annotate CADDSuite/data/OpenBabel/superatom.txt @ 3:ff6df146c0d5

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# Translations of superatom labels to SMILES.
# First atom of SMILES string should be the one connected to the rest of
# the molecule.
# Empty lines and lines starting with # are ignored.
# Originally from http://cactus.nci.nih.gov/osra/
# The left-aligned form is the one recognized in MDL alias lines;
# the right-aligned form may be used in 2D depiction.
# The whole list is used to look up alias names;
# only the part up to a line starting with ## is used to generate aliases.
# and here the largest fragments should be first; 
#left    right    SMILES		color
CO2Et    EtO2C    C(=O)OCC
COOEt    EtOOC    C(=O)OCC
OiBu     iBuO     OCC(C)C
tBu      tBu      C(C)(C)C
nBu      nBu      CCCC
iPr      iPr      C(C)C
nPr      nPr      CCC
Et       Et       CC
NCF3     F3CN     NC(F)(F)F
CF3      F3C      C(F)(F)F
CCl3	 Cl3C     C(Cl)(Cl)Cl
CN       NC       C#N
NC       CN       [N+]#[C-]
N(OH)CH3 CH3(OH)N N(O)C
NO2      O2N      N(=O)=O
NO       ON       N=O
SO3H     HO3S     S(=O)(=O)O
COOH     HOOC     C(=O)O		blue
OEt      EtO      OCC
OAc      AcO      OC(=O)C
NHAc     AcNH     NC(=O)C
Ac       Ac       C(=O)C
CHO      OHC      C=O
NMe      MeN      NC
SMe      MeS      SC
OMe      MeO      OC
COO-     -OOC     C(=O)[O-]
## Only entries above this line are used to *generate* aliases.
Ph       Ph       c1ccccc1
OR       RO       O*
R        R        *
OBz      BzO      OCc1ccccc1
THPO     THPO     O[C@@H]1OCCCC1
NOH      HON      NO 
CO2Me    MeO2C    C(=O)OC
COOMe    MeOOC    C(=O)OC
SO2Me    MeO2S    S(=O)(=O)C
NMe2     Me2N     N(C)C
CO2R     RO2C     C(=O)O*
COOR     ROOC     C(=O)O*
NHZ      ZNH      NC(=O)OCC1=CC=CC=C1
CH2OH    HOCH2    CO
CH2NH2   H2NCH2   CN
Me       Me       C
OBn      BnO      OCC1=CC=CC=C1
NHAm     AmNH     NCCCCC
OAm      AmO      OCCCCC
CO2Am    AmO2C    C(=O)OCCCCC
COOAm    AmOOC    C(=O)OCCCCC
SAm      AmS      SCCCCC
NHBn     BnNH     NCC1=CC=CC=C1
CO2Bn    BnO2C    C(=O)OCC1=CC=CC=C1
SnBu3    Bu3Sn    [Sn](CCCC)(CCCC)CCCC
NHBu     BuNH     NCCCC
OBu      BuO      OCCCC
CO2Bu    BuO2C    C(=O)OCCCC
COOBu    BuOOC    C(=O)OCCCC
SBu      BuS      SCCCC
CBr3	 Br3C     C(Br)(Br)Br
NHCbz    CbzNH    NC(=O)OCC1=CC=CC=C1
SO2Cl    ClSO2    S(Cl)(=O)=O
COBr     BrCO     C(=O)Br
COBu     BuCO     C(=O)CCCC
COCF3    F3CCO    C(=O)C(F)(F)F
COCl     ClCO     C(=O)Cl
COCO     COCO     C(=O)C=O
COEt     EtCO     C(=O)CC
COF      FCO      C(=O)F
COMe     MeCO     C(=O)C
CONEt2   Et2NCO   C(=O)(CC)NCC
CONH2    H2NCO    C(=O)N
CONHEt   EtHNCO   C(=O)NCC
CONHMe   MeHNCO   C(=O)NC
CONMe2   Me2NCO   C(=O)(C)NC
COSH     HSOC     C(=O)S
NEt2     Et2N     N(CC)CC
NEt3     Et3N     N(CC)(CC)CC
NHEt     EtNH     NCC
SO2NH2   H2NSO2   S(=O)(N)=O
NHOH     HONH     ON
NMe2     Me2N     N(C)C
OMs      MsO      CS(O)(=O)=O
OCN      NCO      N=C=O
SCN      NCS      N=C=S
NHAm     AmHN     NCCCCC
NHBn     BuHN     NCC1=CC=CC=C1
NHBu     BuHN     NCCCC
NHEt     EtHB     NCC
NHOH     HOHN     NO
NHPr     PrHN     NCCC
NO       ON       N=O
POEt2    EtO2P    P(OCC)OCC
POEt3    EtO3P    P(OCC)(OCC)OCC
POOEt2   Et2OOP   P(=O)(OCC)OCC
PrNH     HNPr     CCCN
SEt      CCS      SCC
#Aliases from samples provided with InChI
CH       HC       [CH]
CH-      HC-      [CH-]
D        D        [2H]
ND2      D2N      [N]([2H])[2H]
DS       SD       [S][2H]