knitr::opts_chunk$set(echo = TRUE)

readLines('https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/water/property/MolecularFormula/txt',warn=FALSE)

readLines('https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/butadiene/property/HeavyAtomCount/txt',warn=TRUE)


# Write your code here



# Write your code here



pugrest <- 'https://pubchem.ncbi.nlm.nih.gov/rest/pug'
pugin <- 'compound/name/water'
pugoper <- 'property/MolecularFormula'
pugout <- 'txt'

url <- paste(pugrest,pugin,pugoper,pugout,sep="/")
url

readLines(url)


chemicals <- c('cytosine', 'benzene', 'motrin', 'aspirin', 'zolpidem')

pugrest <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
pugoper <- "property/CanonicalSMILES"
pugout  <- "txt"

# loop over each element in the 'chemicals' list
for(chemical in chemicals) {    
    pugin <- paste('compound/name/',chemical,sep="")
    url <- paste(pugrest,pugin,pugoper,pugout,sep="/")
    res <- readLines(url,warn=TRUE)
    print(paste(chemical, ": ", res,sep=""))
}

chemicals <- c('water', 'benzene', 'methanol', 'ethene', 'ethanol',
               'propene','1-propanol', '2-propanol', 'butadiene',
               '1-butanol', '2-butanol', 'tert-butanol')

pugrest <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
pugoper <- "property/CanonicalSMILES"
pugout  <- "txt"

# loop over each element in the 'chemicals' list
for(chemical in chemicals) {    
    pugin <- paste('compound/name/',chemical,sep="")
    url <- paste(pugrest,pugin,pugoper,pugout,sep="/")
    res <- readLines(url,warn=TRUE)
    print(paste(chemical, ": ", res,sep=""))
    Sys.sleep(.3)
}

# Write your code here



# Write your code here



pugrest <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
pugin   <- "compound/cid/4485,4499,5026,5734,8082"
pugoper <- "property/HBondDonorCount,HBondDonorCount,XLogP,TPSA"
pugout  <- "csv"

url <- paste(pugrest,pugin,pugoper,pugout,sep="/")
url

# Print "-" 30 times (to print a line for readability)
cat(strrep("-",30))   

read.table(url,sep=",",header=TRUE)

cids <- c(443422, 72301, 8082, 4485, 5353740, 5282230, 5282138, 1547484,
          941361, 5734, 5494, 5422, 5417, 5290, 5245, 5026, 4746, 4507, 
          4499, 4497, 4494, 4474, 4418, 4386, 4009, 4008, 3949, 3926, 3878,
          3784, 3698, 3547, 3546, 3336, 3333, 3236, 3076, 2585, 2520, 2351,
          2312, 2162, 1236, 1234, 292331, 275182, 235244, 108144, 104972, 77157,
          5942250, 5311217, 4564402, 4715169, 5311501)
chunk_size <- 10
num_chunks <- ceiling(length(cids) / chunk_size)

paste("# Number of CIDs:", length(cids) )
paste("# Number of chunks:", num_chunks )

pugrest <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
pugoper <- "property/HBondDonorCount,HBondDonorCount,XLogP,TPSA"
pugout  <- "csv"

pugin <- paste("compound/cid/",
               paste(cids[1:10],collapse=","),sep="")

url <- paste(pugrest,pugin,pugoper,pugout,sep="/")
df <- read.table(url,sep=",",header=TRUE)


for (i in 2:num_chunks) {
    idx1 = chunk_size * (i - 1) + 1
    idx2 = chunk_size * i

    pugin <- paste("compound/cid/",
                   paste(cids[idx1:pmin(idx2,length(cids))],collapse=","),sep="")
    
    url <- paste(pugrest,pugin,pugoper,pugout,sep="/")
    df <- rbind(df,read.table(url,sep=",",header=TRUE))
    Sys.sleep(10)
}

df

cids <-  c(471, 1981, 2005, 2097, 2151, 2198, 2206, 2214, 2244, 2307, 2308, 2313,
2355, 2396, 2449, 2462, 2466, 2581, 2662, 2794, 2863, 3000, 3003, 3033, 3056,
3059, 3111, 3177, 3194, 3230, 3242, 3282, 3308, 3332, 3335, 3342, 3360, 3371,
3379, 3382, 3384, 3394, 3495, 3553, 3612, 3672, 3715, 3716, 3718, 3778, 3824,
3825, 3826, 3935, 3946, 3965, 4009, 4037, 4038, 4044, 4075, 4159, 4237, 4386,
4409, 4413, 4487, 4488, 4495, 4534, 4553, 4614, 4641, 4671, 4692, 4781, 4888, 
4895, 4921, 5059, 5090, 5147, 5161, 5208, 5228, 5339, 5352, 5359, 5362, 5468, 
5469, 5475, 5480, 5509, 5733, 5743, 5744, 5745, 5753, 5754, 5755, 5834, 5865, 
5875, 5876, 5877, 6094, 6213, 6215, 6247, 6436, 6741, 7090, 7497, 8522, 9053, 
9231, 9642, 9782, 9878, 10114, 10154, 10170, 10185, 10206, 12555, 12938, 13802, 
14982, 15209, 16490, 16533, 16623, 16639, 16752, 16923, 17198, 19161, 20469, 
21102, 21700, 21800, 21826, 21975, 22419, 23205, 26098, 26248, 26318, 28718, 
28871, 30869, 30870, 30951, 31307, 31378, 31508, 31635, 31799, 31800, 32153, 
32327, 32798, 33958, 35375, 35455, 35935, 36833, 37425, 38081, 38503, 39212, 
39941, 40000, 40632, 41643, 43261, 44219, 47462, 47795, 50294, 50295, 51717, 
54445, 54585, 57782, 59757, 60164, 60490, 60542, 60712, 60726, 60864, 61486, 
62074, 62924, 63006, 63019, 64704, 64738, 64746, 64747, 64927, 64945, 64971, 
64982, 65394, 65464, 65655, 65679, 65762, 66249, 67417, 68700, 68704, 68706, 
68731, 68749, 68819, 68865, 68869, 68917, 71246, 71354, 71364, 71386, 71398, 
71414, 71415, 71771, 72158, 72300, 73400, 82153, 84003, 84429, 90763, 91626,
91670, 100472, 102011, 104762, 104943, 107641, 107738, 107793, 108068, 108130, 
114753, 114840, 114917, 114999, 115239, 119032, 119286, 119365, 119607, 119828, 
119871, 121928, 121957, 122139, 122179, 122182, 123619, 123673, 123723, 124978, 
128191, 128229, 128571, 133021, 134896, 146364, 151075, 151166, 152165, 155354, 
155761, 156391, 158103, 159557, 162666, 164676, 167928, 168928, 174093, 174277, 
176155, 177976, 180604, 183088, 189821, 192156, 196122, 196840, 196841, 200674, 
201587, 219121, 222786, 229860, 235244, 236702, 259846, 263373, 275182, 292331, 
425990, 439503, 439533, 441335, 441336, 442534, 442993, 443943, 443949, 443967, 
444036, 445154, 445858, 446925, 479503, 485711, 490428, 501254, 522325, 546807, 
578771, 584547, 610479, 633091, 633097, 636374, 636398, 656604, 656656, 656852, 
657238, 667550, 927704, 969510, 969516, 1548887, 1548910, 2737488, 3033890, 
3033980, 3045402, 3051696, 3055172, 4129359, 4306515, 4483645, 5018304, 5185849, 
5280802, 5280914, 5280915, 5281004, 5281071, 5281515, 5281522, 5281792, 5282183, 
5282193, 5282230, 5282387, 5282402, 5282492, 5283542, 5283734, 5284538, 5284539, 
5311051, 5311052, 5311066, 5311067, 5311093, 5311101, 5311108, 5311169, 5311180, 
5318517, 5320420, 5322111, 5352624, 5353725, 5353726, 5353740, 5353864, 5354499, 
5377381, 5420804, 5420805, 5458396, 5472495, 5481958, 5701991, 5702036, 5702148, 
5702212, 5702252, 5702287, 5745214, 5942250, 6420050, 6429274, 6437368, 6437387, 
6438873, 6447131, 6453785, 6473881, 6509979, 6708733, 6710677, 6714002, 6917783, 
6917852, 6917894, 6918172, 6918173, 6918332, 6918445, 6918452, 6918612, 6925666, 
7060958, 7251185, 9554199, 9798098, 9799453, 9841438, 9843941, 9846332, 9865808, 
9868219, 9869053, 9871508, 9875547, 9883509, 9897518, 9897771, 9907157, 9913795, 
9919776, 9926694, 9934547, 10363606, 10918539, 11158972, 11513733, 11561674, 
11616712, 11870423, 11949636, 11954221, 11954316, 11954353, 11954369, 11957468, 
11961431, 11972243, 11972532, 12300053, 12313906, 12313911, 12606303, 12634263, 
12714644, 12874922, 13018150, 13020033, 13041095, 14010989, 14515707, 14798494, 
15895902, 16051947, 16132369, 16213022, 16213698, 16218996, 16219353, 16220118, 
16759566, 16760658, 17750985, 17753757, 18526330, 18632363, 18647121, 18943026, 
20054915, 21120116, 21637635, 21637642, 21893738, 21893804, 21982135, 22141508, 
22811280, 23509770, 23631982, 23653552, 23657872, 23663407, 23663409, 23663418, 
23663959, 23663989, 23665411, 23665999, 23667642, 23669636, 23674183, 23674255, 
23674745, 23675763, 23680530, 23681059, 23684814, 23688663, 23693301, 23694214, 
23702389, 24181458, 24721429, 24761485, 24799587, 24847961, 24847981, 24867460, 
24867465, 24867475, 24883465, 24916955, 25077872, 25113755, 25796773, 40469526, 
44119558, 44202892, 44260118, 44266812, 44386560, 45006151, 45006158, 45039955, 
45356876, 45356931, 45357558, 45357932, 45358013, 45358120, 45358130, 45358140, 
45358148, 45358149, 45488525, 46174093, 46397498, 46780650, 46780910, 46783539, 
46783786, 46783814, 46863906, 46878350, 46882877, 50989825, 51026956, 51340230, 
51398089, 53384387, 53394893, 53486221, 53486290, 53486322, 54194814, 54605501, 
54675840, 54676228, 54677470, 54677971, 54677972, 54677977, 54682045, 54684589, 
54690031, 54697648, 54708862, 54714524, 56841932, 56842111, 56845155, 57347755, 
57486087, 67668959, 67804972, 67986221, 70470286, 70678885, 71306882, 71587162, 
72774967, 72941490, 72941625, 73758129, 73759663, 73759808, 74787565, 77906397, 
78577433, 90488794, 91711382, 91826463, 91873711, 91881846, 92131836, 92462493, 
102004404, 102601886, 117072385, 117072403, 117072410, 118701141, 118701402, 
118984459, 122130078, 122130111, 122130185, 122130213, 122130768, 122173054, 
122173183, 122361610, 123134657, 124081055, 124463365, 126968472, 126968501, 
126968801, 126969212, 126969455, 129009998, 129010022, 129010033, 129010043, 
129316829, 129317859, 129317898, 129628207, 129628892, 129670532, 129735029, 
131632430, 131635023, 131676243, 131750284, 131954647, 131954667, 132399051, 
132399058, 133112890, 133126366, 133126370, 133562807, 133659920, 133687604, 
134129698, 134159361, 134460917, 134612785, 134687786, 134688123, 134688323, 
134688977, 134689786, 134693106, 134693125, 134693234, 134694728, 134694860, 
135413496, 135413505, 135414247, 135484078, 135515521, 135565709, 136040192, 
137177332, 137699687, 137705034, 137705717, 137705725, 137705994, 137706376, 
137706400, 137795135, 138059757, 138107776, 138113311, 138113507, 138113581, 
138114182, 138114743)

length(cids)


# Write your code here