def main(self):
import cgi, cgitb, time, os, sys, shutil
cgitb.enable() ## enable traceback, which reports non-syntax errors
## set jobid
timetuple = time.gmtime(time.time())
timestr = str(timetuple[0])+str(timetuple[1]).zfill(2)+str(timetuple[2]).zfill(2)+str(timetuple[3]).zfill(2)+str(timetuple[4]).zfill(2)+str(timetuple[5]).zfill(2)
form = cgi.FieldStorage()
if form.has_key("timestr"):
timestr = form["timestr"].value
## set paths
self.path_tmp = '/var/www/cgi-bin/goodvibes/tmp/'
self.path_results = '/var/www/html/goodvibes/results/'
self.path_pdbs = '/data/pdb/'
self.path_python = '/var/www/cgi-bin/goodvibes/'
## initiate fasthtml
print 'Content-type: text/html\n\n'
print '''
<html>
<head><title>UCD GoodVibes</title></head>
<body>
'''
## check form for erros and terminate fasthtml if any errors
self.errorcheckfile(form)
## if no errors then queue job
if os.path.isfile(self.path_tmp+'queue.txt'):
fd = open(self.path_tmp+'queue.txt', 'a')
fd.write(timestr+'\n')
fd.close()
queuemanager = False
else:
fd = open(self.path_tmp+'queue.txt', 'w')
fd.write(timestr+'\n')
fd.close()
queuemanager = True
## if no errors and job queued, then write fast output and slow 1st temporary output
sys.stdout.flush()
sys.stderr.flush()
pid = os.fork()
if pid:
htmlbody = 'Dear user. Your input data has been queued for processing. Your job is still in the queue.'
self.slowhtml(htmlbody, timestr, self.path_results)
htmlbody = 'Dear user. Your input data is being processed. Your results or an estimated time for the completion of your calculation will be available from <a href="http://peat.ucd.ie/goodvibes/results/'+timestr+'.html" target="_blank">http://peat.ucd.ie/goodvibes/results/'+timestr+'.html</a>'
self.fasthtml(htmlbody)
## flush the output from fasthtml
sys.stdout.flush()
## os._exit(0)
##
## sys.stdout.flush() # double flush used in pKD
## os.close(0)
## os.close(1)
## os.close(2)
## fd=open('junkout','w')
## sys.stderr=fd
## sys.stdout=fd
################################################################################
## parse html form
if form.has_key("amplitude_average"): amplitude_average = form["amplitude"].value
else: amplitude_average = 2
if form.has_key("mutations"): mutations = form["mutations"].value
else: mutations = 0
if form.has_key("quarternary"): quarternary = form["quarternary"].value
else: quarternary = 'monomeric'
if form.has_key("frames"): frames = form['frames'].value
else: frames = 50
if form["pdb1_id"].value != "":
fd = open(self.path_pdbs+form["pdb1_id"].value.lower()+'.pdb', 'r')
pdb_lines = fd.readlines()
fd.close()
fd = open(self.path_tmp+timestr+'_reference.pdb', 'w')
fd.writelines(pdb_lines)
fd.close()
if form["pdb1_file"].value:
fd = open(self.path_tmp+timestr+'_reference.pdb', 'w')
fd.writelines(form["pdb1_file"].file.readlines())
fd.close()
if form["pdb1_txt"].value:
fd = open(self.path_tmp+timestr+'_reference.pdb', 'w')
fd.writelines(form["pdb1_txt"].file.readlines())
fd.close()
if form["chains1"].value: chains1 = form["chains1"].value.upper()
else: chains1 = ''
## resranges need to refer to chains. resranges dont need to be updated when building biomolecules from remark350 because residues not parsed.
## self.residue_terminal_n = {'A':-9999, 'B':-9999, 'C':-9999, 'D':-9999, 'E':-9999, 'F':-9999, 'G':-9999, 'H':-9999, 'I':-9999, 'J':-9999, 'K':-9999, 'L':-9999, 'M':-9999, 'N':-9999, 'O':-9999, 'P':-9999, 'Q':-9999, 'R':-9999, 'S':-9999, 'T':-9999, 'U':-9999, 'V':-9999, 'W':-9999, 'X':-9999, 'Y':-9999, 'Z':-9999, ' ':-9999,}
## self.residue_terminal_c = {'A':9999, 'B':9999, 'C':9999, 'D':9999, 'E':9999, 'F':9999, 'G':9999, 'H':9999, 'I':9999, 'J':9999, 'K':9999, 'L':9999, 'M':9999, 'N':9999, 'O':9999, 'P':9999, 'Q':9999, 'R':9999, 'S':9999, 'T':9999, 'U':9999, 'V':9999, 'W':9999, 'X':9999, 'Y':9999, 'Z':9999, ' ':9999,}
if form.has_key("resrange1start"): resrange1start = form["resrange1start"].value
else: resrange1start = -99999
if form.has_key("resrange1end"): resrange1end = form["resrange1end"].value
else: resrange1end = 99999
if form.has_key("model1"): model1 = form["model1"].value
else: model1 = ''
if not form.has_key("atoms"):
atoms_hessian = ['CA']
else:
l_atoms = form.getlist("atoms")
import sets
all = sets.Set(['OXT'])
for chemical_symbol in ['C','O','H','N','S']:
all.add(chemical_symbol)
for remoteness_indicator in ['A','B','G','D','E','Z','H']:
all.add(chemical_symbol+remoteness_indicator)
for branch_designator in range(10):
all.add(chemical_symbol+remoteness_indicator+str(branch_designator))
mainchain = sets.Set(['C', 'O', 'N', 'CA'])
sidechain = all-mainchain
alpha = sets.Set(['CA'])
beta = sets.Set(['CB'])
atoms_hessian = sets.Set()
for s_atoms in l_atoms:
if s_atoms == 'yall':
atoms_hessian |= all
break
if s_atoms == 'ymainchain':
atoms_hessian |= mainchain
if s_atoms == 'ysidechain':
atoms_hessian |= sidechain
if s_atoms == 'yalpha':
atoms_hessian |= alpha
if s_atoms == 'ybeta':
atoms_hessian |= beta
for s_atoms in l_atoms:
if s_atoms == 'nmainchain':
atoms_hessian -= mainchain
if s_atoms == 'nsidechain':
atoms_hessian -= sidechain
if s_atoms == 'nalpha':
atoms_hessian -= alpha
if s_atoms == 'nbeta':
atoms_hessian -= beta
atoms_hessian = list(atoms_hessian)
if form.has_key("pdb2_id"):
fd = open(self.path_pdbs+form["pdb2_id"].value.lower()+'.pdb', 'r')
pdb_lines = fd.readlines()
fd.close()
fd = open(self.path_tmp+timestr+'_conformer.pdb', 'w')
fd.writelines(pdb_lines)
fd.close()
if form.has_key("pdb2_file"):
fd = open(self.path_tmp+timestr+'_conformer.pdb', 'w')
fd.write(form["pdb2_file"].value)
fd.close()
if form.has_key("chains2"): chains2 = form["chains2"].value.upper()
else: chains2 = ''
if form.has_key("resrange2start"): resrange2start = form["resrange2start"].value
else: resrange2start = -99999
if form.has_key("resrange2end"): resrange2end = form["resrange2end"].value
else: resrange2end = 99999
if form.has_key("model2"): model2 = form["model2"].value
else: model2 = ''
## write job input to job file
lines_input = []
lines_input.append('%s;%s\n' %('chains', chains1))
lines_input.append('%s;%s\n' %('model', model1))
lines_input.append('%s;%s\n' %('resrangestart', resrange1start))
lines_input.append('%s;%s\n' %('resrangeend', resrange1end))
lines_input.append('%s;%s\n' %('amplitude', amplitude_average))
lines_input.append('%s;%s\n' %('atoms_hessian', ','.join(atoms_hessian)))
lines_input.append('%s;%s\n' %('mutations', mutations))
lines_input.append('%s;%s\n' %('quarternary', quarternary))
lines_input.append('%s;%s\n' %('frames', frames))
fd = open(self.path_tmp+'job_'+timestr+'.txt', 'w')
fd.writelines(lines_input)
fd.close()
## send mail via SMTP server to user about job being queued
import smtplib
from email.MIMEText import MIMEText
mailfrom = 'GoodVibes'
mailto = form['mail'].value
msg = MIMEText('Dear user. Your input data is being processed. Your results or an estimated time for the completion of your calculation will be available from http://peat.ucd.ie/goodvibes/results/'+timestr+'.html <http://peat.ucd.ie/goodvibes/results/'+timestr+'.html>.')
msg['Subject'] = 'Your GoodVibes job with the ID %s has been queued for processing' %timestr
msg['From'] = mailfrom
msg['Reply-To'] = '*****@*****.**'
msg['To'] = mailto
server=smtplib.SMTP('mail.ucd.ie')
server.set_debuglevel(1)
server.sendmail(mailfrom, mailto, msg.as_string())
server.close()
################################################################################
## end if not queue manager
if not queuemanager:
return
################################################################################
## process queue if queue manager
## change dir in case of any goodvibes outputs (dislin etc.)
os.chdir(self.path_results)
## append the python library to sys.paths after change of dir
sys.path.append(self.path_python)
import goodvibes3
instance_NMA = goodvibes3.vibration()
## process queue while it exists
while os.path.isfile(self.path_tmp+'queue.txt'):
## parse job id
fd = open(self.path_tmp+'queue.txt', 'r')
job = fd.readline().strip()
fd.close()
## write slow 2nd temporary output
htmlbody = 'Dear user. Your input is being processed. Return to this page in a few seconds to get an estimate of the end time of the calculations.'
self.slowhtml(htmlbody, job, self.path_results)
## parse parameters from job txt file to goodvibes
fd = open(self.path_tmp+'job_'+job+'.txt', 'r')
lines_job = fd.readlines()
fd.close()
input_job = {}
for line in lines_job:
input_job[line.split(';')[0]] = line.split(';')[1][:-1]
if input_job['chains'] != '': chains1 = input_job['chains'].split(',')
else: chains1 = []
model1 = input_job['model'].strip()
resrange1start = int(input_job['resrangestart'].strip())
resrange1end = int(input_job['resrangeend'].strip())
amplitude_average = float(input_job['amplitude'].strip())
atoms_hessian = input_job['atoms_hessian'].split(',')
quarternary = input_job['quarternary'].strip()
frames = float(input_job['frames'])
fd = open(self.path_tmp+job+'_reference.pdb', 'r')
pdblines1 = fd.readlines()
fd.close()
## run goodvibes
## try:
self.queue()
N = instance_NMA.main(
job,pdblines1,
atoms_hessian = atoms_hessian,
frames = frames,
chains = chains1,
path_html = self.path_results, path_python = self.path_python,
paralleldir = self.path_tmp,
)
## except 'chainerror', error:
## ## if expected error then remove from queue and report to user
## self.slowhtml(error, job, self.path_results)
## self.queue()
## continue
## except IOError, (errno,strerror):
## self.slowhtml(str(errno)+str(strerror), job, self.path_results)
## self.queue()
## results = instance_NMA.main(pdblines1,chains1,model1, atoms_hessian, quarternary, job, frames, [1], path_html = self.path_results, path_python = self.path_python)
## continue
## except:
## print chains1,model1, atoms_hessian, quarternary, job, cutoffs,
## ## if not expected error (not syntax errors) then remove from queue and report to user
## self.slowhtml('There was a bug. Please email your input to <a href="mailto:[email protected]?subject=GoodVibes Server&body=Hi Tommy,">the administrator</a>.', job, self.path_results)
## self.queue()
## results = instance_NMA.main(pdblines1,chains1,model1, atoms_hessian, quarternary, job, cutoffs, [1], path_html = self.path_results, path_python = self.path_python)
## continue
###################################
## write output if no exceptions ##
###################################
## define dictionary of img files
img_files = ['combo_displacement', 'displacement',
'combo_crosscorrelation', 'crosscorrelation',
'overlaps_combined', 'overlaps_single',
'mmo', 'emo']
# {'2D_atom_displacement': ['combo', 'atom displacement per coordinate'], 'crosscorrelation': ['combo', 'cross correlation'], 'emo': ['single', 'perturbed eigenvalues of max overlap'], 'mmo': ['single', 'perturbed modes of max overlap'], 'overlaps': ['combo', 'overlaps'], 'eigenvalues' : ['single', 'perturbed eigenvalues']}
## define html header
header = [
'<html>\n<head>\n<title>GoodVibes results for job %s</title>\n</head>\n<body>\n' %(job),
'<a href="http://peat.ucd.ie/goodvibes"><img src="http://peat.ucd.ie/goodvibes/logo.png" alt="GoodVibes" border="0"></a>\n<br>\n<hr>\n<br>\n'
]
##
## initiate main html
##
html = header+['<table border="1">\n']
##
## write html output
##
html += [
'<tr><td>Job</td><td>%s</td></tr>\n' %(job),
'<tr><td>Chains</td><td>%s</td></tr>\n' %(chains1),
'<tr><td>Number (3N-6) of Non-Zero Eigenvalues</td><td>%s</td></tr>\n' %(3*N-6),
'<tr><td>Distance Cutoff (Angstrom)</td><td>%s</td></tr>\n' %(10),
'</table>\n<table border="1">\n'
]
##
## write html, pdb and gif output
## write results to subhtml per mode
##
html += [
'<tr>\n'
'<td>mode</td>\n',
'<td>pdb trajectory</td>\n',
'<td>calculation results</td>\n',
'</tr>\n'
]
for mode in range(6,12):
fd = open('%s_mode%s.pdb' %(job, str(mode+1).zfill(2)), 'r')
lines_vmd = fd.readlines()
fd.close()
## loop over frames and read/write rasmol input/output
for frame in range(frames):
## write rasmol pdb for frame (speed up by avoiding reading the lines from the beginning every time)
rasmol_pdb = job+'_'+str(frame)+'.pdb'
line_first = 0
for line_current in range(len(lines_vmd)):
if lines_vmd[line_current] == 'HEADER frame t=%2i.000\n' %frame:
line_first = line_current+2
if lines_vmd[line_current] == 'TER\n' and line_first != 0:
fd = open(rasmol_pdb, 'w')
fd.writelines(lines_vmd[line_first:line_current])
fd.close()
break
## write rasmol script
rasmol_script = self.path_tmp+'rasmol.script'
fd = open(rasmol_script,'w')
fd.write('/software/bin/rasmol -nodisplay '+rasmol_pdb+' << EOF\n')
fd.write('color temperature\n') ## color by displacement
## execute rasmol script and write rasmol img
## somehow center at center of wildtype... by translation only! no rotation!
rasmol_img = job+'_'+str(frame)+'.ppm'
fd.write('write '+self.path_tmp+rasmol_img+'\n')
fd.write('exit\n')
fd.close()
## execute rasmol script to open pdb frame file and do screen shot
os.system('source '+rasmol_script+' > '+self.path_tmp+'rasmol.log') ## write image
os.system('/usr/bin/convert '+self.path_tmp+rasmol_img+' -resize 15% '+self.path_tmp+job+'_'+str(frame)+'.gif') ## resize image
## convert screen shots to gif animation
ImageMagick_script = '/usr/bin/convert -loop 0 -delay 2x'+str(frames) ## -delay fps (sxf)
for frame in range(frames):
rasmol_gif = job+'_'+str(frame)+'.gif'
ImageMagick_script += ' '+self.path_tmp+rasmol_gif
for frame in range(frames-1,-1+1,-1):
rasmol_gif = job+'_'+str(frame)+'.gif'
ImageMagick_script += ' '+self.path_tmp+rasmol_gif
ImageMagick_script += ' %s%s_mode%s.gif' %(self.path_results,job,str(mode+1).zfill(2))
os.system(ImageMagick_script)
## write results to table
html += [
'<tr>\n'
'<td>mode %s</td>\n' %(mode+1),
'<td><a href="%s_mode%s.pdb"><img src="%s_mode%s.gif" border="0" alt="pdb trajectory mode%s"></a></td>\n' %(job, str(mode+1).zfill(2), job, str(mode+1), str(mode+1).zfill(2)),
'<td><a href="%s_mode%s.html">results</a></td>\n' %(job, mode+1),
'</tr>\n',
]
## write results to subhtml per mode
subhtml = header+['<table border="1">\n']
for img_file in img_files:
subhtml += [
'<tr><td><img src="%s_%s_mode%s.png" border="0" alt="%s"></td></tr>\n' %(job, img_file, mode+1, img_file),
]
subhtml += ['</table>\n</body>\n</html>']
fd = open('%s_mode%s.html' %(job, mode+1), 'w')
fd.writelines(subhtml)
fd.close()
## terminate mode result table and initiate plot result table
html += ['</table>\n<table border="1">\n']
##
## write img output to main html
## write results to subhtml per img file type
##
for img_file in img_files:
## write subhtml per img file type
subhtml = header+['<table border="1">\n']
for mode in range(6,12):
subhtml += ['<tr>\n']
subhtml += ['<td><img src="%s_%s_mode%s.png" border="0" alt="mode%s"></td>\n' %(job, img_file, str(mode+1).zfill(2), str(mode+1).zfill(2))]
subhtml += ['</tr>\n']
if img_file == 'overlapscombined':
subhtml += [
'<tr><td><img src="%s_overlapscombined_mode3N" border="0" alt="mode3N"></td></tr>\n' %(job),
]
subhtml += ['</table>\n</body>\n</html>']
fd = open('%s_%s.html' %(job, img_file), 'w')
fd.writelines(subhtml)
fd.close()
## write main html
html += ['<tr><td><a href="%s_%s.html">%s</a></td></tr>\n' %(job, img_file, img_file)]
##
## terminate main html
##
html += ['</table>\n</body>\n</html>']
## delete temporary files
for frame in range(frames):
os.remove('%s%s_%s.ppm' %(self.path_tmp, job, frame))
os.remove('%s%s_%s.gif' %(self.path_tmp, job, frame))
##
## write html to file (this output cannot be written prior to the subpages outputs)
##
fd = open(self.path_results+job+'.html', 'w') ## implicit path
fd.writelines(html)
fd.close()
###############################################################
## remove the job from the queue and continue the while loop ##
###############################################################
self.queue()
continue
## return/end when no more jobs to process in queue
return
def main(self):
import cgi, cgitb, time, os, sys, shutil
cgitb.enable() ## enable traceback, which reports non-syntax errors
## set jobid
timetuple = time.gmtime(time.time())
timestr = str(timetuple[0]) + str(timetuple[1]).zfill(2) + str(
timetuple[2]).zfill(2) + str(timetuple[3]).zfill(2) + str(
timetuple[4]).zfill(2) + str(timetuple[5]).zfill(2)
form = cgi.FieldStorage()
if form.has_key("timestr"):
timestr = form["timestr"].value
## set paths
self.path_tmp = '/var/www/cgi-bin/goodvibes/tmp/'
self.path_results = '/var/www/html/goodvibes/results/'
self.path_pdbs = '/data/pdb/'
self.path_python = '/var/www/cgi-bin/goodvibes/'
## initiate fasthtml
print 'Content-type: text/html\n\n'
print '''
<html>
<head><title>UCD GoodVibes</title></head>
<body>
'''
## check form for erros and terminate fasthtml if any errors
self.errorcheckfile(form)
## if no errors then queue job
if os.path.isfile(self.path_tmp + 'queue.txt'):
fd = open(self.path_tmp + 'queue.txt', 'a')
fd.write(timestr + '\n')
fd.close()
queuemanager = False
else:
fd = open(self.path_tmp + 'queue.txt', 'w')
fd.write(timestr + '\n')
fd.close()
queuemanager = True
## if no errors and job queued, then write fast output and slow 1st temporary output
sys.stdout.flush()
sys.stderr.flush()
pid = os.fork()
if pid:
htmlbody = 'Dear user. Your input data has been queued for processing. Your job is still in the queue.'
self.slowhtml(htmlbody, timestr, self.path_results)
htmlbody = 'Dear user. Your input data is being processed. Your results or an estimated time for the completion of your calculation will be available from <a href="http://peat.ucd.ie/goodvibes/results/' + timestr + '.html" target="_blank">http://peat.ucd.ie/goodvibes/results/' + timestr + '.html</a>'
self.fasthtml(htmlbody)
## flush the output from fasthtml
sys.stdout.flush()
## os._exit(0)
##
## sys.stdout.flush() # double flush used in pKD
## os.close(0)
## os.close(1)
## os.close(2)
## fd=open('junkout','w')
## sys.stderr=fd
## sys.stdout=fd
################################################################################
## parse html form
if form.has_key("amplitude_average"):
amplitude_average = form["amplitude"].value
else:
amplitude_average = 2
if form.has_key("mutations"): mutations = form["mutations"].value
else: mutations = 0
if form.has_key("quarternary"): quarternary = form["quarternary"].value
else: quarternary = 'monomeric'
if form.has_key("frames"): frames = form['frames'].value
else: frames = 50
if form["pdb1_id"].value != "":
fd = open(self.path_pdbs + form["pdb1_id"].value.lower() + '.pdb',
'r')
pdb_lines = fd.readlines()
fd.close()
fd = open(self.path_tmp + timestr + '_reference.pdb', 'w')
fd.writelines(pdb_lines)
fd.close()
if form["pdb1_file"].value:
fd = open(self.path_tmp + timestr + '_reference.pdb', 'w')
fd.writelines(form["pdb1_file"].file.readlines())
fd.close()
if form["pdb1_txt"].value:
fd = open(self.path_tmp + timestr + '_reference.pdb', 'w')
fd.writelines(form["pdb1_txt"].file.readlines())
fd.close()
if form["chains1"].value: chains1 = form["chains1"].value.upper()
else: chains1 = ''
## resranges need to refer to chains. resranges dont need to be updated when building biomolecules from remark350 because residues not parsed.
## self.residue_terminal_n = {'A':-9999, 'B':-9999, 'C':-9999, 'D':-9999, 'E':-9999, 'F':-9999, 'G':-9999, 'H':-9999, 'I':-9999, 'J':-9999, 'K':-9999, 'L':-9999, 'M':-9999, 'N':-9999, 'O':-9999, 'P':-9999, 'Q':-9999, 'R':-9999, 'S':-9999, 'T':-9999, 'U':-9999, 'V':-9999, 'W':-9999, 'X':-9999, 'Y':-9999, 'Z':-9999, ' ':-9999,}
## self.residue_terminal_c = {'A':9999, 'B':9999, 'C':9999, 'D':9999, 'E':9999, 'F':9999, 'G':9999, 'H':9999, 'I':9999, 'J':9999, 'K':9999, 'L':9999, 'M':9999, 'N':9999, 'O':9999, 'P':9999, 'Q':9999, 'R':9999, 'S':9999, 'T':9999, 'U':9999, 'V':9999, 'W':9999, 'X':9999, 'Y':9999, 'Z':9999, ' ':9999,}
if form.has_key("resrange1start"):
resrange1start = form["resrange1start"].value
else:
resrange1start = -99999
if form.has_key("resrange1end"):
resrange1end = form["resrange1end"].value
else:
resrange1end = 99999
if form.has_key("model1"): model1 = form["model1"].value
else: model1 = ''
if not form.has_key("atoms"):
atoms_hessian = ['CA']
else:
l_atoms = form.getlist("atoms")
import sets
all = sets.Set(['OXT'])
for chemical_symbol in ['C', 'O', 'H', 'N', 'S']:
all.add(chemical_symbol)
for remoteness_indicator in [
'A', 'B', 'G', 'D', 'E', 'Z', 'H'
]:
all.add(chemical_symbol + remoteness_indicator)
for branch_designator in range(10):
all.add(chemical_symbol + remoteness_indicator +
str(branch_designator))
mainchain = sets.Set(['C', 'O', 'N', 'CA'])
sidechain = all - mainchain
alpha = sets.Set(['CA'])
beta = sets.Set(['CB'])
atoms_hessian = sets.Set()
for s_atoms in l_atoms:
if s_atoms == 'yall':
atoms_hessian |= all
break
if s_atoms == 'ymainchain':
atoms_hessian |= mainchain
if s_atoms == 'ysidechain':
atoms_hessian |= sidechain
if s_atoms == 'yalpha':
atoms_hessian |= alpha
if s_atoms == 'ybeta':
atoms_hessian |= beta
for s_atoms in l_atoms:
if s_atoms == 'nmainchain':
atoms_hessian -= mainchain
if s_atoms == 'nsidechain':
atoms_hessian -= sidechain
if s_atoms == 'nalpha':
atoms_hessian -= alpha
if s_atoms == 'nbeta':
atoms_hessian -= beta
atoms_hessian = list(atoms_hessian)
if form.has_key("pdb2_id"):
fd = open(self.path_pdbs + form["pdb2_id"].value.lower() + '.pdb',
'r')
pdb_lines = fd.readlines()
fd.close()
fd = open(self.path_tmp + timestr + '_conformer.pdb', 'w')
fd.writelines(pdb_lines)
fd.close()
if form.has_key("pdb2_file"):
fd = open(self.path_tmp + timestr + '_conformer.pdb', 'w')
fd.write(form["pdb2_file"].value)
fd.close()
if form.has_key("chains2"): chains2 = form["chains2"].value.upper()
else: chains2 = ''
if form.has_key("resrange2start"):
resrange2start = form["resrange2start"].value
else:
resrange2start = -99999
if form.has_key("resrange2end"):
resrange2end = form["resrange2end"].value
else:
resrange2end = 99999
if form.has_key("model2"): model2 = form["model2"].value
else: model2 = ''
## write job input to job file
lines_input = []
lines_input.append('%s;%s\n' % ('chains', chains1))
lines_input.append('%s;%s\n' % ('model', model1))
lines_input.append('%s;%s\n' % ('resrangestart', resrange1start))
lines_input.append('%s;%s\n' % ('resrangeend', resrange1end))
lines_input.append('%s;%s\n' % ('amplitude', amplitude_average))
lines_input.append('%s;%s\n' %
('atoms_hessian', ','.join(atoms_hessian)))
lines_input.append('%s;%s\n' % ('mutations', mutations))
lines_input.append('%s;%s\n' % ('quarternary', quarternary))
lines_input.append('%s;%s\n' % ('frames', frames))
fd = open(self.path_tmp + 'job_' + timestr + '.txt', 'w')
fd.writelines(lines_input)
fd.close()
## send mail via SMTP server to user about job being queued
import smtplib
from email.MIMEText import MIMEText
mailfrom = 'GoodVibes'
mailto = form['mail'].value
msg = MIMEText(
'Dear user. Your input data is being processed. Your results or an estimated time for the completion of your calculation will be available from http://peat.ucd.ie/goodvibes/results/'
+ timestr + '.html <http://peat.ucd.ie/goodvibes/results/' +
timestr + '.html>.')
msg['Subject'] = 'Your GoodVibes job with the ID %s has been queued for processing' % timestr
msg['From'] = mailfrom
msg['Reply-To'] = '*****@*****.**'
msg['To'] = mailto
server = smtplib.SMTP('mail.ucd.ie')
server.set_debuglevel(1)
server.sendmail(mailfrom, mailto, msg.as_string())
server.close()
################################################################################
## end if not queue manager
if not queuemanager:
return
################################################################################
## process queue if queue manager
## change dir in case of any goodvibes outputs (dislin etc.)
os.chdir(self.path_results)
## append the python library to sys.paths after change of dir
sys.path.append(self.path_python)
import goodvibes3
instance_NMA = goodvibes3.vibration()
## process queue while it exists
while os.path.isfile(self.path_tmp + 'queue.txt'):
## parse job id
fd = open(self.path_tmp + 'queue.txt', 'r')
job = fd.readline().strip()
fd.close()
## write slow 2nd temporary output
htmlbody = 'Dear user. Your input is being processed. Return to this page in a few seconds to get an estimate of the end time of the calculations.'
self.slowhtml(htmlbody, job, self.path_results)
## parse parameters from job txt file to goodvibes
fd = open(self.path_tmp + 'job_' + job + '.txt', 'r')
lines_job = fd.readlines()
fd.close()
input_job = {}
for line in lines_job:
input_job[line.split(';')[0]] = line.split(';')[1][:-1]
if input_job['chains'] != '':
chains1 = input_job['chains'].split(',')
else:
chains1 = []
model1 = input_job['model'].strip()
resrange1start = int(input_job['resrangestart'].strip())
resrange1end = int(input_job['resrangeend'].strip())
amplitude_average = float(input_job['amplitude'].strip())
atoms_hessian = input_job['atoms_hessian'].split(',')
quarternary = input_job['quarternary'].strip()
frames = float(input_job['frames'])
fd = open(self.path_tmp + job + '_reference.pdb', 'r')
pdblines1 = fd.readlines()
fd.close()
## run goodvibes
## try:
self.queue()
N = instance_NMA.main(
job,
pdblines1,
atoms_hessian=atoms_hessian,
frames=frames,
chains=chains1,
path_html=self.path_results,
path_python=self.path_python,
paralleldir=self.path_tmp,
)
## except 'chainerror', error:
## ## if expected error then remove from queue and report to user
## self.slowhtml(error, job, self.path_results)
## self.queue()
## continue
## except IOError, (errno,strerror):
## self.slowhtml(str(errno)+str(strerror), job, self.path_results)
## self.queue()
## results = instance_NMA.main(pdblines1,chains1,model1, atoms_hessian, quarternary, job, frames, [1], path_html = self.path_results, path_python = self.path_python)
## continue
## except:
## print chains1,model1, atoms_hessian, quarternary, job, cutoffs,
## ## if not expected error (not syntax errors) then remove from queue and report to user
## self.slowhtml('There was a bug. Please email your input to <a href="mailto:[email protected]?subject=GoodVibes Server&body=Hi Tommy,">the administrator</a>.', job, self.path_results)
## self.queue()
## results = instance_NMA.main(pdblines1,chains1,model1, atoms_hessian, quarternary, job, cutoffs, [1], path_html = self.path_results, path_python = self.path_python)
## continue
###################################
## write output if no exceptions ##
###################################
## define dictionary of img files
img_files = [
'combo_displacement', 'displacement', 'combo_crosscorrelation',
'crosscorrelation', 'overlaps_combined', 'overlaps_single',
'mmo', 'emo'
]
# {'2D_atom_displacement': ['combo', 'atom displacement per coordinate'], 'crosscorrelation': ['combo', 'cross correlation'], 'emo': ['single', 'perturbed eigenvalues of max overlap'], 'mmo': ['single', 'perturbed modes of max overlap'], 'overlaps': ['combo', 'overlaps'], 'eigenvalues' : ['single', 'perturbed eigenvalues']}
## define html header
header = [
'<html>\n<head>\n<title>GoodVibes results for job %s</title>\n</head>\n<body>\n'
% (job),
'<a href="http://peat.ucd.ie/goodvibes"><img src="http://peat.ucd.ie/goodvibes/logo.png" alt="GoodVibes" border="0"></a>\n<br>\n<hr>\n<br>\n'
]
##
## initiate main html
##
html = header + ['<table border="1">\n']
##
## write html output
##
html += [
'<tr><td>Job</td><td>%s</td></tr>\n' % (job),
'<tr><td>Chains</td><td>%s</td></tr>\n' % (chains1),
'<tr><td>Number (3N-6) of Non-Zero Eigenvalues</td><td>%s</td></tr>\n'
% (3 * N - 6),
'<tr><td>Distance Cutoff (Angstrom)</td><td>%s</td></tr>\n' %
(10), '</table>\n<table border="1">\n'
]
##
## write html, pdb and gif output
## write results to subhtml per mode
##
html += [
'<tr>\n'
'<td>mode</td>\n', '<td>pdb trajectory</td>\n',
'<td>calculation results</td>\n', '</tr>\n'
]
for mode in range(6, 12):
fd = open('%s_mode%s.pdb' % (job, str(mode + 1).zfill(2)), 'r')
lines_vmd = fd.readlines()
fd.close()
## loop over frames and read/write rasmol input/output
for frame in range(frames):
## write rasmol pdb for frame (speed up by avoiding reading the lines from the beginning every time)
rasmol_pdb = job + '_' + str(frame) + '.pdb'
line_first = 0
for line_current in range(len(lines_vmd)):
if lines_vmd[
line_current] == 'HEADER frame t=%2i.000\n' % frame:
line_first = line_current + 2
if lines_vmd[
line_current] == 'TER\n' and line_first != 0:
fd = open(rasmol_pdb, 'w')
fd.writelines(lines_vmd[line_first:line_current])
fd.close()
break
## write rasmol script
rasmol_script = self.path_tmp + 'rasmol.script'
fd = open(rasmol_script, 'w')
fd.write('/software/bin/rasmol -nodisplay ' + rasmol_pdb +
' << EOF\n')
fd.write('color temperature\n') ## color by displacement
## execute rasmol script and write rasmol img
## somehow center at center of wildtype... by translation only! no rotation!
rasmol_img = job + '_' + str(frame) + '.ppm'
fd.write('write ' + self.path_tmp + rasmol_img + '\n')
fd.write('exit\n')
fd.close()
## execute rasmol script to open pdb frame file and do screen shot
os.system('source ' + rasmol_script + ' > ' +
self.path_tmp + 'rasmol.log') ## write image
os.system('/usr/bin/convert ' + self.path_tmp +
rasmol_img + ' -resize 15% ' + self.path_tmp +
job + '_' + str(frame) + '.gif') ## resize image
## convert screen shots to gif animation
ImageMagick_script = '/usr/bin/convert -loop 0 -delay 2x' + str(
frames) ## -delay fps (sxf)
for frame in range(frames):
rasmol_gif = job + '_' + str(frame) + '.gif'
ImageMagick_script += ' ' + self.path_tmp + rasmol_gif
for frame in range(frames - 1, -1 + 1, -1):
rasmol_gif = job + '_' + str(frame) + '.gif'
ImageMagick_script += ' ' + self.path_tmp + rasmol_gif
ImageMagick_script += ' %s%s_mode%s.gif' % (
self.path_results, job, str(mode + 1).zfill(2))
os.system(ImageMagick_script)
## write results to table
html += [
'<tr>\n'
'<td>mode %s</td>\n' % (mode + 1),
'<td><a href="%s_mode%s.pdb"><img src="%s_mode%s.gif" border="0" alt="pdb trajectory mode%s"></a></td>\n'
% (job, str(mode + 1).zfill(2), job, str(mode + 1),
str(mode + 1).zfill(2)),
'<td><a href="%s_mode%s.html">results</a></td>\n' %
(job, mode + 1),
'</tr>\n',
]
## write results to subhtml per mode
subhtml = header + ['<table border="1">\n']
for img_file in img_files:
subhtml += [
'<tr><td><img src="%s_%s_mode%s.png" border="0" alt="%s"></td></tr>\n'
% (job, img_file, mode + 1, img_file),
]
subhtml += ['</table>\n</body>\n</html>']
fd = open('%s_mode%s.html' % (job, mode + 1), 'w')
fd.writelines(subhtml)
fd.close()
## terminate mode result table and initiate plot result table
html += ['</table>\n<table border="1">\n']
##
## write img output to main html
## write results to subhtml per img file type
##
for img_file in img_files:
## write subhtml per img file type
subhtml = header + ['<table border="1">\n']
for mode in range(6, 12):
subhtml += ['<tr>\n']
subhtml += [
'<td><img src="%s_%s_mode%s.png" border="0" alt="mode%s"></td>\n'
% (job, img_file, str(mode + 1).zfill(2),
str(mode + 1).zfill(2))
]
subhtml += ['</tr>\n']
if img_file == 'overlapscombined':
subhtml += [
'<tr><td><img src="%s_overlapscombined_mode3N" border="0" alt="mode3N"></td></tr>\n'
% (job),
]
subhtml += ['</table>\n</body>\n</html>']
fd = open('%s_%s.html' % (job, img_file), 'w')
fd.writelines(subhtml)
fd.close()
## write main html
html += [
'<tr><td><a href="%s_%s.html">%s</a></td></tr>\n' %
(job, img_file, img_file)
]
##
## terminate main html
##
html += ['</table>\n</body>\n</html>']
## delete temporary files
for frame in range(frames):
os.remove('%s%s_%s.ppm' % (self.path_tmp, job, frame))
os.remove('%s%s_%s.gif' % (self.path_tmp, job, frame))
##
## write html to file (this output cannot be written prior to the subpages outputs)
##
fd = open(self.path_results + job + '.html', 'w') ## implicit path
fd.writelines(html)
fd.close()
###############################################################
## remove the job from the queue and continue the while loop ##
###############################################################
self.queue()
continue
## return/end when no more jobs to process in queue
return
def errorcheckfile(self, form):
import os, sys
sys.path.append(self.path_python)
import goodvibes3
## check for essential input
if not ( form["pdb1_id"].value or form["pdb1_file"].value or form["pdb1_txt"].value ):
self.fasthtml('Dear user. You need to specify a pdb to be used.', error = True)
self.queue()
## check for multiple input
if ( form["pdb1_id"].value and form["pdb1_file"].value ) or ( form["pdb1_id"].value and form["pdb1_txt"].value ) or ( form["pdb1_file"].value and form["pdb1_txt"].value ):
self.fasthtml('Dear user. You must use *either* a PDB ID, an attached PDB file *or* a pasted PDB file as input.', error = True)
self.queue()
## check for valid pdb ids if specified
if form["pdb1_id"].value:
if not os.path.isfile(self.path_pdbs+form["pdb1_id"].value.lower()+'.pdb'):
self.fasthtml('The PDB ID you have specified is not found in the protein data bank.', error = True)
self.queue()
## check that a mail address has been given
if not form["mail"].value:
self.fasthtml('Please specify an address where you want status about your job sent to.', error = True)
self.queue()
## check for valid or missing chain id(s)
## parse chains
if form["pdb1_id"].value:
fd = open(self.path_pdbs+form["pdb1_id"].value.lower()+'.pdb', 'r')
pdb_lines = fd.readlines()
fd.close()
if form["pdb1_file"].value != "":
pdb_lines = form["pdb1_file"].file.readlines()
if form["pdb1_txt"].value != "":
pdb_lines = form["pdb1_txt"].file.readlines()
instance_NMA = goodvibes3.vibration()
d_coordinates = instance_NMA.parse_pdb(pdb_lines)[3]
## check for valid chain ids
if form["chains1"].value:
if not form["chains1"].value.upper() in d_coordinates['chains'].keys():
self.fasthtml('Specified chain ID not present in PDB. Only chains (%s) are present in pdb.' %d_coordinates['chains'].keys(), error = True)
self.queue()
## check that only 1 chain is present if none specified by user
if form["chains1"].value == "":
## error if no chains present
if len(d_coordinates['chains'].keys()) == 0:
self.fasthtml('No protein chains present in pdb. GoodVibes does not compute polynucleotides at present.', error = True)
self.queue()
## error if multiple chains
if len(d_coordinates['chains'].keys()) > 1:
self.fasthtml('Multiple chains (%s) present in pdb. Please specify which one to use.' %d_coordinates['chains'].keys(), error = True)
self.queue()
## check if input exceeds a certain allwed length
## check for valid number of frames
if form.has_key("frames"):
if int(form["frames"].value) > 500 or int(form["frames"].value) < 2:
self.fasthtml('Please change the number of frames to be within the range 10 to 500.', error = True)
self.queue()
## acummulate error messages and then return them in errorhtml if there is any...
return
def errorcheckfile(self, form):
import os, sys
sys.path.append(self.path_python)
import goodvibes3
## check for essential input
if not (form["pdb1_id"].value or form["pdb1_file"].value
or form["pdb1_txt"].value):
self.fasthtml('Dear user. You need to specify a pdb to be used.',
error=True)
self.queue()
## check for multiple input
if (form["pdb1_id"].value and form["pdb1_file"].value) or (
form["pdb1_id"].value
and form["pdb1_txt"].value) or (form["pdb1_file"].value
and form["pdb1_txt"].value):
self.fasthtml(
'Dear user. You must use *either* a PDB ID, an attached PDB file *or* a pasted PDB file as input.',
error=True)
self.queue()
## check for valid pdb ids if specified
if form["pdb1_id"].value:
if not os.path.isfile(self.path_pdbs +
form["pdb1_id"].value.lower() + '.pdb'):
self.fasthtml(
'The PDB ID you have specified is not found in the protein data bank.',
error=True)
self.queue()
## check that a mail address has been given
if not form["mail"].value:
self.fasthtml(
'Please specify an address where you want status about your job sent to.',
error=True)
self.queue()
## check for valid or missing chain id(s)
## parse chains
if form["pdb1_id"].value:
fd = open(self.path_pdbs + form["pdb1_id"].value.lower() + '.pdb',
'r')
pdb_lines = fd.readlines()
fd.close()
if form["pdb1_file"].value != "":
pdb_lines = form["pdb1_file"].file.readlines()
if form["pdb1_txt"].value != "":
pdb_lines = form["pdb1_txt"].file.readlines()
instance_NMA = goodvibes3.vibration()
d_coordinates = instance_NMA.parse_pdb(pdb_lines)[3]
## check for valid chain ids
if form["chains1"].value:
if not form["chains1"].value.upper(
) in d_coordinates['chains'].keys():
self.fasthtml(
'Specified chain ID not present in PDB. Only chains (%s) are present in pdb.'
% d_coordinates['chains'].keys(),
error=True)
self.queue()
## check that only 1 chain is present if none specified by user
if form["chains1"].value == "":
## error if no chains present
if len(d_coordinates['chains'].keys()) == 0:
self.fasthtml(
'No protein chains present in pdb. GoodVibes does not compute polynucleotides at present.',
error=True)
self.queue()
## error if multiple chains
if len(d_coordinates['chains'].keys()) > 1:
self.fasthtml(
'Multiple chains (%s) present in pdb. Please specify which one to use.'
% d_coordinates['chains'].keys(),
error=True)
self.queue()
## check if input exceeds a certain allwed length
## check for valid number of frames
if form.has_key("frames"):
if int(form["frames"].value) > 500 or int(
form["frames"].value) < 2:
self.fasthtml(
'Please change the number of frames to be within the range 10 to 500.',
error=True)
self.queue()
## acummulate error messages and then return them in errorhtml if there is any...
return
