On 08/17/2017 03:19 AM, Bennion, Brian wrote:
Hello All,I am parsing a set of 2D sd files in rdkit in order to generate a 3D structure. The code is below and is based on what I could find on the list for errors in generating 3D coordinates.Temp.mol is the downloaded molfile from chembl for compound CHEMBL500809. I must be doing something incorrectly in the code below as it still throws a -1 at the embed step.
I have a script that can handle the smi for this compound and produce a 3D SDF file (input and output files are attached). The code is there: https://github.com/UnixJunkie/smi2sdf3d Regards, F.
>>suppl = Chem.SDMolSupplier('temp.mol')
>>ms = [x for x in suppl if x is not None]
>>print ("This is the number of entries read in",len(ms))
1
>>for m in ms:
>>tmp=AllChem.Compute2DCoords(m)
>>m3=Chem.AddHs(m)
>>print (AllChem.EmbedMolecule(m3,useRandomCoords=True))
-1
Just finished embedding Molecule
Traceback (most recent call last):
File "sdf2D2Canonical3DSDF.py", line 45, in <module>
AllChem.UFFOptimizeMolecule(m3,4000)
ValueError: Bad Conformer Id
This is the 2D structure from CHEMBL
SciTegic12231509382D CHEMBL500809
68 77 0 0 0 0 999 V2000
-1.7837 1.4355 0.0000 C 0 0
-2.4967 1.0206 0.0000 C 0 0 1 0 0 0
-3.2126 1.4306 0.0000 C 0 0 1 0 0 0
-3.2155 2.2556 0.0000 O 0 0
-3.9256 1.0156 0.0000 C 0 0 1 0 0 0
-4.7139 0.7721 0.0000 O 0 0
-2.9339 1.0873 0.0000 O 0 0
-2.8213 0.3944 0.0000 C 0 0
-3.2069 -0.2194 0.0000 C 0 0 1 0 0 0
-3.2040 -1.0444 0.0000 C 0 0 1 0 0 0
-3.9170 -1.4594 0.0000 C 0 0
-4.6329 -1.0494 0.0000 C 0 0 1 0 0 0
-5.3460 -1.4644 0.0000 C 0 0
-6.0619 -1.0543 0.0000 C 0 0
-6.0647 -0.2293 0.0000 C 0 0
-6.7806 0.1807 0.0000 O 0 0
-5.3517 0.1856 0.0000 C 0 0 1 0 0 0
-5.3546 1.0106 0.0000 O 0 0
-4.6358 -0.2244 0.0000 C 0 0 1 0 0 0
-4.8935 0.5594 0.0000 C 0 0
-3.9228 0.1906 0.0000 C 0 0 1 0 0 0
-5.3431 -2.2894 0.0000 C 0 0
-2.4881 -1.4544 0.0000 O 0 0
-1.7751 -1.0394 0.0000 C 0 0
-1.0592 -1.4495 0.0000 O 0 0
-1.7779 -0.2144 0.0000 C 0 0 2 0 0 0
-1.0649 0.2005 0.0000 O 0 0
-0.3490 -0.2095 0.0000 C 0 0
-0.3461 -1.0345 0.0000 O 0 0
0.3640 0.2055 0.0000 C 0 0
0.3612 1.0305 0.0000 O 0 0
1.0799 -0.2045 0.0000 O 0 0
1.7930 0.2105 0.0000 C 0 0 2 0 0 0
2.2833 -0.1399 0.0000 C 0 0 1 0 0 0
2.5117 -1.0245 0.0000 C 0 0 1 0 0 0
1.7987 -1.4395 0.0000 C 0 0
3.2276 -1.4346 0.0000 C 0 0 1 0 0 0
3.2305 -2.2595 0.0000 O 0 0
3.9407 -1.0196 0.0000 C 0 0 1 0 0 0
4.7289 -0.7761 0.0000 O 0 0
2.9489 -1.0912 0.0000 O 0 0
2.6107 -0.3387 0.0000 C 0 0
3.2219 0.2154 0.0000 C 0 0 2 0 0 0
3.2190 1.0404 0.0000 C 0 0 1 0 0 0
3.9321 1.4554 0.0000 C 0 0
4.6480 1.0454 0.0000 C 0 0 1 0 0 0
5.3610 1.4604 0.0000 C 0 0
6.0769 1.0504 0.0000 C 0 0
6.0798 0.2254 0.0000 C 0 0
6.7957 -0.1846 0.0000 O 0 0
5.3667 -0.1896 0.0000 C 0 0 1 0 0 0
5.3696 -1.0146 0.0000 O 0 0
4.6508 0.2204 0.0000 C 0 0 1 0 0 0
4.9085 -0.5633 0.0000 C 0 0
3.9378 -0.1946 0.0000 C 0 0 1 0 0 0
5.3581 2.2854 0.0000 C 0 0
2.5031 1.4504 0.0000 O 0 0
1.7901 1.0355 0.0000 C 0 0
1.0742 1.4455 0.0000 O 0 0
-2.4938 0.1956 0.0000 C 0 0 1 0 0 0
-1.6295 0.6986 0.0000 H 0 0
4.8056 -0.6916 0.0000 H 0 0
4.6445 2.0454 0.0000 H 0 0
3.2155 2.0404 0.0000 H 0 0
1.4588 -0.7058 0.0000 H 0 0
-4.7905 0.6876 0.0000 H 0 0
-4.6294 -2.0494 0.0000 H 0 0
-3.2005 -2.0444 0.0000 H 0 0
2 1 1 6
2 3 1 0
3 4 1 6
3 5 1 0
5 6 1 6
5 7 1 0
7 8 1 0
9 8 1 1
9 10 1 0
10 11 1 0
12 11 1 0
12 13 1 0
13 14 2 0
14 15 1 0
15 16 2 0
15 17 1 0
17 18 1 1
17 19 1 0
19 12 1 0
19 20 1 1
21 19 1 0
21 5 1 0
21 9 1 0
13 22 1 0
10 23 1 0
23 24 1 0
24 25 2 0
24 26 1 0
26 27 1 1
27 28 1 0
28 29 2 0
28 30 1 0
30 31 2 0
30 32 1 0
33 32 1 1
34 33 1 0
34 35 1 0
35 36 1 6
35 37 1 0
37 38 1 6
37 39 1 0
39 40 1 6
39 41 1 0
41 42 1 0
43 42 1 1
43 34 1 0
43 44 1 0
44 45 1 0
46 45 1 0
46 47 1 0
47 48 2 0
48 49 1 0
49 50 2 0
49 51 1 0
51 52 1 1
51 53 1 0
53 46 1 0
53 54 1 1
55 53 1 0
55 39 1 0
55 43 1 0
47 56 1 0
44 57 1 0
57 58 1 0
58 33 1 0
58 59 2 0
60 26 1 0
60 2 1 0
60 9 1 0
60 61 1 1
55 62 1 6
46 63 1 6
44 64 1 1
34 65 1 1
21 66 1 6
12 67 1 6
10 68 1 1
M END
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CHEMBL500809.sdf
Description: StarMath document
CHEMBL500809.smi
Description: application/smil
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