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BenzDB results

Whatever the considered query, the result is returned as a JSON file. The JSON format makes it possible to structure results in a format that is both human-readable and easy to process. The returned information only depends on the chosen query (see below). Each query returns a given collection of pairs (label,value).

Description of the returned labels

Here is a list of possible labels and their descriptions:

The returned information depending on the desired query

A filtered request only differs from the corresponding unfiltered request by the benzenoids it involved. While an unfiltered request involves all the benzenoids of the database, the filtered one only considers a selection of benzenoids characterized by the given criteria. In other words, the return information is the same for a filtered request or an unfiltered one.

The table below specifies the type of each label and the queries in which it is returned:

Queries
Type Label benzenoids ir ims2d1a nics clar_covers properties irregularities
integer duo
idBenzenoid
kekule
nbCarbons
nbHexagons
nbHydrogens
nbPointsX
nbPointsY
quartet
solo
trio
vectorX
vectorY
float finalEnergy
irregularity
weight
zeroPointEnergy
string amesFormat
clarCover
frequencies
geometry
graphFile
inchi
intensities
label
nics
origin
picture
points
symmetry
Boolean catacondensed
coronenoid
coronoid

Example

For instance, let us consider again the criteria {"nbHexagons": "= 6", "nbCarbons": "IN 22 28"} with the query benzenoids (see Requests page). BenzDB returns the following JSON file:

[{"idBenzenoid":104,"inchi":"1S/C25H40/c1-4-9-21-16(6-1)12-13-18-15-19-14-17-7-2-3-8-20(17)22-10-5-11-23(24(18)21)25(19)22/h16-25H,1-15H2","label":"1-7-8-15-21-22","nbHexagons":6,"nbCarbons":25,"nbHydrogens":15,"irregularity":0.7333,"graphFile":"p DIMACS 25 30 6\ne -1_1 -1_2\ne -1_1 0_0\ne -1_2 -2_3\ne -1_2 0_3\ne -2_3 -3_2\ne -2_3 -2_4\ne -3_2 -4_3\ne 0_0 1_1\ne 1_1 1_2\ne 1_2 0_3\ne 1_2 2_3\ne 0_3 0_4\ne 3_1 3_2\ne 3_1 4_0\ne 3_2 2_3\ne 3_2 4_3\ne 2_3 2_4\ne 4_0 5_1\ne 5_1 5_2\ne 5_2 4_3\ne 4_3 4_4\ne -2_4 -3_5\ne -2_4 -1_5\ne -3_5 -4_4\ne -4_4 -4_3\ne 0_4 -1_5\ne 0_4 1_5\ne 2_4 1_5\ne 2_4 3_5\ne 4_4 3_5\nh 0_0 1_1 1_2 0_3 -1_2 -1_1\nh -1_2 0_3 0_4 -1_5 -2_4 -2_3\nh 1_2 2_3 2_4 1_5 0_4 0_3\nh -3_2 -2_3 -2_4 -3_5 -4_4 -4_3\nh 3_2 4_3 4_4 3_5 2_4 2_3\nh 4_0 5_1 5_2 4_3 3_2 3_1\n","geometry":"C -1.78217 2.37253 -0.42189\nC -2.00012 1.00371 -0.16679\nC -0.49889 2.85417 -0.67021\nC -3.34654 0.45983 0.03158\nC -0.86824 0.12786 -0.13325\nC -4.50085 1.27269 0.10200\nC -3.51395 -0.96013 0.16274\nC -5.76579 0.72614 0.28398\nC 0.60792 2.01171 -0.59240\nC 0.46791 0.64441 -0.25536\nC 1.61108 -0.25897 -0.11984\nC -1.07690 -1.30138 -0.03860\nC 3.34632 1.46498 0.57970\nC 2.98215 0.17198 0.10202\nC 4.67111 1.83310 0.75546\nC 4.05086 -0.77714 -0.07437\nC 1.35780 -1.66320 -0.20873\nC 5.71305 0.92578 0.47120\nC 5.39710 -0.36448 0.08184\nC 3.74436 -2.15281 -0.33889\nC -4.82073 -1.49599 0.34304\nC -2.38085 -1.80764 0.10103\nC -5.92870 -0.67104 0.40240\nC 0.03772 -2.15381 -0.15657\nC 2.45263 -2.58589 -0.34406\nH -2.61786 3.05891 -0.47534\nH -0.35876 3.89658 -0.93838\nH -4.41073 2.34961 0.02393\nH -6.63153 1.37830 0.33730\nH 1.58090 2.40595 -0.84784\nH 2.57371 2.16357 0.86871\nH 4.90522 2.82297 1.13445\nH 6.74844 1.22607 0.59431\nH 6.18336 -1.09577 -0.08375\nH 4.56597 -2.84937 -0.47743\nH -4.92985 -2.57273 0.43670\nH -2.52472 -2.88291 0.16229\nH -6.91896 -1.09228 0.54256\nH -0.12249 -3.22810 -0.18508\nH 2.21972 -3.63925 -0.46858\n","weight":315.3876},{"idBenzenoid":172,"inchi":"1S/C26H16/c1-3-7-22-17(5-1)10-13-20-15-21-14-12-19-11-9-18-6-2-4-8-23(18)26(19)25(21)16-24(20)22/h1-16H","label":"2-7-10-15-16-17","nbHexagons":6,"nbCarbons":26,"nbHydrogens":16,"irregularity":0.5,"graphFile":"p DIMACS 26 31 6\ne -1_1 -1_2\ne -1_1 0_0\ne -1_2 0_3\ne 0_0 1_1\ne 1_1 1_2\ne 1_2 0_3\ne 1_2 2_3\ne 0_3 0_4\ne 2_3 2_4\ne -3_5 -4_4\ne -3_5 -3_6\ne -4_4 -5_5\ne 0_4 -1_5\ne 0_4 1_5\ne -1_5 -1_6\ne 2_4 1_5\ne 1_5 1_6\ne -3_6 -4_7\ne -3_6 -2_7\ne -4_7 -5_6\ne -4_7 -4_8\ne -5_6 -5_5\ne -1_6 -2_7\ne -1_6 0_7\ne -2_7 -2_8\ne 1_6 0_7\ne 0_7 0_8\ne -4_8 -3_9\ne -2_8 -3_9\ne -2_8 -1_9\ne 0_8 -1_9\nh 0_0 1_1 1_2 0_3 -1_2 -1_1\nh 1_2 2_3 2_4 1_5 0_4 0_3\nh 0_4 1_5 1_6 0_7 -1_6 -1_5\nh -1_6 0_7 0_8 -1_9 -2_8 -2_7\nh -3_6 -2_7 -2_8 -3_9 -4_8 -4_7\nh -4_4 -3_5 -3_6 -4_7 -5_6 -5_5\n","geometry":"C 3.72782 2.80170 -0.54233\nC 2.66807 1.91377 -0.41050\nC 5.05563 2.34990 -0.41298\nC 2.88441 0.53938 -0.14823\nC 5.29873 1.00990 -0.15351\nC 4.23472 0.08646 -0.01769\nC 4.50213 -1.30508 0.25048\nC 1.79283 -0.42702 0.00120\nC 3.49226 -2.20868 0.37485\nC -1.80071 1.81052 0.76235\nC -2.31987 3.08960 0.87769\nC -2.53898 0.75127 0.15771\nC -3.61541 3.38599 0.40060\nC 0.44131 -0.06341 -0.09110\nC 2.11489 -1.80652 0.24891\nC -0.62020 -0.97909 0.05913\nC 1.07595 -2.74135 0.31101\nC -3.89914 1.03991 -0.21371\nC -2.03342 -0.60502 -0.00784\nC -4.39337 2.36762 -0.11596\nC -4.76726 -0.02394 -0.61069\nC -0.27217 -2.37489 0.18526\nC -2.97741 -1.63831 -0.25204\nC -1.29743 -3.37423 0.09716\nC -4.33595 -1.31980 -0.56720\nC -2.58350 -3.01839 -0.17772\nH 3.52983 3.84926 -0.74584\nH 1.65848 2.29407 -0.51414\nH 5.88086 3.04706 -0.51573\nH 6.31784 0.64770 -0.05068\nH 5.53808 -1.61703 0.34676\nH 3.70530 -3.25598 0.56830\nH -0.83411 1.60497 1.20053\nH -1.73191 3.86435 1.35971\nH -4.00803 4.39463 0.47782\nH 0.20097 0.95742 -0.34191\nH 1.32181 -3.79414 0.42527\nH -5.41507 2.56138 -0.43044\nH -5.78865 0.21432 -0.89222\nH -1.01496 -4.41801 0.19663\nH 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Exploiting the files returned by BenzDB

The .graph format

The .graph file format is a format used by the BenzAI software in order to describe benzenoids. This format has the following syntax. The first line is of the form p DIMACS nc nl nh where nc, nl and nh are respectively the number of carbons, C-C bonds and hexagons of the described benzenoid.

The nl next lines are of the form e x1_y1 x2_y2. Each of these lines specify the existence of a bond linking the carbons located at the coordinates (x1, y1) and (x2, y2).

Finally, the file ends with nh lines respecting the form h x1_y1 x2_y2 x3_y3 x4_y4 x5_y5 x6_y6. Each of these lines specify that a hexagon is formed by the vertices located at the coordinates (x1, y1), (x2, y2), ..., (x6, y6).

For instance, here is a possible .graph file to describe phenanthrene:

p DIMACS 14 16 3
e 0_0 1_1
e 0_0 -1_1
e 1_1 1_2
e 1_2 0_3
e 0_3 -1_2
e 0_3 0_4
e -1_2 -1_1
e -1_2 -2_3
e -3_2 -2_3
e -3_2 -4_3
e -2_3 -2_4
e -2_4 -3_5
e -2_4 -1_5
e -3_5 -4_4
e -4_4 -4_3
e 0_4 -1_5
h 0_0 1_1 1_2 0_3 -1_2 -1_1
h -3_2 -2_3 -2_4 -3_5 -4_4 -4_3
h -1_2 0_3 0_4 -1_5 -2_4 -2_3

Retrieving the images

The PNG images contained in the database are encoded in base 64. So they cannot be viewed directly. They must first be decoded. This can be achieved, for instance, thanks to the following steps:

  1. save the string corresponding to the image encoded in base 64 into a file,
  2. apply an encoder/decoder tool to this file,
  3. save the produced string into a file which corresponds to the PNG image.

Many tools allow the decoding of such files. We can cite, for instance, base64 for Linux users. For this tool, if the image encoded in base 64 is saved in a file filename, the PNG image can be obtained by typing base64 -d filename.

Again, if we consider phenanthrene, the Clar cover image encoded in base 64 is as follow:

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

The resulting image after decoding:

phenanthrene.png