def test_enm_1():
'''Tests C2-C2 calculation'''
# initialize class. Only PDB are accepted
SBP_enm = enm.Enm(fname,sele_atoms=["C2","C1\'","P"])
# print eigenvectors
evecs = SBP_enm.print_evec(3)
fh = open("%s/enm_01.test.dat" % outdir,'w')
fh.write(evecs)
fh.close()
# print eigenvalues
evals = SBP_enm.print_eval()
fh = open("%s/enm_02.test.dat" % outdir,'w')
fh.write(evals)
fh.close()
# print mean square fluctuations
fluc = SBP_enm.get_MSF()
np.savetxt("%s/enm_03b.test.dat" % outdir,fluc,fmt='%.6e')
# print C2'-C2' fluctuations
fluc,res = SBP_enm.c2_fluctuations()
fh = open("%s/enm_03.test.dat" % outdir,'w')
stri = "# %19s %s \n" % ("Residues","Fluctuations")
for i in range(len(fluc)):
stri += "%10s/%-10s %.6e \n" % (res[i],res[i+1],fluc[i])
fh.write(stri)
fh.close()
comp("%s/enm_01.test.dat" % refdir)
comp("%s/enm_02.test.dat" % refdir)
comp("%s/enm_03.test.dat" % refdir)
comp("%s/enm_03b.test.dat" % refdir)
def test_enm_3():
'''Tests sparse diagonalization'''
# initialize class. Only PDB are accepted
AA_enm = enm.Enm(fname,sele_atoms="AA",sparse=True,cutoff=0.7)
# print eigenvalues
evals = AA_enm.print_eval()
fh = open("%s/enm_06.test.dat" % outdir,'w')
fh.write(evals)
fh.close()
# print eigenvectors
evecs = AA_enm.print_evec(3)
fh = open("%s/enm_07.test.dat" % outdir,'w')
fh.write(evecs)
fh.close()
# print C2'-C2' fluctuations
fluc,res = AA_enm.c2_fluctuations()
fh = open("%s/enm_08.test.dat" % outdir,'w')
stri = "# %19s %s \n" % ("Residues","Fluctuations")
for i in range(len(fluc)):
stri += "%10s/%-10s %.6e \n" % (res[i],res[i+1],fluc[i])
fh.write(stri)
fh.close()
comp("%s/enm_06.test.dat" % refdir)
comp("%s/enm_07.test.dat" % refdir)
comp("%s/enm_08.test.dat" % refdir)
def test_enm_4():
'''Tests RNA+protein complex'''
# initialize class. Only PDB are accepted
SBP_enm = enm.Enm(fname_prot,sparse=False)
# print eigenvalues
evals = SBP_enm.print_eval()
fh = open("%s/enm_09.test.dat" % outdir,'w')
fh.write(evals)
fh.close()
# print eigenvectors
evecs = SBP_enm.print_evec(3)
fh = open("%s/enm_10.test.dat" % outdir,'w')
fh.write(evecs)
fh.close()
# print C2'-C2' fluctuations
fluc,res = SBP_enm.c2_fluctuations()
fh = open("%s/enm_11.test.dat" % outdir,'w')
stri = "# %19s %s \n" % ("Residues","Fluctuations")
for i in range(len(fluc)):
stri += "%10s/%-10s %.6e \n" % (res[i],res[i+1],fluc[i])
fh.write(stri)
fh.close()
comp("%s/enm_09.test.dat" % refdir)
comp("%s/enm_10.test.dat" % refdir)
comp("%s/enm_11.test.dat" % refdir)
def test_enm_6():
"""Tests modes output"""
# initialize class. Only PDB are accepted
#SBP_enm = enm.Enm(fname,sparse=True)
SBP_enm = enm.Enm(fname,sparse=True)
import mdtraj as md
traj_mode=SBP_enm.get_mode_traj(6)
traj_mode.save_pdb("%s/enm_14.test.pdb" % outdir)
comp("%s/enm_14.test.pdb" % refdir)
def test_enm_2():
'''Tests different bead choices'''
# initialize class. Only PDB are accepted
S_enm = enm.Enm(fname,sele_atoms=["C1\'"],cutoff=1.5)
SB_enm = enm.Enm(fname,sele_atoms=["C2","C1\'"],cutoff=1.1)
# print eigenvalues S-ENM
evals = S_enm.print_eval()
fh = open("%s/enm_04.test.dat" % outdir,'w')
fh.write(evals)
fh.close()
# print eigenvalues SB-ENM
evals = SB_enm.print_eval()
fh = open("%s/enm_05.test.dat" % outdir,'w')
fh.write(evals)
fh.close()
comp("%s/enm_04.test.dat" % refdir)
comp("%s/enm_05.test.dat" % refdir)
def test_enm_5():
'''Tests RNA+protein complex (sparse)'''
# initialize class. Only PDB are accepted
AA_enm = enm.Enm(fname,sele_atoms="AA",sparse=True,cutoff=0.7)
# print eigenvalues
evals = AA_enm.print_eval()
fh = open("%s/enm_12.test.dat" % outdir,'w')
fh.write(evals)
fh.close()
# print eigenvectors
evecs = AA_enm.print_evec(3)
fh = open("%s/enm_13.test.dat" % outdir,'w')
fh.write(evecs)
fh.close()
def enm(args):
import barnaba.enm as enm
if(args.type=="AA"):
sele = "AA"
else:
sele = []
sele.append("CA")
if("P" in args.type):
sele.append("P")
if("S" in args.type):
sele.append("C1\'")
if("B" in args.type):
sele.append("C2")
if(args.type=="SBP"):
sele.append("CB")
net = enm.Enm(args.pdbs,sele_atoms=sele,sparse=args.sparse,ntop=args.ntop,cutoff=args.cutoff)
# print eigenvectors
eigvecs = net.print_evec(args.ntop)
fh = open(args.name + ".eigvecs.out",'w')
fh.write(eigvecs)
fh.close()
# print eigenvalues
eigvals = net.print_eval()
fh = open(args.name + ".eigvals.out",'w')
fh.write(eigvals)
fh.close()
if(args.shape):
fluc,res = net.c2_fluctuations()
stri = "# %19s %s \n" % ("Residues","Fluctuations")
stri += "".join(["%10s/%-10s %.6e \n" % (res[i],res[i+1],fluc[i]) for i in range(len(fluc)) ])
fh = open(args.name + ".shape.out",'w')
fh.write(stri)
fh.close()
