def cyclic_shift(monomer_file,fit_file,fits_dir,N,symetry_axis = (0,0,1) ,symetry_center = (0,0,0)):
os.system("mkdir cycledFits")
rc("open " + monomer_file)
rc("cd "+fits_dir)
transArray=[]
for i in range(N):
print fit_file
rc("open " + fit_file)
if i == 0:
rc("match #" + str(i+1) + " #0 showMatrix true move false")
continue
command = get_turn_command(i*360/N,symetry_axis,symetry_center,i+1) #changed for output
if DEBUG:
print command
rc(command)
rc("match #" + str(i+1) + " #0 showMatrix true move false")
#FIX
filePath= "after"+fit_file
rc("close 0")
rc("combine #0,#1 close 1")
rc("cd ..")
saveReplyLog("transformsLog.txt")
transform= findTranform(fit_file)
return transform
def fitToSegment(monomer_file):
"""
Fits the monomer to each of the segments maps in segmentationsDir
"""
os.system("rm -r fitDir ; mkdir fitDir")
i=0
for segmentedMapFile in os.listdir( "segmentationsDir" ) :
rc( "open " + monomer_file)
v= VolumeViewer.open_volume_file("segmentationsDir/" + segmentedMapFile)[0]
d=v.data
#We move the monomer close to the segmented-region map to improve FitMap, so we measure the position of the monomer in atomic coordinates
#measure the position of the segmented-map in grid indices, convert it to atomic corrdinates, and move the monomer in the coordinates
#difference axis, then running fitmap to fit the monomer to the region-map when they are closed to each other
rc( "measure center #0")
rc( "measure center #1")
saveReplyLog("log.txt")
log= open("log.txt", 'r')
lines=log.readlines()
centerLine1=lines[len(lines)-2]
centerLine0=lines[len(lines)-3]
line0Array=centerLine0.split()
line1Array=centerLine1.split()
monomerCenter= (float(line0Array[-3][1:-1]), float(line0Array[-2][:-1]), float(line0Array[-1][:-1]))
segmentCenter= (float(line1Array[-3][1:-1]), float(line1Array[-2][:-1]), float(line1Array[-1][:-1]))
x,y,z= d.ijk_to_xyz(segmentCenter)
moveAxis= (x-monomerCenter[0], y-monomerCenter[1], z-monomerCenter[2])
rc("move "+str(moveAxis[0]) +","+ str(moveAxis[1]) + "," + str(moveAxis[2])
+ " models #0")
rc( "fitmap #0 #1" )
rc("write format pdb #0 fitDir/model" + str(i)+".pdb")
rc("close all")
i+=1
def get_principal_axes(map_file):
"""
Recives a map file, returns it's three axes and the center of it.
The return value is: [axis 1, axis 2, axis 3, center]
Each component is a tuple of three numbers
"""
rc("open "+map_file)
rc("measure inertia #0")
saveReplyLog("log.txt")
log= open("log.txt", 'r')
for line in log:
if "v1" in line:
lineVec1=line.split()
elif "v2" in line:
lineVec2=line.split()
elif "v3" in line:
lineVec3=line.split()
elif "center" in line:
centerLine=line.split()
break
rc("close all")
for i in range(2,5):
lineVec1[i]=float(lineVec1[i])
lineVec2[i]=float(lineVec2[i])
lineVec3[i]=float(lineVec3[i])
centerLine[i]=float(centerLine[i])
vec1= (lineVec1[2], lineVec1[3], lineVec1[4])
vec2= (lineVec2[2], lineVec2[3], lineVec2[4])
vec3= (lineVec3[2], lineVec3[3], lineVec3[4])
centerTup= (centerLine[2], centerLine[3], centerLine[4])
return [vec1, vec2, vec3, centerTup]
def get_score(map_file, N, density):
#We make a density map out of the structure of the protein we made in cycle_shift
rc("molmap #"+ str(N) + " " + str(density))
rc("open " + str(map_file))
rc("measure correlation #0 #" +str(N)) #Assumption: the cycled protein map is model #0 and the map we just opened is model #1
#again, reading from reply log
saveReplyLog("log.txt")
log= open("log.txt", 'r')
for line in log:
if "Correlation" in line:
corrLine=line.split()
ind= corrLine.index("=")
score= float((corrLine[ind+1])[:-1])
score*=1000 #in order to make the score nicer than a number between -1 to 1.
return score
def get_score(map_file, N, density):
"""
Given a map, the number of symm and the density, computes and returns the
correlation between the original map and the current tested model.
Assums that the current model is open.
"""
rc("molmap #"+str(N)+" " + str(density))
rc("open " + str(map_file))
rc("measure correlation #0 #"+str(N)) #Assumption: the cycled protein map is model #0 and the map we just opened is model #1
#again, reading from reply log
saveReplyLog("log.txt")
log= open("log.txt", 'r')
for line in log:
if "Correlation" in line:
corrLine=line.split()
ind= corrLine.index("=")
score= float((corrLine[ind+1])[:-1])
score*=1000 #in order to make the score nicer than a number between -1 to 1.
return score
def get_principal_axes(map_file):
rc("open "+map_file)
rc("measure inertia #0")
saveReplyLog("log.txt")
log= open("log.txt", 'r')
for line in log:
if "v3" in line:
symVec=line.split()
elif "center" in line:
centerLine=line.split()
break
rc("close all")
for i in range(2,5):
symVec[i]=float(symVec[i])
centerLine[i]=float(centerLine[i])
vecTup= (symVec[2], symVec[3], symVec[4])
centerTup= (centerLine[2], centerLine[3], centerLine[4])
return [vecTup, centerTup] #array of the two tupples
def cyclicForOutput(monomer_file,fit_file,fits_dir,N,symetry_axis,symetry_center):
"""
Shifting again the monomer in cyclic transformation to compute the translations and rotations
of the monomers to the original monomer. Chimera's match outputs the rotation matrix between two same structures
"""
rc("open " + monomer_file)
rc("cd " + fits_dir)
for i in range(N):
rc("open " + fit_file)
if i == 0:
print "Calculating transformations and translations " + fit_file #important! Do not remove
rc("match #" + str(i+1) + " #0 showMatrix true move false")
continue
command = get_turn_command(i*360/N,symetry_axis,symetry_center,i+1)
rc(command)
print "Calculating transformations and translations " + fit_file #important! Do not remove
rc("match #" + str(i+1) + " #0 showMatrix true move false")
rc("cd ..")
saveReplyLog("log.txt")
transform= findTransform(fit_file)
rc("close all")
return transform
for i in range(1,pdbno+1):
rc('match #'+str(i)+':1500-1600@ca #0:1500-1600@ca')
# Save matrix file for restoring structural alignmemnt
rc('matrixget '+dir+'/RMSD/RMSD_alignment_matrix')
# Clear reply log ready for gathering RMSD
clearReplyLog()
# Do RMSD measurements in a matrix
for i in range(1,pdbno+1):
for j in range(1,pdbno+1):
rc('rmsd #'+str(i)+' #'+str(j))
# Save reply log ready for calculated RMSD values
saveReplyLog(dir+'/RMSD/RMSD.log')
# Save session
rc('~modeldisplay #; modeldisplay #0; focus; ~modeldisplay #; modeldisplay #1-#'+str(pdbno))
rc('save '+dir+'/RMSD/RMSD_'+str(signature)+'_session.py')
#####################################################################################
# Make images of fits and set up directory with PDB's and images with geometry signature prefix
#####################################################################################
# Open map for cross-correlation and making images, into #999
rc('open #999 '+str(cwd)+'/map/'+str(map))
rc('volume #999 sdLevel 4 color grey transparency 0.8')
#Save default cage and model orientation
rc('savepos p2')
rc('combine #1 modelId #0; combine #2 modelId #0; combine #3 modelId #0; combine #4 modelId #0; combine #5 modelId #0'
)
rc('close #1-5')
rc('write #0 ' + str(dir) + '/' + str(directory) + '_angles/' + str(name) +
'_segments.pdb')
clearReplyLog()
#Run inertiapdb_coc.py script to calculate principal axes for all segments
rc('runscript ' + str(dir) + '/scripts/angles/inertiapdb_coc.py')
#Ready for next round
rc('close #')
#Save reply log with key principal axes definitions
saveReplyLog(
str(dir) + '/' + str(directory) + '_angles/' + str(name) + '.axes')
#Call shell script for parsing angle data
subprocess.call(str(dir) + '/scripts/angles/seshscriptrun.sh', shell=True)
rc('stop')
#####################################################################################
# Save the session and data
#####################################################################################
#Move angles folder to directory you were working in
shutil.move(
str(dir) + '/PDB_angles',
str(dir) + '/' + str(directory) + '/PDB_angles')
print(fn)
replyobj.status("Processing " + fn) # show what file we're working on
rc("open " + fn)
if args.sec_struct:
if args.sec_frac:
rc("mm #0 #1 ss {}".format(args.sec_frac))
else:
rc("mm #0 #1")
else:
rc("mm #0 #1 ss False")
from chimera.tkgui import saveReplyLog
## could probably strip extensions if you want shorter file name for reply log file
try:
saveReplyLog("{}_{}_match.txt".format(file_names[0], file_names[1]))
except IndexError:
print("Need 2 files")
"""
Not implemented Match > Align
1) Getting the list of open molecules:
from chimera import openModels, Molecule
mols = openModels.list(modelTypes=[Molecule])
2) Getting the list of chains to use. This example code assumes they're chain A:
chains = [m.sequence('A') for m in mols]
3) Call Match->Align to create the alignment.
PDB = filelist[i - 1]
#measure cmm markers, centre of map mass, cmm_markers will be in #1, model in #2
#rc('measure center #0 mark true radius 10 color red model '+str(i))
#Place center of rotation origin cmm marker if not using centre of mass marker
rc('volume #0 showOutlineBox true')
rc('reset; cofr #0; ac mc')
#measure cmm marker centre of PDB defining subparticle
rc('open #2 ' + str(dir) + '/PDB/' + str(PDB))
rc('measure center #2 mark true radius 10 color blue model #1')
#save cmm marker as vector for localrec subparticle extraction
rc('savemarkers #1 "' + str(dir) + '/cmm_markers/marker_' + str(i) +
'.cmm"')
#Record the distance between centre and subparticle marker
clearReplyLog()
rc('distance #1:1 #1:2')
rc('getcrd #1:1')
rc('getcrd #1:2')
saveReplyLog(str(dir) + "/cmm_markers/marker_" + str(i) + "_distance.log")
#Close ready for next round
rc('close #1')
rc('close #2')
rc('close #')
#close chimera
rc('stop')
if i < 4:
volSAXS = 2.0 * vol[prots[i]]
else:
volSAXS = 2.0 * vol[prots[i]]
runCommand('volume #' + str(i) +
' step 1 transparency 0.50 encloseVolume ' + str(volSAXS))
num += 1
for i in range(len(prots)):
print i, num
runCommand('open ' + prots[i] + ".mrc")
runCommand('color #FFCCCC #' + str(num))
runCommand('volume #' + str(num) +
' step 1 transparency 0.50 encloseVolume ' + str(vol[prots[i]]))
runCommand('move cofr mod #' + str(num))
runCommand('vop gaussian #' + str(num) + ' sd ' + str(stdev[prots[i]]))
num += 1
runCommand('volume #' + str(num) +
' step 1 transparency 0.50 encloseVolume ' + str(vol[prots[i]]))
runCommand('fitmap #' + str(i) + ' #' + str(num) +
' metric correlation listFits false search 1000 placement rs')
runCommand('measure correlation #' + str(i) + ' #' + str(num))
runCommand('measure correlation #' + str(num) + ' #' + str(i))
num += 1
saveReplyLog("Results_cross_correlation.txt")
##exit()