modifications.txt

2024-11-06:
- problem patched that happened when column 3 of the last line in resNo_diff.txt was bigger than 2
- patch added to account if ACE or NME residues would be in the original pdb and to be included in truncated protein. (In this case no additional residues are retained at N-term or C-term peptide end.)
- patch added to include additional C atom of ACE or NME residues (LEaP has tendency to place the missing heavy atom in a weird spot, so retaining the additional carbon prevents this issue.) 

2024-09-27:
- added 'debug' boolean (this prevents output files to be removed if set to True)
- added 'remove_single_residues' boolean (this prevents the removal of single residues if set to False)
- added variable to pass original pdb file
- radius to truncate is variable (set at start of script)
- starts from cleaned pdb (only ATOM or HETATM records)
- added test if pdb is configured with or withour chainID (this is used for truncating from predefined list ; this is not yet implemented)
- generation of residue list to retain now possible if chainID is present
- residue list is checked versus internal cpptraj numbering (this is required for irregular numbering in the original pdb)
- LigandRes is checked for numeric input or not
- NtermRes and CtermRes strings are only written if more than one peptide string are required and first residue is not 1 or last residue is not last protein residue, respectively
- lines_to_patch bugfix if following residue number is smaller than previous residue number