actually SOL CU2P CU2 in flag and docs

jamesmkrieger · Sep 18, 2024 · e592c58 · e592c58
1 parent 2106747
commit e592c58
Showing 1 changed file with 8 additions and 3 deletions.
diff --git a/prody/atomic/flags.py b/prody/atomic/flags.py
@@ -148,12 +148,12 @@
     'pyrimidine': set(['CYT', 'C', 'THY', 'T', 'URA', 'U']),
 
     'water': set(['HOH', 'DOD', 'WAT', 'TIP3', 'H2O', 'OH2', 'TIP', 'TIP2',
-                  'TIP4', 'SPC']),
+                  'TIP4', 'SPC', 'SOL']),
 
     'ion': set(['AL', 'BA', 'CA', 'CD', 'CL', 'CO', 'CS', 'CU', 'CU1', 'CUA',
                 'HG', 'IN', 'IOD', 'K', 'MG', 'MN', 'MN3', 'NA', 'PB', 'PT', 'RB',
                 'TB', 'TL', 'WO4', 'YB', 'ZN']),
-    'ion_other': set(['CAL', 'CES', 'CLA', 'POT', 'SOD', 'ZN2']),
+    'ion_other': set(['CAL', 'CES', 'CLA', 'POT', 'SOD', 'ZN2', 'CU2', 'CU2P']),
 
 
     'lipid': set(['GPE', 'LPP', 'OLA', 'SDS', 'STE']),
@@ -553,10 +553,15 @@ def changeBackbone(flag, names):
       POT      potassium           No     CHARMM    Yes
       SOD      sodium              No     CHARMM    Yes
       ZN2      zinc                No     CHARMM    No
+      CU2P     copper (ii)         No     CHARMM    No
+      CU2      copper (ii)         No     CHARMM    No
       =======  ==================  =====  ========  ==========
 
       Ion identifiers that are obsoleted by *PDB* (MO3, MO4, MO5, MO6, NAW,
-      OC7, and ZN1) are removed from this definition.
+      OC7, and ZN1) are removed from this definition. 
+
+      CU2 comes from CU2P if parsing PDB files without long_resname
+      or writing them again (always trims to 3-character resnames).
 
 
    lipid