https://github.com/openbabel/openbabel/blob/master/src/residue.cpp
static unsigned int GetAtomIDNumber(const char *atomid) seems to be broken.
always returns -1. All ch1-ch4 characters are misaligned to the left by 1 (ch1
contains 'C' for example when in the code it expects ' ').
conv.SetInAndOutFormats("smi", "mol2");
conv.ReadString(&mol, "OC([C@@H](N)CCSC)=O"); //methionine
mol.AddHydrogens(false, false, 7.0);
build.Build(mol);
and then looping through displaying the number.
Resulting mol2 file is correct:
@<TRIPOS>MOLECULE
*****
20 19 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 O 1.0572 -0.0682 -0.0456 O.3 1 MET1 -0.4795
2 C 0.3827 -0.9526 0.7176 C.2 1 MET1 0.3217
3 CA 1.1237 -1.9243 1.5561 C.3 1 MET1 0.1040
4 HA 0.8652 -1.7783 2.5841 H 1 MET1 0.0574
5 N 0.7685 -3.2920 1.1511 N.3 1 MET1 -0.3184
6 CB 2.6181 -1.7140 1.3747 C.3 1 MET1 -0.0183
7 CG 2.9853 -1.9214 -0.0856 C.3 1 MET1 -0.0047
8 SD 2.0803 -0.7347 -1.1097 S.3 1 MET1 -0.1641
9 CE 0.3007 -0.9851 -0.8937 C.3 1 MET1 -0.0181
10 OXT -0.8449 -0.9526 0.7176 O.2 1 MET1 -0.2493
11 H 2.0572 -0.0682 -0.0456 H 1 MET1 0.2951
12 H1 1.2785 -3.9608 1.7282 H 1 MET1 0.1190
13 H2 -0.2343 -3.4332 1.2729 H 1 MET1 0.1190
14 HB1 2.8766 -0.7185 1.6695 H 1 MET1 0.0293
15 HB2 3.1531 -2.4156 1.9801 H 1 MET1 0.0293
16 HG1 4.0373 -1.7734 -0.2134 H 1 MET1 0.0377
17 HG2 2.7268 -2.9170 -0.3805 H 1 MET1 0.0377
18 HE1 0.0423 -1.9807 -1.1885 H 1 MET1 0.0340
19 HE2 0.0423 -0.8391 0.1343 H 1 MET1 0.0340
20 HE3 -0.2343 -0.2836 -1.4991 H 1 MET1 0.0340
@<TRIPOS>BOND
1 1 11 1
2 1 2 1
3 2 10 2
4 2 3 1
5 3 6 1
6 6 15 1
7 6 14 1
8 6 7 1
9 7 17 1
10 7 16 1
11 7 8 1
12 8 9 1
13 9 20 1
14 9 19 1
15 9 18 1
16 3 5 1
17 5 13 1
18 5 12 1
19 3 4 1
Nick
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