[ghemical-devel] PDB export with ghemical 1.51

[Tommi Hassinen]

On Thu, 17 Feb 2005, Geoff Hutchison wrote:

> On Feb 17, 2005, at 10:15 AM, Avell Diroll wrote:
>
> > I am using ghemical 1.51 "before bonobo branch" (great soft !) and I
> > was wondering if there is a way to export
> > ghemical 1.51 gpr file format into pdb file format ?
> > I have the latest release of openbabel (1.100.2) which only understand
> > the "old" gpr format (from ghemical 1.01).
> > Did anyone try the openbabel cvs to check if support for gpr 1.51 was
> > added ? or found another way ?
>
> Uh, that would be my responsibility.
>
> Since I don't use 1.51 much, I haven't looked at the differences
> between the gpr 1.5x and 1.0x file formats, so there is not currently
> any way to do that. At first glance, it doesn't look like it's a huge
> change, but the Open Babel CVS won't work.

Hello,

I have been aware about the format change, but have not yet sent patches
to OpenBabel or elsewhere since I haven't been sure if the changes are
final. However now I have not changed the format anymore so it seems to be
OK for now... Following is a sample of the new format (H2O molecule):

!Header gpr 111
!Info 1 allmm 241
!Atoms 3
0 8 +0 0
1 1 +0 0
2 1 +0 0
!Bonds 2
0 1 S
0 2 S
!Coord
0 +0.0041421358473599 +0.0248528141528368 +0
1 +0.00978504773229361 +0.0233618784695864 +0.109845049679279
2 +0.0844260603189468 +0.0885083079338074 -0.0400308668613434
!PartialCharges
0 +0
1 +0
2 +0
!End

Now I repeat here the parts that have changed, and explain a bit...

!Header gpr 111
           ^^^^^	a new version number is added...
!Info 1 allmm 241
       ^^^^^^^^^^^	a "setup" class name and an "engine" class ID
			number is printed here ; this is for saving the
			state of the project so that if it was saved as
			a MM project it will open as such and the same
			for QM. valid "setups" are allmm and allqm.
			the "engine" ID can be -1 if not known, it is
			checked and subject to change anyway...

!Atoms 3
0 8 +0 0
   ^^^^^^	at atom records there are two new numbers ; first (here
		printed with sign) one is a formal charge for the atom,
		and second one is "flags" for this atom ; the flags can
		be set to zero by default. for example if the atom is
		selected and then saved the "flags" value will be
		nonzero.

I'm right now working with molecular mechanics so that it would become
better aware of the resonance structures of some organic molecules, and
also to better describe the molecules/ions. For example the structure

        \
         C--
        /

can be either a cation, a radical, or an anion. By adding the formal
charge setting these species can be properly detected in future.

!PartialCharges
 ^^^^^^^		The old !Charges section is now renamed into
			!PartialCharges (just for clarity since the formal
			charge values were added, and those are not the
			same thing as atomic partial charges).

Regards,

	Tommi