def test_ssmotif():
dist = bb.ds_motif(fname,
fname1,
l1=8,
l2=7,
bulges=0,
threshold=0.65,
out='%s/ds_motif' % outdir)
stri = ""
for el in dist:
stri += " %8.5f " % el[1]
for jj in el[2]:
stri += "%s-" % jj
stri += "\n"
fh = open("%s/dsmotif_01.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/dsmotif_01.test.dat" % refdir)
# compare all pdbs
of = glob.glob('%s/ds_motif*.pdb' % refdir)
for f in of:
comp(f)
def test_dump():
fh = open("%s/dump_01.test.dat" % outdir,'w')
rvecs,resi = bb.dump_rvec(fname,cutoff=1.7)
stri = ""
for i1 in range(len(resi)):
for i2 in range(len(resi)):
if(sum((rvecs[0,i1,i2])**2) > 1.0e-5):
stri += "%10s %10s %14e %14e %14e \n" % (resi[i1],resi[i2],rvecs[0,i1,i2,0],rvecs[0,i1,i2,1],rvecs[0,i1,i2,2])
fh.write(stri)
fh.close()
gvecs,resi = bb.dump_gvec(fname)
fh = open("%s/dump_02.test.dat" % outdir,'w')
stri = ""
for i1 in range(len(resi)):
for i2 in range(len(resi)):
if(sum((gvecs[0,i1,i2])**2) > 1.0e-5):
stri += "%10s %10s %14e %14e %14e %14e \n" % (resi[i1],resi[i2],gvecs[0,i1,i2,0],gvecs[0,i1,i2,1],gvecs[0,i1,i2,2],gvecs[0,i1,i2,3])
fh.write(stri)
fh.close()
comp("%s/dump_01.test.dat" % refdir)
comp("%s/dump_02.test.dat" % refdir)
def test_cluster():
# first, calculate all g-vectors
print("# Calculating G-vectors")
gvec,seq = bb.dump_gvec(traj,top)
lent = gvec.shape[0]
gvec = gvec.reshape(lent,-1)[::5]
print("# Calculating PCA. gvec shape: ", gvec.shape)
# calculate PCA
v,w = cc.pca(gvec,nevecs=3)
print("# Cumulative explained variance of component: 1=%5.1f 2:=%5.1f 3=%5.1f" % (v[0]*100,v[1]*100,v[2]*100))
print("# DBSCAN clustering...")
# do DBSCAN clustering. eps and min_samples need to be adjusted.
new_labels, center_idx = cc.dbscan(gvec,range(gvec.shape[0]),eps=0.6/np.sqrt(8.),min_samples=10)
print("DONE!")
# create color palette. gray, small points for unassigned clusters.
#cp = sns.color_palette("hls",len(center_idx)+1)
#colors = [cp[j-1] if(j!=0) else (0.77,0.77,0.77) for j in new_labels]
size = [5 if(j!=0) else 0.25 for j in new_labels]
# do scatterplot
#plt.scatter(w[:,0],w[:,1],s=size,c=colors)
# now dump centroids and print labels on plot
print("# Dump PDB centroids")
t = md.load(traj, top=top)
idxs = [ii for ii,kk in enumerate(new_labels) if(kk==0)]
for i,k in enumerate(center_idx):
t[k].save_pdb("%s/cluster_%03d.test.pdb" % (outdir,i))
comp("%s/cluster_%03d.test.pdb" % (refdir,i))
#plt.text(w[k,0],w[k,1],str(i),ha='center',va='center')
idxs = [ii for ii,kk in enumerate(new_labels) if(kk==i+1)]
def test_dump():
fh = open("%s/dump_01.test.dat" % outdir, 'w')
rvecs, resi = bb.dump_rvec(fname, cutoff=1.7)
stri = ""
for i1 in range(len(resi)):
for i2 in range(len(resi)):
if (sum((rvecs[0, i1, i2])**2) > 1.0e-5):
stri += "%10s %10s %14e %14e %14e \n" % (
resi[i1], resi[i2], rvecs[0, i1, i2, 0],
rvecs[0, i1, i2, 1], rvecs[0, i1, i2, 2])
fh.write(stri)
fh.close()
gvecs, resi = bb.dump_gvec(fname)
fh = open("%s/dump_02.test.dat" % outdir, 'w')
stri = ""
for i1 in range(len(resi)):
for i2 in range(len(resi)):
if (sum((gvecs[0, i1, i2])**2) > 1.0e-5):
stri += "%10s %10s %14e %14e %14e %14e \n" % (
resi[i1], resi[i2], gvecs[0, i1, i2, 0],
gvecs[0, i1, i2, 1], gvecs[0, i1, i2, 2], gvecs[0, i1, i2,
3])
fh.write(stri)
fh.close()
comp("%s/dump_01.test.dat" % refdir)
comp("%s/dump_02.test.dat" % refdir)
def test_score():
# set "force-field"
ee = escore.Escore([ffname])
ss = ee.score(traj,topology=fname)
fh = open("%s/score_01.test.dat" % outdir,'w')
stri = " ".join(["%10.4e \n" % (ss[e]) for e in range(len(ss))])
fh.write(stri)
fh.close()
comp("%s/score_01.test.dat" % refdir)
def test_score():
# set "force-field"
ee = escore.Escore([ffname])
ss = ee.score(traj, topology=fname)
fh = open("%s/score_01.test.dat" % outdir, 'w')
stri = " ".join(["%10.4e \n" % (ss[e]) for e in range(len(ss))])
fh.write(stri)
fh.close()
comp("%s/score_01.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_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_rmsd_2():
# align pdb to pdb with different sequence
fname = "%s/test/data/4v7t-pdb-bundle3_G521_00006.align.pdb" % cwd
fname1 = "%s/test/data/centroid_10.pdb" % cwd
dist = bb.rmsd(fname, fname1, out='%s/aligned_2.pdb' % outdir)
stri = "".join(["%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_02.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_02.test.dat" % refdir)
comp("%s/aligned_2.pdb" % refdir)
def test_rmsd_2():
# align pdb to pdb with different sequence
fname = "%s/test/data/4v7t-pdb-bundle3_G521_00006.align.pdb" % cwd
fname1 = "%s/test/data/centroid_10.pdb" % cwd
dist = bb.rmsd(fname,fname1,out='%s/aligned_2.pdb' % outdir)
stri = "".join([ "%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_02.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_02.test.dat" % refdir)
comp("%s/aligned_2.pdb" % refdir)
def test_ermsd_3():
fname = "%s/test/data/4v7t-pdb-bundle3_G521_00006.align.pdb" % cwd
fname1 = "%s/test/data/centroid_10.pdb" % cwd
dist = bb.ermsd(fname,fname1,cutoff=5.0)
stri = "".join([ "%14e \n" % (dd) for dd in dist])
fh = open("%s/ermsd_03.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/ermsd_03.test.dat" % refdir)
return 0
def test_rmsd_1():
# align pdb to pdb with the same sequence
fname = "%s/test/data/sample1.pdb" % cwd
fname1 = "%s/test/data/sample2.pdb" % cwd
dist = bb.rmsd(fname,fname1,out='%s/aligned_1.pdb' % outdir,heavy_atom=True)
stri = "".join([ "%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_01.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_01.test.dat" % refdir)
comp("%s/aligned_1.pdb" % refdir)
def test_couplings_2():
angles,rr = bb.jcouplings(traj,topology=top,raw=True)
fh = open("%s/couplings_02.test.dat" % outdir,'w')
for e in range(angles.shape[0]):
stri = ""
for k in range(angles.shape[1]):
for l in range(angles.shape[2]):
stri += " %10.4f " % angles[e,k,l]
stri += "\n"
fh.write(stri)
fh.close()
comp("%s/couplings_02.test.dat" % refdir)
def test_ermsd_3():
fname = "%s/test/data/4v7t-pdb-bundle3_G521_00006.align.pdb" % cwd
fname1 = "%s/test/data/centroid_10.pdb" % cwd
dist = bb.ermsd(fname, fname1, cutoff=5.0)
stri = "".join(["%14e \n" % (dd) for dd in dist])
fh = open("%s/ermsd_03.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/ermsd_03.test.dat" % refdir)
return 0
def test_rmsd_1():
# align pdb to pdb with the same sequence
fname = "%s/test/data/sample1.pdb" % cwd
fname1 = "%s/test/data/sample2.pdb" % cwd
dist = bb.rmsd(fname, fname1, out='%s/aligned_1.pdb' % outdir)
stri = "".join(["%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_01.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_01.test.dat" % refdir)
comp("%s/aligned_1.pdb" % refdir)
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_ermsd_4():
# align trajectory to pdb
fname = "%s/test/data/sample1.pdb" % cwd
fname1 = "%s/test/data/samples.xtc" % cwd
dist = bb.ermsd(fname,fname1,topology=fname)
stri = "".join([ "%14e \n" % (dd) for dd in dist])
fh = open("%s/ermsd_04.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/ermsd_04.test.dat" % refdir)
return 0
def test():
print("# TEST %02d: %s" % (num, spec))
# initialize reweighting class
rew = bme.Reweight()
# load data
rew.load(exp_train1, calc_train1)
rew.load(exp_train2, calc_train2)
rew.load(exp_train3, calc_train3)
# do optimization using theta=2
chib, chia, srel = rew.optimize(theta=50)
# compare NOE before and after optimization .
# output is written to files with prefix 'example1_noe'
chi2_b, chi2_a = rew.weight_exp(exp_train1, calc_train1,
'%s/test_%02d_train1' % (outdir, num))
chi2_b, chi2_a = rew.weight_exp(exp_train2, calc_train2,
'%s/test_%02d_train2' % (outdir, num))
chi2_b, chi2_a = rew.weight_exp(exp_train3, calc_train3,
'%s/test_%02d_train3' % (outdir, num))
ww = rew.get_weights()
fh = open("%s/test_%02d_weights.dat" % (outdir, num), "w")
fh.write(" ".join(["%8.4f " % x for x in ww]))
fh.close()
comp("%s/test_%02d_weights.dat" % (refdir, num))
comp("%s/test_%02d_train1.stats.dat" % (refdir, num))
comp("%s/test_%02d_train2.stats.dat" % (refdir, num))
comp("%s/test_%02d_train3.stats.dat" % (refdir, num))
print("# TEST %02d: %s" % (num, spec))
print("# DONE #")
def test_rmsd_3():
# align trajectory to pdb
fname = "%s/test/data/sample1.pdb" % cwd
fname1 = "%s/test/data/samples.xtc" % cwd
dist = bb.rmsd(fname,fname1,topology=fname,out='%s/aligned_3.xtc' % outdir,heavy_atom=True)
stri = "".join([ "%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_03.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_03.test.dat" % refdir)
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_ermsd_4():
# align trajectory to pdb
fname = "%s/test/data/sample1.pdb" % cwd
fname1 = "%s/test/data/samples.xtc" % cwd
dist = bb.ermsd(fname, fname1, topology=fname)
stri = "".join(["%14e \n" % (dd) for dd in dist])
fh = open("%s/ermsd_04.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/ermsd_04.test.dat" % refdir)
return 0
def test_ermsd_1():
# align pdb to pdb with the same sequence
fname = "%s/test/data/sample1.pdb" % cwd
fname1 = "%s/test/data/sample2.pdb" % cwd
dist = bb.ermsd(fname,fname1)
stri = "".join([ "%14e \n" % (dd) for dd in dist])
fh = open("%s/ermsd_01.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/ermsd_01.test.dat" % refdir)
return 0
def test_angles_4():
resi = ["RG_69_0","RU_37_0"]
angles = ["gamma","alpha"]
angles_b,rr = bb.backbone_angles(fname1,topology=fname,residues=resi,angles=angles)
stri = ""
for p in range(angles_b.shape[0]):
for k in range(angles_b.shape[2]):
stri += " %10.4f %10.4f " % (angles_b[p,0,k],angles_b[p,1,k])
stri += "\n"
fh = open("%s/angles_04.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/angles_04.test.dat" % refdir)
def test_rmsd_3():
# align trajectory to pdb
fname = "%s/test/data/sample1.pdb" % cwd
fname1 = "%s/test/data/samples.xtc" % cwd
dist = bb.rmsd(fname,
fname1,
topology=fname,
out='%s/aligned_3.xtc' % outdir)
stri = "".join(["%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_03.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_03.test.dat" % refdir)
def test_angles_1():
angles_b,rr = bb.backbone_angles(fname)
fh = open("%s/angles_01.test.dat" % outdir,'w')
stri = "%20s " % "#"
for pp in dd.bb_angles:
stri += " %10s " % pp
stri += "\n"
for e in range(angles_b.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles_b.shape[2]):
stri += " %10.4f " % angles_b[0,e,k]
stri += "\n"
fh.write(stri)
fh.close()
comp("%s/angles_01.test.dat" % refdir)
def test_sugar_1():
sugar_b, rr = bb.sugar_angles(fname)
fh = open("%s/sugar_01.test.dat" % outdir, 'w')
stri = "%20s " % "#"
for pp in dd.sugar_angles:
stri += " %10s " % pp
stri += "\n"
for e in range(sugar_b.shape[1]):
stri += "%20s " % (rr[e])
for k in range(sugar_b.shape[2]):
stri += " %10.4f " % sugar_b[0, e, k]
stri += "\n"
fh.write(stri)
fh.close()
comp("%s/sugar_01.test.dat" % refdir)
def test_sugar_3():
resi = ["RG_69_0", "RU_37_0"]
na = ["Phase", "tm"]
angles, rr = bb.pucker_angles(fname, residues=resi)
stri = "".join([" %10s " % pp for pp in na])
stri += "\n"
for e in range(angles.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles.shape[2]):
stri += " %10.4f " % angles[0, e, k]
stri += "\n"
fh = open("%s/sugar_03.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/sugar_03.test.dat" % refdir)
def test_angles_4():
resi = ["RG_69_0", "RU_37_0"]
angles = ["gamma", "alpha"]
angles_b, rr = bb.backbone_angles(fname1,
topology=fname,
residues=resi,
angles=angles)
stri = ""
for p in range(angles_b.shape[0]):
for k in range(angles_b.shape[2]):
stri += " %10.4f %10.4f " % (angles_b[p, 0, k], angles_b[p, 1, k])
stri += "\n"
fh = open("%s/angles_04.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/angles_04.test.dat" % refdir)
def test_sugar_3():
resi = ["RG_69_0","RU_37_0"]
na = ["Phase","tm"]
angles,rr = bb.pucker_angles(fname,residues=resi,altona=True)
stri = "".join([" %10s " % pp for pp in na])
stri += "\n"
for e in range(angles.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles.shape[2]):
stri += " %10.4f " % angles[0,e,k]
stri += "\n"
fh = open("%s/sugar_03.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/sugar_03.test.dat" % refdir)
def test_ssmotif():
dist = bb.ss_motif(fname,fname1,bulges=1,threshold=0.6,out='%s/ss_motif' % outdir)
stri = ""
for el in dist:
stri += " %8.5f " % el[1]
for jj in el[2]:
stri += "%s-" % jj
stri += "\n"
fh = open("%s/ssmotif_01.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/ssmotif_01.test.dat" % refdir)
# compare all pdbs
of = glob.glob('%s/ss_motif*.pdb' % refdir)
for f in of:
comp(f)
def test_sugar_2():
resi = ["RC5_1_0","RG_69_0"]
angles = ["nu1","nu4","nu3"]
sugar_b,rr = bb.sugar_angles(fname,residues=resi,angles=angles)
stri = "%20s " % "#"
for pp in angles:
stri += " %10s " % pp
stri += "\n"
for e in range(sugar_b.shape[1]):
stri += "%20s " % (rr[e])
for k in range(sugar_b.shape[2]):
stri += " %10.4f " % sugar_b[0,e,k]
stri += "\n"
fh = open("%s/sugar_02.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/sugar_02.test.dat" % refdir)
def test_sugar_2():
resi = ["RC5_1_0", "RG_69_0"]
angles = ["nu1", "nu4", "nu3"]
sugar_b, rr = bb.sugar_angles(fname, residues=resi, angles=angles)
stri = "%20s " % "#"
for pp in angles:
stri += " %10s " % pp
stri += "\n"
for e in range(sugar_b.shape[1]):
stri += "%20s " % (rr[e])
for k in range(sugar_b.shape[2]):
stri += " %10.4f " % sugar_b[0, e, k]
stri += "\n"
fh = open("%s/sugar_02.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/sugar_02.test.dat" % refdir)
def test_enm_5():
'''Tests RNA+protein complex (sparse)'''
# initialize class. Only PDB are accepted
AA_enm = enm.Enm(fname_prot, 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()
comp("%s/enm_12.test.dat" % refdir)
comp("%s/enm_13.test.dat" % refdir)
def test():
print("# TEST %02d: %s" % (num,spec))
# initialize reweighting class
rew_bme = bme.Reweight()
rows = range(0,20000,100)
# load data
rew_bme.load(exp_train,calc_train,rows=rows)
# do optimization using theta=2, method MAXENT (default)
chib,chia, srel = rew_bme.optimize(theta=2,method="MAXENT")
ww_bme = rew_bme.get_weights()
# initialize reweighting class
rew_eros = bme.Reweight()
# load data
rew_eros.load(exp_train,calc_train,rows=rows)
# do optimization using theta=2
chib,chia, srel = rew_eros.optimize(theta=2,method="BER")
ww_ber = rew_eros.get_weights()
diff=np.sqrt(np.sum(((ww_ber-ww_bme)**2))/len(ww_ber))
print(" rms difference between BER and BME: %10.5e" % diff)
fh = open("%s/test_%02d_weights_bme.dat" % (outdir,num) ,"w")
fh.write(" ".join(["%10.5e \n" % x for x in ww_bme]) )
fh.close()
fh = open("%s/test_%02d_weights_ber.dat" % (outdir,num) ,"w")
fh.write(" ".join(["%10.5e \n" % x for x in ww_ber]) )
fh.close()
comp("%s/test_%02d_weights_ber.dat" % (refdir,num))
comp("%s/test_%02d_weights_bme.dat" % (refdir,num))
print("# TEST %02d: %s" % (num,spec))
print("# DONE #")
def test_enm_5():
'''Tests RNA+protein complex (sparse)'''
# initialize class. Only PDB are accepted
AA_enm = enm.Enm(fname_prot,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()
comp("%s/enm_12.test.dat" % refdir)
comp("%s/enm_13.test.dat" % 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_angles_3():
resi = ["RG_69_0","RU_37_0"]
angles = ["gamma","alpha"]
angles_b,rr = bb.backbone_angles(fname,residues=resi,angles=angles)
stri = "%20s " % "#"
for pp in angles:
stri += " %10s " % pp
stri += "\n"
for e in range(angles_b.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles_b.shape[2]):
stri += " %10.4f " % angles_b[0,e,k]
stri += "\n"
fh = open("%s/angles_03.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/angles_03.test.dat" % refdir)
def test_angles_3():
resi = ["RG_69_0", "RU_37_0"]
angles = ["gamma", "alpha"]
angles_b, rr = bb.backbone_angles(fname, residues=resi, angles=angles)
stri = "%20s " % "#"
for pp in angles:
stri += " %10s " % pp
stri += "\n"
for e in range(angles_b.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles_b.shape[2]):
stri += " %10.4f " % angles_b[0, e, k]
stri += "\n"
fh = open("%s/angles_03.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/angles_03.test.dat" % 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_sugar_4():
resi = ["RC5_1_0","RG_69_0","RU_37_0"]
na = ["Phase","tm"]
angles_b,rr = bb.pucker_angles(fname,residues=resi)
stri = "%20s " % "#"
for pp in na:
stri += " %10s " % pp
stri += "\n"
for e in range(angles_b.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles_b.shape[2]):
stri += " %10.4f " % angles_b[0,e,k]
stri += "\n"
fh = open("%s/sugar_04.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/sugar_04.test.dat" % refdir)
def test_annotate_2():
fname = "%s/test/data/1S72.pdb" % cwd
stackings, pairings, res = bb.annotate(fname)
dotbr,ss = bb.dot_bracket(pairings,res)
fh = open("%s/stackings_02.test.dat" % outdir,'w')
stri = "# STACKING \n"
for e in range(len(stackings[0][0])):
stri += "%15s " % (res[stackings[0][0][e][0]])
stri += "%15s " % (res[stackings[0][0][e][1]])
stri += " %4s \n" % (stackings[0][1][e])
fh.write(stri)
fh.close()
fh = open("%s/pairings_02.test.dat" % outdir,'w')
stri = "# PAIRING \n"
for e in range(len(pairings[0][0])):
stri += "%15s " % (res[pairings[0][0][e][0]])
stri += "%15s " % (res[pairings[0][0][e][1]])
stri += " %4s \n" % (pairings[0][1][e])
fh.write(stri)
fh.close()
fh = open("%s/dotbracket_02.test.dat" % outdir,'w')
fh.write(str(dotbr[0]))
fh.close()
comp("%s/stackings_02.test.dat" % refdir)
comp("%s/pairings_02.test.dat" % refdir)
comp("%s/dotbracket_02.test.dat" % refdir)
def test():
print("# TEST %02d: %s" % (num,spec))
# initialize reweighting class, use non-uniform initial weights
bias = [float(line.split()[1]) for line in open(bias_file)]
rew = bme.Reweight(w0=bias,kbt=kbt)
# load data
rew.load(exp_train,calc_train)
# do optimization using theta=2
chib,chia, srel = rew.optimize(theta=1)
# compare NOE before and after optimization .
# output is written to files with prefix 'example1_noe'
chi2_b,chi2_a = rew.weight_exp(exp_train,calc_train, '%s/test_%02d_train' % (outdir,num))
chi2_b,chi2_a = rew.weight_exp(exp_test,calc_test, '%s/test_%02d_test' % (outdir,num))
ww = rew.get_weights()
fh = open("%s/test_%02d_weights.dat" % (outdir,num) ,"w")
fh.write(" ".join(["%8.4f " % x for x in ww]) )
fh.close()
comp("%s/test_%02d_weights.dat" % (refdir,num))
comp("%s/test_%02d_train.stats.dat" % (refdir,num))
comp("%s/test_%02d_test.stats.dat" % (refdir,num))
print("# TEST %02d: %s" % (num,spec))
print("# DONE #")
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_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_0():
"""Tests command line interface"""
cl.main(['ENM','--pdb',fname,'-o',"%s/enm_00.test" % outdir,'--ntop','4','--shape'])
comp("%s/enm_00.test.ENM.eigvecs.out" % refdir)
comp("%s/enm_00.test.ENM.eigvals.out" % refdir)
comp("%s/enm_00.test.ENM.shape.out" % refdir)
def test_annotate_2():
fname = "%s/test/data/1S72.pdb" % cwd
stackings, pairings, res = bb.annotate(fname)
dotbr, ss = bb.dot_bracket(pairings, res)
fh = open("%s/stackings_02.test.dat" % outdir, 'w')
stri = "# STACKING \n"
for e in range(len(stackings[0][0])):
stri += "%15s " % (res[stackings[0][0][e][0]])
stri += "%15s " % (res[stackings[0][0][e][1]])
stri += " %4s \n" % (stackings[0][1][e])
fh.write(stri)
fh.close()
fh = open("%s/pairings_02.test.dat" % outdir, 'w')
stri = "# PAIRING \n"
for e in range(len(pairings[0][0])):
stri += "%15s " % (res[pairings[0][0][e][0]])
stri += "%15s " % (res[pairings[0][0][e][1]])
stri += " %4s \n" % (pairings[0][1][e])
fh.write(stri)
fh.close()
fh = open("%s/dotbracket_02.test.dat" % outdir, 'w')
fh.write(str(dotbr[0]))
fh.close()
comp("%s/stackings_02.test.dat" % refdir)
comp("%s/pairings_02.test.dat" % refdir)
comp("%s/dotbracket_02.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_cluster():
# first, calculate all g-vectors
print("# Calculating G-vectors")
gvec, seq = bb.dump_gvec(traj, top)
lent = gvec.shape[0]
gvec = gvec.reshape(lent, -1)[::5]
print("# Calculating PCA. gvec shape: ", gvec.shape)
# calculate PCA
v, w = cc.pca(gvec, nevecs=3)
print(
"# Cumulative explained variance of component: 1=%5.1f 2:=%5.1f 3=%5.1f"
% (v[0] * 100, v[1] * 100, v[2] * 100))
print("# DBSCAN clustering...")
# do DBSCAN clustering. eps and min_samples need to be adjusted.
new_labels, center_idx = cc.dbscan(gvec,
range(gvec.shape[0]),
eps=0.6 / np.sqrt(8.),
min_samples=10)
print("DONE!")
# create color palette. gray, small points for unassigned clusters.
#cp = sns.color_palette("hls",len(center_idx)+1)
#colors = [cp[j-1] if(j!=0) else (0.77,0.77,0.77) for j in new_labels]
size = [5 if (j != 0) else 0.25 for j in new_labels]
# do scatterplot
#plt.scatter(w[:,0],w[:,1],s=size,c=colors)
# now dump centroids and print labels on plot
print("# Dump PDB centroids")
t = md.load(traj, top=top)
idxs = [ii for ii, kk in enumerate(new_labels) if (kk == 0)]
for i, k in enumerate(center_idx):
t[k].save_pdb("%s/cluster_%03d.test.pdb" % (outdir, i))
comp("%s/cluster_%03d.test.pdb" % (refdir, i))
#plt.text(w[k,0],w[k,1],str(i),ha='center',va='center')
idxs = [ii for ii, kk in enumerate(new_labels) if (kk == i + 1)]
def test_enm_0():
"""Tests command line interface"""
cl.main([
'ENM', '--pdb', fname, '-o',
"%s/enm_00.test" % outdir, '--ntop', '4', '--shape'
])
comp("%s/enm_00.test.ENM.eigvecs.out" % refdir)
comp("%s/enm_00.test.ENM.eigvals.out" % refdir)
comp("%s/enm_00.test.ENM.shape.out" % refdir)
def test_annotate_1():
stackings, pairings, res = bb.annotate(fname1,topology=fname)
dotbr,ss = bb.dot_bracket(pairings,res)
fh = open("%s/stackings_01.test.dat" % outdir,'w')
stri = "# STACKING \n"
for k in range(len(stackings)):
stri += "# frame %d \n" % k
for e in range(len(stackings[k][0])):
stri += "%15s " % (res[stackings[k][0][e][0]])
stri += "%15s " % (res[stackings[k][0][e][1]])
stri += " %4s \n" % (stackings[k][1][e])
stri += "\n"
fh.write(stri)
fh.close()
fh = open("%s/pairings_01.test.dat" % outdir,'w')
stri = "# PAIRING \n"
for k in range(len(pairings)):
stri += "# frame %d \n" % k
for e in range(len(pairings[k][0])):
stri += "%15s " % (res[pairings[k][0][e][0]])
stri += "%15s " % (res[pairings[k][0][e][1]])
stri += " %4s \n" % (pairings[k][1][e])
fh.write(stri)
fh.close()
fh = open("%s/dotbracket_01.test.dat" % outdir,'w')
stri = ""
for k in range(len(pairings)):
stri += " %06d " % k
stri += "%s \n" % dotbr[k]
fh.write(stri)
fh.close()
comp("%s/stackings_01.test.dat" % refdir)
comp("%s/pairings_01.test.dat" % refdir)
comp("%s/dotbracket_01.test.dat" % refdir)
def test_annotate_1():
stackings, pairings, res = bb.annotate(fname1, topology=fname)
dotbr, ss = bb.dot_bracket(pairings, res)
fh = open("%s/stackings_01.test.dat" % outdir, 'w')
stri = "# STACKING \n"
for k in range(len(stackings)):
stri += "# frame %d \n" % k
for e in range(len(stackings[k][0])):
stri += "%15s " % (res[stackings[k][0][e][0]])
stri += "%15s " % (res[stackings[k][0][e][1]])
stri += " %4s \n" % (stackings[k][1][e])
stri += "\n"
fh.write(stri)
fh.close()
fh = open("%s/pairings_01.test.dat" % outdir, 'w')
stri = "# PAIRING \n"
for k in range(len(pairings)):
stri += "# frame %d \n" % k
for e in range(len(pairings[k][0])):
stri += "%15s " % (res[pairings[k][0][e][0]])
stri += "%15s " % (res[pairings[k][0][e][1]])
stri += " %4s \n" % (pairings[k][1][e])
fh.write(stri)
fh.close()
fh = open("%s/dotbracket_01.test.dat" % outdir, 'w')
stri = ""
for k in range(len(pairings)):
stri += " %06d " % k
stri += "%s \n" % dotbr[k]
fh.write(stri)
fh.close()
comp("%s/stackings_01.test.dat" % refdir)
comp("%s/pairings_01.test.dat" % refdir)
comp("%s/dotbracket_01.test.dat" % refdir)
def test_snippet():
bb.snippet(fname,"AAANU",outdir="%s" % outdir)
for f in glob.glob("%s/1S72*.pdb" %outdir):
comp(f)
def test_snippet():
bb.snippet(fname, "AAANU", outdir="%s" % outdir)
for f in glob.glob("%s/1S72*.pdb" % outdir):
comp(f)
