Protein-Prep: Support prep direct from RCSB

[jthorton]

Running our protein-prep CLI on a supported target but using a PDB structure file directly from RCSB results in a failure see the following example:

wget https://files.rcsb.org/download/5SQ1.pdb
asap-prep --target "SARS-CoV-2-Mac1"  --pdb-file 5SQ1.pdb --output-dir mac1  

DPI: 0.02, RFree: 0.17, Resolution: 1.05
Processing BU # 1 with title: NON-STRUCTURAL PROTEIN 3_, chains A
Found unresolved N-terminal with 2 residues before VAL 3 A 0 , with sequence SM
Warning: There was a problem building some missing pieces, built as much as was possible
Processing BU # 2 with title: NON-STRUCTURAL PROTEIN 3_, chains B
Warning: No ligand or sites detected, please revise inputs and/or options

In this case the prep workflow can not find the ligand, however changing the residue name to LIG fixes the issue.

cc @hmacdope @JenkeScheen

[JenkeScheen]

solution would be to expose a flag to pass the ligand entry in the PDB file. Annoying that OE doesn't catch the ligand automatically.