[Open Babel] Hydrophobic carbons

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?

[Open Babel] Determining if carbons are hydrophobic

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

Re: [Open Babel] Math multiplication symbol in SMARTs

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 < outlook_ea1c3adb71ba7...@outlook.com> wrote: > I am

[Open Babel] filtering conformers based on RMSD

Hi, I would like to remove duplicate conformers judged by RMSD from MD frames to generated many unique conformers for a system. Is obabel capable of doing that? -Tayeb Tayeb Kakeshpour Graduate Research Assistant Jackson Research Group Michigan State University Department of Chemistry 578 S.

[Open Babel] Math multiplication symbol in SMARTs

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

Re: [Open Babel] Math multiplication symbol in SMARTs

It's probably a capital X4 without spaces messed up by the journal. What's the ref? On Tue, 20 Nov 2018, 17:21 Leif Peterson < outlook_ea1c3adb71ba7...@outlook.com wrote: > I am using OB and SmartsPattern fetching in 2D compounds, and need to > fetch a published SMARTS which looks like the