def splitInput(filename):
"""
Split the parallel input file into multiple async file names
Parameters
filename: The path to the original parallel input
file (string)
"""
nproc = 0
file = open(filename)
text = ""
while 1:
line = file.readline()
if line == "": break
text += line
line = string.strip(line)
if line.startswith("pdime"): # Get # Procs
words = string.split(line)
nproc = int(words[1]) * int(words[2]) * int(words[3])
if nproc == 0:
sys.stderr.write("%s is not a valid APBS parallel input file!\n" % filename)
sys.stderr.write("The inputgen script was unable to asynchronize this file!\n")
sys.exit(2)
period = string.find(filename,".")
for i in range(nproc):
outname = filename[0:period] + "-PE%i.in" % i
outtext = string.replace(text, "mg-para\n","mg-para\n async %i\n" % i)
outfile = open(outname, "w")
outfile.write(outtext)
outfile.close()
def parseLines(self, lines):
""" Parse the lines """
for line in lines:
if string.find(line, "ATOM") == 0:
subline = string.replace(line[30:], "-", " -")
words = string.split(subline)
if len(words) < 4:
#sys.stderr.write("Can't parse following line:\n")
#sys.stderr.write("%s\n" % line)
#sys.exit(2)
continue
self.gotatom = self.gotatom + 1
self.q = self.q + float(words[3])
rad = float(words[4])
center = []
for word in words[0:3]:
center.append(float(word))
for i in range(3):
self.minlen[i] = min(center[i] - rad, self.minlen[i])
self.maxlen[i] = max(center[i] + rad, self.maxlen[i])
elif string.find(line, "HETATM") == 0:
self.gothet = self.gothet + 1
def setID(time):
"""
Given a floating point time.time(), generate an ID.
Use the tenths of a second to differentiate.
Parameters
time: The current time.time() (float)
Returns
id : The file id (string)
"""
strID = "%s" % time
period = string.find(strID, ".")
id = "%s%s" % (strID[:period], strID[(period+1):(period+2)])
return id
def formatName(self, at):
altLoc = None
name = at.name
#if len(name)>2 and name[-2]=='@':
if string.find(name, '@') > -1:
ind = string.index(name, '@')
altLoc = name[ind + 1:]
#altLoc = name[-1]
name = name[:ind]
if len(name) == 4:
if at.element == 'H':
name = name[-1] + name[:-1]
nameStr = '%-4.4s' % name
else:
nameStr = '%4.4s' % name
elif len(at.element) == 2:
nameStr = '%-4.4s' % at.element
else:
nameStr = ' %-3s' % name
return nameStr, altLoc
def cleanTmpdir():
"""
Clean up the temp directory for CGI. If the size of the directory
is greater than LIMIT, delete the older half of the files. Since
the files are stored by system time of creation, this is an
easier task.
"""
newdir = []
size = 0.0
count = 0
path = LOCALPATH + TMPDIR
dir = os.listdir(path)
for filename in dir:
size = size + os.path.getsize("%s%s" % (path, filename))
period = string.find(filename,".")
id = filename[:period]
if id not in newdir:
newdir.append(id)
count += 1
newdir.sort()
size = size / (1024.0 * 1024.0)
newcount = 0
if size >= LIMIT:
for filename in newdir:
if newcount > count/2.0: break
try:
os.remove("%s%s.pqr" % (path, filename))
except OSError: pass
try:
os.remove("%s%s.in" % (path, filename))
except OSError: pass
try:
os.remove("%s%s.html" % (path, filename))
except OSError: pass
newcount += 1
def printInputFiles(self):
"""
Make the input file(s) associated with this object
"""
period = string.find(self.pqrpath,".")
if self.asyncflag == 1:
outname = self.pqrpath[0:period] + "-para.in"
# Temporarily disable async flag
for elec in self.elecs:
elec.asyncflag = 0
file = open(outname, "w")
file.write(str(self))
file.close()
# Now make the async files
elec = self.elecs[0]
nproc = elec.pdime[0] * elec.pdime[1] * elec.pdime[2]
for i in range(int(nproc)):
outname = self.pqrpath[0:period] + "-PE%i.in" % i
for elec in self.elecs:
elec.asyncflag = 1
elec.async = i
file = open(outname, "w")
file.write(str(self))
file.close()
else:
if period > 0:
outname = self.pqrpath[0:period] + ".in"
else:
outname = self.pqrpath + ".in"
file = open(outname, "w")
file.write(str(self))
file.close()
def getTestSummaryResults(testroot, testreportdir):
"""Parse the test report files created by tester.
testroot - directory containing the MGLTools packages ;
testreportdir - directory containing testreports """
#print "testreportdir:", testreportdir
assert os.path.exists(testreportdir)
assert os.path.exists(testroot)
# list of directories containing Tests ( created when the tests ran last for this platform)
cwd = os.getcwd()
testdirs = []
os.chdir(testroot)
for p in mglpacks:
os.path.walk(p, getTestsDirs, testdirs)
#print "testdirs" ,testdirs
os.chdir(cwd)
reports = []
for p in testdirs:
reports.append(p.replace(os.sep, '.'))
# a dictionary containing the names of test reports
rantests = {}
# a dictionary containing the names of test reports (with -s option)
rantestsS = {}
# a list of test modules for which we did not get a report
noreports = []
modules = []
# string containing time when the directory was last modified
reporttime = time.asctime(
time.localtime(os.stat(testreportdir)[stat.ST_MTIME]))
# remove time (##:##:##) from reporttime string (leave only the date)
rd = string.split(reporttime)
rd.pop(-2)
reportdate = "%s %s %s %s" % tuple(rd)
import sys
for r in reports:
f1 = os.path.join(testroot, testreportdir,
"report-" + r + sys.platform + ".txt")
f2 = os.path.join(testroot, testreportdir,
"sReport-" + r + sys.platform + ".txt")
if os.path.exists(f1):
rantests[f1] = r
elif os.path.exists(f2):
rantestsS[f2] = r
else:
noreports.append(r)
numtests = 0
numerrors = 0
results = {}
for file in list(rantestsS.keys()):
test = None
ntests = 0
testerrors = 0
f = open(file, "r")
st = f.readline()
l = string.split(st)
if len(l) == 5:
if l[0] == "RAN":
test = rantestsS[file]
ntests = float(l[1])
numtests = numtests + ntests
modules.append(test)
results[test] = {}
results[test]['ntests'] = ntests
txt = f.readlines()
f.close()
testname = None
errlist = []
errtxt = ""
for line in txt:
if string.find(line, "Tests.test_") > 0:
if string.find(line, "ERROR:") == 0 or string.find(
line, "FAIL:") == 0:
errlist.append(line)
continue
testname = line
if len(errlist) > 0:
errtxt = errtxt + "\n" + testname
for err in errlist:
errtxt = errtxt + err
testerrors = testerrors + len(errlist)
errlist = []
continue
elif string.find(line, "ERROR:") == 0 or string.find(
line, "FAIL:") == 0:
errlist.append(line)
elif line.startswith("RAN "):
if test == None:
test = rantestsS[file]
modules.append(test)
results[test] = {}
#print test, file, ntests, numtests,
nt = float(line.split()[1])
ntests = ntests + nt
numtests = numtests + nt
#print ntests, numtests
results[test]['ntests'] = ntests
#this is for the case when error is in the last test:
if len(errlist) > 0:
errtxt = errtxt + "\n" + testname
for err in errlist:
errtxt = errtxt + err
testerrors = testerrors + len(errlist)
errlist = []
if testerrors:
numerrors = numerrors + testerrors
results[test]['failed'] = testerrors
results[test]['errtxt'] = errtxt
for file in list(rantests.keys()):
testerrors = 0
f = open(file, "r")
st = f.readline()
l = string.split(st)
if len(l) == 5:
if l[0] == "RAN":
test = rantests[file]
modules.append(test)
ntests = float(l[1])
numtests = numtests + ntests
results[test] = {}
results[test]['ntests'] = ntests
txt = f.readlines()
f.close()
testname = None
errlist = []
errtxt = ""
for line in txt:
if string.find(line, "FAILED (") == 0:
if len(errlist) > 0:
for err in errlist:
errtxt = errtxt + err
testerrors = testerrors + len(errlist)
errlist = []
continue
elif string.find(line, "ERROR:") == 0 or string.find(
line, "FAIL:") == 0:
errlist.append(line)
if testerrors:
numerrors = numerrors + testerrors
results[test]['failed'] = testerrors
results[test]['errtxt'] = errtxt
perc = numerrors / numtests * 100.0
if len(noreports):
endstr = "No test report for the following module(s) (tests possibly crashed): \n"
for f in noreports:
endstr = endstr + "%s \n" % f
results['tail'] = endstr
results['reportdate'] = reportdate
results['numtests'] = numtests
results['numerrors'] = numerrors
results['perc'] = perc
return results, modules
def read(self, filename):
"""
1.5 2.0 binding
0 0 0 0 0.000 0.000 0.000 -14.645
1 0 1 0 2.449 0.000 0.000 -14.636
0 1 0 1 1.281 1.281 1.281 -14.424
1 1 1 1 2.548 1.014 1.014 -14.210
| | |
| | |-rmsd from cluster seed @ 2.0 tolerance
| |-rmsd from cluster seed @ 1.0 tolerance
|-rmsd from overall reference structure
"""
file_ptr = open(filename)
lines = file_ptr.readlines() # read the file
file_ptr.close()
d = self.clustering_dict # local copy
# see if there's the last char is a 'd' or 'b' or 'e'to denote energy
word_list = string.split(lines[0])
if word_list[-1][0] in ['b', 'd', 'e']:
file_energy_used = word_list[-1]
ind = string.find(lines[0], file_energy_used)
lines[0] = lines[0][:ind] # strip energy symbol
else:
file_energy_used = 'binding'
# ??? make sure we're consistent with the argsort
#check that self has done some clustering before this
if len(self.clustering_dict)>0:
assert file_energy_used[0] == self.energy_used[0], 'Cluster energy mismatch'
else:
#here the dlg had no clustering in it
self.energy_used = file_energy_used
#redo argsort with file_energy_used
if file_energy_used[0] == 'd':
energy_list = [conf.docking_energy for conf in self.data]
else:
energy_list = [conf.binding_energy for conf in self.data]
# sort the conformations by energy
self.argsort = numpy.argsort(energy_list)
#print "self.argsort=", self.argsort
t_list = list(map(float, string.split(lines[0])))
#t_list for the example is [0.5, 2.0]
num_t = len(t_list) #number of clusterings
for tolerance in t_list: # initialize the keys
if tolerance in d:
raise RuntimeError("overwriting existing clustering")
c = d[tolerance] = Clustering()
c.tolerance = tolerance
# cx is the index into self.data, the list of conformatons
# NEW FORMAT:
# 0 0 0 0 0.000 0.000 0.000 -14.645
#first line has list of tolerances
for cx, l in enumerate(lines[1:]):
ll = l.split()
#eg: 2 tolerances gives [ 0, 0, 0, 0, 0.000, 0.000, 0.000,-14.645]
#num_t *2
c_list = list(map(int, ll[:num_t*2]))
data_list = list(map(float, ll[num_t*2:]))
for t, i in zip(t_list, range(len(c_list)/2)):
cluster_index = c_list[2*i]
cluster_rank = c_list[2*i+1]
conf = self.data[int(self.argsort[cx])]
if cluster_rank == 0:
assert len(d[t]) == cluster_index
d[t].append(Cluster(conf))
else:
# add conformation to its cluster
assert len(d[t][cluster_index]) == cluster_rank
d[t][cluster_index].append(conf)
# tell the conformation what cluster(s) it belongs to...
conf.cluster_dict[t] = (cluster_index, cluster_rank)
conf.refRMS = data_list[0]
conf.clRMS = data_list[1]