Is there a chemical input format that is-
- Supported by Open Babel (and hence supports visualization in avogadro??)
- Can represent a bond connecting an atom to its partner in a neighbouring unit cell, for crystals/systems with periodic boundary conditions
Follow up (added later):
I could not understand how cif
does it, or cml
. But it would be nice if I could get rid of the symmetry folds in the markup given below.
Here is the cif
file. The cml
output using babel
is --
<?xml version="1.0"?>
<molecule id="Calcium titanate" xmlns="http://www.xml-cml.org/schema">
<crystal>
<scalar title="a" units="units:angstrom">5.380000</scalar>
<scalar title="b" units="units:angstrom">5.440000</scalar>
<scalar title="c" units="units:angstrom">7.639000</scalar>
<scalar title="alpha" units="units:degree">90.000003</scalar>
<scalar title="beta" units="units:degree">90.000003</scalar>
<scalar title="gamma" units="units:degree">90.000003</scalar>
<symmetry spaceGroup="-P 2c 2ab">
<transform3>1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1</transform3>
<transform3>1 0 0 0.5 0 -1 0 0.5 0 0 -1 0 0 0 0 1</transform3>
<transform3>-1 0 0 0 0 -1 0 0 0 0 1 0.5 0 0 0 1</transform3>
<transform3>-1 0 0 0.5 0 1 0 0.5 0 0 -1 0.5 0 0 0 1</transform3>
<transform3>-1 0 0 0 0 -1 0 0 0 0 -1 0 0 0 0 1</transform3>
<transform3>-1 0 0 0.5 0 1 0 0.5 0 0 1 0 0 0 0 1</transform3>
<transform3>1 0 0 0 0 1 0 0 0 0 -1 0.5 0 0 0 1</transform3>
<transform3>1 0 0 0.5 0 -1 0 0.5 0 0 1 0.5 0 0 0 1</transform3>
</symmetry>
</crystal>
<atomArray>
<atom id="a1" elementType="Ti" formalCharge="4" xFract="0.000000" yFract="0.500000" zFract="0.000000"/>
<atom id="a2" elementType="Ca" formalCharge="2" xFract="0.006480" yFract="0.035600" zFract="0.250000"/>
<atom id="a3" elementType="O" formalCharge="-2" xFract="0.571100" yFract="-0.016100" zFract="0.250000"/>
<atom id="a4" elementType="O" formalCharge="-2" xFract="0.289700" yFract="0.288800" zFract="0.037300"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a4" order="1"/>
<bond atomRefs2="a4 a2" order="1"/>
</bondArray>
</molecule>