[ghemical-devel] Exporting from GChemPaint to Ghemical

[Jean Bréfort]

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Le mar 29/06/2004 =C3=A0 12:51, Tommi Hassinen a =C3=A9crit :
> On Tue, 29 Jun 2004, Jean Br=C3=A9fort wrote:
>=20
> > Hi,
> >
> > I am currently implementing the export of a molecule from GChemPaint to
> > Ghemical (using a temporary gpr file written with OpenBabel). I would
> > like that the molecule appears centered in Ghemical's view but I don't
>=20
> Hello,
>=20
> the molecule should appear centered when the sum (or average) of all x, y
> and z coordinates are zero. You can do this by calculating first averages
> of x, y and z coordinates and then translating like this:
>=20
> 	new_x =3D old_x - average_x;
> 	new_y =3D old_y - average_y;
> 	new_z =3D old_z - average_z;
>=20
> > understand the coordinate system used in Ghemical. I can easily
> > translate the molecule but the question is where?
>=20
> The graphics code work so that actually the atom coordinates are always
> the same, but instead the "camera" coordinates are changed. That is more
> complicated but perhaps you can look at camera.cpp and tools.cpp to see
> how the translations/rotations work in the mouse tools.
>=20
> But averaging the coordinates should do the centering trick.
>=20

Thanks, it works. I must now try to transfer as far as possible the
stereochemistry (not so simple). At the moment, when I transfer a
molecule such as cholesterol with all z coordinates set at 0., I cannot
optimize the geometry (nan values everywhere). More simple molecules
work. Have a nice summer.

Regards,

Jean

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