def two_pdb_chains(pdb,
ch1='',
ch2='',
dock=None,
file1=None,
file2=None,
surface=False,
allres=False,
cutoff1=15,
cutoff2=2):
if dock == None:
from use_dock import DockTool
dock = DockTool()
p1, ch1, p2, ch2 = dock.prepare_data(pdb,
ch1,
pdb,
ch2,
file1=file1,
file2=file2)
area1 = get_area(dock.chain1, dock.chain1_id, ch1)
area2 = get_area(dock.chain2, dock.chain2_id, ch2)
areac = get_area(dock.combine, dock.chain1_id + dock.chain2_id, ch1 + ch2)
dock.clean_temp_path()
res1 = area1.keys()
res2 = area2.keys()
outer1 = get_outer(area1, cutoff1)
outer2 = get_outer(area2, cutoff1)
inter1 = get_interface(area1, areac, cutoff2)
inter2 = get_interface(area2, areac, cutoff2)
if allres:
return inter1 & outer1, inter2 & outer2, outer1, outer2, res1, res2
if surface:
return inter1 & outer1, inter2 & outer2, outer1, outer2
return inter1 & outer1, inter2 & outer2
def change_of_rel_asa(pdb, ch1='', ch2='', dock=None, file1=None, file2=None):
if dock == None:
from use_dock import DockTool
dock = DockTool()
p1, ch1, p2, ch2 = dock.prepare_data(pdb, ch1, pdb, ch2, file1=file1, file2=file2)
area1 = get_area(dock.chain1, dock.chain1_id, ch1)
area2 = get_area(dock.chain2, dock.chain2_id, ch2)
areac = get_area(dock.combine, dock.chain1_id+dock.chain2_id, ch1+ch2)
dock.clean_temp_path()
data = []
for p in area1:
data.append([pdb, ch1, p, area1[p][1] - areac[p][1]])
for p in area2:
data.append([pdb, ch2, p, area2[p][1] - areac[p][1]])
return data
def change_of_rel_asa(pdb, ch1='', ch2='', dock=None, file1=None, file2=None):
if dock == None:
from use_dock import DockTool
dock = DockTool()
p1, ch1, p2, ch2 = dock.prepare_data(pdb,
ch1,
pdb,
ch2,
file1=file1,
file2=file2)
area1 = get_area(dock.chain1, dock.chain1_id, ch1)
area2 = get_area(dock.chain2, dock.chain2_id, ch2)
areac = get_area(dock.combine, dock.chain1_id + dock.chain2_id, ch1 + ch2)
dock.clean_temp_path()
data = []
for p in area1:
data.append([pdb, ch1, p, area1[p][1] - areac[p][1]])
for p in area2:
data.append([pdb, ch2, p, area2[p][1] - areac[p][1]])
return data
def two_pdb_chains(pdb, ch1='', ch2='', dock=None, file1=None, file2=None,
surface=False, allres=False, cutoff1=15, cutoff2=2):
if dock == None:
from use_dock import DockTool
dock = DockTool()
p1, ch1, p2, ch2 = dock.prepare_data(pdb, ch1, pdb, ch2, file1=file1, file2=file2)
area1 = get_area(dock.chain1, dock.chain1_id, ch1)
area2 = get_area(dock.chain2, dock.chain2_id, ch2)
areac = get_area(dock.combine, dock.chain1_id+dock.chain2_id, ch1+ch2)
dock.clean_temp_path()
res1 = area1.keys()
res2 = area2.keys()
outer1 = get_outer(area1, cutoff1)
outer2 = get_outer(area2, cutoff1)
inter1 = get_interface(area1, areac, cutoff2)
inter2 = get_interface(area2, areac, cutoff2)
if allres:
return inter1 & outer1, inter2 & outer2, outer1, outer2, res1, res2
if surface:
return inter1 & outer1, inter2 & outer2, outer1, outer2
return inter1 & outer1, inter2 & outer2