Update/extend PolyBuild documentation

polybuild/polybuild/RTPcharge.py

@@ -11,6 +11,28 @@
     conda activate polyconstruct-env
     RTPcharge
 
+**How monomer charges are adjusted by RTPCharge:**
+
+Once the connectivity information has been generated by ITP2RTP, the .rtp file
+is processed using RTPCharge to modify partial changes to ensure that each
+monomer contains an integer (or zero) net charge. The user specifies which
+atoms should be kept, and any unselected atoms are removed. Since removing
+atoms can alter the net charge, the script calculates the total charge of the
+remaining atoms and applies proportional adjustments to partial charges to
+restore the defined charge. Initially, it attempts to distribute the correction
+within a 5% tolerance of each atom's original charge. If defined charge cannot
+be achieved, it increases the tolerance to 10%. If neither threshold is
+sufficient, the script stops execution, notifying the user. Since these
+adjustments are done to all the atoms in monomer level, the relative charge
+distribution across the monomer remains similar. Therefore, the dipole moments,
+hydrogen bonding patterns, and overall electrostatic potential should not
+deviate significantly from the original system. However, the charge adjustment
+tolerance is capped at 10% to limit major alterations to partial charges. If
+the net charge of a monomer cannot be corrected within this 10% threshold,
+manual adjustment by the user is required to ensure essential chemical
+properties are accurately maintained. The final output is a modified .rtp file
+in the pdb2gmx format required to extract the monomer parameters for the final
+polymer topology.
 """
 
 import os

polytop/polytop/Dihedrals.py

@@ -13,7 +13,7 @@ class Dihedral_type(IntEnum):
     Enum to track Dihedral types including proper (1) and improper (2).
 
     Proper dihedrals also include: Ryckaert-Bellemans (3), Fourier (5),
-        proper (multiple) (9), tabulated (8) and restricted (10).
+    proper (multiple) (9), tabulated (8) and restricted (10).
     Improper dihedrals also include: periodic improper (4).
 
     For more information, see