In shell:
balloon/balloon -f balloon/MMFF94.mff --nconfs 1 --nGenerations 300 "[H]OC(=O)C([H])([H])[C##]1([H])C2=C([H])C([H])=C(OC([H])([H])C([H])([H])C([H])([H])OC3=C(OC([H])([H])[H])C([H])=C(C([H])=C3[H])C3=NC(OC([H])([H])C([H])([H])[H])=C(S3)C([H])([H])[H])C([H])=C2C([H])([H])C1([H])[H]" AAA.pdb
It works very well. However, when I try to implement use ipython, there is an error, my code as follows:
import os
str3="[H]OC(=O)C([H])([H])[C##]1([H])C2=C([H])C([H])=C(OC([H])([H])C([H]([H])C([H([H])OC3=C(OC([H])([H])[H])C([H])=C(C([H])=C3[H])C3=NC(OC([H])([H])C([H])([H][H])=C(S3)C([H])([H])[H])C([H])=C2C([H])([H])C1([H])[H]"
str4="balloon/balloon -f balloon/MMFF94.mff --nconfs 1 --nGenerations 300 str3 AAC.pdb"
#os.system('balloon_options')
os.system(str4)
The error is:
Cannot parse input str3 SMILES parser said: Syntax error after s
Skipping.
What is wrong with the problem?
By the way, balloon is the software which can put SMILES STRING into mol2 or pdb format.(SMILES STRING is like [H]OC(=O)C([H])([H])[C##]1([H])C2=C([H])C([H])=C(OC([H])([H])C(HC([H([H])OC3=C(OC([H])([H])[H])C([H])=C(C([H])=C3[H])C3=NC(OC([H])([H])C([H])([H][H])=C(S3)C([H])([H])[H])C([H])=C2C([H])([H])C1([H])[H])
You want to give the contents of the string str3 as an argument to balloon/balloon, but instead you're giving the string "str3" as the argument, and the string "str3" isn't valid SMILES.
Try using this line:
str4="balloon/balloon -f balloon/MMFF94.mff --nconfs 1 --nGenerations 300 " + str3 + " AAC.pdb"
Related
I have the following string:
{\"Id\":\"135\",\"Type\":0}
The number in the Id field will vary, but will always be an integer with no comma separator. I'm not sure how to get just that value from that string given that it's string data type and not real "XML". I was toying with the replace() function, but the special characters are making it more complex than it seems it needs to be.
is there a way to convert that to XML or something that I can reference the Id value directly?
Maybe use a regular expression, e.g.
import re
txt = "{\"Id\":\"135\",\"Type\":0}"
x = re.search('"Id":"([0-9]+)"', txt)
if x:
print(x.group(1))
gives
135
It is assumed here that the ids are numeric and consist of at least one digit.
Non-regex answer as you asked
\" is an escape sequence in python.
So if {\"Id\":\"135\",\"Type\":0} is a raw string and if you put it into a python variable like
a = '{\"Id\":\"135\",\"Type\":0}'
gives
>>> a
'{"Id":"135","Type":0}'
OR
If the above string is python string which has \" which is already escaped, then do a.replace("\\","") which will give you the string without \.
Now just load this string into a dict and access element Id like below.
import json
d = json.loads(a)
d['Id']
Output :
135
When using triple quotes in an indented position I for sure get indentation in the output js string too:
Comparing these two in a nested let
let input1 = "T1\nX55.555Y-44.444\nX52.324Y-40.386"
let input2 = """T1
X66.324Y-40.386
X52.324Y-40.386"""
giving
// single quotes with \n
"T1\x0aX55.555Y-44.444\x0aX52.324Y-40.386"
// triple quoted
"T1\x0a X66.324Y-40.386\x0a X52.324Y-40.386"
Is there any agreed upon thing like stripMargin in Scala so I can use those without having to unindent to top level?
Update, just to clarify what I mean, I'm currently doing:
describe "header" do
it "should parse example header" do
let input = """M48
;DRILL file {KiCad 4.0.7} date Wednesday, 31 January 2018 'AMt' 11:08:53
;FORMAT={-:-/ absolute / metric / decimal}
FMAT,2
METRIC,TZ
T1C0.300
T2C0.400
T3C0.600
T4C0.800
T5C1.000
T6C1.016
T7C3.400
%
"""
doesParse input header
describe "hole" do
it "should parse a simple hole" do
doesParse "X52.324Y-40.386" hole
Update:
I was asked to clarify stripMargin from Scala. It's used like so:
val speech = """T1
|X66.324Y-40.386
|X52.324Y-40.386""".stripMargin
which then removes the leading whitespace. stripMargin can take any separator, but defaults to |.
More examples:
Rust has https://docs.rs/trim-margin/0.1.0/trim_margin/
Kotlin has in stdlib: https://kotlinlang.org/api/latest/jvm/stdlib/kotlin.text/trim-margin.html
I guess it might sound like asking for left-pad ( :) ) but if there's something there already I'd rather not brew it myself…
I'm sorry you didn't get a prompt response to this one, but I have implemented this function here. In case the pull request isn't merged, here's an implementation that just depends on purescript-strings:
import Data.String (joinWith, split) as String
import Data.String.CodeUnits (drop, dropWhile) as String
import Data.String.Pattern (Pattern(..))
stripMargin :: String -> String
stripMargin =
let
lines = String.split (Pattern "\n")
unlines = String.joinWith "\n"
mapLines f = unlines <<< map f <<< lines
in
mapLines (String.drop 1 <<< String.dropWhile (_ /= '|'))
I try to get stdin from readLine() in Swift, but the following two string to become the same one, but they should be different, while the latter one got more space.
//Console
abcd
abcd
//
let a = readline()!
let b = readline()!
print(a==b)
The second line from stdin got four more space in the end.
Is there any Swift api to solve this problem?
I am running python 3.5, I have imported pandas. My csv file (payinfo.csv) looks like:
"01 DEC",1234.45,2344,11,1212.66
"01 NOV", 9898.33, 2343,12,1009.33
When I run the following:
dateparse = lambda x: pd.datetime.strptime(x,"%d %b")
pay_data = pd.read_csv('payinfo.csv', parse_dates = ['Date'], date_parse
I always get
"ValueError: time data '“01 DEC”' does not match format '%d %b'
I am a new programmer to python, and would appreciate any help.
I think it was just the double quotes around string that caused that error. Try stripping away any hardcoded (not 'python generated') single or double quote marks with .strip('"')
Example:
a = '"01 DEC"'
# Gives error
#a = pd.datetime.strptime(a,"%d %b")
# string without unneccessary quote marks
a = pd.datetime.strptime(a.strip('"'),"%d %b")
print a
Output:
1900-12-01 00:00:00
You haven't included the headers in the question. But this works:
import io
import pandas as pd
a = io.StringIO(u""""01 DEC",1234.45,2344,11,1212.66
"01 NOV", 9898.33, 2343,12,1009.33""")
dateparse = lambda x: pd.datetime.strptime(x,"%d %b")
df = pd.read_csv(a,header=None, parse_dates=[0], date_parser=dateparse)
print df
You can append custom year to x before converting it to datetime
.strptime(year + x,"%Y%d %b")
Output:
0 1 2 3 4
0 1900-12-01 1234.45 2344 11 1212.66
1 1900-11-01 9898.33 2343 12 1009.33
Thank you both for your input. From your answers I modified the csv file to remove the quotes around the date entry, then things worked fine! I am puzzled because I have used the read_csv method before on similar data that looked like this:
"12/31/2016","The UPS Store","THE UPS STORE 031","10.74","debit","Business Services","Interest Checking","",""
"12/31/2016","Hospice of The East Bay","HOSPICE OF THE EAST","14.00","debit","Clara","Interest Checking","",""
and had no problems – in fact I didn't need to parse the data at all and the reader was able to correctly identify the date. Huh! I guess the real issue was that the date was stored in an unconventional format. In any case, I have the answer and thank you both for your answers.
My prototype data line looks like this:
(1) 11 July England 0-0 Uruguay # Wembley Stadium, London
Currently I'm using this:
[no,dd,mm,t1,p1,p2,t2,loc]=textread('1966.txt','(%d) %d %s %s %d-%d %s # %[%s \n]');
But it gives me the following error:
Error using dataread
Trouble reading string from file (row 1, field 12) ==> Wembley Stadium, London\n
Error in textread (line 174)
[varargout{1:nlhs}]=dataread('file',varargin{:}); %#ok<REMFF1>
So it seems to have trouble with reading a string that contains a comma, or it's the at sign that causes trouble. I read the documentation thoroughly but nowhere does it mention what to do when you have special characters such as # or if you want to read a string that contains a delimiter even though it I don't want it recognized as a delimiter.
You want
[no,dd,mm,t1,p1,p2,t2,loc] = ...
textread('1966.txt','(%d) %d %s %s %d-%d %s # %[^\n]');