#2 Connectivity between atoms

[Anonymous]

Originally created by: perdig...@yahoo.com
Originally owned by: perdig...@yahoo.com

1. Opening molecular structure files in control that do not contain
information about connectivity between atoms. This applies to XYZ files and
PDB files without CONNECT lines

Some atoms may form connections when they are not expected. In other cases,
two atoms are not connected when they were supposed to be.

Code:

In LPMolecule, the AUTOCONNECTDISTANCE is used when connectivity
information is not provided. The value is set to 1.85 (Angstrons) as default.

Solution:

1. Avoid molecular structure files without connectivity information
2. Come up with a smarter autoconnectivity algorithm.