fmcstest: SD file stored in 'SDFset' object

In fmcsR: Mismatch Tolerant Maximum Common Substructure Searching

Description

Sample compound structures stored in SDF format.

Usage

data(fmcstest)

Format

Object of class SDFset

Details

Object stores X molecules from a sample SD file.

Source

ftp://ftp.ncbi.nih.gov/pubchem/

References

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

Examples

data(fmcstest)
sdfset <- fmcstest
view(sdfset)

Example output

Loading required package: ChemmineR
$Caffeine
An instance of "SDF"

<<header>>
                            Molecule_Name 
                                   "2519" 
                                   Source 
                 "  -OEChem-07141219402D" 
                                  Comment 
                                       "" 
                              Counts_Line 
" 24 25  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      2   0   0   0   0   0   0   0   0   0   0   0   0   0
O_2       2     -1   0   0   0   0   0   0   0   0   0   0   0   0   0
...     ...    ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_23 1.4631   1.31   0   0   0   0   0   0   0   0   0   0   0   0   0
H_24   1.69 0.4631   0   0   0   0   0   0   0   0   0   0   0   0   0

<<bondblock>>
     C1  C2  C3  C4  C5  C6  C7
1     1   9   2   0   0   0   0
2     2  10   2   0   0   0   0
... ... ... ... ... ... ... ...
24   14  23   1   0   0   0   0
25   14  24   1   0   0   0   0

<<datablock>> (33 data items)
          PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED 
                        "2519"                            "1" 
     PUBCHEM_CACTVS_COMPLEXITY  PUBCHEM_CACTVS_HBOND_ACCEPTOR 
                         "293"                            "3" 
                               
                         "..." 

$Viagra
An instance of "SDF"

<<header>>
                            Molecule_Name 
                                   "5212" 
                                   Source 
                 "  -OEChem-07141219392D" 
                                  Comment 
                                       "" 
                              Counts_Line 
" 63 66  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   5.4641   -0.5   0   0   0   0   0   0   0   0   0   0   0   0   0
O_2   4.9641  0.366   0   0   0   0   0   0   0   0   0   0   0   0   0
...      ...    ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_62 10.3312   3.31   0   0   0   0   0   0   0   0   0   0   0   0   0
H_63  9.4842 3.5369   0   0   0   0   0   0   0   0   0   0   0   0   0

<<bondblock>>
     C1  C2  C3  C4  C5  C6  C7
1     1   2   2   0   0   0   0
2     1   3   2   0   0   0   0
... ... ... ... ... ... ... ...
65   33  62   1   0   0   0   0
66   33  63   1   0   0   0   0

<<datablock>> (33 data items)
          PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED 
                        "5212"                            "1" 
     PUBCHEM_CACTVS_COMPLEXITY  PUBCHEM_CACTVS_HBOND_ACCEPTOR 
                         "838"                            "7" 
                               
                         "..." 

$`5866133`
An instance of "SDF"

<<header>>
                                         Molecule_Name 
                                                    "" 
                                                Source 
"          07141217122D 1   1.00000     0.00000     0" 
                                               Comment 
                                                    "" 
                                           Counts_Line 
             " 25 27  0     0  0            999 V2000" 

<<atomblock>>
          C1      C2  C3  C5  C6  C7  C8  C9 C10 C11 C12 C13
C_1  -3.2458 -0.8542   0   0   0   0   0   0   0   0   0   0
C_2  -3.2458 -0.1042   0   0   0   0   0   0   0   0   0   0
...      ...     ... ... ... ... ... ... ... ... ... ... ...
O_24    1.85  1.0333   0   0   0   0   0   0   0   0   0   0
C_25  2.3542  0.4833   0   0   0   0   0   0   0   0   0   0

<<bondblock>>
     C1  C2  C3  C4  C5  C6
1     2   1   2   0   0   0
2     3   1   1   0   0   0
... ... ... ... ... ... ...
26    6   4   1   0   0   0
27   22  19   2   0   0   0

<<datablock>> (8 data items)
       ID     cLogP     LogSW        RB           
"5866133"    "0.76"   "-2.35"       "3"     "..." 

fmcsR documentation built on Nov. 8, 2020, 6:57 p.m.