Hello,
I looked through the archives and found similar problems, but couldn't find
an exact solution for my case. Apologies if I missed the solution somewhere.
I'm reading through a list of sdf files and calculating descriptors for
each compound. For some (but not all) of the files, I get an error (see
below) about specific valence. I know that this is an error having to do
with 'sanitizing' the molecule, but I'm not sure exactly how to proceed.
I've included a clip from my python script, the error, and one of the sdf
files that is causing the problem.
Any ideas on how to fix this?
--Wendy
---------------------------------------
Excerpt from script
---------------------------------------
stringWithMolData = file('10104489.sdf','r').read()
mol = Chem.MolFromMolBlock(stringWithMolData)
AllChem.ComputeGasteigerCharges(mol)
---------------------------------------
Error message
---------------------------------------
Explicit valence for atom # 4 N, 4, is greater than permitted
Pre-condition Violation
bad molecule
Violation occurred on line 81 in file
/tmp/rdkit-HNQR/rdkit-Release_2014_03_1/Code/GraphMol/PartialCharges/GasteigerCharges.cpp
Failed Expression: mol
---------------------------------------
10104489.sdf file contents
---------------------------------------
10104489
TRC 05231419153D
PM6 optimization, min free energy conformation
14 14 0 0 0 0 0 0 0 0999 V2000
-0.4307 2.0889 0.2792 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0407 1.1071 0.2148 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4008 0.9484 0.5227 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6973 -0.0195 -0.1759 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9941 1.8122 0.8291 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9923 -0.3134 0.4365 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1378 -1.2635 -0.2668 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.1710 0.0301 -0.5321 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0439 -0.4753 0.6673 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1631 -1.3724 0.0355 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8766 0.5689 0.4954 F 0 0 0 0 0 0 0 0 0 0 0 0
-2.3775 0.9405 -1.5182 F 0 0 0 0 0 0 0 0 0 0 0 0
-2.6216 -0.9493 -0.8245 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6684 -3.1599 -0.1690 Br 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
2 3 1 0 0 0 0
3 5 1 0 0 0 0
4 2 1 0 0 0 0
6 3 2 0 0 0 0
6 9 1 0 0 0 0
7 4 2 0 0 0 0
7 10 2 0 0 0 0
8 4 1 0 0 0 0
8 11 1 0 0 0 0
10 6 1 0 0 0 0
12 8 1 0 0 0 0
13 8 1 0 0 0 0
14 10 1 0 0 0 0
M RAD 1 2 2
M END
> <Symmetry>
Cs(1)
> <Energy>
-76.2319210753677
> <FreeEnergy>
-105.218958525368
> <Freq>
36.3827 1.8490
118.9528 0.6797
121.3287 1.7880
146.7422 3.2258
230.2547 4.6726
300.5702 5.7138
328.8019 1.4348
361.6117 0.5034
402.5823 0.1183
552.4995 20.1778
573.7578 0.7088
621.4207 13.4753
682.9353 27.8339
701.6618 5.4059
844.3396 76.4557
881.5112 51.8745
935.0009 0.0366
986.5135 4.6250
1020.1213 12.4436
1073.2578 27.3170
1132.0055 17.4835
1149.0508 5.7188
1174.1069 3.8183
1193.8903 14.3170
1225.8361 3.1755
1250.0146 94.6662
1258.0689 25.6122
1333.4544 115.3666
1444.9060 96.2140
1474.6392 0.2878
1604.5610 58.4422
1630.9742 34.4613
2636.6222 77.6239
2737.5860 21.2480
2745.9489 233.0648
2756.3587 214.6328
> <gAAFreq>
1046.34084166667
> <gAlpha>
72.95
> <gCOSMO_DPSA1>
-16.3678412270001
> <gCOSMO_DPSA2>
-8.0618952540101
> <gCOSMO_NCD>
-0.00499623410644148
> <gCOSMO_NEG>
-0.492544809359508
> <gCOSMO_PCD>
0.00599090900680561
> <gCOSMO_PNSA1>
98.5832126490001
> <gCOSMO_PNSA2>
-48.5566496802496
> <gCOSMO_POS>
0.492544809149928
> <gCOSMO_PPSA1>
82.215371422
> <gCOSMO_PPSA2>
40.4947544262395
> <gCOSMO_SA>
180.798584071
> <gCOSMO_SKW>
0.546436666002523
> <gCOSMO_VAR>
0.00692393043054713
> <gCOSMO_Vol>
167.141981607954
> <gCvib>
12.6954699037459
> <gDPSA1>
-65.71527629439
> <gDPSA2>
-76.6311751243748
> <gDipole>
2.8934
> <gEN>
-5.447286492133e+02
> <gEnergy>
-76.2319210753677
> <gGAFreq>
745.714161110022
> <gHLgap>
0.33918
> <gHOMO>
-0.37718
> <gIRAFreq>
1836.33033030781
> <gKE>
-3.721651577705e+01
> <gLUMO>
-0.03800
> <gNCD>
-0.0105562568746138
> <gNEG>
-1.166109
> <gNN>
3.105243637196e+02
> <gPCD>
0.0260577959728786
> <gPNSA1>
110.4661447567
> <gPNSA2>
-128.815565596091
> <gPOS>
1.166109
> <gPPSA1>
44.75086846231
> <gPPSA2>
52.1843904717159
> <gSumIR>
1276.4724
> <gVol>
177.358428355517
> <gvdWSA>
155.217013219
> <gvdWV>
120.158277876
$$$$
------------------------------------------------------------------------------
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
