Molecules from CDXML Parser have inverted, unrealistic atomic coordinates

[greglandrum]

First the illustration. Here's a simple molecule in Chemdraw:

This is what it looks like if you read that CDXML into the RDKit:

There are two things going on here:

1. The coordinates are all much too large
2. The coordinate system is inverted: y increases from top to bottom instead of bottom to top

Configuration (please complete the following information):

• RDKit version: release and master
• OS: all