def get_residue_list(self, pdb_struct, domain, getchainid=None):
"""
Return list of Bio.PDB Residue objects in this domain, and optionally
in the specified chain.,
Parameters:
pdb_struct - Bio.PDB parsed PDB struct for the protein
domain - PTDomain (ptdomain.py) object listing the segment(s)
that make up this domain (only one domain processed at a
time).
getchainid - chain identifier to get residues in (default None -
all chains).
Return value:
list of Bio.PDB Residue objects in the domain (and optionally chain).
Raises exceptions:
NoSSE_Exception for empty structure (happens eg on d1oayi_.ent)
"""
residue_list = []
try:
pdb_model = self.pdb_struct[0] # TODO always using model 0 for now
except KeyError:
raise NoSSE_Exception
for chain in pdb_model:
chainid = ptsecstruct.pdb_chainid_to_stride_chainid(chain.get_id())
if getchainid and getchainid != chainid:
continue # this is not the chain we want
# Build a list of Bio.PDB Residue objects that are in this
# domain.
# id of a residue in Bio.PDB is tuple (hetatm, resseqnum, icode)
# so we choose those where residue PDB number
# (in the current chain) is in the domain.
# TODO: maybe should use polypeptide builder for this instead
# (and indeed should probably use it right from the beginning) -
residue_list += [
residue for residue in chain.get_unpacked_list() if
is_aa(residue) and domain.is_in_domain(chainid,
residue.get_id()[1])
]
if getchainid:
break # if getchainid specified, we now have it so can quit
return residue_list
def get_residue_list(self, pdb_struct, domain, getchainid=None):
"""
Return list of Bio.PDB Residue objects in this domain, and optionally
in the specified chain.,
Parameters:
pdb_struct - Bio.PDB parsed PDB struct for the protein
domain - PTDomain (ptdomain.py) object listing the segment(s)
that make up this domain (only one domain processed at a
time).
getchainid - chain identifier to get residues in (default None -
all chains).
Return value:
list of Bio.PDB Residue objects in the domain (and optionally chain).
Raises exceptions:
NoSSE_Exception for empty structure (happens eg on d1oayi_.ent)
"""
residue_list = []
try:
pdb_model = self.pdb_struct[0] # TODO always using model 0 for now
except KeyError:
raise NoSSE_Exception
for chain in pdb_model:
chainid = ptsecstruct.pdb_chainid_to_stride_chainid(chain.get_id())
if getchainid and getchainid != chainid:
continue # this is not the chain we want
# Build a list of Bio.PDB Residue objects that are in this
# domain.
# id of a residue in Bio.PDB is tuple (hetatm, resseqnum, icode)
# so we choose those where residue PDB number
# (in the current chain) is in the domain.
# TODO: maybe should use polypeptide builder for this instead
# (and indeed should probably use it right from the beginning) -
residue_list += [
residue
for residue in chain.get_unpacked_list()
if is_aa(residue) and domain.is_in_domain(chainid, residue.get_id()[1])
]
if getchainid:
break # if getchainid specified, we now have it so can quit
return residue_list
def accept_residue(self, residue):
"""
overrides the base accept_residue() function to accept only
residues in our domain. Also reject HETATMS.
Paramteters:
residue - Bio.PDB Residue object of residue to test
Return value:
1 to accept residue, 0 to reject.
"""
chain = residue.get_parent()
chainid = pdb_chainid_to_stride_chainid(chain.get_id())
# id of a residue in Bio.PDB is tuple (hetatm, resseqnum, icode)
# so we choose those where chain and residue PDB number
# is in the domain.
resnum = residue.get_id()[1]
if (self.domain.is_in_domain(chainid, resnum)
and residue.get_id()[0] == ' '):
return 1
else:
return 0
def accept_residue(self, residue):
"""
overrides the base accept_residue() function to accept only
residues in our domain. Also reject HETATMS.
Paramteters:
residue - Bio.PDB Residue object of residue to test
Return value:
1 to accept residue, 0 to reject.
"""
chain = residue.get_parent()
chainid = pdb_chainid_to_stride_chainid(chain.get_id())
# id of a residue in Bio.PDB is tuple (hetatm, resseqnum, icode)
# so we choose those where chain and residue PDB number
# is in the domain.
resnum = residue.get_id()[1]
if (self.domain.is_in_domain(chainid, resnum) and
residue.get_id()[0] == ' '):
return 1
else:
return 0
def build_graph_from_secstruct(self,
secstruct,
domain,
chainid=None,
ignore_insertion_codes=False):
"""
Build the list of nodes from the the supplied PTSecStruct
object.
Parameters:
secstruct - PTSecStruct (ptsecstruct.py) object to build from
domain - PTDomain (ptdomain.py) object listing the segment(s)
that make up this domain (only one domain processed at a
time).
(in/out) NOTE: may be modified by having a segment
added if SSE is only partly in domain.
chainid - chain identifier to build graph for only this chain,
or None for all chains (default)
ignore_insertion_codes - If True, a hack to make it work with
PMML (only) which does not report insertion codes
unlike DSSP and STRIDE
Uses member data (write):
chain_dict - dict of { chainid : node_list } where node_list is
list of nodes in order, built in this function
secstruct - keeps a pointer to the supplied secstruct
(readonly):
pdb_struct - The Bio.PDB parsed PDB struct (atomic co-ordinates)
for this protein.
include_310_helices, include_pi_helices - if true, include
these kinds of helices.
Raises exceptions:
NoSSE_Exception if no helices or strands found
Return value:
None.
"""
self.secstruct = secstruct
helix_num = 1
strand_num = 1
num_helices_in_domain = 0
num_strands_in_domain = 0
#
# Build dictionary mapping (chainid, pdb_resid) to index in residue_list
# for ALL residues, not just those in this domain.
#
self.residue_list = self.get_residue_list(self.pdb_struct,
PTDomain(None, None))
self.pdb_resid_dict = {}
seq_indx = 0
while seq_indx < len(self.residue_list):
residue = self.residue_list[seq_indx]
self.pdb_resid_dict[(ptsecstruct.pdb_chainid_to_stride_chainid(
residue.get_full_id()[2]),
biopdbresid_to_pdbresseq(
residue.get_id(),
ignore_insertion_codes))] = seq_indx
seq_indx += 1
# Note that now we are only adding elements in the supplied domain,
# so the so-called 'chains' may really be segments, i.e. subsequences
# of chains (rest of chain may be in other domain(s)
self.chain_dict = {} # dict of {chainid : node_list}
for (start_chainid, start_resnum, end_chainid, end_resnum, helixtype) \
in secstruct.helix_list:
assert (start_chainid == end_chainid) #helix must be same chain
if chainid and chainid != start_chainid:
continue # chainid specified, skip ones not in that chain
# will consider structures in domain if first residue is in domain
if domain.is_in_domain(start_chainid,
get_int_icode(start_resnum)[0]):
num_helices_in_domain += 1
if helixtype == "H":
idprefix = "ALPHAHELIX_"
htype = "ALPHA"
this_helix_num = helix_num
helix_num += 1
elif helixtype == "I":
if not self.include_pi_helices:
continue
idprefix = "PIHELIX_"
htype = "PI"
this_helix_num = helix_num
helix_num += 1
elif helixtype == "G":
if not self.include_310_helices:
continue
idprefix = "310HELIX_"
htype = "310"
this_helix_num = helix_num
helix_num += 1
else: # shouldn't happen
sys.stderr.write("ERROR: bad helix type " + helixtype +
"\n")
ah_node = PTNodeHelix(htype,
idprefix + start_chainid+"_" +\
str(this_helix_num),
this_helix_num,
start_resnum, end_resnum, start_chainid,
domain.domainid,
self.residue_list, self.pdb_resid_dict)
if not self.chain_dict.has_key(start_chainid):
self.chain_dict[start_chainid] = []
self.chain_dict[start_chainid].append(ah_node)
# we must already have handled the case of SSEs that cross
# domain boundaries (by moving whole SSE to one of the domains)
assert (domain.is_in_domain(end_chainid,
get_int_icode(end_resnum)[0]))
for (start_chainid, start_resnum, end_chainid, end_resnum) \
in secstruct.strand_list:
assert (start_chainid == end_chainid) # must be in same chain
if chainid and chainid != start_chainid:
continue # chainid specified, skip ones not in that chain
if domain.is_in_domain(start_chainid,
get_int_icode(start_resnum)[0]):
num_strands_in_domain += 1
bs_node = PTNodeStrand("STRAND_"+start_chainid +"_"+\
str(strand_num),
strand_num,
start_resnum, end_resnum, start_chainid,
domain.domainid,
self.residue_list,
self.pdb_resid_dict)
strand_num += 1
if not self.chain_dict.has_key(start_chainid):
self.chain_dict[start_chainid] = []
# we must already have handled the case of SSEs that cross
# domain boundaries (by moving whole SSE to one of the domains)
assert (domain.is_in_domain(end_chainid,
get_int_icode(end_resnum)[0]))
self.chain_dict[start_chainid].append(bs_node)
# raise an exception if there are no SSEs at all in this domain
if num_helices_in_domain == 0 and num_strands_in_domain == 0:
raise NoSSE_Exception
delete_chainid_list = [] # list of chainids to delete from chain_dict
for (chainid, nodelist) in self.chain_dict.iteritems():
# sort in order of start residue id ascending (all must be disjoint)
nodelist.sort()
if len(nodelist) < 1:
# There are no SSEs in this chain, get rid of it.
sys.stderr.write('WARNING: no SSEs in chain ' + chainid +
'; chain ignored\n')
delete_chainid_list.append(
chainid) # don't delete while in loop
continue
else:
# Check for chain with only SSEs that will not be drawn
# (i.e. pi or 310 helices), and delete those too
found_useful_node = False
for ptnode in nodelist:
if isinstance(ptnode, PTNodeStrand):
found_useful_node = True
break
elif isinstance(ptnode, PTNodeHelix):
if ptnode.get_type() == "ALPHA":
found_useful_node = True
break
elif ((ptnode.get_type() == "310"
and self.include_310_helices)
or (ptnode.get_type() == "PI"
and self.include_pi_helices)):
found_useful_node = True
break
if not found_useful_node:
sys.stderr.write(
'WARNING: only pi or 310 helices in chain ' + chainid +
'; chain ignored\n')
delete_chainid_list.append(chainid)
continue
# delete chains from chain_dict that were marked earlier for deletion
for chainid in delete_chainid_list:
self.chain_dict.pop(chainid)
# -------------------------------------------------------------------
# This is needed only for labelling sheets for HH and KK codes
# (see dfs_strands() etc. below)
# add edges for hydrogen bonds
# uses secstruct and chainid member data
# these are used for determining which side bridge partners are
# on (and also for drawing a hydrogen bond graph if requested)
self.add_hbond_edges_from_secstruct()
# add edges for bridge partners
# uses secstruct and chainid member data
self.add_bridge_edges_from_secstruct()
#---------------------------------------------------------------------
# for sequential numbering, we'll build this dictionary mapping
# sequential number (note NOT restarting for each chain)
# to PTNode
# so that sequential numbers as used in ptgraph2 -b sequential
# option.
# this is a dictionary of { seqnum : PTNode }
self.seqnum2node = {}
for (seqnum, node) in \
enumerate([node for node in self.iter_nodes() if \
not ( (isinstance(node, PTNodeTerminus)) or
(isinstance(node, PTNodeHelix) and
( (node.get_type() == "310" and
not self.include_310_helices) or
(node.get_type() == "PI" and
not self.include_pi_helices) ) ) ) ]):
self.seqnum2node[seqnum + 1] = node # start at 1 not 0
def build_graph_from_secstruct(self, secstruct, domain, chainid=None, ignore_insertion_codes=False):
"""
Build the list of nodes from the the supplied PTSecStruct
object.
Parameters:
secstruct - PTSecStruct (ptsecstruct.py) object to build from
domain - PTDomain (ptdomain.py) object listing the segment(s)
that make up this domain (only one domain processed at a
time).
(in/out) NOTE: may be modified by having a segment
added if SSE is only partly in domain.
chainid - chain identifier to build graph for only this chain,
or None for all chains (default)
ignore_insertion_codes - If True, a hack to make it work with
PMML (only) which does not report insertion codes
unlike DSSP and STRIDE
Uses member data (write):
chain_dict - dict of { chainid : node_list } where node_list is
list of nodes in order, built in this function
secstruct - keeps a pointer to the supplied secstruct
(readonly):
pdb_struct - The Bio.PDB parsed PDB struct (atomic co-ordinates)
for this protein.
include_310_helices, include_pi_helices - if true, include
these kinds of helices.
Raises exceptions:
NoSSE_Exception if no helices or strands found
Return value:
None.
"""
self.secstruct = secstruct
helix_num = 1
strand_num = 1
num_helices_in_domain = 0
num_strands_in_domain = 0
#
# Build dictionary mapping (chainid, pdb_resid) to index in residue_list
# for ALL residues, not just those in this domain.
#
self.residue_list = self.get_residue_list(self.pdb_struct, PTDomain(None, None))
self.pdb_resid_dict = {}
seq_indx = 0
while seq_indx < len(self.residue_list):
residue = self.residue_list[seq_indx]
self.pdb_resid_dict[
(
ptsecstruct.pdb_chainid_to_stride_chainid(residue.get_full_id()[2]),
biopdbresid_to_pdbresseq(residue.get_id(), ignore_insertion_codes),
)
] = seq_indx
seq_indx += 1
# Note that now we are only adding elements in the supplied domain,
# so the so-called 'chains' may really be segments, i.e. subsequences
# of chains (rest of chain may be in other domain(s)
self.chain_dict = {} # dict of {chainid : node_list}
for (start_chainid, start_resnum, end_chainid, end_resnum, helixtype) in secstruct.helix_list:
assert start_chainid == end_chainid # helix must be same chain
if chainid and chainid != start_chainid:
continue # chainid specified, skip ones not in that chain
# will consider structures in domain if first residue is in domain
if domain.is_in_domain(start_chainid, get_int_icode(start_resnum)[0]):
num_helices_in_domain += 1
if helixtype == "H":
idprefix = "ALPHAHELIX_"
htype = "ALPHA"
this_helix_num = helix_num
helix_num += 1
elif helixtype == "I":
if not self.include_pi_helices:
continue
idprefix = "PIHELIX_"
htype = "PI"
this_helix_num = helix_num
helix_num += 1
elif helixtype == "G":
if not self.include_310_helices:
continue
idprefix = "310HELIX_"
htype = "310"
this_helix_num = helix_num
helix_num += 1
else: # shouldn't happen
sys.stderr.write("ERROR: bad helix type " + helixtype + "\n")
ah_node = PTNodeHelix(
htype,
idprefix + start_chainid + "_" + str(this_helix_num),
this_helix_num,
start_resnum,
end_resnum,
start_chainid,
domain.domainid,
self.residue_list,
self.pdb_resid_dict,
)
if not self.chain_dict.has_key(start_chainid):
self.chain_dict[start_chainid] = []
self.chain_dict[start_chainid].append(ah_node)
# we must already have handled the case of SSEs that cross
# domain boundaries (by moving whole SSE to one of the domains)
assert domain.is_in_domain(end_chainid, get_int_icode(end_resnum)[0])
for (start_chainid, start_resnum, end_chainid, end_resnum) in secstruct.strand_list:
assert start_chainid == end_chainid # must be in same chain
if chainid and chainid != start_chainid:
continue # chainid specified, skip ones not in that chain
if domain.is_in_domain(start_chainid, get_int_icode(start_resnum)[0]):
num_strands_in_domain += 1
bs_node = PTNodeStrand(
"STRAND_" + start_chainid + "_" + str(strand_num),
strand_num,
start_resnum,
end_resnum,
start_chainid,
domain.domainid,
self.residue_list,
self.pdb_resid_dict,
)
strand_num += 1
if not self.chain_dict.has_key(start_chainid):
self.chain_dict[start_chainid] = []
# we must already have handled the case of SSEs that cross
# domain boundaries (by moving whole SSE to one of the domains)
assert domain.is_in_domain(end_chainid, get_int_icode(end_resnum)[0])
self.chain_dict[start_chainid].append(bs_node)
# raise an exception if there are no SSEs at all in this domain
if num_helices_in_domain == 0 and num_strands_in_domain == 0:
raise NoSSE_Exception
delete_chainid_list = [] # list of chainids to delete from chain_dict
for (chainid, nodelist) in self.chain_dict.iteritems():
# sort in order of start residue id ascending (all must be disjoint)
nodelist.sort()
if len(nodelist) < 1:
# There are no SSEs in this chain, get rid of it.
sys.stderr.write("WARNING: no SSEs in chain " + chainid + "; chain ignored\n")
delete_chainid_list.append(chainid) # don't delete while in loop
continue
else:
# Check for chain with only SSEs that will not be drawn
# (i.e. pi or 310 helices), and delete those too
found_useful_node = False
for ptnode in nodelist:
if isinstance(ptnode, PTNodeStrand):
found_useful_node = True
break
elif isinstance(ptnode, PTNodeHelix):
if ptnode.get_type() == "ALPHA":
found_useful_node = True
break
elif (ptnode.get_type() == "310" and self.include_310_helices) or (
ptnode.get_type() == "PI" and self.include_pi_helices
):
found_useful_node = True
break
if not found_useful_node:
sys.stderr.write("WARNING: only pi or 310 helices in chain " + chainid + "; chain ignored\n")
delete_chainid_list.append(chainid)
continue
# delete chains from chain_dict that were marked earlier for deletion
for chainid in delete_chainid_list:
self.chain_dict.pop(chainid)
# -------------------------------------------------------------------
# This is needed only for labelling sheets for HH and KK codes
# (see dfs_strands() etc. below)
# add edges for hydrogen bonds
# uses secstruct and chainid member data
# these are used for determining which side bridge partners are
# on (and also for drawing a hydrogen bond graph if requested)
self.add_hbond_edges_from_secstruct()
# add edges for bridge partners
# uses secstruct and chainid member data
self.add_bridge_edges_from_secstruct()
# ---------------------------------------------------------------------
# for sequential numbering, we'll build this dictionary mapping
# sequential number (note NOT restarting for each chain)
# to PTNode
# so that sequential numbers as used in ptgraph2 -b sequential
# option.
# this is a dictionary of { seqnum : PTNode }
self.seqnum2node = {}
for (seqnum, node) in enumerate(
[
node
for node in self.iter_nodes()
if not (
(isinstance(node, PTNodeTerminus))
or (
isinstance(node, PTNodeHelix)
and (
(node.get_type() == "310" and not self.include_310_helices)
or (node.get_type() == "PI" and not self.include_pi_helices)
)
)
)
]
):
self.seqnum2node[seqnum + 1] = node # start at 1 not 0