Thanks Noel, got it working. However, I am using the following molecule as a
use case “"CCOc1nc2c(n1Cc1ccc(cc1)c1ccccc1c1n[nH]nn1)c(ccc2)C(=O)O”, and its
fitted 3D coordinates (MMFF94) change slightly whenever they are fitted. Would
lowering the convergence criteria for steepest descent (i.e., 0.0001) or
increasing the rotors from 25 make the fits more robust, or is it a fact of
life that the coordinates can change from fit to fit? The #iters and
conjugate gradient convergence look okay.
pFF->SteepestDescent(250, 0.0001)
pFF->WeightedRotorSearch(200, 25)
pFF->ConjugateGradients(250, 0.000001)
pFF->UpdateCoordinates(Mol2)
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On Fri, Jul 20, 2018 at 7:50 AM, Noel O'Boyle<baoille...@gmail.com> wrote:
You need to check the return values of your functions or you will have
segfaults left, right and center. For example, the return value of
SetInAndOutFormats() and ReadString(). Also, check the value of gen3d in your
debugger. It may be a NULL pointer if FindType failed.
- Noel
On 19 July 2018 at 15:30, Leif Peterson <leifepeter...@sbcglobal.net> wrote:
Using the .NET code below to generate 3D coordinates from a SMILES, Visual
Studio 15 simply exits the run-time. Thus, some type of an exception is being
thrown, which indicates gen3d may be a python or java method/function? Is
there an Imports that perhaps needs to be used to allow gen3d to run.
Dim OBConv2 As New OBConver sion()
OBConv2.SetInAndOutFormats(" smi", "sdf")
Dim Mol2 As New OBMol()
OBConv2.ReadString(Mol2, "C( Cl)(=O)CCC(=O)Cl")
Dim gen3d As OBOp = OBOp. FindType("Gen3D")
gen3d.Do(Mol2)
MsgBox(OBConv2.WriteString( Mol2))
FYI, when I don’t use gen3d and OBOp, but rather a conversion from SMILES to
xyz format, all of the coordinates are zero.
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