#1 Output errors when input molecule has disjoint pieces

[Matthew Baumgartner]

When the input file has multiple disjoint compounds, such as in the attached files where there are two residues in the input pdb file, smina produces a seemingly valid output file that pymol reads without error. However, babel fails to convert the output file with the error:

==============================
*** Open Babel Warning in ReadMolecule
WARNING: Problems reading a MDL file
Invalid bond specification

To reproduce:
smina -r MDM2_1YCR.pdb -l pyrvinium_pamoate.pdb -o docked_out.sdf --autobox_ligand MDM2_1YCR.pdb

[David Koes]

Fixed by stripping the molecule of all but the largest component.
cc3aa927a1cc480236aed2a5ca83a4d167bd47ec