indices, acsi=acsi, unique=True,
selstr=selstr)
_dict[s] = segment
_segments.append(segment)
LOGGER.info('Hierarchical view contains segments.')
else:
_segments = None
else:
ps = None # previous segment name
for i, s in enumerate(sgnms):
if s == ps or s in _dict:
continue
ps = s
idx = _indices[i:][sgnms[i:] == s]
segment = Segment(ag, idx, acsi=acsi, unique=True,
selstr=selstr)
if set_indices:
segindex += 1
segindices[idx] = segindex
_dict[s] = segment
_segments.append(segment)
LOGGER.info('Hierarchical view contains segments.')
if set_indices:
ag._data['segindices'] = segindices
chindex = -1
chindices = zeros(n_atoms, int)
# identify chains
chids = ag._getChids()
if chids is None:
_chains = None
else:
if selstr:
chids = chids[_indices]
if _segments is None:
if len(unique(chids)) == 1:
chain = Chain(ag, _indices, acsi=acsi, unique=True,
selstr=selstr)
_dict[(None, chids[0] or None)] = chain
_chains.append(chain)
else:
pc = None
for i, c in enumerate(chids):
if c == pc or (None, c) in _dict:
continue
pc = c
idx = _indices[i:][chids[i:] == c]
chain = Chain(ag, idx, acsi=acsi, unique=True,
selstr=selstr)
if set_indices:
chindex += 1
chindices[idx] = chindex
_dict[(None, c)] = chain
_chains.append(chain)
else:
pc = chids[0]
ps = sgnms[0]
_i = 0
for i, c in enumerate(chids):
s = sgnms[i]
if c == pc and s == ps:
continue
s_c = (ps, pc or None)
chain = _dict.get(s_c)
if chain is None:
segment = _dict[ps]
idx = _indices[_i:i]
chain = Chain(ag, idx, acsi=acsi, segment=segment,
unique=True, selstr=selstr)
if set_indices:
chindex += 1
chindices[idx] = chindex
_dict[s_c] = chain
_chains.append(chain)
else:
idx = _indices[_i:i]
chindices[idx] = chain._indices[0]
chain._indices = concatenate((chain._indices, idx))
pc = c
ps = s
_i = i
s_c = (ps, pc or None)
chain = _dict.get(s_c)
idx = _indices[_i:]
if chain is None:
segment = _dict[ps]
if set_indices:
chindex += 1
chindices[idx] = chindex
chain = Chain(ag, idx, acsi=acsi, segment=segment,
unique=True, selstr=selstr)
_dict[s_c] = chain
_chains.append(chain)
else:
if set_indices:
chindices[idx] = chain._indices[0]
chain._indices = concatenate((chain._indices, idx))
if set_indices:
ag._data['chindices'] = chindices
if kwargs.get('chain') == True:
return
if set_indices:
resindex = -1
resindices = zeros(n_atoms, int)
rnums = ag._getResnums()
if rnums is None:
raise ValueError('resnums are not set')
if selstr:
rnums = rnums[_indices]
nones = None
if _segments is None:
if nones is None:
nones = [None] * len(rnums)
sgnms = nones
if _chains is None:
if nones is None:
nones = [None] * len(rnums)
chids = nones
icods = ag._getIcodes()
if icods is None:
if nones is None:
nones = [None] * len(rnums)
icods = nones
elif selstr:
icods = icods[_indices]
pr = rnums[0]
pi = icods[0] or None
pc = chids[0]
ps = sgnms[0]
_j = 0
_append = _residues.append
_get = _dict.get
_set = _dict.__setitem__
for j, r in enumerate(rnums):
i = icods[j] or None
c = chids[j]
s = sgnms[j]
if r != pr or i != pi or c != pc or s != ps:
s_c_r_i = (ps, pc, pr, pi)
res = _get(s_c_r_i)
if res is None:
chain = _get((ps, pc))
idx = _indices[_j:j]
res = Residue(ag, idx, acsi=acsi, chain=chain,
unique=True, selstr=selstr)
if set_indices:
resindex += 1
resindices[idx] = resindex
_append(res)
_set(s_c_r_i, res)
else:
res._indices = concatenate((res._indices, _indices[_j:j]))
ps = s
pc = c
pr = r
pi = i
_j = j
s_c_r_i = (ps, pc, pr, pi)
res = _get(s_c_r_i)
idx = _indices[_j:]
if res is None:
chain = _get((ps, pc))
res = Residue(ag, idx, acsi=acsi, chain=chain, unique=True,
selstr=selstr)
if set_indices:
resindex += 1
resindices[idx] = resindex
_append(res)
_set(s_c_r_i, res)
else:
if set_indices:
resindices[idx] = res._indices[0]
res._indices = concatenate((res._indices, idx))
if set_indices:
ag._data['resindices'] = resindices
resobject_list = []
for residue in contact_residues:
new_residue = Residue(resSeq = residue[1], chain_id = residue[0])
resobject_list.append(new_residue)
return(resobject_list)
#CHOOSE RESIDUES:
bp_4dkl = md.load("/home/enf/md_simulations/MOR/4dkl_bp_6pt6.pdb")
bp_5c1m = md.load("/home/enf/md_simulations/MOR/5c1m_bp_6pt6.pdb")
bp_4dkl_residues = set([r.resSeq for r in bp_4dkl.topology.residues if r.is_protein])
bp_5c1m_residues = set([r.resSeq for r in bp_4dkl.topology.residues if r.is_protein])
bp_residues = sorted(list(bp_4dkl_residues | bp_5c1m_residues))
bp_residue_objects = convert_list_to_resobject_list([("R", i) for i in bp_residues])
cutoff = 1.
feature_name = "bp_residues_4dkl_5c1m_under_cutoff%dA" %(int(10*cutoff))
common_residues_pkl = get_common_residues_pkl(base)
contact_residues = find_common_residues([inactive_dir, active_dir, simulation_structure], common_residues_pkl)
contact_resSeq = [r.resSeq for r in contact_residues]
bfna_resobj = Residue(resSeq = 601, res_name = "BF0")
_, bp_4dkl_residues = find_binding_pocket_residues(bfna_resobj, contact_residues, inactive_dir, cutoff=cutoff)
bu72_resobj = Residue(resSeq = 401, res_name = "4VO")
_, bp_5c1m_residues = find_binding_pocket_residues(bu72_resobj, contact_residues, active_dir, cutoff=cutoff)
bp_residue_objects = sorted(list(set(bp_4dkl_residues) | set(bp_5c1m_residues)))
#bp_residue_objects = [res for res in bp_residue_objects if res.resSeq in contact_resSeq]
def getStubs(self):
"""returns a list of dicts with peptide and stub glycopeptide ions """
for i in self.pep_seq:
res = Residue()
res.bySymbol(i)
if i == 'C':
self.mass += Carbamidomethyl
self.mass += res.mass
if self.mod_type == "Deamidated":
self.mass += (Deamidation * self.n_mod)
elif self.mod_type == '':
pass
stubs =[]
stubs.append({"key":"peptide", "mass": (self.mass + Proton)})
sites = self.glyco_num
if sites == 0 :
pass
elif sites>0:
if self.dHex==0:
for i in range(1,sites+1,1):
for j in range(1,3,1):
if j ==1:
key = "pep+"+str(j)+"HexNAc+"+"0Hexose"+"-"+str(i)+"sites"
mass = self.mass+Proton+(i*(j*HexNAc))
#print key, mass
stubs.append({"key":key,"mass": mass})
elif (j == 2):
for k in range(0,4,1):
key = "pep+"+str(j)+"HexNAc+"+str(k)+"Hexose"+"-"+str(i)+"sites"
mass = self.mass+Proton+(i*((j*HexNAc)+(k*Hex)))
#print key, mass
stubs.append({"key":key,"mass": mass})
else:
pass
elif self.dHex>0:
for i in range(1,sites+1,1):
for j in range(1,3,1):
if j ==1:
key = "pep+"+str(j)+"HexNAc+"+"0Hexose"+"-"+str(i)+"sites"
mass = self.mass+Proton+(i*(j*HexNAc))
#print key, mass
stubs.append({"key":key,"mass": mass})
if (j == 2):
for l in range (0,2,1):
for k in range(0,4,1):
key = "pep+"+str(j)+"HexNAc+"+str(k)+"Hexose"+str(l)+"dHex"+"-"+str(i)+"sites"
mass = self.mass+Proton+(i*((j*HexNAc)+(k*Hex)+(l*dHex)))
#print key, mass
stubs.append({"key":key,"mass": mass})
else:
pass
j +=1
return stubs