def PDBHelix_vs_helixBunble(pdb,limits_file = 0):
"""
Allows to compute the angle between an helix and the protein axis on a pdb
file.
Args : a pdb file and a limits file (optional)
Return : a file which contain all the angle calculation
"""
if limits_file == 0:
ss = fct.secondary_structure(pdb) # compute the helix position
else:
ss = fct.get_ss(limits_file,pdb)# get the helix position from helix list
list_helix = fct.search_helix(pdb,ss) # extract helix from a pdb
fct.print_limits(list_helix) # print and write the helix position
fct.get_inertie_mtx(list_helix) # compute the inertia matrix
fct.helix_evec(list_helix)# compute the eigen vector for each helix
hb_axis = fct.helix_bundle_evec(list_helix) # compute the helix bundle axis
output = open("prot_angle.dat","w")
output.write("#Helix angle(degrees)\n")
axis1 = hb_axis[:,0]
i = 1
print "\nResults : "
for helix in list_helix:
axis2 = helix.eig_vec[:,0]
#Compute the helix-helix bundle angle :
angle = math.acos(axis1.dot(axis2))*57.3
out = "%s-helix_bundle_axis %.3f\n"%(helix.name,angle)
output.write(out)
print out
i += 1
output.close()
def PDBhelix_torsion_angle(pdb,limits_file = 0):
"""
Compute the torsion angle for helix which is contact in a pdbfile
"""
if limits_file == 0:
ss = fct.secondary_structure(pdb) # compute the helix position
else:
ss = fct.get_ss(limits_file,pdb)# get the helix position from helix list
list_helix = fct.search_helix(pdb,ss) # extract helix from a pdb
fct.print_limits(list_helix) # print and write the helix position
contact = fct.WhichIsInContact(list_helix)# Compute which helix is in contact
fct.get_inertie_mtx(list_helix) # compute the inertia matrix
fct.helix_evec(list_helix) # Compute the eigen vectors for each helix
output = open("torsion_angle.dat","w")
header = "#Helix torsion_angle(degrees)\n"
output.write(header)
print header
start = 1
for i in range(len(list_helix)):
h1 = list_helix[i]
for j in range(start,len(list_helix)):
h2 = list_helix[j]
ang = "%s-%s"%(h1.name,h2.name)
if ang in contact:
# Compute the torsion angle :
angle = ma.compute_torsion_angle(h1,h2)
out = "%s-%s %.3f\n"%(h1.name,h2.name,angle)
output.write(out)
print out
start += 1
output.close()
def MDhelix_vs_helix(top,traj,output = 0,limits = 0):
"""
Compute the helix - helix angle during a MD simulation.
If output = "w", an output file is write.
Args : a topology, a trajectory file and an output (optional)
Return : a numpy matrix which contain all angle and a list which contain all
angle couple.
"""
#mk a directory and compute the number of frame in the trajectory:
last_frame,dir_name = fct.get_pdb(top,traj) #number of frame
row = 0
if output == "w":
output = open('results_helix_vs_helix.dat','w')
for i in range(last_frame):
print 'Compute helix-helix angle for frame : %i'%(i+1)
if i == 0:
if limits == 0:
# Compute the helix positions:
ss = fct.secondary_structure("%s/dssp_input.pdb"%dir_name)
else :
# Extract the helix positions from an input file
ss = fct.get_ss(limits,"%s/dssp_input.pdb"%dir_name)
#Extract helix from the frame:
list_helix = fct.search_helix("%s/frame_1.pdb"%dir_name,ss)
if i == 0:
#Print and write the helix positions
fct.print_limits(list_helix,"w")
# Create a numpy matrix with the good dimensions:
results_mtx = fct.mk_results_mtx(last_frame,list_helix)
names = fct.header_hvsh(output,list_helix)
# Extract helix from the frame:
list_helix = fct.search_helix("%s/frame_%i.pdb"%(dir_name,i+1),ss)
# Compute the inertia matrix:
fct.get_inertie_mtx(list_helix)
#Compute the eigen vectors :
fct.helix_evec(list_helix)
results_mtx,row = fct.compute_hvsh(i,output,list_helix,results_mtx,row)
if output != 0:
output.close()
# os.system("rm -rf %s"%dir_name)
return results_mtx,names
def MDhelix_vs_helixbundle(top,traj,output = 0,limits = 0):
"""
Compute the helix - helix bundle angle during a MD simulation.
If output = "w", an output file is write.
Args : a topology, a trajectory file and an output (optional)
Return : a numpy matrix which contain all angle and a list which contain all
the combination of angle.
"""
#mk a directory and compute the number of frame in the trajectory:
last_frame,dir_name = fct.get_pdb(top,traj)
row = 0
if output == "w":
output = open('results_helix_vs_helixbundle.dat','w')
for i in range(last_frame):
print 'Compute helix - helix bundle angle for frame : %i'%(i+1)
if i == 0:
if limits == 0 :
# Compute the helix positions:
ss = fct.secondary_structure("%s/dssp_input.pdb"%dir_name)
else:
# Extract the helix positions from an input file:
ss = fct.get_ss(limits,"%s/dssp_input.pdb"%dir_name)
list_helix = fct.search_helix("%s/frame_1.pdb"%dir_name,ss)
for helix in list_helix:
print helix.name,helix.res_start,helix.res_finish
if i == 0:
fct.print_limits(list_helix,"w")
results_mtx = np.zeros((last_frame,len(list_helix)))
names = fct.header_hvshb(output,list_helix)
list_helix = fct.search_helix("%s/frame_%i.pdb"%(dir_name,i+1),ss)
#Compute the inertia matrix :
fct.get_inertie_mtx(list_helix)
#Compute the eigen vectors :
fct.helix_evec(list_helix)
# Compute the helixbundle axis:
baxe = fct.helix_bundle_evec(list_helix)
results_mtx,row = fct.compute_hvshb(i,output,list_helix,baxe[:,0],\
results_mtx,row)
if output != 0:
output.close()
os.system("rm -rf %s"%dir_name)
return results_mtx,names
def PDBHelix_vs_helix(pdb,limits_file = 0):
"""
Compute the angle between for all combination of two diffrents helix.
all the results is write on an output file.
Args : a pdb file and a limits file (optional)
"""
if limits_file == 0:
ss = fct.secondary_structure(pdb) # compute the helix position
else:
ss = fct.get_ss(limits_file,pdb)# get the helix position from helix list
list_helix = fct.search_helix(pdb,ss) # extract helix from a pdb
fct.print_limits(list_helix) # print and write the helix position
fct.get_inertie_mtx(list_helix) # compute the inertia matrix
fct.helix_evec(list_helix) # compute the eigen vector for each helix
print "\n"
print "Results :"
output = open("helix_helix_angle.dat","w")
header = "#Helix angle(degrees)\n"
output.write(header) # write the header on the output file
print header
start = 1
# this double loop allows to compute angle between each helix couple
for i in range(len(list_helix)):
axis1 = list_helix[i].eig_vec[:,0] # axis of helix 1
for j in range(start,len(list_helix)):
axis2 = list_helix[j].eig_vec[:,0] # axis for helix 2
axis1 = fct.check_vec_sens(axis1,axis2) # check the vectors direction
angle = math.acos(axis1.dot(axis2))*57.3
out = "%s-%s %.3f"%(list_helix[i].name,list_helix[j].name,angle)
output.write("%s\n"%out) # write the angle on the output file
print out
start += 1
print "The resutls file : helix_helix_angle.dat"
print ""
output.close()
def MDhelix_torsion_angle(top,traj,output = 0):
#mk a directory and compute the number of frame in the trajectory:
last_frame,dirname = fct.get_pdb(top,traj)
row = 0
if output == "w":
output = open('results_helix_torsion_angle.dat','w')
for i in range(last_frame):
print 'Compute helix - helix torsion angle for frame : %i'%(i+1)
if i == 0:
ss = fct.secondary_structure("%s/dssp_input.pdb"%dirname)
list_helix = fct.search_helix("%s/frame_%i.pdb"%(dirname,i+1),ss)
if i == 0:
fct.print_limits(list_helix,"w")
contact = fct.WhichIsInContact(list_helix)
results_mtx = np.zeros((last_frame,len(contact)))
if output != 0:
fct.header_hta(output,contact)
fct.get_inertie_mtx(list_helix) #Compute inertia matrix
fct.helix_evec(list_helix) # Compute eigen vectors
fct.evec_correction(list_helix) # Correct the vector direction
fct.get_mass_center(list_helix) # Compute the mass center
results_mtx,row = fct.compute_hta(i,output,list_helix,\
contact,results_mtx,row)
if output != 0:
output.close()
os.system("rm -rf %s"%dirname)
return results_mtx,contact