From e592c58bae2f377169d0c4e93965d69c49979309 Mon Sep 17 00:00:00 2001 From: James Krieger Date: Wed, 18 Sep 2024 12:52:56 +0200 Subject: [PATCH] actually SOL CU2P CU2 in flag and docs --- prody/atomic/flags.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/prody/atomic/flags.py b/prody/atomic/flags.py index 63768d466..1247077f1 100644 --- 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