sdfsample: SD file in 'SDFset' object

Description Usage Format Details Source References Examples

Description

First 100 compounds from PubChem SD file: Compound_00650001_00675000.sdf.gz

Usage

1

Format

Object of class sdfset

Details

Object stores 100 molecules from a sample SD file.

Source

ftp://ftp.ncbi.nih.gov/pubchem/Compound/CURRENT-Full/SDF/Compound_00650001_00675000.sdf.gz

References

SDF format definition: http://www.symyx.com/downloads/public/ctfile/ctfile.jsp

Examples

1
2
3
data(sdfsample)
sdfset <- sdfsample
view(sdfset[1:4])

Example output

$CMP1
An instance of "SDF"

<<header>>
                            Molecule_Name 
                                 "650001" 
                                   Source 
                 "  -OEChem-07071010512D" 
                                  Comment 
                                       "" 
                              Counts_Line 
" 61 64  0     0  0  0  0  0  0999 V2000" 

<<atomblock>>
          C1      C2  C3  C5  C6  C7  C8  C9 C10 C11 C12 C13 C14 C15 C16
O_1   7.0468  0.0839   0   0   0   0   0   0   0   0   0   0   0   0   0
O_2  12.2708  1.0492   0   0   0   0   0   0   0   0   0   0   0   0   0
...      ...     ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_60  1.8411 -1.5985   0   0   0   0   0   0   0   0   0   0   0   0   0
H_61  2.6597 -1.2843   0   0   0   0   0   0   0   0   0   0   0   0   0

<<bondblock>>
     C1  C2  C3  C4  C5  C6  C7
1     1  16   2   0   0   0   0
2     2  23   1   0   0   0   0
... ... ... ... ... ... ... ...
63   33  60   1   0   0   0   0
64   33  61   1   0   0   0   0

<<datablock>> (33 data items)
          PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED 
                      "650001"                            "1" 
     PUBCHEM_CACTVS_COMPLEXITY  PUBCHEM_CACTVS_HBOND_ACCEPTOR 
                         "700"                            "7" 
                               
                         "..." 

$CMP2
An instance of "SDF"

<<header>>
                            Molecule_Name 
                                 "650002" 
                                   Source 
                 "  -OEChem-07071010512D" 
                                  Comment 
                                       "" 
                              Counts_Line 
" 49 51  0     0  0  0  0  0  0999 V2000" 

<<atomblock>>
          C1     C2  C3  C5  C6  C7  C8  C9 C10 C11 C12 C13 C14 C15 C16
O_1    3.732  0.997   0   0   0   0   0   0   0   0   0   0   0   0   0
O_2        2 -2.003   0   0   0   0   0   0   0   0   0   0   0   0   0
...      ...    ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_48 10.6863 2.6555   0   0   0   0   0   0   0   0   0   0   0   0   0
H_49 10.4379 -3.272   0   0   0   0   0   0   0   0   0   0   0   0   0

<<bondblock>>
     C1  C2  C3  C4  C5  C6  C7
1     1  15   2   0   0   0   0
2     2  18   2   0   0   0   0
... ... ... ... ... ... ... ...
50   25  47   1   0   0   0   0
51   26  48   1   0   0   0   0

<<datablock>> (33 data items)
          PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED 
                      "650002"                            "1" 
     PUBCHEM_CACTVS_COMPLEXITY  PUBCHEM_CACTVS_HBOND_ACCEPTOR 
                         "497"                            "5" 
                               
                         "..." 

$CMP3
An instance of "SDF"

<<header>>
                            Molecule_Name 
                                 "650003" 
                                   Source 
                 "  -OEChem-07071010512D" 
                                  Comment 
                                       "" 
                              Counts_Line 
" 44 47  0     0  0  0  0  0  0999 V2000" 

<<atomblock>>
         C1      C2  C3  C5  C6  C7  C8  C9 C10 C11 C12 C13 C14 C15 C16
S_1   4.326  1.9917   0   0   0   0   0   0   0   0   0   0   0   0   0
O_2  2.5369 -1.0961   0   0   0   0   0   0   0   0   0   0   0   0   0
...     ...     ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_43 2.4361  3.5824   0   0   0   0   0   0   0   0   0   0   0   0   0
H_44 3.1175  3.0307   0   0   0   0   0   0   0   0   0   0   0   0   0

<<bondblock>>
     C1  C2  C3  C4  C5  C6  C7
1     1  23   1   0   0   0   0
2     1  24   1   0   0   0   0
... ... ... ... ... ... ... ...
46   26  43   1   0   0   0   0
47   26  44   1   0   0   0   0

<<datablock>> (28 data items)
          PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED 
                      "650003"                            "1" 
     PUBCHEM_CACTVS_COMPLEXITY  PUBCHEM_CACTVS_HBOND_ACCEPTOR 
                         "638"                            "6" 
                               
                         "..." 

$CMP4
An instance of "SDF"

<<header>>
                            Molecule_Name 
                                 "650004" 
                                   Source 
                 "  -OEChem-07071010512D" 
                                  Comment 
                                       "" 
                              Counts_Line 
" 59 61  0     0  0  0  0  0  0999 V2000" 

<<atomblock>>
          C1     C2  C3  C5  C6  C7  C8  C9 C10 C11 C12 C13 C14 C15 C16
S_1   7.1279 1.5981   0   0   0   0   0   0   0   0   0   0   0   0   0
O_2    3.732 3.5981   0   0   0   0   0   0   0   0   0   0   0   0   0
...      ...    ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_58 15.4379  0.403   0   0   0   0   0   0   0   0   0   0   0   0   0
H_59  14.591  0.176   0   0   0   0   0   0   0   0   0   0   0   0   0

<<bondblock>>
     C1  C2  C3  C4  C5  C6  C7
1     1  15   1   0   0   0   0
2     1  22   1   0   0   0   0
... ... ... ... ... ... ... ...
60   32  58   1   0   0   0   0
61   32  59   1   0   0   0   0

<<datablock>> (33 data items)
          PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED 
                      "650004"                            "1" 
     PUBCHEM_CACTVS_COMPLEXITY  PUBCHEM_CACTVS_HBOND_ACCEPTOR 
                         "698"                            "6" 
                               
                         "..." 

ChemmineR documentation built on May 31, 2018, 6 p.m.