def __init__(self, fasta_align, m1, m2, si=0, sj=1):
"""
fasta_align --- Alignment object
m1, m2 --- two models
si, sj --- the sequences in the Alignment object that
correspond to the structures
"""
l=fasta_align.get_alignment_length()
# Get the residues in the models
rl1=Selection.unfold_entities(m1, 'R')
rl2=Selection.unfold_entities(m2, 'R')
# Residue positions
p1=0
p2=0
# Map equivalent residues to each other
map12={}
map21={}
# List of residue pairs (None if -)
duos=[]
for i in range(0, l):
column=fasta_align.get_column(i)
aa1=column[si]
aa2=column[sj]
if aa1!="-":
# Position in seq1 is not -
while True:
# Loop until an aa is found
r1=rl1[p1]
p1=p1+1
if is_aa(r1):
break
self._test_equivalence(r1, aa1)
else:
r1=None
if aa2!="-":
# Position in seq2 is not -
while True:
# Loop until an aa is found
r2=rl2[p2]
p2=p2+1
if is_aa(r2):
break
self._test_equivalence(r2, aa2)
else:
r2=None
if r1:
# Map residue in seq1 to its equivalent in seq2
map12[r1]=r2
if r2:
# Map residue in seq2 to its equivalent in seq1
map21[r2]=r1
# Append aligned pair (r is None if gap)
duos.append((r1, r2))
self.map12=map12
self.map21=map21
self.duos=duos
def __init__(self, fasta_align, m1, m2, si=0, sj=1):
"""
fasta_align --- Alignment object
m1, m2 --- two models
si, sj --- the sequences in the Alignment object that
correspond to the structures
"""
l = fasta_align.get_alignment_length()
# Get the residues in the models
rl1 = Selection.unfold_entities(m1, 'R')
rl2 = Selection.unfold_entities(m2, 'R')
# Residue positions
p1 = 0
p2 = 0
# Map equivalent residues to each other
map12 = {}
map21 = {}
# List of residue pairs (None if -)
duos = []
for i in range(0, l):
column = fasta_align.get_column(i)
aa1 = column[si]
aa2 = column[sj]
if aa1 != "-":
# Position in seq1 is not -
while True:
# Loop until an aa is found
r1 = rl1[p1]
p1 = p1 + 1
if is_aa(r1):
break
self._test_equivalence(r1, aa1)
else:
r1 = None
if aa2 != "-":
# Position in seq2 is not -
while True:
# Loop until an aa is found
r2 = rl2[p2]
p2 = p2 + 1
if is_aa(r2):
break
self._test_equivalence(r2, aa2)
else:
r2 = None
if r1:
# Map residue in seq1 to its equivalent in seq2
map12[r1] = r2
if r2:
# Map residue in seq2 to its equivalent in seq1
map21[r2] = r1
# Append aligned pair (r is None if gap)
duos.append((r1, r2))
self.map12 = map12
self.map21 = map21
self.duos = duos
def __init__(self, model, radius=12.0, offset=0):
"""
A residue's exposure is defined as the number of CA atoms around
that residues CA atom. A dictionary is returned that uses a L{Residue}
object as key, and the residue exposure as corresponding value.
@param model: the model that contains the residues
@type model: L{Model}
@param radius: radius of the sphere (centred at the CA atom)
@type radius: float
@param offset: number of flanking residues that are ignored in the calculation of the number of neighbors
@type offset: int
"""
assert(offset>=0)
ppb=CaPPBuilder()
ppl=ppb.build_peptides(model)
fs_map={}
fs_list=[]
fs_keys=[]
for pp1 in ppl:
for i in range(0, len(pp1)):
fs=0
r1=pp1[i]
if not is_aa(r1) or not r1.has_id('CA'):
continue
ca1=r1['CA']
for pp2 in ppl:
for j in range(0, len(pp2)):
if pp1 is pp2 and abs(i-j)<=offset:
continue
r2=pp2[j]
if not is_aa(r2) or not r2.has_id('CA'):
continue
ca2=r2['CA']
d=(ca2-ca1)
if d<radius:
fs+=1
res_id=r1.get_id()
chain_id=r1.get_parent().get_id()
# Fill the 3 data structures
fs_map[(chain_id, res_id)]=fs
fs_list.append((r1, fs))
fs_keys.append((chain_id, res_id))
# Add to xtra
r1.xtra['EXP_CN']=fs
AbstractPropertyMap.__init__(self, fs_map, fs_keys, fs_list)
def annotate(m, ss_seq):
"""Apply seconardary structure information to residues in model."""
c = m.get_list()[0]
all = c.get_list()
residues = []
# Now remove HOH etc.
for res in all:
if is_aa(res):
residues.append(res)
L = len(residues)
if not (L == len(ss_seq)):
raise ValueError("Length mismatch %i %i" % (L, len(ss_seq)))
for i in range(0, L):
residues[i].xtra["SS_PSEA"] = ss_seq[i]
def annotate(m, ss_seq):
"""Apply seconardary structure information to residues in model."""
c=m.get_list()[0]
all=c.get_list()
residues=[]
# Now remove HOH etc.
for res in all:
if is_aa(res):
residues.append(res)
L=len(residues)
if not (L==len(ss_seq)):
raise ValueError("Length mismatch %i %i" % (L, len(ss_seq)))
for i in range(0, L):
residues[i].xtra["SS_PSEA"]=ss_seq[i]
def __init__(self, model, pdb_file):
depth_dict={}
depth_list=[]
depth_keys=[]
# get_residue
residue_list=Selection.unfold_entities(model, 'R')
# make surface from PDB file
surface=get_surface(pdb_file)
# calculate rdepth for each residue
for residue in residue_list:
if not is_aa(residue):
continue
rd=residue_depth(residue, surface)
ca_rd=ca_depth(residue, surface)
# Get the key
res_id=residue.get_id()
chain_id=residue.get_parent().get_id()
depth_dict[(chain_id, res_id)]=(rd, ca_rd)
depth_list.append((residue, (rd, ca_rd)))
depth_keys.append((chain_id, res_id))
# Update xtra information
residue.xtra['EXP_RD']=rd
residue.xtra['EXP_RD_CA']=ca_rd
AbstractPropertyMap.__init__(self, depth_dict, depth_keys, depth_list)
def __init__(self, model, pdb_file):
depth_dict = {}
depth_list = []
depth_keys = []
# get_residue
residue_list = Selection.unfold_entities(model, 'R')
# make surface from PDB file
surface = get_surface(pdb_file)
# calculate rdepth for each residue
for residue in residue_list:
if not is_aa(residue):
continue
rd = residue_depth(residue, surface)
ca_rd = ca_depth(residue, surface)
# Get the key
res_id = residue.get_id()
chain_id = residue.get_parent().get_id()
depth_dict[(chain_id, res_id)] = (rd, ca_rd)
depth_list.append((residue, (rd, ca_rd)))
depth_keys.append((chain_id, res_id))
# Update xtra information
residue.xtra['EXP_RD'] = rd
residue.xtra['EXP_RD_CA'] = ca_rd
AbstractPropertyMap.__init__(self, depth_dict, depth_keys, depth_list)
def __init__(self, model, radius, offset, hse_up_key, hse_down_key,
angle_key=None):
"""
@param model: model
@type model: L{Model}
@param radius: HSE radius
@type radius: float
@param offset: number of flanking residues that are ignored in the calculation
of the number of neighbors
@type offset: int
@param hse_up_key: key used to store HSEup in the entity.xtra attribute
@type hse_up_key: string
@param hse_down_key: key used to store HSEdown in the entity.xtra attribute
@type hse_down_key: string
@param angle_key: key used to store the angle between CA-CB and CA-pCB in
the entity.xtra attribute
@type angle_key: string
"""
assert(offset>=0)
# For PyMOL visualization
self.ca_cb_list=[]
ppb=CaPPBuilder()
ppl=ppb.build_peptides(model)
hse_map={}
hse_list=[]
hse_keys=[]
for pp1 in ppl:
for i in range(0, len(pp1)):
if i==0:
r1=None
else:
r1=pp1[i-1]
r2=pp1[i]
if i==len(pp1)-1:
r3=None
else:
r3=pp1[i+1]
# This method is provided by the subclasses to calculate HSE
result=self._get_cb(r1, r2, r3)
if result is None:
# Missing atoms, or i==0, or i==len(pp1)-1
continue
pcb, angle=result
hse_u=0
hse_d=0
ca2=r2['CA'].get_vector()
for pp2 in ppl:
for j in range(0, len(pp2)):
if pp1 is pp2 and abs(i-j)<=offset:
# neighboring residues in the chain are ignored
continue
ro=pp2[j]
if not is_aa(ro) or not ro.has_id('CA'):
continue
cao=ro['CA'].get_vector()
d=(cao-ca2)
if d.norm()<radius:
if d.angle(pcb)<(pi/2):
hse_u+=1
else:
hse_d+=1
res_id=r2.get_id()
chain_id=r2.get_parent().get_id()
# Fill the 3 data structures
hse_map[(chain_id, res_id)]=(hse_u, hse_d, angle)
hse_list.append((r2, (hse_u, hse_d, angle)))
hse_keys.append((chain_id, res_id))
# Add to xtra
r2.xtra[hse_up_key]=hse_u
r2.xtra[hse_down_key]=hse_d
if angle_key:
r2.xtra[angle_key]=angle
AbstractPropertyMap.__init__(self, hse_map, hse_keys, hse_list)
