# This rename rule file defines how to standardize atom and residue names.
# Its main goal is to convert residue names to the 3-character MCCE format
# and split large cofactors into smaller components.
#
# Each rule consists of two fields, separated by exactly two spaces.
# Both fields are exactly 14 characters long, corresponding to the atom name,
# residue name, chain ID, and sequence number in a PDB file.
# The first field is the pattern to match; the second is the replacement.
#
# The "*" character in the first field acts as a wildcard, matching any character.
# In the replacement field, "*" means "keep the original character".
#
# Rules are applied sequentially in the order they appear in this file.
#
####_###_#_###  ####_###_#_###
***** ********  *****_********
****** *******  ******_*******
******* ******  *******_******
 D***** ******   H*****_******
 D************   H************
DD***** ******  HD*****_******
DD************  HD************
DE***** ******  HE*****_******
DE************  HE************
*****HEA******  *****HEM******
*****HEC******  *****HEM******
*CAA*HEM******  *****PAA******      extract propionate PAA from heme
*CBA*HEM******  *****PAA******
*CGA*HEM******  *****PAA******
*O1A*HEM******  *****PAA******
*O2A*HEM******  *****PAA******
HAA**HEM******  *****PAA******
HBA**HEM******  *****PAA******
*H1A*HEM******  *****PAA******
*H2A*HEM******  *****PAA******
*CAD*HEM******  *****PDD******      extract propionate PDD from heme
*CBD*HEM******  *****PDD******
*CGD*HEM******  *****PDD******
*O1D*HEM******  *****PDD******
*O2D*HEM******  *****PDD******
HAD**HEM******  *****PDD******
HBD**HEM******  *****PDD******
*H1D*HEM******  *****PDD******
*H2D*HEM******  *****PDD******

*C11*HEM******  *****FAR******      extract aliphatic farnesyl tail FAR from heme
*O11*HEM******  *****FAR******
*C12*HEM******  *****FAR******
*C13*HEM******  *****FAR******
*C14*HEM******  *****FAR******
*C15*HEM******  *****FAR******
*C16*HEM******  *****FAR******
*C17*HEM******  *****FAR******
*C18*HEM******  *****FAR******
*C19*HEM******  *****FAR******
*C20*HEM******  *****FAR******
*C21*HEM******  *****FAR******
*C22*HEM******  *****FAR******
*C23*HEM******  *****FAR******
*C24*HEM******  *****FAR******
*C25*HEM******  *****FAR******
*C26*HEM******  *****FAR******
*C27*HEM******  *****FAR******

*CAA*CYC******  *****PAA******      extract proprionate PAA from cyc  added by Gehan (07/26/22)
*CBA*CYC******  *****PAA******
*CGA*CYC******  *****PAA******
*O1A*CYC******  *****PAA******
*O2A*CYC******  *****PAA******
*H02*CYC******  HAA1*PAA******
*H24*CYC******  HAA2*PAA******
*H07*CYC******  HBA1*PAA******
*H28*CYC******  HBA2*PAA******
*CAD*CYC******  *****PDD******      extract propionate PDD from cyc  added by Gehan (07/26/22)
*CBD*CYC******  *****PDD******
*CGD*CYC******  *****PDD******
*O1D*CYC******  *****PDD******
*O2D*CYC******  *****PDD******
*H05*CYC******  HAD1*PDD******
*H27*CYC******  HAD2*PDD******
*H10*CYC******  HBD1*PDD******
*H31*CYC******  HBD2*PDD******

 O **ACT******   O_***********
 C **ACT******   C_***********
 O **CMO******   O_***********
 C **CMO******   C_***********
 O **CSS******   O_***********
 C **CSS******   C_***********
 N **CSS******   N_***********
 O **PCA******   O_***********
 C **PCA******   C_***********
 N **PCA******   N_***********
 O **ACN******   O_***********
 C **ACN******   C_***********
***** ZN******  *****_ZN******
***** NA******  *****_NA******

*NA  CLA******  *N1A CLA******      rename Chl a/b/d/f atoms - added by Gehan 
*NB  CLA******  *N1B CLA******          
*NC  CLA******  *N1C CLA******      
*ND  CLA******  *N1D CLA******      
*NA  CLB******  *N1A CLB******      
*NB  CLB******  *N1B CLB******      
*NC  CLB******  *N1C CLB******      
*ND  CLB******  *N1D CLB******      
*NA  CL7******  *N1A CL7******      
*NB  CL7******  *N1B CL7******      
*NC  CL7******  *N1C CL7******      
*ND  CL7******  *N1D CL7******      
*NA  F6C******  *N1A F6C******      
*NB  F6C******  *N1B F6C******      
*NC  F6C******  *N1C F6C******      
*ND  F6C******  *N1D F6C******      
*NA  CHL******  *N1A CHL******      
*NB  CHL******  *N1B CHL******      
*NC  CHL******  *N1C CHL******      
*ND  CHL******  *N1D CHL******      
*NA  AvB******  *N1A AvB******      rename Chl a vs b atoms           - added by Gehan
*NB  AvB******  *N1B AvB******
*NC  AvB******  *N1C AvB******
*ND  AvB******  *N1D AvB******   
*NA  FRL******  *N1A FRL******      rename FRL-Chl a vs d vs f atoms  - added by Gehan
*NB  FRL******  *N1B FRL******
*NC  FRL******  *N1C FRL******
*ND  FRL******  *N1D FRL******
*NA  AOB******  *N1A AOB******      rename Chl a vs b atoms           - added by Gehan
*NB  AOB******  *N1B AOB******
*NC  AOB******  *N1C AOB******
*ND  AOB******  *N1D AOB******

*C1  CL*******  *C1  CT1******      create Chl a/b/d aliphatic tail - added by Gehan
*C2  CL*******  *C2  CT1******
*C3  CL*******  *C3  CT1******
*C4  CL*******  *C4  CT1******
*C5  CL*******  *C5  CT1******
*C6  CL*******  *C6  CT2******
*C7  CL*******  *C7  CT2******
*C8  CL*******  *C8  CT2******
*C9  CL*******  *C9  CT2******
*C10 CL*******  *C10 CT2******
*C11 CL*******  *C11 CT3******
*C12 CL*******  *C12 CT3******
*C13 CL*******  *C13 CT3******
*C14 CL*******  *C14 CT3******
*C15 CL*******  *C15 CT3******
*C16 CL*******  *C16 CT4******
*C17 CL*******  *C17 CT4******
*C18 CL*******  *C18 CT4******
*C19 CL*******  *C19 CT4******
*C20 CL*******  *C20 CT4******

*C1  CHL******  *C1  CT1******      create CHL aliphatic tail - added by Gehan
*C2  CHL******  *C2  CT1******
*C3  CHL******  *C3  CT1******
*C4  CHL******  *C4  CT1******
*C5  CHL******  *C5  CT1******
*C6  CHL******  *C6  CT2******
*C7  CHL******  *C7  CT2******
*C8  CHL******  *C8  CT2******
*C9  CHL******  *C9  CT2******
*C10 CHL******  *C10 CT2******
*C11 CHL******  *C11 CT3******
*C12 CHL******  *C12 CT3******
*C13 CHL******  *C13 CT3******
*C14 CHL******  *C14 CT3******
*C15 CHL******  *C15 CT3******
*C16 CHL******  *C16 CT4******
*C17 CHL******  *C17 CT4******
*C18 CHL******  *C18 CT4******
*C19 CHL******  *C19 CT4******
*C20 CHL******  *C20 CT4******

*C1  AvB******  *C1  CT1******      create chlorophyll aliphatic tail for A vs B - added by Gehan
*C2  AvB******  *C2  CT1******
*C3  AvB******  *C3  CT1******
*C4  AvB******  *C4  CT1******
*C5  AvB******  *C5  CT1******
*C6  AvB******  *C6  CT2******
*C7  AvB******  *C7  CT2******
*C8  AvB******  *C8  CT2******
*C9  AvB******  *C9  CT2******
*C10 AvB******  *C10 CT2******
*C11 AvB******  *C11 CT3******
*C12 AvB******  *C12 CT3******
*C13 AvB******  *C13 CT3******
*C14 AvB******  *C14 CT3******
*C15 AvB******  *C15 CT3******
*C16 AvB******  *C16 CT4******
*C17 AvB******  *C17 CT4******
*C18 AvB******  *C18 CT4******
*C19 AvB******  *C19 CT4******
*C20 AvB******  *C20 CT4******

*C1  FRL******  *C1  CT1******      create chlorophyll aliphatic tail for FRL-CHL a vs d vs f - added by Gehan
*C2  FRL******  *C2  CT1******
*C3  FRL******  *C3  CT1******
*C4  FRL******  *C4  CT1******
*C5  FRL******  *C5  CT1******
*C6  FRL******  *C6  CT2******
*C7  FRL******  *C7  CT2******
*C8  FRL******  *C8  CT2******
*C9  FRL******  *C9  CT2******
*C10 FRL******  *C10 CT2******
*C11 FRL******  *C11 CT3******
*C12 FRL******  *C12 CT3******
*C13 FRL******  *C13 CT3******
*C14 FRL******  *C14 CT3******
*C15 FRL******  *C15 CT3******
*C16 FRL******  *C16 CT4******
*C17 FRL******  *C17 CT4******
*C18 FRL******  *C18 CT4******
*C19 FRL******  *C19 CT4******
*C20 FRL******  *C20 CT4******

*C1  F6C******  *C1  CT1******      create Chl f aliphatic tail - added by Gehan
*C2  F6C******  *C2  CT1******
*C3  F6C******  *C3  CT1******
*C4  F6C******  *C4  CT1******
*C5  F6C******  *C5  CT1******
*C6  F6C******  *C6  CT2******
*C7  F6C******  *C7  CT2******
*C8  F6C******  *C8  CT2******
*C9  F6C******  *C9  CT2******
*C10 F6C******  *C10 CT2******
*C11 F6C******  *C11 CT3******
*C12 F6C******  *C12 CT3******
*C13 F6C******  *C13 CT3******
*C14 F6C******  *C14 CT3******
*C15 F6C******  *C15 CT3******
*C16 F6C******  *C16 CT4******
*C17 F6C******  *C17 CT4******
*C18 F6C******  *C18 CT4******
*C19 F6C******  *C19 CT4******
*C20 F6C******  *C20 CT4******

*C1A DGD******  *C1A DGA******      create DGD subheads, DGA and DGB head - added by Gehan (11/17/22)
*C2A DGD******  *C2A DGA******
*O1A DGD******  *O1A DGA******
*C1B DGD******  *C1B DGA******
*C2B DGD******  *C2B DGA******
*O1B DGD******  *O1B DGA******
*O1G DGD******  *O1G DGA******
*C1G DGD******  *C1G DGA******
*C2G DGD******  *C2G DGA******
*O2G DGD******  *O2G DGA******
*C3G DGD******  *C3G DGA******
*O3G DGD******  *O3G DGA******
*C1D DGD******  *C1D DGA******
*C2D DGD******  *C2D DGA******
*O2D DGD******  *O2D DGA******
*C3D DGD******  *C3D DGA******
*O3D DGD******  *O3D DGA******
*C4D DGD******  *C4D DGA******
*O4D DGD******  *O4D DGA******
*C5D DGD******  *C5D DGA******
*O6D DGD******  *O6D DGA******
*O5D DGD******  *O5D DGB******      start create DGB subhead - added by Gehan (11/17/22)
*C6D DGD******  *C6D DGB******
*C1E DGD******  *C1E DGB******
*C2E DGD******  *C2E DGB******
*O2E DGD******  *O2E DGB******
*C3E DGD******  *C3E DGB******
*O3E DGD******  *O3E DGB******
*C4E DGD******  *C4E DGB******
*O4E DGD******  *O4E DGB******
*C5E DGD******  *C5E DGB******
*O6E DGD******  *O6E DGB******
*C6E DGD******  *C6E DGB******
*O5E DGD******  *O5E DGB******

*C3A DGD******  *C3A dgd******      create DGD aliphatic tail dgd - added by Gehan (07/28/22)
*C4A DGD******  *C4A dgd******
*C5A DGD******  *C5A dgd******
*C6A DGD******  *C6A dgd******
*C7A DGD******  *C7A dgd******
*C8A DGD******  *C8A dgd******
*C9A DGD******  *C9A dgd******
*CAA DGD******  *CAA dgd******
*CBA DGD******  *CBA dgd******
*CCA DGD******  *CCA dgd******
*CDA DGD******  *CDA dgd******
*CEA DGD******  *CEA dgd******
*CFA DGD******  *CFA dgd******
*CGA DGD******  *CGA dgd******
*CHA DGD******  *CHA dgd******
*CIA DGD******  *CIA dgd******
*C3B DGD******  *C3B dgd******
*C4B DGD******  *C4B dgd******
*C5B DGD******  *C5B dgd******
*C6B DGD******  *C6B dgd******
*C7B DGD******  *C7B dgd******
*C8B DGD******  *C8B dgd******
*C9B DGD******  *C9B dgd******
*CAB DGD******  *CAB dgd******
*CBB DGD******  *CBB dgd******
*CCB DGD******  *CCB dgd******
*CDB DGD******  *CDB dgd******
*CEB DGD******  *CEB dgd******
*CFB DGD******  *CFB dgd******
*CGB DGD******  *CGB dgd******
*CHB DGD******  *CHB dgd******
*CIB DGD******  *CIB dgd******      

*C11 LMG******  *C11 lmg******     create LMG aliphatic tail lmg - added by Gehan (01/23/23)
*C12 LMG******  *C12 lmg******
*C13 LMG******  *C13 lmg******
*C14 LMG******  *C14 lmg******
*C15 LMG******  *C15 lmg******
*C16 LMG******  *C16 lmg******
*C17 LMG******  *C17 lmg******
*C18 LMG******  *C18 lmg******
*C19 LMG******  *C19 lmg******
*C20 LMG******  *C20 lmg******
*C21 LMG******  *C21 lmg******
*C22 LMG******  *C22 lmg******
*C23 LMG******  *C23 lmg******
*C24 LMG******  *C24 lmg******
*C25 LMG******  *C25 lmg******
*C26 LMG******  *C26 lmg******
*C27 LMG******  *C27 lmg******    # Skip 28
*C29 LMG******  *C29 lmg******
*C30 LMG******  *C30 lmg******
*C31 LMG******  *C31 lmg******
*C32 LMG******  *C32 lmg******
*C33 LMG******  *C33 lmg******
*C34 LMG******  *C34 lmg******
*C35 LMG******  *C35 lmg******
*C36 LMG******  *C36 lmg******
*C37 LMG******  *C37 lmg******
*C38 LMG******  *C38 lmg******
*C39 LMG******  *C39 lmg******
*C40 LMG******  *C40 lmg******
*C41 LMG******  *C41 lmg******
*C42 LMG******  *C42 lmg******
*C43 LMG******  *C43 lmg******
*C44 LMG******  *C44 lmg******
*C45 LMG******  *C45 lmg******

*C2  LMT******  *C2  lmt******     create LMT aliphatic tail lmg - added by Gehan (01/23/23)
*C3  LMT******  *C3  lmt******
*C4  LMT******  *C4  lmt******
*C5  LMT******  *C5  lmt******
*C6  LMT******  *C6  lmt******
*C7  LMT******  *C7  lmt******
*C8  LMT******  *C8  lmt******
*C9  LMT******  *C9  lmt******
*C10 LMT******  *C10 lmt******
*C11 LMT******  *C11 lmt******
*C12 LMT******  *C12 lmt******

*C9  LHG******  *C9  lhg******     create LHG aliphatic tail lhg - added by Gehan (08/02/22)
*C10 LHG******  *C10 lhg******
*C11 LHG******  *C11 lhg******
*C12 LHG******  *C12 lhg******
*C13 LHG******  *C13 lhg******
*C14 LHG******  *C14 lhg******
*C15 LHG******  *C15 lhg******
*C16 LHG******  *C16 lhg******
*C17 LHG******  *C17 lhg******
*C18 LHG******  *C18 lhg******
*C19 LHG******  *C19 lhg******
*C20 LHG******  *C20 lhg******
*C21 LHG******  *C21 lhg******
*C22 LHG******  *C22 lhg******
*C25 LHG******  *C25 lhg******
*C26 LHG******  *C26 lhg******
*C27 LHG******  *C27 lhg******
*C28 LHG******  *C28 lhg******
*C29 LHG******  *C29 lhg******
*C30 LHG******  *C30 lhg******
*C31 LHG******  *C31 lhg******
*C32 LHG******  *C32 lhg******
*C33 LHG******  *C33 lhg******
*C34 LHG******  *C34 lhg******
*C35 LHG******  *C35 lhg******
*C36 LHG******  *C36 lhg******
*C37 LHG******  *C37 lhg******
*C38 LHG******  *C38 lhg******

*C9  SQD******  *C9  sqd******     create SQD aliphatic tail sqd - added by Gehan (09/19/22)
*C10 SQD******  *C10 sqd******
*C11 SQD******  *C11 sqd******
*C12 SQD******  *C12 sqd******
*C13 SQD******  *C13 sqd******
*C14 SQD******  *C14 sqd******
*C15 SQD******  *C15 sqd******
*C16 SQD******  *C16 sqd******
*C17 SQD******  *C17 sqd******
*C18 SQD******  *C18 sqd******
*C19 SQD******  *C19 sqd******
*C20 SQD******  *C20 sqd******
*C21 SQD******  *C21 sqd******
*C22 SQD******  *C22 sqd******
*C25 SQD******  *C25 sqd******
*C26 SQD******  *C26 sqd******
*C27 SQD******  *C27 sqd******
*C28 SQD******  *C28 sqd******
*C29 SQD******  *C29 sqd******
*C30 SQD******  *C30 sqd******
*C31 SQD******  *C31 sqd******
*C32 SQD******  *C32 sqd******
*C33 SQD******  *C33 sqd******
*C34 SQD******  *C34 sqd******
*C35 SQD******  *C35 sqd******
*C36 SQD******  *C36 sqd******
*C37 SQD******  *C37 sqd******
*C38 SQD******  *C38 sqd******

*C **BCT******  *CT**BCT******      added by Gehan 
CA    CA******   CA  CA ******      added by Gehan
CL    CL******   CL  CL ******      added by Gehan
MG    MG******   MG  MG ******      added by Gehan
*****OEX******  *****OEC******
*C8  UNL******  *C8  UNL******      added by Gehan
SE  *MSE******   SD *MET******
*****MSE******  *****MET******
*****HIE******  *****HIS******
*****HID******  *****HIS******

*NA  CCC******  *N1A CCC******      rename CCC-Chl a vs d vs f atoms  - added by Gehan
*NB  CCC******  *N1B CCC******
*NC  CCC******  *N1C CCC******
*ND  CCC******  *N1D CCC******
*C1  CCC******  *C1  CT1******      create Chl a/b/d tail - added by Gehan
*C2  CCC******  *C2  CT1******
*C3  CCC******  *C3  CT1******
*C4  CCC******  *C4  CT1******
*C5  CCC******  *C5  CT1******
*C6  CCC******  *C6  CT2******
*C7  CCC******  *C7  CT2******
*C8  CCC******  *C8  CT2******
*C9  CCC******  *C9  CT2******
*C10 CCC******  *C10 CT2******
*C11 CCC******  *C11 CT3******
*C12 CCC******  *C12 CT3******
*C13 CCC******  *C13 CT3******
*C14 CCC******  *C14 CT3******
*C15 CCC******  *C15 CT3******
*C16 CCC******  *C16 CT4******
*C17 CCC******  *C17 CT4******
*C18 CCC******  *C18 CT4******
*C19 CCC******  *C19 CT4******
*C20 CCC******  *C20 CT4******

*NA  HOC******  *N1A HOC******      rename HOC-Chl a vs b atoms  - added by Gehan
*NB  HOC******  *N1B HOC******
*NC  HOC******  *N1C HOC******
*ND  HOC******  *N1D HOC******
*C1  HOC******  *C1  CT1******      create Chl a/b/d aliphatic tails - added by Gehan
*C2  HOC******  *C2  CT1******
*C3  HOC******  *C3  CT1******
*C4  HOC******  *C4  CT1******
*C5  HOC******  *C5  CT1******
*C6  HOC******  *C6  CT2******
*C7  HOC******  *C7  CT2******
*C8  HOC******  *C8  CT2******
*C9  HOC******  *C9  CT2******
*C10 HOC******  *C10 CT2******
*C11 HOC******  *C11 CT3******
*C12 HOC******  *C12 CT3******
*C13 HOC******  *C13 CT3******
*C14 HOC******  *C14 CT3******
*C15 HOC******  *C15 CT3******
*C16 HOC******  *C16 CT4******
*C17 HOC******  *C17 CT4******
*C18 HOC******  *C18 CT4******
*C19 HOC******  *C19 CT4******
*C20 HOC******  *C20 CT4******

*C1  AOB******  *C1  CT1******      create chlorophyll aliphatic tail for A vs B  noMethyl - added by Gehan
*C2  AOB******  *C2  CT1******
*C3  AOB******  *C3  CT1******
*C4  AOB******  *C4  CT1******
*C5  AOB******  *C5  CT1******
*C6  AOB******  *C6  CT2******
*C7  AOB******  *C7  CT2******
*C8  AOB******  *C8  CT2******
*C9  AOB******  *C9  CT2******
*C10 AOB******  *C10 CT2******
*C11 AOB******  *C11 CT3******
*C12 AOB******  *C12 CT3******
*C13 AOB******  *C13 CT3******
*C14 AOB******  *C14 CT3******
*C15 AOB******  *C15 CT3******
*C16 AOB******  *C16 CT4******
*C17 AOB******  *C17 CT4******
*C18 AOB******  *C18 CT4******
*C19 AOB******  *C19 CT4******
*C20 AOB******  *C20 CT4******
