def f_eigenvectors(path, pdb):
import sys
sys.path.append('/home/people/tc/python/goodvibes/')
import goodvibes
instance_goodvibes = goodvibes.vibration()
fd = open('%saverage/%s' %(path,pdb))
pdb1lines = fd.readlines()
fd.close()
chains1 = ['A']
pdb1model = [1]
atoms_hessian = ['CA']
cutoff_distance = 10.
verbose = True
jobid = pdb[:-4]
pdb1ATOM_all, HEADERdepDate1, REMARK350transformations1, REMARK2resolution1, COMPNDchains1, helices1, strands1 = instance_goodvibes.parse_pdb(pdb1lines, chains1, pdb1model)
coordinates1 = []
vectors_difference = []
for chain1 in chains1:
for residue in pdb1ATOM_all[chain1]['residues'].keys():
for atom in pdb1ATOM_all[chain1]['residues'][residue]['atoms'].keys():
if atom in atoms_hessian:
coordinates1.append(pdb1ATOM_all[chain1]['residues'][residue]['atoms'][atom]['coordinates'])
pdb1ATOM_all[chain1]['residues'][residue]['atoms'][atom]['hessian'] = 1
matrix_hessian = instance_goodvibes.hessian_calculation(coordinates1, float(cutoff_distance), verbose) ## calculate with coordinates2 as well... and compare results to switching pdb1 and pdb2
eigenvectors_nonperturbed, eigenvalues_nonperturbed, eigenvectors_combined_nonperturbed = instance_goodvibes.eigenv_calccomb(matrix_hessian, jobid, verbose)
stop
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/python/'
## 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://polymerase.ucd.ie/goodvibes/results/'+timestr+'.html" target="_blank">http://polymerase.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("cutoffs"):
cutoffs = form.getlist("cutoffs")
else: cutoffs = ['10']
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
calctype = form['calctype'].value
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' %('cutoffs', ','.join(cutoffs)))
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))
lines_input.append('%s;%s\n' %('calctype', calctype))
fd = open(self.path_tmp+'job_'+timestr+'.txt', 'w')
fd.writelines(lines_input)
fd.close()
## fd = open(self.path_tmp+'job_'+timestr+'.txt', 'w')
## fd.write(
## str(chains1)+'\n'+str(model1)+'\n'+str(resrange1start)+'\n'+str(resrange1end)+'\n'+
## str(cutoffs)+'\n'+str(amplitude_average)+'\n'+str(atoms_hessian)+'\n'+str(mutations)+'\n'+str(quarternary)+'\n'+
## str(frames)+'\n'+str(inputfiles)+'\n'+str(calctype)+'\n'+
## str(chains2)+'\n'+str(model2)+'\n'+str(resrange2start)+'\n'+str(resrange2end)+'\n'
## )
## 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://polymerase.ucd.ie/goodvibes/results/'+timestr+'.html <http://polymerase.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()
## delete timestr to avoid use of this variable beyond this point (not really necessary)
del timestr
################################################################################
## 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 goodvibes
instance_NMA = goodvibes.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())
cutoffs = input_job['cutoffs'].split(',')
for i in range(len(cutoffs)):
cutoffs[i] = float(cutoffs[i])
amplitude_average = float(input_job['amplitude'].strip())
atoms_hessian = input_job['atoms_hessian'].split(',')
quarternary = input_job['quarternary'].strip()
frames = float(input_job['frames'])
calctype = int(input_job['calctype'].strip())
fd = open(self.path_tmp+job+'_reference.pdb', 'r')
pdblines1 = fd.readlines()
fd.close()
## run goodvibes
try:
results = instance_NMA.main(pdblines1,chains1,model1, atoms_hessian, quarternary, job, frames, cutoffs, calctype, [1], path_html = self.path_results, path_python = self.path_python)
## 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, cutoffs, calctype, [1], path_html = self.path_results, path_python = self.path_python)
continue
except:
def errorcheckfile(self, form):
import os, sys
sys.path.append(self.path_python)
import goodvibes
## ## check for essential settings
## if not (form["cutoffs"] and form["amplitude"] and
## form["mutations"] and form["atoms"] and form["frames"]):
## self.fasthtml('Dear User. You need to set cutoff distance, amplitude, number of allowed mutations, frames and atoms to be used.', error = True)
## 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 that either of the radio buttons for method of calculation is checked
if not form["calctype"].value:
self.fasthtml('You need to specify which calculation you want to perform.', 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 = goodvibes.vibration()
pdb1ATOM_all = instance_NMA.parse_pdb(pdb_lines, pdb_chain = [], pdb_model = None)[0]
## check for valid chain ids
if form["chains1"].value:
if not form["chains1"].value.upper() in pdb1ATOM_all.keys():
self.fasthtml('Specified chain ID not present in PDB. Only chains (%s) are present in pdb.' %pdb1ATOM_all.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(pdb1ATOM_all.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(pdb1ATOM_all.keys()) > 1:
self.fasthtml('Multiple chains (%s) present in pdb. Please specify which one to use.' %pdb1ATOM_all.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 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/python/'
## check form for erros
if form["inputfiles"].value == '1':
inputfiles = 1
self.errorcheck1file(form)
elif form["inputfiles"].value == '2':
inputfiles = 2
self.errorcheck2files(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
## write fast output and slow 1st temporary output
## pid = os.fork()
pid = 11
if pid:
htmlbody = 'Dear user. Your input data has been queued for processing. Your job is still in the queu.'
self.slowhtml(htmlbody, timestr)
htmlbody = 'Dear user. Your input data is being processed. Your results will be available from <a href="http://polymerase.ucd.ie/goodvibes/results/'+timestr+'.html">http://polymerase.ucd.ie/goodvibes/results/'+timestr+'.html</a> in a minute...'
self.fasthtml(htmlbody)
## sys.stdout.flush()
## os.close(0)
##
## os.close(1)
## os.close(2)
################################################################################
## parse html form
if form.has_key("cutoffs"):
cutoffs = form.getlist("cutoffs")
for i in range(len(cutoffs)):
cutoffs[i] = float(cutoffs[i])
else: cutoffs = [10]
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.has_key("pdb1_id"):
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.has_key("pdb1_file"):
fd = open(self.path_tmp+timestr+'_reference.pdb', 'w')
fd.write(form["pdb1_file"].value)
fd.close()
if form.has_key("chains1"): 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
fd = open(self.path_tmp+'job_'+timestr+'.txt', 'w')
fd.write(
str(chains1)+'\n'+str(model1)+'\n'+str(resrange1start)+'\n'+str(resrange1end)+'\n'+
str(cutoffs)+'\n'+str(amplitude_average)+'\n'+str(atoms_hessian)+'\n'+str(mutations)+'\n'+str(quarternary)+'\n'+
str(frames)+'\n'+str(inputfiles)+'\n'+
str(chains2)+'\n'+str(model2)+'\n'+str(resrange2start)+'\n'+str(resrange2end)+'\n'
)
fd.close()
del timestr
################################################################################
## 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 goodvibes
instance_NMA = goodvibes.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. Your results - or an error if you gave an invalid input - will be here in less than 30 minutes.'
self.slowhtml(htmlbody, job)
## parse parameters from job txt file to goodvibes
fd = open(self.path_tmp+'job_'+job+'.txt', 'r')
lines_job = fd.readlines()
fd.close()
if lines_job[0].strip() != '': chains1 = lines_job[0].strip().split(',')
else: chains1 = []
model1 = lines_job[1].strip()
resrange1start = int(lines_job[2].strip())
resrange1end = int(lines_job[3].strip())
cutoffs = lines_job[4].strip()[1:-1].split(', ')
for i in range(len(cutoffs)):
cutoffs[i] = float(cutoffs[i])
amplitude_average = float(lines_job[5].strip())
atoms_hessian = lines_job[6].strip()[2:-2].split(',')
mutations = int(lines_job[7].strip())
quarternary = lines_job[8].strip()
frames = float(lines_job[9].strip())
inputfiles = int(lines_job[10].strip())
fd = open(self.path_tmp+job+'_reference.pdb', 'r')
pdblines1 = fd.readlines()
fd.close()
if inputfiles == 2:
fd = open(self.path_tmp+job+'_conformer.pdb', 'r')
pdblines2 = fd.readlines()
fd.close()
if lines_job[11].strip() != '': chains2 = lines_job[11].strip().split(',')
else: chains2 = []
model2 = lines_job[12].strip()
resrange2start = int(lines_job[13].strip())
resrange2end = int(lines_job[14].strip())
else:
pdblines2 = None
chains2 = None
model2 = None
## run goodvibes
try:
results = instance_NMA.main(pdblines1,chains1,model1, atoms_hessian, amplitude_average, cutoffs, mutations, quarternary, job, frames, pdblines2, chains2, model2)
except 'chainerror', error:
## if expected error then remove from queue and report to user
self.slowhtml(error, job)
self.queue()
continue
except:
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/python/'
## check form for erros
if form["inputfiles"].value == '1':
inputfiles = 1
self.errorcheck1file(form)
elif form["inputfiles"].value == '2':
inputfiles = 2
self.errorcheck2files(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
## write fast output and slow 1st temporary output
## pid = os.fork()
pid = 11
if pid:
htmlbody = 'Dear user. Your input data has been queued for processing. Your job is still in the queu.'
self.slowhtml(htmlbody, timestr)
htmlbody = 'Dear user. Your input data is being processed. Your results will be available from <a href="http://polymerase.ucd.ie/goodvibes/results/' + timestr + '.html">http://polymerase.ucd.ie/goodvibes/results/' + timestr + '.html</a> in a minute...'
self.fasthtml(htmlbody)
## sys.stdout.flush()
## os.close(0)
##
## os.close(1)
## os.close(2)
################################################################################
## parse html form
if form.has_key("cutoffs"):
cutoffs = form.getlist("cutoffs")
for i in range(len(cutoffs)):
cutoffs[i] = float(cutoffs[i])
else:
cutoffs = [10]
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.has_key("pdb1_id"):
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.has_key("pdb1_file"):
fd = open(self.path_tmp + timestr + '_reference.pdb', 'w')
fd.write(form["pdb1_file"].value)
fd.close()
if form.has_key("chains1"): 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
fd = open(self.path_tmp + 'job_' + timestr + '.txt', 'w')
fd.write(
str(chains1) + '\n' + str(model1) + '\n' + str(resrange1start) +
'\n' + str(resrange1end) + '\n' + str(cutoffs) + '\n' +
str(amplitude_average) + '\n' + str(atoms_hessian) + '\n' +
str(mutations) + '\n' + str(quarternary) + '\n' + str(frames) +
'\n' + str(inputfiles) + '\n' + str(chains2) + '\n' + str(model2) +
'\n' + str(resrange2start) + '\n' + str(resrange2end) + '\n')
fd.close()
del timestr
################################################################################
## 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 goodvibes
instance_NMA = goodvibes.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. Your results - or an error if you gave an invalid input - will be here in less than 30 minutes.'
self.slowhtml(htmlbody, job)
## parse parameters from job txt file to goodvibes
fd = open(self.path_tmp + 'job_' + job + '.txt', 'r')
lines_job = fd.readlines()
fd.close()
if lines_job[0].strip() != '':
chains1 = lines_job[0].strip().split(',')
else:
chains1 = []
model1 = lines_job[1].strip()
resrange1start = int(lines_job[2].strip())
resrange1end = int(lines_job[3].strip())
cutoffs = lines_job[4].strip()[1:-1].split(', ')
for i in range(len(cutoffs)):
cutoffs[i] = float(cutoffs[i])
amplitude_average = float(lines_job[5].strip())
atoms_hessian = lines_job[6].strip()[2:-2].split(',')
mutations = int(lines_job[7].strip())
quarternary = lines_job[8].strip()
frames = float(lines_job[9].strip())
inputfiles = int(lines_job[10].strip())
fd = open(self.path_tmp + job + '_reference.pdb', 'r')
pdblines1 = fd.readlines()
fd.close()
if inputfiles == 2:
fd = open(self.path_tmp + job + '_conformer.pdb', 'r')
pdblines2 = fd.readlines()
fd.close()
if lines_job[11].strip() != '':
chains2 = lines_job[11].strip().split(',')
else:
chains2 = []
model2 = lines_job[12].strip()
resrange2start = int(lines_job[13].strip())
resrange2end = int(lines_job[14].strip())
else:
pdblines2 = None
chains2 = None
model2 = None
## run goodvibes
try:
results = instance_NMA.main(pdblines1, chains1, model1,
atoms_hessian, amplitude_average,
cutoffs, mutations, quarternary,
job, frames, pdblines2, chains2,
model2)
except 'chainerror', error:
## if expected error then remove from queue and report to user
self.slowhtml(error, job)
self.queue()
continue
except:
def errorcheckfile(self, form):
import os, sys
sys.path.append(self.path_python)
import goodvibes
## ## check for essential settings
## if not (form["cutoffs"] and form["amplitude"] and
## form["mutations"] and form["atoms"] and form["frames"]):
## self.fasthtml('Dear User. You need to set cutoff distance, amplitude, number of allowed mutations, frames and atoms to be used.', error = True)
## 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)
## 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)
## 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)
## 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)
## check that either of the radio buttons for method of calculation is checked
if not form["calctype"].value:
self.fasthtml('You need to specify which calculation you want to perform.', error = True)
## 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 = goodvibes.vibration()
pdb1ATOM_all = instance_NMA.parse_pdb(pdb_lines, pdb_chain = [], pdb_model = None)[0]
## check for valid chain ids
if form["chains1"].value:
if not form["chains1"].value.upper() in pdb1ATOM_all.keys():
self.fasthtml('Specified chain ID not present in PDB. Only chains (%s) are present in pdb.' %pdb1ATOM_all.keys(), error = True)
## check that only 1 chain is present if none specified by user
if form["chains1"].value == "":
## error if no chains present
if len(pdb1ATOM_all.keys()) == 0:
self.fasthtml('No protein chains present in pdb. GoodVibes does not compute polynucleotides at present.', error = True)
## error if multiple chains
if len(pdb1ATOM_all.keys()) > 1:
self.fasthtml('Multiple chains (%s) present in pdb. Please specify which one to use.' %pdb1ATOM_all.keys(), error = True)
## 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)
## acummulate error messages and then return them in errorhtml if there is any...
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/python/"
## 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://polymerase.ucd.ie/goodvibes/results/'
+ timestr
+ '.html" target="_blank">http://polymerase.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("cutoffs"):
cutoffs = form.getlist("cutoffs")
else:
cutoffs = ["10"]
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
calctype = form["calctype"].value
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" % ("cutoffs", ",".join(cutoffs)))
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))
lines_input.append("%s;%s\n" % ("calctype", calctype))
fd = open(self.path_tmp + "job_" + timestr + ".txt", "w")
fd.writelines(lines_input)
fd.close()
## fd = open(self.path_tmp+'job_'+timestr+'.txt', 'w')
## fd.write(
## str(chains1)+'\n'+str(model1)+'\n'+str(resrange1start)+'\n'+str(resrange1end)+'\n'+
## str(cutoffs)+'\n'+str(amplitude_average)+'\n'+str(atoms_hessian)+'\n'+str(mutations)+'\n'+str(quarternary)+'\n'+
## str(frames)+'\n'+str(inputfiles)+'\n'+str(calctype)+'\n'+
## str(chains2)+'\n'+str(model2)+'\n'+str(resrange2start)+'\n'+str(resrange2end)+'\n'
## )
## 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://polymerase.ucd.ie/goodvibes/results/"
+ timestr
+ ".html <http://polymerase.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()
## delete timestr to avoid use of this variable beyond this point (not really necessary)
del timestr
################################################################################
## 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 goodvibes
instance_NMA = goodvibes.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())
cutoffs = input_job["cutoffs"].split(",")
for i in range(len(cutoffs)):
cutoffs[i] = float(cutoffs[i])
amplitude_average = float(input_job["amplitude"].strip())
atoms_hessian = input_job["atoms_hessian"].split(",")
quarternary = input_job["quarternary"].strip()
frames = float(input_job["frames"])
calctype = int(input_job["calctype"].strip())
fd = open(self.path_tmp + job + "_reference.pdb", "r")
pdblines1 = fd.readlines()
fd.close()
## run goodvibes
try:
results = instance_NMA.main(
pdblines1,
chains1,
model1,
atoms_hessian,
quarternary,
job,
frames,
cutoffs,
calctype,
[1],
path_html=self.path_results,
path_python=self.path_python,
)
## 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,
cutoffs,
calctype,
[1],
path_html=self.path_results,
path_python=self.path_python,
)
continue
except:
