We Keep Coding

OSError: The topology is loaded by filename extension, and the detected ".pd" format is not supported

I'm writing a code to generate features of ligands. Code is:
def parsePDB(self):
top = self.pdb.topology
residues = [str(residue)[:3] for residue in top.residues]
residues_cp = residues.copy()
# number of all groups in the complex except the ligand
LIG_number = residues.index('LIG')
self.residues_indices = [i for i in range(top.n_residues) if i != LIG_number]
# Get the types of atoms in the protein and ligand
self.rec_indices = top.select('protein')
self.lig_indices = top.select('resname LIG')
table, bond = top.to_dataframe()
self.all_ele = table['element']
self.lig_ele = table['element'][self.lig_indices]
H_num = []
for num, i in enumerate(self.all_ele):
if i == 'H':
H_num.append(num)
# Get the serial number of the atom in each residue or group
removes = []
for i in self.residues_indices:
atoms = top.residue(i).atoms
each_atoms = [j.index for j in atoms]
heavy_atoms = [x for x in each_atoms if not x in H_num]
if len(heavy_atoms) == 0:
removes.append(i)
else:
self.atoms_indices.append(heavy_atoms)
if len(removes) != 0:
for i in removes:
self.residues_indices.remove(i)
self.residues = [residues_cp[x] for x in self.residues_indices]
# Get the 3D coordinates for all atoms
self.xyz = self.pdb.xyz[0]
return self
I'm getting this error:
OSError: The topology is loaded by filename extension, and the detected ".pd" format is not supported. Supported topology formats include ".pdb", ".pdb.gz", ".h5", ".lh5", ".prmtop", ".parm7", ".prm7", ".psf", ".mol2", ".hoomdxml", ".gro", ".arc", ".hdf5" and ".gsd".
Can anyone please suggest me how to resolve this issue? Thanks

I am getting 'index out of bound error' when reading from csv in pandas but not when I extract the data via api. What could be the reason?

So for my bot, I am first extracting data via api and storing it in csv. When I run my for loop on data via api, it gives no error and runs smoothly.
But when the csv file is read and run, it gives out of bound error.
This is my function to generate data:
full_list = pd.DataFrame(columns=("date","open","high","low","close","volume","ticker","RSI","ADX","20_sma","max_100"))
def stock_data(ticker):
create_data = fetchOHLC(ticker,'minute',60)
create_data["ticker"] = ticker
create_data["RSI"] = round(rsi(create_data,25),2)
create_data["ADX"] = round(adx(create_data,14),2)
create_data["20_sma"] = round(create_data.close.rolling(10).mean().shift(),2)
create_data["max_100"] = create_data.close.rolling(100).max().shift()
create_data.dropna(inplace=True,axis=0)
create_data.reset_index(inplace=True)
return create_data
stocklist = open("stocklist.txt","r+")
tickers = stocklist.readlines()
for x in tickers:
try:
full_list = full_list.append(stock_data(x.strip()))
except:
print(f'{x.strip()} did not work')
full_list.to_csv("All_Data")
full_list
So when I run the same code below on dataframe created I got no error. But when I run the same code on the csv file, I get out of bound error.
list_tickers = full_list["ticker"].unique()
for y in list_tickers[:2]:
main = full_list[full_list["ticker"]==y]
pos = 0
num = 0
tick = y
signal_time = 0
signal_rsi = 0
signal_adx = 0
buy_time = 0
buy_price = 0
sl = 0
#to add trailing sl in this.
for x in main.index:
maxx = main.iloc[x]["max_100"]
rsi = main.iloc[x]["RSI"]
adx = main.iloc[x]["ADX"]
sma = main.iloc[x]["20_sma"]
close = main.iloc[x]["close"]
high = main.iloc[x]["high"]
if rsi > 80 and adx > 35 and close > maxx:
if pos == 0:
buy_price = main.iloc[x+1]["open"]
buy_time = main.iloc[x+1]["date"]
pos=1
signal_time = main.iloc[x]["date"]
signal_rsi = main.iloc[x]["RSI"]
signal_adx = main.iloc[x]["ADX"]
elif close < sma:
if pos == 1:
sell_time = main.iloc[x]["date"]
sell_price = sma*.998
pos=0
positions.loc[positions.shape[0]] = [y,signal_time,signal_rsi,signal_adx,buy_time,buy_price,sell_time,sell_price]
Any idea why?
Here is a cleanup and file call code:
full_list = pd.read_csv("All_data")
full_list.dropna(inplace=True,axis=0)
full_list.drop(labels="Unnamed: 0",axis=1) < index of previous dataframe
full_list.head(5)
Thanks

While loop incrementer not functioning properly

Right now, my code is correctly spitting out the first game (identified by start_id) in games. I am trying to increment in the bottom two lines, but the while loop doesn't seem to read the fact that I'm incrementing. So the input of this with start_id 800 and end_id 802 is just the information from 800, for some reason.
Am I using the incrementers correctly? Should I be initializing one of i or start_id elsewhere?
games = console(start_id, end_id)
final_output = []
while start_id < (end_id + 1):
single_game = []
i = 0
game_id = games[i][0]
time_entries = games[i][1][2][0]
play_entries = games[i][1][2][1]
score_entries = games[i][1][2][2]
team_entries = games[i][1][2][3]
bovada = games[i][1][0][0][0]
at_capacity = games[i][1][0][1]
idisagree_yetrespect_thatcall = games[i][1][0][2][0]
imsailingaway = games[i][1][1][0][0]
homeiswheretheheartis = games[i][1][1][1][0]
zipper = zip(time_entries, play_entries, score_entries, team_entries)
for play_by_play in zipper:
single_game.append(game_id)
single_game.append(play_by_play)
single_game.append(bovada)
single_game.append(at_capacity)
single_game.append(idisagree_yetrespect_thatcall)
single_game.append(imsailingaway)
single_game.append(homeiswheretheheartis)
start_id += 1
i += 1
final_output.append(single_game)
return final_output

Your problem is that you initialize the increment-er i inside the while loop so every time your loop iterates i is reset to zero.
Try changing it to:
i = 0
while start_id < (end_id + 1):
...

TypeError: object is not subscriptable

I`ve obtain this error
File "/class.py", line 246, in __init__
if d and self.rf == 2 and d["descriptionType"] in ["900000000000003001"] and d["conceptId"] in konZer.zerrenda:
TypeError: 'Desk' object is not subscriptable
I created this object
class Desk:
descriptionId = ""
descriptionStatus = ""
conceptId = ""
term = ""
And I called it in another class
class DescriptionList():
def deskJ(self,line):
er = line.strip().split('\t')
desc = Desk()
if er[1] == "0":
desc.descriptionId = er[0]
desc.descriptionStatus = er[1]
desc.conceptId = er[2]
desc.term = er[3]
return description
Then I called the function "deskJ" at init and I get the error at this part (I've deleted some parts of the function):
def __init__(self,fitx,konZer,lanZer={}):
with codecs.open(fitx,encoding='utf-8') as fitx:
lines = fitx.read().split('\n')[1:-1]
for line in lines:
d = self.deskJ(line)
if d and self.rf == 2 and d["descriptionType"] in ["900000000000003001"] and d["conceptId"] in konZer.zerrenda:
c = konZer.zerrenda[d["conceptId"]]
c["fullySpecifiedName"] = d["term"]
What am I doing wrong?

Using d["descriptionType"] is trying to access d with the key "descriptionType". That doesn't work, though, because d is a Desk object that doesn't have keys. Instead, get the attributes:
if d and self.rf == 2 and d.descriptionType in ["900000000000003001"] and d.conceptId in konZer.zerrenda:

Error 'numpy.int32' object does not support item assignment

I get this error
Traceback (most recent call last):
File "C:\Users\User1\Desktop\cellh5_scripts\ewa_pnas_fate.py", line 90, in <module>
ec.combine_classifiers("Event labels combined")
File "C:\Users\User1\Desktop\cellh5_scripts\ewa_pnas_fate.py", line 53, in combine_classifiers
pnas_class[pnas_class==3] = 1
TypeError: 'numpy.int32' object does not support item assignment
by runing the code
def combine_classifiers(self, output_name):
all_combined_classes = []
for _, (plate_name, w, p, t1, t2, track_ids, track_labels) in self.mapping[['Plate',
'Well',
'Site',
'Gene Symbol',
'siRNA ID',
'Event track ids',
'Event track labels']].iterrows():
combined_classes = []
ch5_file_handle = self.cellh5_handles[plate_name]
ch5_pos = ch5_file_handle.get_position(w, str(p))
for track_id, track_label in zip(track_ids, track_labels):
h2b_class = track_label.copy()
print(track_id)
pnas_class = ch5_pos.get_class_prediction('secondary__expanded')[track_id]['label_idx'] + 1
print(pnas_class)
inter_idx = h2b_class == 1
pnas_class[pnas_class==3] = 1
pnas_class[pnas_class==2]+=2
combined_class = h2b_class
combined_class[inter_idx] = pnas_class[inter_idx]
combined_classes.append(combined_class)
all_combined_classes.append(combined_classes)
self.mapping[output_name] = pandas.Series(all_combined_classes)
I print pnas_class which is 1, and track_id which is 50708. I'm wondering what the designer of code want to do in the part:
inter_idx = h2b_class == 1
pnas_class[pnas_class==3] = 1
pnas_class[pnas_class==2]+=2
combined_class = h2b_class
combined_class[inter_idx] = pnas_class[inter_idx]
How can I change that to have the same meaning?

pnas_class is a an integer so you can't select item from an integer by [pnas_class==3] = 1.
Maybe you are trying to affect 1 to pnas_class if it's equal to 3. In this case try this:
pnas_class= 1*(pnas_class == 3) + pnas_class*(pnas_class != 3 )

Ok I found the mistake. You arer right the pnas_class should not be an integer and I know why is it integer instead of array.