Version 1.1.0

Various bug fixes and improvements.

Improvements (general):

• Documentation has been streamlined
• Configuration files are now useable to specify input parameters
• martinize2 is now a core dependency
• To install all optional dependencies, the command is now CCD2MD[membrane] to avoid issues pulling all versions with CCD2MD[all]

Improvements (conversion, everything but pos2cif):

• MD operations can now be specified
• Solvated boxes can now be created for non-membrane proteins
• Steering of predicted ligands to reference structure for chirality fixes
• Can specify own titles for output files

Improvements (pos2cif):

• pos2cif can now create AF3 input files without needing to convert a ligand
• pos2cif can create a userCCD file utilising converted ligands, user
  specified cif files and CCD2MD.cif
• Number of ligands can now be specified numerically, allowing for lipid/detergent flooding

Bug fixes:

• Changed (incorrect) CCD code for POPE
• Fixing issue from Chai where cif files had split lines
• pos2cif now accepts tabs in input files
• Fixing issue where inputting optional arguments caused crashes