system_path = system['path']
print('Analyzing', system_path)
try:
if system['UNITEDATOM_DICT']:
#continue
print('United atom simulation')
except:
pass
output_name = ""
trj_name = system['path'] + system['TRJ'][0][0]
tpr_name = system['path'] + system['TPR'][0][0]
trj_url = download_link(system['DOI'], system['TRJ'][0][0])
tpr_url = download_link(system['DOI'], system['TPR'][0][0])
socket.setdefaulttimeout(15)
download_failed = False
# make a function like this
if (not os.path.isfile(tpr_name)):
try:
url_size = urllib.request.urlopen(tpr_url).length
response = urllib.request.urlretrieve(tpr_url, tpr_name)
except ContentTooShortError:
download_failed = True
print("Content too short error.")
filepath = subdir + os.sep + filename1
if filepath.endswith("README.yaml"):
READMEfilepathSimulation = subdir + '/README.yaml'
with open(READMEfilepathSimulation) as yaml_file_sim:
#print('toimii')
readme = yaml.load(yaml_file_sim, Loader=yaml.FullLoader)
indexingPath = "/".join(filepath.split("/")[4:8])
print(indexingPath)
DATAdir = '../../../../tst/FlipFlop/' + indexingPath + '/' #change directory when code works properly!!!
doi = readme['DOI']
trj=readme['TRJ'][0][0]
tpr=readme['TPR'][0][0]
trj_name = subdir + '/' + trj
tpr_name = subdir + '/' + tpr
trj_url = download_link(doi, trj)
tpr_url = download_link(doi, tpr)
EQtime=float(readme['TIMELEFTOUT'])*1000
#Download tpr and xtc files to a tmp directory in dir wrk defined in readme file / or should these be put into the same directory as README.yaml ???
if (not os.path.isfile(tpr_name)):
response = urllib.request.urlretrieve(tpr_url, tpr_name)
if (not os.path.isfile(trj_name)):
response = urllib.request.urlretrieve(trj_url, trj_name)
xtcwhole=subdir + '/whole.xtc'
if (not os.path.isfile(xtcwhole)):
os.system('echo System | gmx trjconv -f ' + trj_name + ' -s ' + tpr_name + ' -o ' + xtcwhole + ' -pbc mol -b ' + str(EQtime))
u = mda.Universe(tpr_name,xtcwhole)
outfilename = path + 'apl.json'
if os.path.isfile(outfilename):
continue
print('Analyzing: ', system['path'])
for molecule in system['COMPOSITION']:
if molecule in lipids_dict:
Nlipid += np.sum(system['COMPOSITION'][molecule]['COUNT'])
doi = system.get('DOI')
trj = system.get('TRJ')
tpr = system.get('TPR')
trj_name = path + system.get('TRJ')[0][0]
tpr_name = path + system.get('TPR')[0][0]
trj_url = download_link(doi, trj[0][0])
tpr_url = download_link(doi, tpr[0][0])
#print(trj_name,tpr_name)
if (not os.path.isfile(tpr_name)):
response = urllib.request.urlretrieve(tpr_url, tpr_name)
if (not os.path.isfile(trj_name)):
response = urllib.request.urlretrieve(trj_url, trj_name)
try:
u = MDAnalysis.Universe(tpr_name, trj_name)
except:
conf = path + '/conf.gro'
print("Generating conf.gro because MDAnalysis cannot read tpr version")
os.system('echo System | gmx trjconv -s ' + tpr_name + ' -f ' +
# ### Check status links
wrong_links = 0
software_sim = software_dict[sim['SOFTWARE'].upper()]
for key_sim, value_sim in sim.items():
#print("key_sim = {0} => value_sim = {1}".format(key_sim, value_sim))
try:
entry_type = software_sim[key_sim]['TYPE']
extension_type = software_sim[key_sim]['EXTENSION']
#print("entry_type = {0}".format(entry_type))
if "file" in entry_type and "txt" not in extension_type:
for file_provided in value_sim:
#print("File={0}".format(file_provided[0]))
file_url = download_link(DOI, file_provided[0])
if file_url == "":
wrong_links += 1
continue
try:
if key_sim == 'INI':
continue
response = urllib.request.urlopen(file_url)
#print("Status of the DOI link: {0}".format(response.msg))
except HTTPError as e:
print("\nkey={0} => file={1}".format(key_sim, file_provided[0]))
print(file_url)
print('The server couldn\'t fulfill the request.')
print('Error code: ', e.code)
wrong_links += 1
except URLError as e: