def pairwise_dist(sel1,
sel2,
max_dist,
output="N",
output_filename="",
sidechain="N",
show="N"):
"""
usage: pairwise_dist sel1, sel2, max_dist, [output=S/P/N, [sidechain=N/Y, [show=Y/N]]]
sel1 and sel2 can be any to pre-existing or newly defined selections
max_dist: maximum distance in Angstrom between atoms in the two selections
--optional settings:
output: accepts Screen/Print/None (default N)
sidechain: limits (Y) results to sidechain atoms (default N)
show: shows (Y) individual distances in pymol menu (default=N)
"""
print ""
cmd.delete("dist*")
extra = ""
if sidechain == "Y": extra = " and not name c+o+n"
#builds models
m1 = cmd.get_model(sel2 + " around " + str(max_dist) + " and " + sel1 +
extra)
m1o = cmd.get_object_list(sel1)
m2 = cmd.get_model(sel1 + " around " + str(max_dist) + " and " + sel2 +
extra)
m2o = cmd.get_object_list(sel2)
#defines selections
cmd.select("__tsel1a",
sel1 + " around " + str(max_dist) + " and " + sel2 + extra)
cmd.select("__tsel1", "__tsel1a and " + sel2 + extra)
cmd.select("__tsel2a",
sel2 + " around " + str(max_dist) + " and " + sel1 + extra)
cmd.select("__tsel2", "__tsel2a and " + sel1 + extra)
cmd.select("IntAtoms_" + max_dist, "__tsel1 or __tsel2")
cmd.select("IntRes_" + max_dist, "byres IntAtoms_" + max_dist)
#controlers-1
if len(m1o) == 0:
print "warning, '" + sel1 + extra + "' does not contain any atoms."
return
if len(m2o) == 0:
print "warning, '" + sel2 + extra + "' does not contain any atoms."
return
#measures distances
s = ""
counter = 0
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
distance = math.sqrt(
sum(
map(lambda f: (f[0] - f[1])**2,
zip(m1.atom[c1].coord, m2.atom[c2].coord))))
if distance < float(max_dist):
s += "%s/%s/%s/%s/%s to %s/%s/%s/%s/%s: %.3f\n" % (
m1o[0], m1.atom[c1].chain, m1.atom[c1].resn,
m1.atom[c1].resi, m1.atom[c1].name, m2o[0],
m2.atom[c2].chain, m2.atom[c2].resn, m2.atom[c2].resi,
m2.atom[c2].name, distance)
counter += 1
if show == "Y":
cmd.distance(
m1o[0] + " and " + m1.atom[c1].chain + "/" +
m1.atom[c1].resi + "/" + m1.atom[c1].name,
m2o[0] + " and " + m2.atom[c2].chain + "/" +
m2.atom[c2].resi + "/" + m2.atom[c2].name)
#controler-2
if counter == 0:
print "warning, no distances were measured! Check your selections/max_dist value"
return
#outputs
if output == "S": print s
if output == "P":
f = open(output_filename, 'w')
f.write("Number of distances calculated: %s\n" % (counter))
f.write(s)
f.close()
print "Results saved in %s" % output_filename
print "Number of distances calculated: %s" % (counter)
cmd.hide("lines", "IntRes_*")
if show == "Y": cmd.show("lines", "IntRes_" + max_dist)
cmd.deselect()
cmd.select("__tsel2",
"__tsel2a and " + sel1 + extra)
cmd.select("IntAtoms_" + max_dist,
"__tsel1 or __tsel2")
cmd.select("IntRes_" + max_dist,
"byres IntAtoms_" + max_dist)
s = ""
counter = 0
atomlist = []
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
distance = math.sqrt(
sum(
map(
lambda f: (f[0] - f[1])**2,
zip(
m1.atom[c1].coord,
m2.atom[c2].coord))))
if distance < float(max_dist):
# s += "%s/%s/%s/%s/%s to %s/%s/%s/%s/%s: %.3f\n" % (
# m1o[0], m1.atom[c1].chain, m1.atom[c1].resn,
# m1.atom[c1].resi, m1.atom[c1].name, m2o[0],
# m2.atom[c2].chain, m2.atom[c2].resn,
# m2.atom[c2].resi,
# m2.atom[c2].name, distance)
counter += 1
atomlist.append(distance)
finList = round(min(atomlist), 1)
goodRuns = goodRuns + 1
def pairwise_dist(pdbfile,sel1, sel2, max_dist, output="P", sidechain="N", show="N",outfile="./"):
"""
usage: pairwise_dist sel1, sel2, max_dist, [output=S/P/N, [sidechain=N/Y, [show=Y/N]]]
sel1 and sel2 can be any to pre-existing or newly defined selections
max_dist: maximum distance in Angstrom between atoms in the two selections
--optional settings:
output: accepts Screen/Print/None (default N)
sidechain: limits (Y) results to sidechain atoms (default N)
show: shows (Y) individual distances in pymol menu (default=N)
"""
print ""
cmd.delete ("dist*")
extra=""
if sidechain=="Y": extra=" and not name c+o+n"
#builds models
m1=cmd.get_model(sel2+" around "+str(max_dist)+" and "+sel1+extra)
m1o=cmd.get_object_list(sel1)
m2=cmd.get_model(sel1+" around "+str(max_dist)+" and "+sel2+extra)
m2o=cmd.get_object_list(sel2)
#defines selections
cmd.select("__tsel1a", sel1+" around "+str(max_dist)+" and "+sel2+extra)
cmd.select("__tsel1", "__tsel1a and "+sel2+extra)
cmd.select("__tsel2a", sel2+" around "+str(max_dist)+" and "+sel1+extra)
cmd.select("__tsel2", "__tsel2a and "+sel1+extra)
cmd.select("IntAtoms_"+str(max_dist), "__tsel1 or __tsel2")
cmd.select("IntRes_"+str(max_dist), "byres IntAtoms_"+str(max_dist))
#controlers-1
if len(m1o)==0:
print "warning, '"+sel1+extra+"' does not contain any atoms."
return
if len(m2o)==0:
print "warning, '"+sel2+extra+"' does not contain any atoms."
return
#measures distances
s=""
counter=0
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
distance=math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(m1.atom[c1].coord,m2.atom[c2].coord))))
if distance<float(max_dist):
s+="%s/%s/%s/%s/%s to %s/%s/%s/%s/%s: %.3f\n" % (m1o[0],m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2o[0],m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
counter+=1
if show=="Y": cmd.distance (m1o[0]+" and "+m1.atom[c1].chain+"/"+m1.atom[c1].resi+"/"+m1.atom[c1].name, m2o[0]+" and "+m2.atom[c2].chain+"/"+m2.atom[c2].resi+"/"+m2.atom[c2].name)
#controler-2
if counter==0:
print "warning, no distances were measured! Check your selections/max_dist value"
return
#outputs
if output=="S": print s
if output=="P":
filename=os.getcwd()+'/interface_analyzer/'+pdbfile+'_distance'+str(max_dist)
f=open(filename,'w')
f.write("Number of distances calculated: %s\n" % (counter))
f.write(s)
f.close()
print "Results saved in _%s" % filename
print "Number of distances calculated: %s" % (counter)
cmd.hide("lines", "IntRes_*")
if show=="Y": cmd.show("lines","IntRes_"+max_dist)
cmd.deselect()