Dear all,
I found some bugs about the calculation of molecular weight:
The first problem:
1) In the "RuleOfFiveDescriptor.java" code, the molecular weight is calculate
as below：
“IAtomContainer mol = rof.readMol2("test.mol2");
IMolecularDescriptor mw = new WeightDescriptor();
Object[] mwparams = { "" };
mw.setParameters(mwparams);
double mwvalue = ((DoubleResult) mw.calculate(mol).getValue()).doubleValue();
"
However, if Object[] mwparams = { "" }; The molecular weigh is 0.0. When I
modify it to "Object[] mwparams = { "*" };" it can calculte the molecular
weight. Is it the bug ofRuleOfFiveDescriptor in CDK?
The second problem:
2) I calculate the molecule weight by using the below code:
“IAtomContainer mol = rof.readMol2("test.mol2");
IMolecularDescriptor mw = new WeightDescriptor();
Object[] mwparams = { "*" };
mw.setParameters(mwparams);
double mwvalue = ((DoubleResult) mw.calculate(mol).getValue()).doubleValue();
"
The calculated molecular weight is different with the results from the website
https://zh.webqc.org/mmcalc.php or
https://www.lenntech.com/calculators/molecular/molecular-weight-calculator.htm
For example, I use the attached "test.mol2" file (formula is: C27H32N5O4S).
The molecular weight of test.mol2 is 522.2175005040009 by using the above CDK
code;
The molecular weight of test.mol2 is 522.6391 by using website
https://zh.webqc.org/mmcalc.php or
https://www.lenntech.com/calculators/molecular/molecular-weight-calculator.htm
In my opinion, It should not the a cumulative rounding off error, some
parameters of atom are err. I had calculated it by Chemoffice, it also is
522.64, please check it.
Is it the bug of molecular weight calculation in CDK code?
I am waiting for somebody to solve this problem. Thanks.
To show the example clearly, I also paste the "test.mol2" content as below:
@<TRIPOS>MOLECULE
ligand.pdb
69 72 1 0 0
SMALL
AMBER ff14SB
@<TRIPOS>ATOM
1 N1 33.4730 12.2860 22.0110 N.am 1 MID 0.0000
2 C2 33.6900 11.1160 21.1670 C.3 1 MID 0.0000
3 C3 32.9400 9.9200 21.7710 C.3 1 MID 0.0000
4 C4 33.3310 9.7150 23.2650 C.3 1 MID 0.0000
5 C5 33.0510 10.9910 24.0860 C.3 1 MID 0.0000
6 C6 33.7560 12.1980 23.4560 C.3 1 MID 0.0000
7 N7 31.5060 14.2480 23.1380 N.am 1 MID 0.0000
8 C8 32.7930 14.5390 22.4860 C.3 1 MID 0.0000
9 C9 32.9780 13.4720 21.4620 C.2 1 MID 0.0000
10 O10 32.7440 13.5950 20.2550 O.2 1 MID 0.0000
11 C11 32.7220 15.8910 21.7900 C.3 1 MID 0.0000
12 C12 32.6760 16.9470 22.8070 C.ar 1 MID 0.0000
13 C13 33.8380 17.4680 23.3090 C.ar 1 MID 0.0000
14 C14 31.4630 17.3550 23.2950 C.ar 1 MID 0.0000
15 C15 33.7800 18.4850 24.2800 C.ar 1 MID 0.0000
16 C16 31.3820 18.3620 24.2600 C.ar 1 MID 0.0000
17 C17 32.5450 18.9280 24.7480 C.ar 1 MID 0.0000
18 N18 29.9850 13.7390 26.3060 N.pl3 1 MID 0.0000
19 C19 30.0460 13.7400 24.8830 C.3 1 MID 0.0000
20 C20 31.4080 14.0330 24.4730 C.2 1 MID 0.0000
21 O21 32.3780 14.1170 25.2350 O.2 1 MID 0.0000
22 S22 29.3410 12.4380 27.0580 S.o2 1 MID 0.0000
23 O23 28.3630 11.8390 26.1820 O.2 1 MID 0.0000
24 O24 29.0620 12.8090 28.4350 O.2 1 MID 0.0000
25 C25 30.5070 10.1480 26.3150 C.ar 1 MID 0.0000
26 C26 30.6400 11.2630 27.1350 C.ar 1 MID 0.0000
27 C27 31.7270 11.4390 27.9370 C.ar 1 MID 0.0000
28 C28 32.7410 10.4530 27.9200 C.ar 1 MID 0.0000
29 C29 32.5820 9.2850 27.1330 C.ar 1 MID 0.0000
30 C30 31.4640 9.1710 26.3000 C.ar 1 MID 0.0000
31 C31 33.8930 10.5930 28.7020 C.ar 1 MID 0.0000
32 C32 34.8520 9.5850 28.6810 C.ar 1 MID 0.0000
33 C33 34.6900 8.4150 27.8780 C.ar 1 MID 0.0000
34 C34 33.5680 8.2670 27.1180 C.ar 1 MID 0.0000
35 C35 32.4750 19.9650 25.7860 C.2 1 MID 0.0000
36 N36 31.2960 20.4290 26.2370 N.pl3 1 MID 0.0000
37 N37 33.5310 20.7490 26.0440 N.pl3 1 MID 0.0000
38 H22 33.3140 11.3140 20.1630 H 1 MID 0.0000
39 H23 34.7560 10.8920 21.1200 H 1 MID 0.0000
40 H32 31.8670 10.1010 21.7050 H 1 MID 0.0000
41 H33 33.1870 9.0200 21.2080 H 1 MID 0.0000
42 H42 34.3930 9.4770 23.3270 H 1 MID 0.0000
43 H43 32.7530 8.8880 23.6780 H 1 MID 0.0000
44 H52 31.9770 11.1740 24.1090 H 1 MID 0.0000
45 H53 33.4150 10.8520 25.1040 H 1 MID 0.0000
46 H62 34.8310 12.0980 23.6020 H 1 MID 0.0000
47 H63 33.4110 13.1090 23.9450 H 1 MID 0.0000
48 H7 30.6700 14.2070 22.5730 H 1 MID 0.0000
49 H8 33.6060 14.5210 23.2120 H 1 MID 0.0000
50 H112 31.8250 15.9380 21.1730 H 1 MID 0.0000
51 H113 33.6040 16.0260 21.1630 H 1 MID 0.0000
52 H13 34.7930 17.1010 22.9620 H 1 MID 0.0000
53 H14 30.5580 16.8930 22.9290 H 1 MID 0.0000
54 H15 34.6910 18.9210 24.6620 H 1 MID 0.0000
55 H16 30.4200 18.6950 24.6210 H 1 MID 0.0000
56 H18 30.3320 14.5240 26.8380 H 1 MID 0.0000
57 H192 29.3730 14.5010 24.4880 H 1 MID 0.0000
58 H193 29.7530 12.7610 24.5040 H 1 MID 0.0000
59 H25 29.6370 10.0520 25.6820 H 1 MID 0.0000
60 H27 31.8120 12.3100 28.5700 H 1 MID 0.0000
61 H30 31.3570 8.3160 25.6490 H 1 MID 0.0000
62 H31 34.0360 11.4720 29.3140 H 1 MID 0.0000
63 H321 35.7400 9.6900 29.2860 H 1 MID 0.0000
64 H331 35.4530 7.6510 27.8730 H 1 MID 0.0000
65 H34 33.4320 7.3840 26.5110 H 1 MID 0.0000
66 H361 30.4340 19.9760 25.9700 H 1 MID 0.0000
67 H362 31.2730 21.2340 26.8460 H 1 MID 0.0000
68 H371 34.4290 20.5490 25.6260 H 1 MID 0.0000
69 H372 33.4290 21.5440 26.6590 H 1 MID 0.0000
@<TRIPOS>BOND
1 11 8 1
2 11 12 1
3 11 50 1
4 11 51 1
5 12 13 ar
6 12 14 ar
7 13 15 ar
8 13 52 1
9 14 16 ar
10 14 53 1
11 15 17 ar
12 15 54 1
13 16 17 ar
14 16 55 1
15 17 35 1
16 19 18 1
17 19 20 1
18 19 57 1
19 19 58 1
20 2 1 1
21 2 3 1
22 2 38 1
23 2 39 1
24 20 7 am
25 20 21 2
26 25 26 ar
27 25 30 ar
28 25 59 1
29 26 22 1
30 26 27 ar
31 27 28 ar
32 27 60 1
33 28 29 ar
34 28 31 ar
35 29 30 ar
36 29 34 ar
37 3 4 1
38 3 41 1
39 3 40 1
40 30 61 1
41 31 32 ar
42 31 62 1
43 32 33 ar
44 32 63 1
45 33 34 ar
46 33 64 1
47 34 65 1
48 35 36 2
49 35 37 2
50 4 5 1
51 4 42 1
52 4 43 1
53 5 6 1
54 5 44 1
55 5 45 1
56 6 1 1
57 6 46 1
58 6 47 1
59 8 7 1
60 8 9 1
61 8 49 1
62 9 1 am
63 9 10 2
64 56 18 1
65 66 36 1
66 67 36 1
67 68 37 1
68 69 37 1
69 48 7 1
70 18 22 1
71 23 22 2
72 24 22 2
@<TRIPOS>SUBSTRUCTURE
1 MID 1 RESIDUE 4 A MID 0 ROOT
test.mol2
Description: Binary data
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