def getTMScoreValues(self):
"""
Calculate the TM-Score value to the input PDB files
@type self: koala.CalculateTMScore.CalculateTMScore
"""
try:
pdbs = list_directory(self.path_runs.get_path_execution(), "*.pdb")
if not pdbs:
raise "getTMScoreValues: No PDB file found.\n"
dict_tmscore = {}
for pdb in pdbs:
if not (pdb == self.opts.inputPDBRefName):
name_pdb, ext = os.path.splitext(pdb)
name_reference, ext = os.path.splitext(self.opts.inputPDBRefName)
aux_command = self.command.replace(
"@PATH@",
self.path_runs.get_path_execute()).replace(
"@MODEL@",
(os.path.join(self.path_runs.get_path_execution(), pdb))).replace(
"@NATIVE@",
(os.path.join(
self.path_runs.get_path_execution(),
self.opts.inputPDBRefName)))
aux_command = aux_command.replace(
"@PATHEXECUTE@",
self.path_runs.get_path_execution()).replace(
"@NAMEMODEL@",
name_pdb).replace(
"@NAMENATIVE@",
name_reference)
os.system(aux_command) # TODO: USAR SUBPROCESS
os.chdir(self.path_runs.get_path_execution())
result_file = name_reference + '_' + name_pdb + '.txt'
temp_tmscore = open(result_file, "r")
for line in temp_tmscore.readlines():
if line.startswith("TM-score"):
tmscore_value = line.split("=", 1)[1].strip()
only_pdb_file_name = os.path.basename(pdb)
dict_tmscore[only_pdb_file_name] = tmscore_value
temp_tmscore.close()
return OrderedDict(sorted(dict_tmscore.items(), key=lambda x: x[1], reverse=True))
except Exception, e:
show_error_message("Erro on getTMScoreValues method:\n%s" % e)
def getRMSDValues(self):
"""
Calculate the RMSD value to the input PDB files
@type self: koala.CalculateRMSD.CalculateRMSD
"""
try:
pdbs = list_directory(self.path_runs.get_path_execution(), "*.pdb")
if not pdbs:
raise Exception("getRMSDValues: No PDB file found.\n")
dict_rmsd = {}
for pdb in pdbs:
if not (pdb == self.opts.inputPDBRefName):
# aux_command = self.command.replace(
# "@PATH_GROMACS@",
# self.ClassColection.getPathGromacs()).replace(
# "@PROT@",
# (os.path.join(self.path_runs.get_path_execution(), pdb))).replace(
# "@NATIVE@",
# (os.path.join(self.path_runs.get_path_execution(), self.opts.inputPDBRefName)))
# os.system(aux_command)
# temp_rmsd = open("temporary_rmsd.xvg", "r")
# for line in temp_rmsd.readlines():
# if line.find("@") < 0 and line.find("#") < 0:
# rmsd_value = float(str(line).split()[1])
# only_pdb_file_name = os.path.basename(pdb)
# dict_rmsd[only_pdb_file_name] = rmsd_value
# temp_rmsd.close()
# os.remove("temporary_rmsd.xvg")
# Load Structures
a = os.path.join(self.path_runs.get_path_execution(), pdb)
aname, ext = os.path.splitext(pdb)
b = os.path.join(self.path_runs.get_path_execution(), self.opts.inputPDBRefName)
bname, ext = os.path.splitext(self.opts.inputPDBRefName)
pymol.cmd.load(a, aname)
pymol.cmd.load(b, bname)
ret = pymol.cmd.align(aname, bname)
rms = list(ret)
print 'rmds %s, atoms %s, residues %s' % (rms[0], rms[1], rms[-1])
only_pdb_file_name = os.path.basename(pdb)
dict_rmsd[only_pdb_file_name] = round(rms[0], 3)
sleep(0.25) # (in seconds)
pymol.cmd.reinitialize()
return OrderedDict(sorted(dict_rmsd.items(), key=lambda x: x[1]))
except Exception, e:
show_error_message("Erro on getRMSDValues method:\n%s" % e)
def getBetterPDBs(self, path):
"""
Get the methods that have been classified on the two first fronts
@type self: koala.SortByFront.SortByFront
"""
try:
front = list_directory(path, "*.front")
if len(front) > 1:
raise Exception("There is more than one .front file.\n")
if len(front) == 0:
raise Exception("There is no .front file.\n")
for l in file(front[0], 'r'):
ln = l.split("\n")
if not ln[0].startswith('#', 0, 1):
ll = ln[0].split("\t")
if(int(ll[1]) < 2): # ll[1] = fronteira fronteiras 0 e 1
self.methods.append(ll[6].strip()) # ll[6] = metodo
except Exception, e:
show_error_message("Error on getBetterPDBs.\n%s" % e)
def run_Random(self):
"""
Create the 2PG Random configuration file and begin the execution.
@type self: koala.Random2PG.Random2PG
"""
try:
self.path_runs.set_path_execute()
if self.opts.inputEmail:
email = validate_email(self.opts.inputEmail)
self.path_runs.set_execution_directory(email)
else:
self.path_runs.set_execution_directory()
self.sequence = create_local_fasta_file(
self.path_runs.get_path_execution(),
self.opts.fromFasta,
self.opts.inputFasta,
self.opts.toolname,
self.framework)
SizePopulation = create_local_pop_file(
self.path_runs.get_path_execution(),
self.opts.inputPop,
self.framework)
if SizePopulation > 1:
show_error_message(
"Error: The population file must contain only one model")
copy_necessary_files(
self.path_runs.get_path_execute(),
self.path_runs.get_path_execution(),
self.framework.get_framework())
self.framework.set_parameter(
'rotamer_library', self.opts.rotamerLibrary)
self.framework.set_parameter(
'StepNumber', self.opts.stepNumber)
self.framework.set_parameter(
'How_Many_Rotation', self.opts.howManyRotation)
self.framework.set_parameter(
'force_field', self.opts.forceField)
self.framework.set_parameter(
'SequenceAminoAcidsPathFileName',
self.path_runs.get_path_execution() + 'fasta.txt')
self.framework.set_parameter(
'Local_Execute', self.path_runs.get_path_execution())
self.framework.set_parameter(
'Path_Gromacs_Programs',
get_path_gromacs())
self.framework.set_parameter(
'NativeProtein', '%s1VII.pdb' % self.path_runs.get_path_execution())
self.framework.set_parameter(
'Database',
'%s/Database/' %
get_path_algorithms('2pg_build_conformation'))
create_configuration_file(
self.path_runs.get_path_execution(), self.framework)
self.framework.set_command(
self.path_runs.get_path_execution(),
'protpred-Gromacs-Random_Algorithm')
config = 'configuration.conf'
cl = [self.framework.get_command(), config, '&']
retProcess = subprocess.Popen(
cl, 0, stdout=None, stderr=subprocess.STDOUT, shell=False)
retCode = retProcess.wait()
if(retCode != 0):
show_error_message(
"The 2PG framework finished wrong.\nContact the system administrator.")
parse_pdb(
self.path_runs.get_path_execution(),
'random_algorithm_solutions.pdb',
20,
'randomSolution')
if(self.opts.runMinimization == 'true'):
self.do_minimization("randomSolution")
pdbs = list_directory(
self.path_runs.get_path_execution(), 'randomSolution-M*.pdb')
build_images(pdbs, self.path_runs.get_path_execution())
path_output, file_output = os.path.split(self.opts.filehtml)
name, ext = os.path.splitext(self.opts.filehtml)
htmldir = os.path.join(path_output, '%s_files' % name)
if not os.path.exists(htmldir):
os.makedirs(htmldir)
self.opts.htmlfiledir = htmldir
result, filesHtml = get_result_files(
self.path_runs.get_path_execution(),
self.opts.toolname,
'randomSolution-M')
send_output_files_html(self.opts.htmlfiledir, filesHtml)
send_output_files_html(self.opts.htmlfiledir, [result])
if self.opts.createCompressFile == "True":
if compress_files(pdbs, self.path_runs.get_path_execution(), "2PGRandom"):
path_output, file_output = os.path.split(self.opts.outputZip)
send_output_results(
path_output,
file_output,
os.path.join(self.path_runs.get_path_execution(), '2PGRandom.zip'))
self.makeHtml()
if(self.opts.useJmol in ('True', 'true')):
self.makeHtmlWithJMol(pdbs[0])
if(self.opts.inputEmail):
send_email(
'*****@*****.**',
email,
'%s Execution on Galaxy - Cloud USP' % self.opts.toolname,
get_message_email(self.opts.toolname),
[],
'smtp.gmail.com')
except Exception, e:
show_error_message(str(e))
def makeHtml(self):
""" Create an HTML file content to list all the artifacts found in the html_dir
@type self: koala.Random2PG.Random2PG
"""
try:
galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Galaxy %s tool output" />
<title></title>
<link rel="stylesheet" href="/static/koala.css" type="text/css" />
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
<script type="text/javascript"
src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
<script src="http://code.highcharts.com/highcharts.js"></script>
<script src="http://code.highcharts.com/highcharts-more.js"></script>
<script src="http://code.highcharts.com/modules/exporting.js"></script>
</head>
<body>
<div class="toolFormBody">"""
galhtmlpostfix = """</div></body></html>\n"""
flist = os.listdir(self.opts.htmlfiledir)
flist.sort()
html = []
html.append(galhtmlprefix % self.progname)
html.append('<div class="sucessmessage">')
html.append('<br>')
html.append('<h1 align="center">2PG Random Ab Initio Algorithm results</h1><br></div>')
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Submitted Primary Sequence.<br><br></div>')
html.append('<div class="code">')
html.append('Length: %s<br>' % len(self.sequence))
html.append('%s<br></div>' % self.sequence)
fhtml = []
fitFiles = []
outputfiles = []
compressedFile = []
imageFiles = []
if len(flist) > 0:
for rownum, fname in enumerate(flist):
dname, e = os.path.splitext(fname)
sfsize = get_file_size(fname, self.opts.htmlfiledir)
if e.lower() == ".fit":
fitFiles.append(fname)
elif e.lower() == ".png":
imageFiles.append(fname)
elif e.lower() in ".zip, .gz":
compressedFile.append(fname)
elif not e.lower() in self.ignoreoutfiles:
outputfiles.append(fname)
# Arquivos fit
for fit in fitFiles:
sfsize = get_file_size(fit, self.opts.htmlfiledir)
fhtml.append('<tr>')
fhtml.append('<td><a href="%s">%s</a></td>' % (fit, fit))
fhtml.append('<td>%s</td>' % (sfsize))
fhtml.append('</tr>')
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Download Calculated values of selected Objectives.<br><br></div>')
fhtml.insert(
0,
'<div class="filetables"><table border="1"><tr><th>File</th>'
'<th>Size</th></tr>\n')
fhtml.append('</table></div><br>')
html += fhtml
fhtml = []
# images (e depois models)
listaArquivosPdb = list_directory(
self.path_runs.get_path_execution(),
'randomSolution-M*.pdb')
if len(listaArquivosPdb) <= 20:
size = int(len(listaArquivosPdb) / 5)
rest = len(listaArquivosPdb) % 5
else:
size = 4 # vai mostrar no máximo 20 imagens
rest = 0
idx = 0 # controla indice das imagens e dos metodos
start = 0
end = 5 # limite de colunas para uma linha
if size < 1:
n = len(listaArquivosPdb)
fhtml.append('<tr>')
idx_linha = idx
for i in range(0, n):
pdbName, ext = os.path.splitext(listaArquivosPdb[idx])
fhtml.append(
'<td><a href="%s.png"><img src="%s.png" '
'title="Click to see %s.png bigger" width="130"/></a></td>'
% (pdbName, pdbName, pdbName))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, n):
fhtml.append(
'<td><a href="%s">%s</a></td>' % (
listaArquivosPdb[idx], listaArquivosPdb[idx]))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, n):
sfsize = get_file_size(
listaArquivosPdb[idx],
self.opts.htmlfiledir)
fhtml.append('<td>%s</td>' % (sfsize))
idx += 1
idx = idx_linha
fhtml.append('</tr>')
else:
for img in range(0, size):
fhtml.append('<tr>')
idx_linha = idx
for i in range(start, end):
pdbName, ext = os.path.splitext(listaArquivosPdb[idx])
fhtml.append(
'<td><a href="%s.png"><img src="%s.png" '
'title="Click to see %s.png bigger" width="130"/></a></td>'
% (pdbName, pdbName, pdbName))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(start, end):
fhtml.append(
'<td><a href="%s">%s</a></td>' % (
listaArquivosPdb[idx], listaArquivosPdb[idx]))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(start, end):
sfsize = get_file_size(
listaArquivosPdb[idx],
self.opts.htmlfiledir)
fhtml.append('<td>%s</td>' % (sfsize))
idx += 1
fhtml.append('</tr>')
fhtml.append('<tr>')
idx_linha = idx
for i in range(0, rest):
pdbName, ext = os.path.splitext(listaArquivosPdb[idx])
fhtml.append(
'<td><a href="%s.png"><img src="%s.png" '
'title="Click to see %s.png bigger" width="130"/></a></td>'
% (pdbName, pdbName, pdbName))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, rest):
fhtml.append(
'<td><a href="%s">%s</a></td>' % (
listaArquivosPdb[idx], listaArquivosPdb[idx]))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, rest):
sfsize = get_file_size(
listaArquivosPdb[idx],
self.opts.htmlfiledir)
fhtml.append('<td>%s</td>' % (sfsize))
idx += 1
idx = idx_linha
fhtml.append('</tr>')
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Best Tertiary Structures<br>')
html.append('<br></div>')
if(self.opts.useJmol == 'true'):
html.append('<div class="active-jmol">')
html.append('<br>')
html.append(
'<a href=/datasets/%s/display/%s.htm>Activate JMol</a>' % (
self.opts.datasetID, self.opts.datasetID))
html.append('<br></div>')
model = ''
if size < 1:
for i in range(0, len(listaArquivosPdb)):
model += '<th>Model</th>'
else:
model = '<th>Model</th>'\
'<th>Model</th>'\
'<th>Model</th>'\
'<th>Model</th>'\
'<th>Model</th>'
fhtml.insert(
0,
'<div class="filetables"><table border="1">'
'<tr>' +
model +
'</tr>\n')
fhtml.append('</table></div><br/>')
html += fhtml
fhtml = []
# Outros arquivos de output
for output in outputfiles:
sfsize = get_file_size(output, self.opts.htmlfiledir)
fhtml.append('<tr>')
fhtml.append('<td><a href="%s">%s</a></td>' % (output, output))
fhtml.append('<td>%s</td>' % (sfsize))
fhtml.append('</tr>')
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Download the output files:<br><br></div>')
fhtml.insert(
0,
'<div class="filetables"><table border="1"><tr><th>Output File</th>'
'<th>Size</th></tr>\n')
fhtml.append('</table></div><br>')
html += fhtml
fhtml = []
# arquivo zipado
for output in compressedFile:
sfsize = get_file_size(output, self.opts.htmlfiledir)
fhtml.append('<tr>')
fhtml.append('<td><a href="%s">%s</a></td>' % (output, output))
fhtml.append('<td>%s</td>' % (sfsize))
fhtml.append('</tr>')
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Compressed file with all the output files<br><br></div>')
fhtml.insert(
0,
'<div class="filetables"><table border="1"><tr><th>File</th>'
'<th>Size</th></tr>\n')
fhtml.append('</table></div><br>')
html += fhtml
self.time_execution.set_job_end(datetime.datetime.now())
self.endTime = datetime.datetime.now()
dif = self.time_execution.calculate_time_execution()
html.append('<div>Time execution:<br>')
html.append('Start: %s<br>' %
self.time_execution.get_job_start().strftime("%d/%m/%Y %H:%M:%S"))
html.append('End: %s<br>' %
self.time_execution.get_job_end().strftime("%d/%m/%Y %H:%M:%S"))
html.append('Total time: ~%dh:%dm:%ds' % (dif[0], dif[1], dif[2]))
html.append('</div>')
html.append('<hr>')
html.append('<div>Citation<br>')
html.append('Please, cite the used algorithm in this tool:<br><br>')
html.append('')
html.append('<br></div>')
html.append(galhtmlpostfix)
htmlf = file(self.opts.filehtml, 'w')
htmlf.write('\n'.join(html))
htmlf.write('\n')
htmlf.close()
except Exception, e:
show_error_message("Error on makeHtml:\n%s" % str(e))
def makeHtmlWithJMol(self, pdbReference):
"""
Create an HTML file content to list all the artifacts found in the html_dir
@type self: koala.SortByFront.SortByFront
"""
try:
galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Galaxy %s tool output" />
<title></title>
<link rel="stylesheet" href="/static/koala.css" type="text/css" />
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
<script type="text/javascript"
src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
<script src="http://code.highcharts.com/highcharts.js"></script>
<script src="http://code.highcharts.com/highcharts-more.js"></script>
<script src="http://code.highcharts.com/modules/exporting.js"></script>
<script type="text/javascript" src="/static/js/JSmol.min.js"></script>
<script type="text/javascript">
Jmol._isAsync = false;
Jmol.getProfile()
var jmolApplet0;
jmol_isReady = function(applet) {
document.title = (applet._id + " is ready")
Jmol._getElement(applet, "appletdiv").style.border="1px solid blue"
}
Info = {
width: 400,
height: 300,
debug: false,
color: "#F0F0F0",
zIndexBase: 20000,
z:{monitorZIndex:100},
addSelectionOptions: false,
serverURL: "/static/js/php/jsmol.php",
use: "HTML5",
jarPath: "/static/js/java",
j2sPath: "/static/js/j2s",
jarFile: "JmolApplet.jar",
isSigned: false,
disableJ2SLoadMonitor: false,
disableInitialConsole: false,
readyFunction: jmol_isReady,
allowjavascript: true,
script: "set antialiasDisplay;set showtiming;load async /datasets/%s/display/%s;cartoons only;color cartoons structure; spin on"
//,defaultModel: ":dopamine"
//,noscript: true
//console: "none", // default will be jmolApplet0_infodiv
//script: "set antialiasDisplay;background white;load data/caffeine.mol;"
//delay 3;background yellow;delay 0.1;background white;for (var i = 0; i < 10; i+=1){rotate y 3;delay 0.01}"
}
</script>
</head>
<body>
<div class="toolFormBody">"""
galhtmlpostfix = """</div></body></html>\n"""
flist = os.listdir(self.opts.htmlfiledir)
flist.sort()
html = []
html.append(galhtmlprefix % (self.progname, self.opts.datasetID, pdbReference))
html.append('<div class="sucessmessage">')
html.append('<br>')
html.append('<h1 align="center">2PG Random Ab Initio Algorithm results</h1><br></div>')
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Submitted Primary Sequence.<br><br></div>')
html.append('<div class="code">')
html.append('Length: %s<br>' % len(self.sequence))
html.append('%s<br></div>' % self.sequence)
fhtml = []
fitFiles = []
outputfiles = []
compressedFile = []
imageFiles = []
if len(flist) > 0:
for rownum, fname in enumerate(flist):
dname, e = os.path.splitext(fname)
sfsize = get_file_size(fname, self.opts.htmlfiledir)
if e.lower() == ".fit":
fitFiles.append(fname)
elif e.lower() == ".png":
imageFiles.append(fname)
elif e.lower() in ".zip, .gz":
compressedFile.append(fname)
elif not e.lower() in self.ignoreoutfiles:
outputfiles.append(fname)
# Arquivos fit
for fit in fitFiles:
sfsize = get_file_size(fit, self.opts.htmlfiledir)
fhtml.append('<tr>')
fhtml.append('<td><a href="%s">%s</a></td>' % (fit, fit))
fhtml.append('<td>%s</td>' % (sfsize))
fhtml.append('</tr>')
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Download Calculated values of selected Objectives.<br><br></div>')
fhtml.insert(
0,
'<div class="filetables"><table border="1"><tr><th>File</th>'
'<th>Size</th></tr>\n')
fhtml.append('</table></div><br>')
html += fhtml
fhtml = []
# images (e depois models)
listaArquivosPdb = list_directory(
self.path_runs.get_path_execution(),
'randomSolution-M*.pdb')
if len(listaArquivosPdb) <= 20:
size = int(len(listaArquivosPdb) / 5)
rest = len(listaArquivosPdb) % 5
else:
size = 4 # vai mostrar no máximo 20 imagens
rest = 0
idx = 0 # controla indice das imagens e dos metodos
start = 0
end = 5 # limite de colunas para uma linha
if size < 1:
n = len(listaArquivosPdb)
fhtml.append('<tr>')
idx_linha = idx
for i in range(0, n):
pdbName, ext = os.path.splitext(listaArquivosPdb[idx])
fhtml.append(
'<td><a href="/datasets/%s/display/%s.png">'
'<img src="/datasets/%s/display/%s.png" '
'title="Click to see %s.png bigger" width="130"/></a></td>'
% (self.opts.datasetID, pdbName, self.opts.datasetID, pdbName, pdbName))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, n):
fhtml.append(
'<td><a href="/datasets/%s/display/%s">%s</a></td>' % (
self.opts.datasetID, listaArquivosPdb[idx], listaArquivosPdb[idx]))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, n):
sfsize = get_file_size(
listaArquivosPdb[idx],
self.opts.htmlfiledir)
fhtml.append('<td>%s</td>' % (sfsize))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, n):
fhtml.append(
'<td>'
'<a href="javascript:Jmol.script(jmolApplet0,'
"'load /datasets/%s/display/%s;cartoons only; \
color cartoons structure; spin on')"
'">Load on Jmol</a></td>' % (
self.opts.datasetID, listaArquivosPdb[idx]))
idx += 1
idx = idx_linha
else:
for img in range(0, size):
fhtml.append('<tr>')
idx_linha = idx
for i in range(start, end):
pdbName, ext = os.path.splitext(listaArquivosPdb[idx])
fhtml.append(
'<td><a href="/datasets/%s/display/%s.png">'
'<img src="/datasets/%s/display/%s.png" '
'title="Click to see %s.png bigger" width="130"/></a></td>'
% (self.opts.datasetID, pdbName, self.opts.datasetID, pdbName, pdbName))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(start, end):
fhtml.append(
'<td><a href="/datasets/%s/display/%s">%s</a></td>'
% (
self.opts.datasetID, listaArquivosPdb[idx], listaArquivosPdb[idx]))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(start, end):
sfsize = get_file_size(
listaArquivosPdb[idx],
self.opts.htmlfiledir)
fhtml.append('<td>%s</td>' % (sfsize))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(start, end):
fhtml.append(
'<td>'
'<a href="javascript:Jmol.script(jmolApplet0,'
"'load /datasets/%s/display/%s;cartoons only; \
color cartoons structure; spin on')"
'">Load on Jmol</a></td>' % (
self.opts.datasetID, listaArquivosPdb[idx]))
idx += 1
fhtml.append('<tr>')
idx_linha = idx
for i in range(0, rest):
pdbName, ext = os.path.splitext(listaArquivosPdb[idx])
fhtml.append(
'<td><a href="/datasets/%s/display/%s.png">'
'<img src="/datasets/%s/display/%s.png" '
'title="Click to see %s.png bigger" width="130"/></a></td>'
% (self.opts.datasetID, pdbName, self.opts.datasetID, pdbName, pdbName))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, rest):
fhtml.append(
'<td><a href="/datasets/%s/display/%s">%s</a></td>' % (
self.opts.datasetID, listaArquivosPdb[idx], listaArquivosPdb[idx]))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, rest):
sfsize = get_file_size(
listaArquivosPdb[idx],
self.opts.htmlfiledir)
fhtml.append('<td>%s</td>' % (sfsize))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, rest):
fhtml.append(
'<td>'
'<a href="javascript:Jmol.script(jmolApplet0,'
"'load /datasets/%s/display/%s;cartoons only; \
color cartoons structure; spin on')"
'">Load on Jmol</a></td>' % (
self.opts.datasetID, listaArquivosPdb[idx]))
idx += 1
idx = idx_linha
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Best Tertiary Structures<br>')
html.append('<br></div>')
model = ''
if size < 1:
for i in range(0, len(listaArquivosPdb)):
model += '<th>Model</th>'
else:
model = '<th>Model</th>'\
'<th>Model</th>'\
'<th>Model</th>'\
'<th>Model</th>'\
'<th>Model</th>'
fhtml.insert(
0,
'<div class="filetables"><table border="1">'
'<tr>' +
model +
'</tr>\n')
fhtml.append('</table></div><br/>')
# html += fhtml
fhtml.append('<div class="jmol-applet">')
fhtml.append('<script>')
fhtml.append('jmolApplet0 = Jmol.getApplet("jmolApplet0", Info)')
fhtml.append("var lastPrompt=0;")
fhtml.append('</script></div>')
html += fhtml
fhtml = []
# Outros arquivos de output
for output in outputfiles:
sfsize = get_file_size(output, self.opts.htmlfiledir)
fhtml.append('<tr>')
fhtml.append('<td><a href="%s">%s</a></td>' % (output, output))
fhtml.append('<td>%s</td>' % (sfsize))
fhtml.append('</tr>')
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Download the output files:<br><br></div>')
fhtml.insert(
0,
'<div class="filetables"><table border="1"><tr><th>Output File</th>'
'<th>Size</th></tr>\n')
fhtml.append('</table></div><br>')
html += fhtml
fhtml = []
# arquivo zipado
for output in compressedFile:
sfsize = get_file_size(output, self.opts.htmlfiledir)
fhtml.append('<tr>')
fhtml.append('<td><a href="%s">%s</a></td>' % (output, output))
fhtml.append('<td>%s</td>' % (sfsize))
fhtml.append('</tr>')
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Compressed file with all the output files<br><br></div>')
fhtml.insert(
0,
'<div class="filetables"><table border="1"><tr><th>File</th>'
'<th>Size</th></tr>\n')
fhtml.append('</table></div><br>')
html += fhtml
self.time_execution.set_job_end(datetime.datetime.now())
self.endTime = datetime.datetime.now()
dif = self.time_execution.calculate_time_execution()
html.append('<div>Time execution:<br>')
html.append('Start: %s<br>' %
self.time_execution.get_job_start().strftime("%d/%m/%Y %H:%M:%S"))
html.append('End: %s<br>' %
self.time_execution.get_job_end().strftime("%d/%m/%Y %H:%M:%S"))
html.append('Total time: ~%dh:%dm:%ds' % (dif[0], dif[1], dif[2]))
html.append('</div>')
html.append('<hr>')
html.append('<div>Citation<br>')
html.append('Please, cite the used algorithm in this tool:<br><br>')
html.append('')
html.append('<br></div>')
html.append(galhtmlpostfix)
htmlf = file("%s.htm" % os.path.join(self.opts.htmlfiledir, self.opts.datasetID), 'w')
htmlf.write('\n'.join(html))
htmlf.write('\n')
htmlf.close()
except Exception, e:
show_error_message("Error on makeHtmlWithJMol:\n%s" % str(e))
def main(self):
"""
Create the ProtPred-EDA configuration file and begin the execution.
@type self: koala.ProtPredEDA.ProtPredEDA
"""
try:
self.path_runs.set_path_execute()
if self.opts.inputEmail:
email = validate_email(self.opts.inputEmail)
self.path_runs.set_execution_directory(email)
else:
self.path_runs.set_execution_directory()
self.sequence = create_local_fasta_file(
self.path_runs.get_path_execution(),
self.opts.fromFasta,
self.opts.SequenceFile,
self.opts.toolname,
self.framework)
copy_necessary_files(
self.path_runs.get_path_execute(),
self.path_runs.get_path_execution(),
self.framework.get_framework())
# Config
self.framework.set_parameter('OptimMethod', 'rboa')
self.framework.set_parameter('MaxEval', self.opts.MaxEval)
self.framework.set_parameter('Threshold', self.opts.Threshold)
# FitnessPSP
self.framework.set_parameter('VanderWaals', self.opts.VanderWaals)
# ClassColection.setParameter('SASA', self.opts.SASA)
self.framework.set_parameter('Coulomb', self.opts.Coulomb)
self.framework.set_parameter('Solvatation', self.opts.Solvatation)
self.framework.set_parameter('HydrogenBond', self.opts.HydrogenBond)
self.framework.set_parameter('Torsion', self.opts.Torsion)
self.framework.set_parameter('UseAngleDB', self.opts.UseAngleDB)
self.framework.set_parameter('AminoAcidL', self.opts.AminoAcidL)
# rboa
self.framework.set_parameter('PopSize', self.opts.PopSize)
self.framework.set_parameter('SelSize', self.opts.SelSize)
self.framework.set_parameter('MaxParents', self.opts.MaxParents)
self.framework.set_parameter('MixtureComponents', self.opts.MixtureComponents)
create_configuration_file(
self.path_runs.get_path_execution(), self.framework)
self.framework.set_command(
self.path_runs.get_path_execution(),
'protpred')
config = 'input.ini'
cl = [self.framework.get_command(), config, '&']
retProcess = subprocess.Popen(
cl, 0, stdout=None, stderr=None, shell=False)
retCode = retProcess.wait()
if(retCode != 0):
show_error_message(
"The ProtPred-EDA framework finished wrong.\nContact the system administrator.")
copy_files_to_execute_folder(
self.path_runs.get_path_execution(),
'ProtPredEDA_rBOA')
if(self.opts.runMinimization == 'true'):
self.do_minimization("ProtPredEDA_rBOA")
pdbs = sorted(list_directory(self.path_runs.get_path_execution(), '*.pdb'))
build_images(pdbs, self.path_runs.get_path_execution())
path_output, file_output = os.path.split(self.opts.filehtml)
name, ext = os.path.splitext(self.opts.filehtml)
htmldir = os.path.join(path_output, '%s_files' % name)
if not os.path.exists(htmldir):
os.makedirs(htmldir)
self.opts.htmlfiledir = htmldir
result, filesHtml = get_result_files(
self.path_runs.get_path_execution(),
self.opts.toolname)
send_output_results(path_output, file_output, result)
send_output_files_html(self.opts.htmlfiledir, filesHtml)
send_output_files_html(self.opts.htmlfiledir, [result])
if self.opts.createCompressFile == "True":
if compress_files(pdbs, self.path_runs.get_path_execution(), "ProtPredEDA-rBOA"):
path_output, file_output = os.path.split(self.opts.outputZip)
send_output_results(
path_output,
file_output,
os.path.join(
self.path_runs.get_path_execution(), 'ProtPredEDA-rBOA.zip'))
self.makeHtml()
if(self.opts.useJmol in ('True', 'true')):
self.makeHtmlWithJMol(pdbs[0])
if(self.opts.inputEmail):
send_email(
'*****@*****.**',
email,
'%s Execution on Galaxy - Cloud USP' % self.opts.toolname,
get_message_email(self.opts.toolname),
[],
'smtp.gmail.com')
except Exception, e:
show_error_message(str(e))
def run_NSGAII(self):
"""
Create the 2PG NSGA-II configuration file and begin the execution.
@type self: koala.NSGAII2PG.NSGAII2PG
"""
try:
self.path_runs.set_path_execute()
if self.opts.inputEmail:
email = validate_email(self.opts.inputEmail)
self.path_runs.set_execution_directory(email)
else:
self.path_runs.set_execution_directory()
self.sequence = create_local_fasta_file(
self.path_runs.get_path_execution(),
self.opts.fromFasta,
self.opts.inputFasta,
self.opts.toolname,
self.framework,
)
SizePopulation = create_local_pop_file(
self.path_runs.get_path_execution(), self.opts.inputPop, self.framework
)
copy_necessary_files(
self.path_runs.get_path_execute(), self.path_runs.get_path_execution(), self.framework.get_framework()
)
self.framework.set_parameter("NumberGeration", self.opts.numberGeration)
self.framework.set_parameter("SizePopulation", SizePopulation)
self.framework.set_parameter(
"SequenceAminoAcidsPathFileName", self.path_runs.get_path_execution() + "fasta.txt"
)
self.framework.set_parameter("How_Many_Rotation", self.opts.howManyRotation)
self.framework.set_parameter("rotamer_library", self.opts.rotamerLibrary)
self.framework.set_parameter("Local_Execute", self.path_runs.get_path_execution())
self.framework.set_parameter("Path_Gromacs_Programs", get_path_gromacs())
self.framework.set_parameter("NativeProtein", "%s1VII.pdb" % self.path_runs.get_path_execution())
self.framework.set_parameter("Database", "%sDatabase/" % get_path_algorithms("2pg_build_conformation"))
NumberObjective, Fitness_Energy = format_fitness(self.opts.inputFitness, self.opts.toolname)
self.framework.set_parameter("NumberObjective", NumberObjective)
self.framework.set_parameter("Fitness_Energy", Fitness_Energy)
create_configuration_file(self.path_runs.get_path_execution(), self.framework)
self.framework.set_command(self.path_runs.get_path_execution(), "protpred-Gromacs-NSGA2")
config = "configuration.conf"
cl = [self.framework.get_command(), config, "&"]
retProcess = subprocess.Popen(cl, 0, stdout=None, stderr=subprocess.STDOUT, shell=False)
retCode = retProcess.wait()
if retCode != 0:
show_error_message("The 2PG framework finished wrong.\nContact the system administrator.")
parse_pdb(
self.path_runs.get_path_execution(),
"pop_NON_DOMINATED_%s.pdb" % self.opts.numberGeration,
20,
"NSGAIISolutions",
)
if self.opts.runMinimization == "true":
self.do_minimization("NSGAIISolutions")
pdbs = list_directory(self.path_runs.get_path_execution(), "NSGAIISolutions-M*.pdb")
build_images(pdbs, self.path_runs.get_path_execution())
path_output, file_output = os.path.split(self.opts.filehtml)
name, ext = os.path.splitext(self.opts.filehtml)
htmldir = os.path.join(path_output, "%s_files" % name)
if not os.path.exists(htmldir):
os.makedirs(htmldir)
self.opts.htmlfiledir = htmldir
result, filesHtml = get_result_files(
self.path_runs.get_path_execution(), self.opts.toolname, "NSGAIISolutions-M"
)
send_output_results(path_output, file_output, result)
send_output_files_html(self.opts.htmlfiledir, filesHtml)
send_output_files_html(self.opts.htmlfiledir, [result])
if self.opts.createCompressFile == "True":
if compress_files(pdbs, self.path_runs.get_path_execution(), "2PGNSGAII"):
path_output, file_output = os.path.split(self.opts.outputZip)
send_output_results(
path_output, file_output, os.path.join(self.path_runs.get_path_execution(), "2PGNSGAII.zip")
)
self.makeHtml()
if self.opts.useJmol in ("True", "true"):
self.makeHtmlWithJMol(pdbs[0])
if self.opts.inputEmail:
send_email(
"*****@*****.**",
email,
"%s Execution on Galaxy - Cloud USP" % self.opts.toolname,
get_message_email(self.opts.toolname),
[],
"smtp.gmail.com",
)
except Exception, e:
show_error_message(str(e))
def buildHighchart(self):
"""
Create a Highchart chart with the algorithm result
@type self: koala.SortByFront.SortByFront
"""
try:
# Load files
files = list_directory(self.path_runs.get_path_execution(), '*.xvg')
methods = self.methods
# Objectivies
obj1 = ""
obj2 = ""
x = [[]]*len(files)
y = [[]]*len(files)
for i, f in enumerate(files):
f = os.path.join(self.path_runs.get_path_execution(), f)
arq = open(f, "r")
# Loading File
x[i] = []
y[i] = []
for line in arq:
if line.find("#") == -1:
x[i].append(float(line.split("\t")[0].strip()))
y[i].append(float(line.split("\t")[1]))
else:
col = line.split("\t")
if len(col) > 1:
obj1 = col[0].replace('#', ' ')
obj2 = col[2]
arq.close()
chart = Highchart(renderTo="container2")
chart.title("Pareto Fronts")
chart.subtitle(
"A graph with %s and %s objectivies showing at most four fronts, "
"but the first as line and the others as scatter"
% (obj1, obj2))
graph_options = {
"xAxis": {
"minPadding": 0.05,
"maxPadding": 0.1,
"title": {
'offset': 30,
'text': obj1,
'rotation': 0,
},
},
"yAxis": {
"minPadding": 0.05,
"maxPadding": 0.1,
"title": {
'offset': 50,
'text': obj2,
'rotation': -90,
},
},
"tooltip": {
"shared": True,
"useHTML": False,
# "valueDecimals": 3,
},
}
data = []
it = {}
i_file = 0
context = Context(prec=3, rounding=ROUND_UP)
if(len(x) > 5):
fronts = 4
else:
fronts = len(x)
for i in range(fronts): # no máximo as duas primeiras fronteiras
data = []
z = x[i]
for ii, w in enumerate(z):
if(i == 0):
it["name"] = methods[i_file]
i_file += 1
else:
it["name"] = "front%d" % i
if(not math.isinf(z[ii])):
it["x"] = (context.create_decimal_from_float(z[ii])).quantize(
Decimal('.2'),
rounding=ROUND_UP)
else:
it["x"] = "0.0"
if(not math.isinf(y[i][ii])):
it["y"] = (context.create_decimal_from_float(y[i][ii])).quantize(
Decimal('.2'),
rounding=ROUND_UP)
else:
it["y"] = "0.0"
data.append(it)
it = {}
if(i == 0):
chart.add_data_set(data, name="front%d" % i, index=i, marker={"enabled": True})
else:
chart.add_data_set(data, series_type="scatter", name="front%d" % i, index=i)
chart.set_options(graph_options)
return chart.generate()
except Exception, e:
show_error_message("Error on building highcharts.\n%s" % e)
def CreateDominanceMatrix(self):
"""
Create a text file with the dominance ranking matrix
@type self: koala.DominanceRanking.DominanceRanking
"""
try:
front = list_directory(self.path_runs.get_path_execution(), "*.front")
if len(front) == 0:
raise Exception("There is no .front file.\n")
objectivies = [[]]*len(front)
ranking = [[]]*len(front)
methods = [[]]*len(front)
values = {}
# matriz to be used on dominance ranking
temp = []
for i, f in enumerate(front):
f = os.path.join(self.path_runs.get_path_execution(), f)
arq = open(f, "r")
# Loading File
objectivies[i] = []
ln_objectives = ''
ranking[i] = []
methods[i] = []
for line in arq:
if line.find("#") == -1:
ranking[i].append(line.split("\t")[0].strip())
methods[i].append(line.split("\t")[6].strip())
if line.split("\t")[6].strip() not in values:
values[line.split("\t")[6].strip()] = [line.split("\t")[0].strip()]
self.headers.append(
[line.split("\t")[6].strip(), 0, 0, 0]) # DOMINANCE, WINS, LOSES
else:
ranks = values[line.split("\t")[6].strip()]
ranks.append(line.split("\t")[0].strip())
values[line.split("\t")[6].strip()] = ranks
else:
col = line.split("\t")
if len(col) > 1:
objectivies[i].append(col[2])
objectivies[i].append(col[4])
ln_objectives += col[2]
ln_objectives += ';'
ln_objectives += col[4]
arq.close()
matrixFile = open(os.path.join(
self.path_runs.get_path_execution(), 'dr_matrix.txt'), 'w+')
# utilizando os metodos como header
for i in range(len(values)):
if i == 0:
matrixFile.write('#%s' % methods[0][i])
else:
matrixFile.write(methods[0][i])
matrixFile.write('\t\t')
matrixFile.write('\n')
# executa a quantidade de x correspondente a qtde de metodos
for i in range(len(values)):
pdb = methods[0][i]
if pdb in values:
ranks = values[pdb]
temp.append(ranks)
for i in range(len(temp[0])):
self.data.append([])
for j in range(len(temp)):
self.data[i].append(temp[j][i])
for i in range(len(temp[0])):
for j in range(len(temp)):
matrixFile.write(temp[j][i])
matrixFile.write('\t\t')
matrixFile.write('\n')
matrixFile.close()
self.CalculateDominance()
self.makeHtml()
pdbsToCopy = [os.path.join(
self.path_runs.get_path_execution(), method) for method in self.methods]
if(self.opts.useJmol == 'true'):
self.makeHtmlWithJMol(pdbsToCopy[0].split('/')[-1])
except Exception, e:
raise Exception("Error on CreateDominanceMatrix.\n%s" % e)
def build_Highchart(self, objectivies, container="container"):
"""
Create a Highchart chart with the algorithm result
@type self: koala.DominanceRanking.DominanceRanking
@type objectivies: string
@type container: string
"""
try:
# Load files
objs = objectivies.split(",")
files = list_directory(
self.path_runs.get_path_execution(), '*%s_%s*.xvg' % (objs[0], objs[1]))
images = self.methods
x = [[]]*len(files)
y = [[]]*len(files)
for i, f in enumerate(files):
f = os.path.join(self.path_runs.get_path_execution(), f)
arq = open(f, "r")
# Loading File
x[i] = []
y[i] = []
for line in arq:
if line.find("#") == -1:
x[i].append(float(line.split("\t")[0].strip()))
y[i].append(float(line.split("\t")[1]))
arq.close()
chart = Highchart(renderTo=container)
chart.title("Pareto Fronts")
chart.subtitle("A graph with %s and %s objectivies" % (objs[0], objs[1]))
graph_options = {
"xAxis": {
"minPadding": 0.05,
"maxPadding": 0.1,
"title": {
'offset': 30,
'text': objs[0],
'rotation': 0,
},
},
"yAxis": {
"minPadding": 0.05,
"maxPadding": 0.1,
"title": {
'offset': 50,
'text': objs[1],
'rotation': -90,
},
},
"tooltip": {
"shared": True,
"useHTML": False,
"valueDecimals": 3,
},
}
data = []
it = {}
i_file = 0
context = Context(prec=3, rounding=ROUND_UP)
if(len(x) >= 4):
fronts = 4
else:
# fronts = 2
fronts = len(x)
for i in range(fronts):
data = []
z = x[i]
for ii, w in enumerate(z):
if(i_file < len(images)):
it["name"] = images[i_file]
i_file += 1
else:
it["name"] = "front%d" % i
it["x"] = (context.create_decimal_from_float(z[ii])).quantize(
Decimal('.1'),
rounding=ROUND_UP)
it["y"] = (context.create_decimal_from_float(y[i][ii])).quantize(
Decimal('.1'),
rounding=ROUND_UP)
data.append(it)
it = {}
if(i == 0):
chart.add_data_set(data, name="front%d" % i, index=i, marker={"enabled": True})
else:
chart.add_data_set(data, series_type="scatter", name="front%d" % i, index=i)
chart.set_options(graph_options)
return chart.generate()
except Exception, e:
show_error_message("Error while building the Highchart:\n%s" % e)
def getGDTValues(self):
"""
Calculate the GDT-TS value to the input PDB files
@type self: koala.CalculateGDTTS.CalculateGDTTS
"""
try:
pdbs = list_directory(self.path_runs.get_path_execution(), "*.pdb")
if not pdbs:
raise "getGDTValues: No PDB file found.\n"
dict_gdtts = None
for pdb in pdbs:
if not (pdb == self.opts.inputPDBRefName):
name_pdb, ext = os.path.splitext(pdb)
name_reference, ext = os.path.splitext(self.opts.inputPDBRefName)
result_file = file(os.path.join(
self.path_runs.get_path_execution(),
name_reference + '_' + name_pdb + '.txt'),
'w')
cl = [
self.path_runs.get_path_execute()+'TMscore',
os.path.join(
self.path_runs.get_path_execution(), self.opts.inputPDBRefName),
os.path.join(
self.path_runs.get_path_execution(), pdb),
'-o',
'TM.sup',
'>',
self.path_runs.get_path_execution()+name_reference+'_'+name_pdb+'.txt',
'&']
retProcess = subprocess.Popen(
cl, 0, stdout=result_file, stderr=None, shell=False)
retCode = retProcess.wait()
if(retCode != 0):
show_error_message(
"The TMscore program finished wrong.\n"
"Contact the system administrator.")
os.chdir(self.path_runs.get_path_execution())
result_file = name_reference + '_' + name_pdb + '.txt'
temp_gdtts = open(result_file, "r")
for line in temp_gdtts.readlines():
if line.startswith("GDT-TS"):
gdt_value = line.split("=", 1)[1].split("%", 1)[0].strip()
only_pdb_file_name = os.path.basename(pdb)
if(dict_gdtts is None):
dict_gdtts = dict([(only_pdb_file_name, [gdt_value])])
else:
dict_gdtts.update(dict([(only_pdb_file_name, [gdt_value])]))
if line.startswith("GDT-HA"):
gdt_value = line.split("=", 1)[1].split("%", 1)[0].strip()
only_pdb_file_name = os.path.basename(pdb)
if(only_pdb_file_name in dict_gdtts):
ts = dict_gdtts.get(only_pdb_file_name)
ts.append(gdt_value)
dict_gdtts.update(dict([(only_pdb_file_name, ts)]))
temp_gdtts.close()
if(dict_gdtts is not None):
return OrderedDict(sorted(dict_gdtts.items(), key=lambda x: x[1]))
else:
return None
except Exception, e:
show_error_message("Error on getGDTValues:\n%s" % e)
def main(self):
"""
Create the MEAMT configuration file and begin
the execution to create a initial population.
@type self: koala.MEAMT.MEAMT
"""
try:
self.path_runs.set_path_execute()
if(self.opts.inputEmail):
email = validate_email(self.opts.inputEmail)
self.path_runs.set_execution_directory(email)
else:
self.path_runs.set_execution_directory()
self.sequence = create_local_fasta_file(
self.path_runs.get_path_execution(),
self.opts.fromFasta,
self.opts.inputFasta,
self.opts.toolname,
self.framework)
SizePopulation = create_local_pop_file(
self.path_runs.get_path_execution(),
self.opts.inputPop,
self.framework)
copy_necessary_files(
self.path_runs.get_path_execute(),
self.path_runs.get_path_execution(),
self.framework.get_framework())
self.framework.set_command(
self.path_runs.get_path_execution(),
'aemt-mo-up2')
size = int(SizePopulation) / 15
cl = [
self.framework.get_command(),
self.opts.numberGeneration,
str(SizePopulation),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(0),
str(0),
self.opts.VanderWaalsWeight,
self.opts.ChargeWeight,
str(0),
str(0),
str(0),
str(0),
str(0),
self.opts.SolvWeight,
self.opts.HbondWeight,
os.path.join(self.path_runs.get_path_execution(), "fasta.txt"),
os.path.join(self.path_runs.get_path_execution(), "result.txt"),
os.path.join(self.path_runs.get_path_execution(), "pop_meamt.txt"),
os.path.join(self.path_runs.get_path_execution(), "MEAMT-M1.pdb"),
os.path.join(self.path_runs.get_path_execution(), "saida1.txt"),
os.path.join(self.path_runs.get_path_execution(), "angles.txt"),
str(0),
os.path.join(self.path_runs.get_path_execution(), "meat.txt"),
'&']
retProcess = subprocess.Popen(
cl, 0, stdout=None, stderr=subprocess.STDOUT, shell=False)
retCode = retProcess.wait()
if(retCode != 0):
show_error_message(
"The MEAMT framework finished wrong.\nContact the system administrator.")
if(self.opts.runMinimization == 'true'):
self.do_minimization()
pdbs = list_directory(self.path_runs.get_path_execution(), '*.pdb')
build_images(pdbs, self.path_runs.get_path_execution())
path_output, file_output = os.path.split(self.opts.filehtml)
name, ext = os.path.splitext(self.opts.filehtml)
htmldir = os.path.join(path_output, '%s_files' % name)
if not os.path.exists(htmldir):
os.makedirs(htmldir)
self.opts.htmlfiledir = htmldir
result, filesHtml = get_result_files(
self.path_runs.get_path_execution(),
self.opts.toolname)
send_output_files_html(self.opts.htmlfiledir, filesHtml)
send_output_files_html(self.opts.htmlfiledir, [result])
if self.opts.createCompressFile == "True":
if compress_files(pdbs, self.path_runs.get_path_execution(), "MEAMT"):
path_output, file_output = os.path.split(self.opts.outputZip)
send_output_results(
path_output,
file_output,
os.path.join(self.path_runs.get_path_execution(), 'MEAMT.zip'))
self.makeHtml()
if(self.opts.useJmol == 'true'):
self.makeHtmlWithJMol(pdbs[0])
if(self.opts.inputEmail):
send_email(
'*****@*****.**',
email,
'%s Execution on Galaxy - Cloud USP' % self.opts.toolname,
get_message_email(self.opts.toolname),
[],
'smtp.gmail.com')
except Exception, e:
show_error_message(str(e))
def get_result_files(path, tool, fileName=None):
try:
resultFile = ''
filesToHtml = []
os.chdir(path)
if tool == '2PG_SortByFront_Tool':
resultFile = '%s%s.zip' % (path, tool)
z = zipfile.ZipFile(resultFile, 'w', zipfile.ZIP_DEFLATED)
listaArquivosFront = list_directory(path, '*.front')
for arq in listaArquivosFront:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosXvg = list_directory(path, '*.xvg')
for arq in listaArquivosXvg:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosPng = list_directory(path, '*.png')
for arq in listaArquivosPng:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosLog = list_directory(path, '*.log')
for arq in listaArquivosLog:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
elif tool in (
'Dominance_Ranking', '2PG_SortMethodByFront_Tool',
'CalculateRMSD', 'CalculateTMScore', 'CalculateGDTTS'):
resultFile = '%s%s.zip' % (path, tool)
z = zipfile.ZipFile(resultFile, 'w', zipfile.ZIP_DEFLATED)
listaArquivosFront = list_directory(path, '*.front')
for arq in listaArquivosFront:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosXvg = list_directory(path, '*.xvg')
for arq in listaArquivosXvg:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosPdf = list_directory(path, '*.pdf')
for arq in listaArquivosPdf:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosPng = list_directory(path, '*.png')
for arq in listaArquivosPng:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosTxt = list_directory(path, '*.txt')
for arq in listaArquivosTxt:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosLog = list_directory(path, '*.log')
for arq in listaArquivosLog:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
elif tool == '2PG_BuildConformation_Tool':
resultFile = '%s%s' % (path, 'pop_0.pdb')
elif tool in (
'2PG_NSGA2_Tool', '2PG_Mono_Tool',
'2PG_MC_Metropolis', '2PG_Random_Tool'):
resultFile = '%s%s.zip' % (path, tool)
z = zipfile.ZipFile(resultFile, 'w', zipfile.ZIP_DEFLATED)
if(fileName):
listaArquivosPDB = list_directory(path, '%s*.pdb' % fileName)
else:
listaArquivosPDB = list_directory(path, '*.pdb')
for arq in listaArquivosPDB:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosXvg = list_directory(path, '*.xvg')
for arq in listaArquivosXvg:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosFit = list_directory(path, '*.fit')
for arq in listaArquivosFit:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosPng = list_directory(path, '*.png')
for arq in listaArquivosPng:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
elif(tool == 'ProtPred_EDA'):
resultFile = '%s%s.zip' % (path, tool)
z = zipfile.ZipFile(resultFile, 'w', zipfile.ZIP_DEFLATED)
listaArquivosPDB = list_directory(path, '*.pdb')
for arq in listaArquivosPDB:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosPng = list_directory(path, '*.png')
for arq in listaArquivosPng:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
elif tool == 'Download_From_Quark':
resultFile = '%s%s' % (path, '/ResultQuark.zip')
z = zipfile.ZipFile(resultFile, 'w', zipfile.ZIP_DEFLATED)
listaArquivosPDB = list_directory(path, '*.pdb')
for arq in listaArquivosPDB:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
listaArquivosTxt = list_directory(path, '*.txt')
for arq in listaArquivosTxt:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
elif(tool == 'MEAMT_BuildConformation_Tool'):
resultFile = '%s%s' % (path, 'pop_meamt.txt')
elif(tool == 'MEAMT_Tool'):
resultFile = '%s%s.zip' % (path, tool)
z = zipfile.ZipFile(resultFile, 'w', zipfile.ZIP_DEFLATED)
listaArquivosPDB = list_directory(path, '*.pdb')
for arq in listaArquivosPDB:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosPng = list_directory(path, '*.png')
for arq in listaArquivosPng:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
listaArquivosTxt = list_directory(path, 'subpop*.txt')
for arq in listaArquivosTxt:
z = zipfile.ZipFile(resultFile, 'a', zipfile.ZIP_DEFLATED)
z.write(arq)
z.close()
filesToHtml.append(os.path.join(path, arq))
return resultFile, filesToHtml
except Exception, e:
show_error_message("Error when getResultFiles:\n%s" % e)
try:
inF = gzip.GzipFile(input_f, 'rb')
f = inF.read()
inF.close()
if f:
extract_gz_file(input_f, self.path_runs.get_path_execution())
except Exception, e:
raise Exception("The input file could not be read.\n%s" % e)
else:
copy_pdbs_from_input(
self.path_runs.get_path_execution(),
self.opts.outputdir,
self.opts.inputnames,
self.opts.inputPDBs)
pdbs = list_directory(self.path_runs.get_path_execution(), "*.pdb")
for pdb in pdbs:
self.check_structue_by_pdb2gmx(
os.path.join(self.path_runs.get_path_execution(), pdb),
get_path_gromacs(),
self.opts.forceField)
path_output, file_output = os.path.split(self.opts.output)
pdbs_accepted = list_directory(self.path_runs.get_path_execution(), "*.pdb")
if compress_files(pdbs_accepted, self.path_runs.get_path_execution(), "PDBsChecked"):
send_output_results(
path_output,
file_output,
