Daylight Conversion Package Appendix

Example Files

Example input and output files are shown below:

SMILES:

CCCCOCCOCCOC(=O)CCCCCCCCC(=O)O
ClCCN(Cl)(C)(C)C 3334
C=CCOc1ccc(cc1)C(C)Cc2ccc(cc2)OCC=C 56XC
 678C2

Isomeric SMILES:

Cc1ccc(NC(=O)C(=O)N/N=C/C=C/c2ccccc2)cc1 S46282
C[C@@]12CC[C@H]3[C@@H](CC[C@@H]4C[C@@H](O)CC[C@@]43C)[C@]2(O)CC[C@H]1c5ccc(=O)oc5 7743
CN1Cc2c(ncn2-c3ccc(F)cc3C1=O)C(=O)OCC[18F]
C[Si](N[Si](C)(C)C)(C)C 4413

SMARTS:

[Cl,Br][C;v4]([C][C]([C])[C][C])[N][C]
[C][c]:1:[c]:[c]:[c]([C]):[c]:[c]1 LST12
[c,n]:[14c]:[!c;!o;H0]:[c;!H0] XCD123

SMIRKS:

[!#6;!#1:1][C@:5]([C,c:2])([F:3])[Cl:4]>>[!S;!N:1][C@:5]([C,c:2])([F:3])[Cl:4] 19
[C]C1=[C][N][C]=C1[N]>>[C]C1=[C][N][C]=C1[N]
[C]c1[c][n]([H])[c]c1[N]>>[C]c1[c][n]([H])[c]c1[N] transform2

molfile:

33456
  DCIS

  7  5  0     0  0              1 V2000
    0.4552    0.3828    0.0000 C   0  0  0  0  0  0  0  0  0
    1.1552   -0.0448    0.0000 C   0  0  0  0  0  0  0  0  0
   -0.2759   -0.0103    0.0000 C   0  0  0  0  0  0  0  0  0
    1.1379   -0.8724    0.0000 O   0  0  0  0  0  0  0  0  0
    1.8862    0.3517    0.0000 O   0  0  0  0  0  0  0  0  0
   -0.9759    0.4172    0.0000 C   0  0  0  0  0  0  0  0  0
   -3.3828   -0.2241    0.0000 Na  0  3  0  0  0  0  0  0  0
  1  2  1  0  0  0
  1  3  1  0  0  0
  2  4  1  0  0  0
  2  5  2  0  0  0
  3  6  1  0  0  0
M  CHG  1   7   1
M  END

molfile (query):

785
  DCIS

 10  9  1  0  0  0  0  0  0  0999 V2000
    3.5875   -6.7958    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
    4.3000   -6.3792    0.0000 L   0  0  0  0  0  0  0  0  0  0  0  0
    2.8708   -6.3833    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8708   -7.2042    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9958   -7.5083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5811   -8.2215    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
    3.9913   -8.9373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7561   -8.2188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8697   -5.5583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8083   -8.9333    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  5  6  1  0  0  0  0
  1  2  1  0  0  0  0
  6  7  1  0  0  0  0
  1  4  1  0  0  0  0
  6  8  1  0  0  0  0
  3  9  1  0  0  0  0
  7 10  1  0  0  0  0
  1  5  1  0  0  0  0
M  ALS   2  4 F F   Cl  Br  I
M  END

SDfile:

90003-X
  smi2mol

  7  7  0     0  0              1 V2000
    0.0000   -0.6828    0.0000 N   0  3  0  0  0  0  0  0  0
    1.2379    0.0483    0.0000 C   0  0  0  0  0  0  0  0  0
   -1.2379    0.0483    0.0000 C   0  0  0  0  0  0  0  0  0
    0.0000   -2.1103    0.0000 O   0  5  0  0  0  0  0  0  0
    1.2379    1.4724    0.0000 C   0  0  0  0  0  0  0  0  0
   -1.2379    1.4724    0.0000 C   0  0  0  0  0  0  0  0  0
    0.0000    2.2034    0.0000 N   0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0
  1  3  2  0  0  0
  1  4  1  0  0  0
  2  5  2  0  0  0
  3  6  1  0  0  0
  5  7  1  0  0  0
  6  7  2  0  0  0
M  END
> <MOLNAME>
90003-X
> <MOL.WEIGHT>
96.088
$$$$

RGfile:

$MDL  REV  1 0107081157
$MOL
$HDR
1R-23
  -ISIS-  01070811572D

$END HDR
$CTAB
  7  7  0  0  0  0  0  0  0  0999 V2000
    4.5000    0.0208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5000   -0.8042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2120   -1.2125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9240   -0.8042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9240    0.0208    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
    5.2120    0.4375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6397    0.4312    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
  5  7  1  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  RGP  1   7   1
M  LOG  1   1   0   0   >0
M  END
$END CTAB
$RGP
   1
TAB
  3  2  0  0  0  0  0  0  0  0999 V2000
   -0.5544   -4.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1600   -3.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5439   -4.8542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
M  APO  1   3   1
M  END
$END CTAB
$CTAB
  3  2  0  0  0  0  0  0  0  0999 V2000
    1.4873   -4.0500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2017   -3.6375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4873   -4.8750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
M  APO  1   3   1
M  END
$END CTAB
$CTAB
  2  1  0  0  0  0  0  0  0  0999 V2000
    3.5542   -5.0666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2686   -4.6541    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  APO  1   1   1
M  END
$END CTAB
$END RGP
$END MOL

RDfile (molecule):

$RDFILE 1
$DATM    12/05/05 22:51
$MFMT $MIREG 1

  smi2rd

  7  7  0     0  0            999 V2000
    0.4483    0.6655    0.0000 C   0  0  0  0  0  0  0  0  0
   -0.8552    1.4172    0.0000 C   0  0  0  0  0  0  0  0  0
    0.4483   -0.8414    0.0000 C   0  0  0  0  0  0  0  0  0
    1.7483    1.4172    0.0000 Se  0  0  0  0  0  0  0  0  0
   -2.1586    0.6655    0.0000 C   0  0  0  0  0  0  0  0  0
   -0.8552   -1.5931    0.0000 C   0  0  0  0  0  0  0  0  0
   -2.1586   -0.8414    0.0000 C   0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0
  1  3  2  0  0  0
  1  4  1  0  0  0
  2  5  2  0  0  0
  3  6  1  0  0  0
  5  7  1  0  0  0
  6  7  2  0  0  0
M  END
$DTYPE MOL:NAME
$DATUM SECC4
$DTYPE MOL:EXTREG
$DATUM 112
$DTYPE MOL:MOLECULAR.WEIGHT
$DATUM 157.073

RDfile (reaction):

$RDFILE 1
$DATM    12/06/05 21:51
$RFMT $RIREG 1
$RXN

  SMI2RD REACTION

  1  2
$MOL

  smi2rd

  6  6  0  0  0  0              1 V2000
    0.0000    1.5422    0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0
   -1.3335    0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  2  0  0
    1.3335    0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  3  0  0
   -1.3335   -0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  4  0  0
    1.3335   -0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  5  0  0
    0.0000   -1.5422    0.0000 C   0  0  0  0  0  0  0  0  0  6  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
$MOL

  smi2rd

  7  7  0  0  0  0              1 V2000
   10.0047    0.6541    0.0000 C   0  0  3  0  0  0  0  0  0  1  0  0
   -1.3315   -0.1191    0.0000 C   0  0  0  0  0  0  0  0  0  2  0  0
   11.3315   -0.1191    0.0000 C   0  0  0  0  0  0  0  0  0  3  0  0
   10.0070    2.1935    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3315   -1.6585    0.0000 C   0  0  0  0  0  0  0  0  0  4  0  0
   11.3315   -1.6585    0.0000 C   0  0  0  0  0  0  0  0  0  5  0  0
   10.0047   -2.4341    0.0000 C   0  0  0  0  0  0  0  0  0  6  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
$MOL

  smi2rd

  7  7  0  0  0  0              1 V2000
    0.0000    0.6445    0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0
    1.3312   -0.1148    0.0000 C   0  0  0  0  0  0  0  0  0  2  0  0
   -1.3312   -0.1148    0.0000 C   0  0  0  0  0  0  0  0  0  3  0  0
    0.0000    2.2006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3312   -1.6569    0.0000 C   0  0  0  0  0  0  0  0  0  4  0  0
   -1.3312   -1.6569    0.0000 C   0  0  0  0  0  0  0  0  0  5  0  0
    0.0000   -2.4420    0.0000 C   0  0  0  0  0  0  0  0  0  6  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  2  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
$DTYPE RXN:VARIATION(1):NAME
$DATUM DD45
$DTYPE RXN:VARIATION(1):CONC
$DATUM (0.25 mmol)
$DTYPE RXN:VARIATION(1):CATALYST(1):REGNO
$DATUM $MFMT $MIREG 432

  smi2rd

  3  2  0  0  0  0              1 V2000
    1.1893   -0.1551    0.0000 C   0  0  0  0  0  0
   -0.1395   -0.9334    0.0000 C   0  0  0  0  0  0
    1.1893    1.3753    0.0000 O   0  0  0  0  0  0
  1  2  1  0  0  0
  1  3  2  0  0  0
M  END

TDT (structure branched on $NAM):

$SMI<Ic1cccc(C=O)c1>
2D<-1.26,5.02,-0.75,4.14,-1.27,3.29,-0.76,2.41,0.25,2.41,0.76,3.27,1.77,3.27,
2.28,2.40,0.25,4.14,,,,,,,,,,>
$NAM<N1a>
CAT<Supplier1;500026271;Fine;62.10/G USD>
$NAM<N1b>
CAT<Supplier2;800045;Fine;65.55/G USD per 5 G>
|

TDT (non-structure):

$NAM<BB2948>
CFLAG<0>
VIS<>
BST<>
EXTREG<XR32D>
RN<CR01050>
COMMENT<Structure unknown>
|

SQLLDR .dat:

XX12;
CODE;
36A
XX12;
Assay1;
45.23

SQLLDR .str:

general_line1;
general_line1;
NC(Br)C(=O)O;
1.215,3.230,0.485,2.510,0.225,1.530,-0.495,2.770,-1.215,2.050,-1.215,3.490;
;
N[C@@H](Br)C(=O)O;
0;
1,1,1,1,1,1,,,1,;
,,,,,,,,,;
,,,,,,,,,;
-1,,,,,,,2,;
1.215,3.230,0.485,2.510,0.225,1.530,-0.495,2.770,-1.215,2.050,-1.215,3.490
,,,,,1.465,2.250,,;