def update_graph(gene2graph, cog, signif_struct_info, struct, radius):
"""Updates the residue neighbor graph based on the current structure.
Residues are linked by edges if they are within the provided radius
and are on the same gene.
Parameters
----------
gene2graph : dict
dictionary with genes as keys pointing to significant hotspot residue
neighbor graph
signif_struct_info : dict
identifies which residues are significant hotspots
struct : Bio.PDB structure
structure under consideration when populating the graph
radius : float
radius deemed close enough to add an edge between two residues
Returns
-------
gene2graph : dict
updated graph based on the provided structure
"""
# get which residues are significant
signif_pdb_pos = signif_struct_info.keys()
possible_res = set(signif_pdb_pos)
# find neighbor residues
cog = {k: cog[k] for k in cog
if (k[2], k[3][1]) in signif_pdb_pos}
neighbors = pstruct.find_neighbors_1D(cog, radius)
#struct_info = struct_chain[pdb_id]
# add edge if residues are neighbors
avail_models = [m.id for m in struct]
for s in signif_pdb_pos:
tmp_chain, tmp_res = s
cur_res = signif_struct_info[s]
cur_gene = cur_res[0]
# update gene2graph
gene2graph.setdefault(cur_gene, {})
gene2graph[cur_gene].setdefault(cur_res, set())
for m in avail_models:
try:
# get neighbors
tmp_id = struct[m][tmp_chain][int(tmp_res)].get_full_id()
tmp_neighbors = set([(n[2], n[3][1]) for n in neighbors[tmp_id]])
# get only neighbors that are significant and in the
# same gene
signif_neighbors = set([signif_struct_info[o]
for o in (tmp_neighbors & possible_res)])
signif_neighbors_gene = set([s for s in signif_neighbors
if s[0] == cur_gene])
# add result to the graph
gene2graph[cur_gene][cur_res] = gene2graph[cur_gene][cur_res] | signif_neighbors_gene
except KeyError:
# skip deleted chains, or models without a chain
# be careful this catches all keyerrors
pass
return gene2graph
def update_graph(struct2graph, all_cogs, signif_struct_info, non_signif_struct_info, struct, radius):
"""Updates the residue neighbor graph based on the current structure.
Residues are linked by edges if they are within the provided radius
and are on the same gene.
Parameters
----------
gene2graph : dict
dictionary with genes as keys pointing to significant hotspot residue
neighbor graph
signif_struct_info : dict
identifies which residues are significant hotspots
struct : Bio.PDB structure
structure under consideration when populating the graph
radius : float
radius deemed close enough to add an edge between two residues
Returns
-------
gene2graph : dict
updated graph based on the provided structure
"""
# get which residues are significant
signif_pdb_pos = signif_struct_info.keys()
non_signif_pdb_pos = non_signif_struct_info.keys()
possible_signif_res = set(signif_pdb_pos)
possible_non_signif_res = set(non_signif_pdb_pos)
# find neighbor residues
signif_cogs = {k: all_cogs[k] for k in all_cogs
if (k[2], k[3][1]) in signif_pdb_pos}
neighbors = pstruct.find_neighbors_1D(signif_cogs, radius)
all_neighbors = pstruct.find_neighbors_for_1D(all_cogs, signif_cogs.keys(), radius)
#struct_info = struct_chain[pdb_id]
# add edge if residues are neighbors
avail_models = [m.id for m in struct]
signif_res_neighbors = {}
for s in signif_pdb_pos:
tmp_chain, tmp_res = s
cur_res = signif_struct_info[s]
cur_pdb = cur_res[0]
# update struct2graph
struct2graph.setdefault(cur_pdb, {})
for m in avail_models:
cur_res = (m, tmp_chain, int(tmp_res))
struct2graph[cur_pdb].setdefault(cur_res, set())
try:
# get neighbors
tmp_id = struct[m][tmp_chain][int(tmp_res)].get_full_id()
tmp_neighbors = set([(n[2], n[3][1]) for n in neighbors[tmp_id]])
all_tmp_neighbors = set([(n[2], n[3][1]) for n in all_neighbors[tmp_id]])
signif_neighbors = set(tmp_neighbors & possible_signif_res)
signif_neighbors_struct = set([(m, o[0], o[1]) for o in signif_neighbors])
non_signif_neighbors = set(all_tmp_neighbors & possible_non_signif_res)
non_signif_neighbors_struct = set([(m, o[0], o[1]) for o in non_signif_neighbors])
signif_res_neighbors[cur_res] = non_signif_neighbors_struct
# add result to the graphs
struct2graph[cur_pdb][cur_res] = struct2graph[cur_pdb][cur_res] | signif_neighbors_struct
except KeyError:
# skip deleted chains, or models without a chain
# be careful this catches all keyerrors
print cur_pdb
pass
return struct2graph, signif_res_neighbors
def update_graph(gene2graph, cog, signif_struct_info, struct, radius):
"""Updates the residue neighbor graph based on the current structure.
Residues are linked by edges if they are within the provided radius
and are on the same gene.
Parameters
----------
gene2graph : dict
dictionary with genes as keys pointing to significant hotspot residue
neighbor graph
signif_struct_info : dict
identifies which residues are significant hotspots
struct : Bio.PDB structure
structure under consideration when populating the graph
radius : float
radius deemed close enough to add an edge between two residues
Returns
-------
gene2graph : dict
updated graph based on the provided structure
"""
# get which residues are significant
signif_pdb_pos = signif_struct_info.keys()
possible_res = set(signif_pdb_pos)
# find neighbor residues
cog = {k: cog[k] for k in cog if (k[2], k[3][1]) in signif_pdb_pos}
neighbors = pstruct.find_neighbors_1D(cog, radius)
#struct_info = struct_chain[pdb_id]
# add edge if residues are neighbors
avail_models = [m.id for m in struct]
for s in signif_pdb_pos:
tmp_chain, tmp_res = s
cur_res = signif_struct_info[s]
cur_gene = cur_res[0]
# update gene2graph
gene2graph.setdefault(cur_gene, {})
gene2graph[cur_gene].setdefault(cur_res, set())
for m in avail_models:
try:
# get neighbors
tmp_id = struct[m][tmp_chain][int(tmp_res)].get_full_id()
tmp_neighbors = set([(n[2], n[3][1])
for n in neighbors[tmp_id]])
# get only neighbors that are significant and in the
# same gene
signif_neighbors = set([
signif_struct_info[o]
for o in (tmp_neighbors & possible_res)
])
signif_neighbors_gene = set(
[s for s in signif_neighbors if s[0] == cur_gene])
# add result to the graph
gene2graph[cur_gene][cur_res] = gene2graph[cur_gene][
cur_res] | signif_neighbors_gene
except KeyError:
# skip deleted chains, or models without a chain
# be careful this catches all keyerrors
pass
return gene2graph
