def myMain():
x=input('Enter x:')
if argv[1] == 'zen':
log.level('info')
log.d('debug')
log.i('info x={}'.format(x))
log.w('warn')
log.e('error')
log.c('critical')
else:
if argv[1] == 'basic':
# see Python Docs logging.html 16.6.7. LogRecord attributes
logging.basicConfig(style='{',format="{asctime:s}:{filename:s}:{lineno:d}:{msg:s}",level='DEBUG')
logging.debug('our debug message x={}'.format(x))
logging.warn('our warn message x={}'.format(x))
else:
print("If we don't want to type logging.debug() etc, we have to create our own logger lg=logging.getLogger({})".format(__name__))
lg=logging.getLogger(__name__)
if argv[1]=='easy':
logging.basicConfig(level='INFO')
else:
lg.setLevel('WARN') # optional: defaults to all levels
lg.addHandler(logging.StreamHandler())
lg.handlers[0].setFormatter(logging.Formatter(style='{',fmt="{filename:s}:{funcName:s}():{lineno:d}:{msg:s}"))
lg.debug('our debug mesage')
lg.info('our info here')
def get_web_page(url):
'''
# Let the user know we are trying to download a webpage
# Construct a request with a User-Agent header
# Send the request and read the webpage from the response
# Convert the webpage from bytes to a string, and return it
'''
url = clean_link(url)
log.i('getting: ' + url)
handle = Request(url)
handle.add_header('User-Agent', 'SPD/1.0')
try:
webpage = urlopen(handle).read()
except HTTPError as err:
log.w('a problem occured when getting ' + url)
if err.code == 404:
message = 'the requested page could not be found'
else:
message = 'the server returned a code of ' + str(err.code)
log.w(message)
webpage = str(err.code) # pass the return code as a string
webpage = str(webpage) # convert from bytes to string
log.d(len(webpage))
soup = BeautifulSoup(webpage, 'html.parser')
return soup
def get_web_page(url):
'''
# Let the user know we are trying to download a webpage
# Construct a request with a User-Agent header
# Send the request and read the webpage from the response
# Convert the webpage from bytes to a string, and return it
'''
url = clean_link(url)
log.i('getting: ' + url)
handle = Request(url)
handle.add_header('User-Agent', 'SPD/1.0')
try:
webpage = urlopen(handle).read()
except HTTPError as err:
log.w('a problem occured when getting ' + url)
if err.code == 404:
message = 'the requested page could not be found'
else:
message = 'the server returned a code of ' + str(err.code)
log.w(message)
webpage = str(err.code) # pass the return code as a string
webpage = str(webpage) # convert from bytes to string
log.d(len(webpage))
soup = BeautifulSoup(webpage, 'html.parser')
return soup
def download_image_gallery(link):
'''
# Fetch the HTML page at the given link
# If it's a gfycat link, alter the url to point at the gif and download it
# Otherwise, find all '//i.imgur.com' links and download each one
'''
global args
if 'gfycat.com/' in link:
log.d('page is gfycat')
if not re.search(r'\.(gif|webm)', link):
link = link.replace('gfycat', 'fat.gfycat') + '.webm'
download_image(link)
elif 'imgur.com/' in link:
webpage = get_web_page(link)
if str(webpage) == '404' and re.search(r'layout/grid', link):
log.w('grid layout not found, trying again')
webpage = get_web_page(link.replace('/layout/grid', ''))
log.d('page is imgur gallery (limited to first 20 images!)')
urls = webpage.find_all('a')
for url in urls:
if re.search(args.imgur_gallery_image_regex, url.get('href')):
log.d('matched imgur_gallery_image_regex in %s' % url)
download_image(url.get('href'))
else:
log.d('page is imgur grid')
urls = webpage.find_all('img')
for url in urls:
if url.get('data-src'):
if re.search(args.imgur_grid_image_regex,
url.get('data-src')):
log.d('matched data-src in %s, grid image link' % url)
download_image(url.get('data-src'))
elif url.get('src'):
if re.search(args.imgur_gallery_image_regex,
url.get('src')):
log.d('matched src in %s, gallery image link' % url)
download_image(url.get('src'))
else:
log.d('no src, data-src in %s' % url)
def download_image(link):
'''
# Let the user know we are trying to download an image at the given link
# Prepare the command (wget) to download the image
# If wget doesn't exist, we raise a FileNotFound error
# Otherwise, if we're on Windows, modify the wget command to avoid an issue
# with GnuWin wget and SSL
# Finally, we run the constructed command to download the image
'''
global args
# --no-check-certificate is used on windows because GnuWin wget fails to
# verify all certificates for some reason
link = clean_link(link)
log.i('downloading: ' + link)
wget_command = [which('wget'), '-b', '-N', '-o', '/dev/null', link]
if (which('wget') is None):
raise WGetNotFoundException('Could not find wget')
elif operating_system() == 'Windows':
log.d('on windows, adjusting wget_command')
wget_command = [
which('wget'), '-b', '-N', '-o', 'NUL', '--no-check-certificate',
link
]
try:
while call(wget_command) != 0:
time.sleep(.05)
log.d('call is not 0')
log.i('retrying...')
except BlockingIOError:
time.sleep(.1)
log.d('BlockingIOError!')
log.w('retrying...')
download_image(link)
def download_image_gallery(link):
'''
# Fetch the HTML page at the given link
# If it's a gfycat link, alter the url to point at the gif and download it
# Otherwise, find all '//i.imgur.com' links and download each one
'''
global args
if 'gfycat.com/' in link:
log.d('page is gfycat')
if not re.search(r'\.(gif|webm)', link):
link = link.replace('gfycat', 'fat.gfycat') + '.webm'
download_image(link)
elif 'imgur.com/' in link:
webpage = get_web_page(link)
if str(webpage) == '404' and re.search(r'layout/grid', link):
log.w('grid layout not found, trying again')
webpage = get_web_page(link.replace('/layout/grid', ''))
log.d('page is imgur gallery (limited to first 20 images!)')
urls = webpage.find_all('a')
for url in urls:
if re.search(args.imgur_gallery_image_regex, url.get('href')):
log.d('matched imgur_gallery_image_regex in %s' % url)
download_image(url.get('href'))
else:
log.d('page is imgur grid')
urls = webpage.find_all('img')
for url in urls:
if url.get('data-src'):
if re.search(args.imgur_grid_image_regex, url.get('data-src')):
log.d('matched data-src in %s, grid image link' % url)
download_image(url.get('data-src'))
elif url.get('src'):
if re.search(args.imgur_gallery_image_regex, url.get('src')):
log.d('matched src in %s, gallery image link' % url)
download_image(url.get('src'))
else:
log.d('no src, data-src in %s' % url)
def download_image(link):
'''
# Let the user know we are trying to download an image at the given link
# Prepare the command (wget) to download the image
# If wget doesn't exist, we raise a FileNotFound error
# Otherwise, if we're on Windows, modify the wget command to avoid an issue
# with GnuWin wget and SSL
# Finally, we run the constructed command to download the image
'''
global args
# --no-check-certificate is used on windows because GnuWin wget fails to
# verify all certificates for some reason
link = clean_link(link)
log.i('downloading: ' + link)
wget_command = [which('wget'), '-b', '-N', '-o', '/dev/null', link]
if (which('wget') is None):
raise WGetNotFoundException('Could not find wget')
elif operating_system() == 'Windows':
log.d('on windows, adjusting wget_command')
wget_command = [which('wget'), '-b', '-N', '-o', 'NUL',
'--no-check-certificate', link]
try:
while call(wget_command) != 0:
time.sleep(.05)
log.d('call is not 0')
log.i('retrying...')
except BlockingIOError:
time.sleep(.1)
log.d('BlockingIOError!')
log.w('retrying...')
download_image(link)
def print_energies_on_file(self, energy_dict, folder_names, args):
time = datetime.datetime.now()
file_name = (f'{USER} - {time.strftime("%d-%m-%y")}.txt')
x = PrettyTable()
folder_names.insert(0, 'Molecule Name')
x.field_names = folder_names
temp_table = list(energy_dict.values())
temp_table2 = list(energy_dict.keys())
err_cont = 0
for j in temp_table:
for i in temp_table2:
cont = 0
lista1 = [i]
while cont < len(j):
try:
valor = list(j[cont].values())[0]
except IndexError:
valor = ' '
lista1.append(valor)
cont += 1
try:
x.add_row(lista1)
except Exception:
if err_cont == 0:
log.w(
'There is not the same number of files in all the directories. Some results might be missing from the table...'
)
err_cont += 1
temp_table2.remove(i)
break
x.sortby = 'Molecule Name'
table_title = (
f'{USER} - {time.strftime("%d-%m-%y")} - Gaussian Energy Calculation Results'
)
x.hrules = prettytable.ALL
print(x.get_string(title=table_title))
with open(file_name, 'w+') as f:
f.write(str(x.get_string(title=table_title)))
image_name = f'{time.strftime("%d-%m-%y")}-molecules.svg'
subprocess.call([f'obabel -i pdb *.pdb -O {image_name} -d -xC'],
shell=True,
stdout=subprocess.DEVNULL,
stderr=subprocess.STDOUT)
log.info(
f'Data correctly saved as \'{file_name}\' in \'{os.getcwd()}\'')
log.info(
f'Molecule structure drawn in \'{time.strftime("%d-%m-%y")}-molecules.svg\' in \'{os.getcwd()}\''
)
if args.mail != ' ':
full_path = os.getcwd()
folder_name = os.path.basename(full_path)
email = args.mail
subprocess.call([
'echo "Calculations from folder \'{}\' done, see results attached..." | mail -s "Results - {}" -A "{}" -A "{}" {}'
.format(folder_name, folder_name, file_name, image_name, email)
],
shell=True,
stdout=subprocess.DEVNULL,
stderr=subprocess.STDOUT)
log.info('Results delivery attempted in \'{}\''.format(email))
return str(x)
def gjf_settings(self):
config_dict = {}
file_list = [file for file in os.listdir() if file.endswith('.pdb')]
if len(file_list) == 0:
log.e(
f'\'.pdb\' files not found in directory \'{os.path.basename(os.getcwd())}\'. Aborting...'
)
quit()
log.i(f'{len(file_list)} files found. Gathering settings...')
while True:
try:
log.d('How many calculations do you wish to perform?')
ncalc = int(input())
log.d(
'Do you want to set number of processors used and memory size available? Default is 8 processors and 1gb of memory. (Y/N) '
)
query = input()
nproc, mem = 8, 1
if query.lower() == 'y':
log.d('How many procesors do you wish to use? ')
nproc = int(input())
log.d('How much memory do you want to use? ')
mem = float(input())
break
except:
log.w('You have not provided a valid input, please try again.')
config_dict['ncalc'] = ncalc
config_dict['nproc'] = nproc
config_dict['mem'] = mem
config_dict['chk'] = 'chkfile.chk'
for calc_number in range(ncalc):
type_list = [
'DFTmin', 'MP2min', 'MP2max', 'M062Xmin', 'M062Xmax', 'Custom'
]
opt_list = [
'Local minimum', 'Transition State', 'Restart from Checkpoint'
]
freq_list = ['Complete', 'no Raman']
method_list = ['B3LYP', 'MP2', 'M062X']
basis_list = ['6-31G(d)', '6-311+G(d,p)']
log.d(
f'For calculation number {calc_number}, choose a calculation type preset by its number or type \'custom\' for custom settings...'
)
for val, name in enumerate(type_list):
print(f'{val:15}) {name}')
calc_type = input()
log.d(
f'For calculation number {calc_number}, do you wish optimization (Y/N):'
)
query = input()
if query.lower() == 'y':
log.d(f'Which optimization type do you wish :')
for val, name in enumerate(opt_list):
print(f'{val:15}) {name}')
opt_type = input()
log.d(
f'For calculation number {calc_number}, do you wish frequency calculations (Y/N):'
)
query = input()
if query.lower() == 'y':
log.d(f'Which frequency calculation do you wish:')
for val, name in enumerate(freq_list):
print(f'{val:15}) {name}')
opt_type = input()
if calc_type.lower() == 'custom':
log.d(
f'For calculation number {calc_number}, select calculation method:'
)
for val, name in enumerate(method_list):
print(f'{val:15}) {name}')
calc_method = input()
log.d(
f'For calculation number {calc_number}, select basis set:')
for val, name in enumerate(basis_list):
print(f'{val:15}) {name}')
basis_set = input()
log.d(
f'For calculation number {calc_number}, do you wish to specify a solvent (Y/N):'
)
query = input()
if query.lower() == 'y':
query_text1 = 'Please input solvent name:'
solvent = input(f'{query_text1:15}')
pp.pprint(config_dict)
return config_dict