1. I loaded all the .dlls in the executable folder, and also Reference
the OBDotNet.dll in the VS 2015 (C#) within the project, and am getting an
exception
Additional information: The type initializer for
'OpenBabel.openbabel_csharpPINVOKE' threw an exception.
Example code is below:
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 wrote:
Using the .NET code below to generate 3D coordinates from a SMILES, Visual
Studio 15 simply exits th
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
I was able to complete the .NET coding for a SMARTS pattern search within an
input SMILES, and am wondering if the loop to check for SMARTS hits (below) in
each vector element of maplist should start at 0 or 1?
As an example, when using Thiophene's SMILES Cc1ccsc1 and the SMARTS pattern
why those options are
provided.
On Thu, 1 Nov 2018, 19:41 Leif Peterson https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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For stripping the counter ion of a salted ligand, I am basically using the
larger smiles string after splitting on "."
It's my understanding that for counter ions, they're pretty much not present in
an aqueous solution (inside cell). So for example, if sodium (+1) is the
counter ion for a
Before performing ligand energy minimization then docking with receptors, I am
adding hydrogens to ligands via the syntax:
Addhydrogens(False, False);
I am pretty sure this adds implicit H since polar-only is false. For docking,
should I only add polar H, or is ...(False, False) the
t;
wrote:
See:
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
Look at the first section, "4.1 SMARTS Atomic Primitives" section. Both "x"
and "X" are valid, but not with spaces.
Craig
On Tue, Nov 20, 2018 at 9:21 AM Leif Peterson
wrote:
I need to determine the number of hydrophobic carbons in a compound. when I
loop through the atoms with OBAtom, I can count carbons by incrementing when
atom.IsCarbon = true. However, what atom.property should I use to determine if
the carbon is polar? Is it heterovalence?
One of the weights for a particular LogS method requires the number of
hydrophobic carbons. So I added hydrogens, transformed to three dimensions,
energy minimized with gradient descent (don't need conformers here), then
parsed the mol2 output to fetch the partial charge on the far right
I am using OB and SmartsPattern fetching in 2D compounds, and need to fetch a
published SMARTS which looks like the following:
[CX4;H]([#6 × 4,c,F,Cl,Br,I])([#6 × 4,c,F,Cl,Br,I])[#6 × 4,c,F,Cl,Br,I]
and there are actually spaces around the × symbols between the 6 and 4.
Question is, should I
Chimera's Viewdock can input a mol2 file containing many ligands, and determine
minimum binding energy for a specific receptor's pocket for each ligand. Can OB
perform energy minimization of ligands in batch mode (loop) and then export all
ligands to a single mol2 file?
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