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name.txt
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name.txt
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# Rename rule file contains rules to format atom names and residue
# names. The purpose is to unify residue names to 3-char mcce names
# and break some big cofactors into small ones.
#
# Each line has two fields separated by at least one space. Each field
# is 14 characters long, matching the atom, residue name, chainID and
# sequence number field of a pdb line. The first string will be
# replaced by the second string.
#
# Symbol "*" in the first string is a wildcard that matchs any character.
# It means "do not replace" in the second string.
#
# The replace is accumulative in the order of appearing in this file.
#
####_###_#_### ####_###_#_###
***** ******** *****_********
****** ******* ******_*******
******* ****** *******_******
D***** ****** H*****_******
*****HEA****** *****HEM******
*CAA*HEM****** *****PAA****** extract 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 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******
*CAA*HEC****** *****PAA****** extract PAA from HECe
*CBA*HEC****** *****PAA******
*CGA*HEC****** *****PAA******
*O1A*HEC****** *****PAA******
*O2A*HEC****** *****PAA******
HAA**HEC****** *****PAA******
HBA**HEC****** *****PAA******
*H1A*HEC****** *****PAA******
*H2A*HEC****** *****PAA******
*CAD*HEC****** *****PDD****** extract PDD from HECe
*CBD*HEC****** *****PDD******
*CGD*HEC****** *****PDD******
*O1D*HEC****** *****PDD******
*O2D*HEC****** *****PDD******
HAD**HEC****** *****PDD******
HBD**HEC****** *****PDD******
*H1D*HEC****** *****PDD******
*H2D*HEC****** *****PDD******
*C11*HEM****** *****FAR****** extract FAR from heme
*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******
*O11*HEM****** *****FAR******
*CAA*CYC****** *****PAA****** extract 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 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 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 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 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 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 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 tail - 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 tail - 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 tail - 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 tail - 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 tail - 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 tail - 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 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******