Re: [Open Babel] aromaticity detection

This is somewhat unrelated but I found that CDK has a well-documented aromaticity algorithm. You could try looking at that before examining Open Babel's implementation. They might be similar. On Wed, Feb 22, 2012 at 8:16 AM, Geoffrey Hutchison < ge...@geoffhutchison.net> wrote: > > Im asking be

[Open Babel] Sum of Gasteiger Partial Charges

Hello, I am trying to assign the Gasteiger partial charges to all the atoms. However, when I implemented the algorithm in molchrg.cpp (separate from OpenBabel), the sum of my partial charges is always 0 whereas the sum of OpenBabel partial charges is sometimes 0, -1, or 1. A similar question was

Re: [Open Babel] GAFF atom assignments

Thanks Geoff, I took some time to really examine the SMARTS language today and it's not so bad - I panicked when I saw things like aliphatic/aromatic. Instead of writing a parser, I am going to try and use a bunch of if/else clauses. Would it be logically sound to proceed from bottom of the list

[Open Babel] Assigning GAFF Torsion Params according to PN value?

In the gaff.dat force field paramater, there are different torsion values of n, gamma, vn_half for c3-c3-c3-c3 chains. I consulted the Amber specification, and it says that if PN is negative, it means that 'additional parameters have to be read'. It was my understanding that the torsional energ

Re: [Open Babel] formal charges

Formal charges for Gasteiger partial charge assignment. typer.cpp seems to indicate that it assigns formal charges but I couldn't find the specific line.. On Wed, Dec 21, 2011 at 8:55 PM, Geoff Hutchison wrote: > > How are formal charges assigned in a molecule? I can't seem to find the > code oth

[Open Babel] formal charges

Hello, How are formal charges assigned in a molecule? I can't seem to find the code other than setPartialCharge and getPartialCharge accessors. Thanks, - Eric -- Write once. Port to many. Get the SDK and tools to simplif

Re: [Open Babel] GAFF atom assignments

solely on bond connectivities. Thanks, - Eric On Mon, Dec 19, 2011 at 8:44 PM, Geoff Hutchison wrote: > > On Dec 19, 2011, at 7:48 PM, Eric Jang wrote: > > *1. Is the assignment of atom types somehow based on the SMARTS string of > a molecule? *It would make sense that ea

Re: [Open Babel] GAFF atom assignments

Thanks for pointing out parsmart.cpp! Sorry, let me rephrase my question (or separate my many related questions): I have a very basic atomic structure (not part of OpenBabel) that I am implementing and I would like to assign GAFF atom types to it. All I know are the element names and the types of

[Open Babel] GAFF atom assignments

Hello, I am trying to figure out how the forcefieldgaff.cpp file reads the gaff.prm file to assign atom types. Given a molecular model where I know the bonds connected between atoms (and I know their basic element name C,N,O,H, etc.), how can I deduce their atom type? (e.g. n2,n1,cp,cd, etc.) wit

[Open Babel] bond stretch constant

hello, I am using the obenergy program and GAFF force field to compute the potential energy of some molecule, according to the following program example: obenergy -ff GAFF /Users/Eric/Desktop/ExampleMolecules/GAFF-test-set/21208702.mol according to forcefieldgaff.cpp, the energy is given by the s

Re: [Open Babel] Fwd: debug openbabel

/ExampleMolecules/GAFF-test-set/twocarbons.mol Sorry again for the bother! On Sat, Dec 10, 2011 at 3:46 PM, Eric Jang wrote: > Oops, I spoke too soon. Turns out that obenergy.cpp prints its promo > message correctly but I think I need to compile all of the .o object files > that get linked into ob

Re: [Open Babel] Fwd: debug openbabel

e and link the .o files myself? Do I need to make modifications to CMakeLists.txt file? Thanks On Sat, Dec 10, 2011 at 3:25 PM, Eric Jang wrote: > Hello, > > I haven't been able to get the XCode generator to work, but what I found > is that if I follow the standard build inst

Re: [Open Babel] Fwd: debug openbabel

at has now been fixed. > > An alternative IDE you could use is Eclipse (with the C++ extensions). > I (think I) have successfully compiled Open Babel under this in the > past. > > - Noel > > On 27 November 2011 18:59, Eric Jang wrote: > > > > > >

[Open Babel] Fwd: debug openbabel

-- Forwarded message -- From: Eric Jang Date: Sat, Nov 26, 2011 at 8:03 PM Subject: Re: [Open Babel] debug openbabel To: Noel O'Boyle I ran cmake -G Xcode ../openbabel-2.3.1 and it produced the xcodeproj file. However when I try to open the file, it says that XCode cannot

[Open Babel] debug openbabel

Hello! I was wondering if someone could show me how to build a debuggable version of OpenBabel? Specifically I want to step through the *obenergy* program. I asked earlier how to port over to XCode (since that would give me a better understanding of where I am and what vars are present), but perha

[Open Babel] port GAFF parameters for use in another program

... Thanks! Eric Jang -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this

[Open Babel] cmake to generate xcode project from OpenBabel

Hello, I am trying to use CMake to auto-generate an xcode project so I can access the debugger interface in XCode. I was wondering if someone could show me how to set up the procedure using the GUI interface to CMake or command line so that I can compile OpenBabel in XCode (and use the GUI debugger