For now the mongodb database has been setup locally.
To run the database script
Before running database script, I assume:
- You're running mongodb server on your machine
- You're mounted the
MSSHARE/Anubhav/darpacme/drive on your system and configured theRESULT_PATHto MSSHARE data location &FILEPATTERNtoCHEM_ID_calc_prop_v2.dat(default) file in database script. - Have a MongoDB GUI client, such Studio 3T or NoSQL Manager downloaded and installed to view the database queries.
Run the database script.
python cme_mongo.py
Example database can be found at smb://pnl.gov/Projects/MSSHARE/Anubhav/darpacme/Oct26/test/darpe_cme.calcProp_uvSpec.json
JSON Schema:
Atomic Number
INCHIKEY index A B C mu HOMO LUMO gap ZPVE U0 U H G Cv
Geometry block with mulliken charges as ==> symbol x y z Mulliken_population_charge
Frequency
Converged SMILE
Converged InChI
------------------UNITS of properties----------------------
I. Property Unit Description
-- -------- ----------- --------------
1 tag - "INCHIKEY"; string constant to ease extraction via grep
2 index - Consecutive, 1-based integer identifier of molecule
3 A cm-1 Rotational constant A
4 B cm-1 Rotational constant B
5 C cm-1 Rotational constant C
6 mu Debye Dipole moment
7 homo Hartree Energy of Highest occupied molecular orbital (HOMO)
8 lumo Hartree Energy of Lowest occupied molecular orbital (LUMO)
9 gap Hartree Gap, difference between LUMO and HOMO
10 zpve Hartree Zero point vibrational energy
11 U0 Hartree Internal energy at 0 K
12 U Hartree Internal energy at 298.15 K
13 H Hartree Enthalpy at 298.15 K
14 G Hartree Free energy at 298.15 K
15 Cv cal/mol-K Heat capacity at 298.15 K
Sample database document
{
"_id" : "KSEBMYQBYZTDHS-HWKANZROSA-M",
"atomic_num" : NumberInt(24),
"INCHIKEY" : "KSEBMYQBYZTDHS-HWKANZROSA-M",
"index" : "KSEBMYQBYZTDHS-HWKANZROSA-M",
"A" : 0.050706,
"B" : 0.018,
"C" : 0.01471,
"mu" : 5.7437844482,
"HOMO" : -0.2054529,
"LUMO" : -0.0135485,
"gap" : 0.1919044,
"ZPVE" : 0.19638889566141512,
"U0" : -592.907702504817,
"U" : -592.700074504817,
"H" : -592.699131504817,
"G" : -592.7484801350587,
"Cv" : 44.502,
"geo_block" : [
[
"C",
2.3887962,
-1.61080755,
-0.1494748,
-0.16999999999999993
],
[
"C",
3.35446709,
-0.58295536,
-0.19870777,
-0.17999999999999972
],
[
"C",
1.03050204,
-1.32182051,
-0.14440963,
-0.23000000000000043
],
[
"C",
2.98190821,
0.75540299,
-0.24768949,
-0.1900000000000004
],
[
"C",
-0.41292119,
2.02944908,
-0.25933631,
-0.019999999999999574
],
[
"C",
-2.29531416,
-0.51334009,
1.3241779,
-0.040000000000000036
],
[
"C",
0.6235709,
0.02374632,
-0.17918187,
0.05999999999999961
],
[
"C",
-0.66251935,
0.68095436,
-0.19067203,
0.009999999999999787
],
[
"C",
1.61277367,
1.04233645,
-0.23757404,
0.29000000000000004
],
[
"C",
-2.00250504,
0.02346523,
-0.08145639,
0.04999999999999982
],
[
"N",
0.94959335,
2.25378711,
-0.28100364,
-0.6799999999999997
],
[
"O",
-3.56213003,
-1.14494106,
1.3823646,
-0.6699999999999999
],
[
"O",
-2.10315637,
-1.1360316,
-0.93004101,
-0.6799999999999997
],
[
"H",
2.71761064,
-2.64592787,
-0.11929648,
0.14
],
[
"H",
4.40962205,
-0.84208893,
-0.20316257,
0.15000000000000002
],
[
"H",
0.28430283,
-2.10930126,
-0.12642897,
0.14
],
[
"H",
3.72487533,
1.54745263,
-0.29261372,
0.16000000000000003
],
[
"H",
-1.10893102,
2.85701722,
-0.28607341,
0.18999999999999995
],
[
"H",
-2.31288238,
0.31826465,
2.03519347,
0.16000000000000003
],
[
"H",
-1.48103132,
-1.19585666,
1.61670757,
0.14
],
[
"H",
-2.79829945,
0.74209614,
-0.33570152,
0.14
],
[
"H",
1.39014313,
3.15813014,
-0.34196153,
0.38
],
[
"H",
-3.57423141,
-1.77154983,
0.63955221,
0.42000000000000004
],
[
"H",
-1.83819691,
-0.87247309,
-1.82443824,
0.43000000000000005
]
],
"freq_block" : [
-0.0,
-0.0,
0.0,
0.0,
0.0,
0.0,
61.353,
85.811,
104.807,
182.776,
203.769,
226.731,
255.782,
315.02,
348.163,
361.193,
424.376,
437.702,
457.636,
465.268,
530.578,
573.782,
588.466,
630.745,
652.505,
758.512,
769.367,
782.277,
800.02,
800.887,
864.421,
889.172,
901.764,
934.546,
976.553,
1040.433,
1043.145,
1072.806,
1090.665,
1099.015,
1121.245,
1164.808,
1192.761,
1203.683,
1247.243,
1277.901,
1301.528,
1319.571,
1356.834,
1367.152,
1390.283,
1403.47,
1422.828,
1456.69,
1462.449,
1499.056,
1529.638,
1540.647,
1606.71,
1633.684,
1678.454,
2992.024,
3009.983,
3111.548,
3179.892,
3190.077,
3204.35,
3220.414,
3263.127,
3668.227,
3722.247,
3755.54
],
"converg_smile" : "c1ccc2c(c1)c(c[nH]2)[C@H](CO)O",
"converg_inchi" : "1S/C10H11NO2/c12-6-10(13)8-5-11-9-4-2-1-3-7(8)9/h1-5,10-13H,6H2/t10-/m0/s1"
}