extractDrugExtended: Calculate the Extended Molecular Fingerprints (in Compact...

In Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Description

Calculate the Extended Molecular Fingerprints (in Compact Format)

Usage

extractDrugExtended(molecules, depth = 6, size = 1024, silent = TRUE)

Arguments

molecules	Parsed molucule object.
depth	The search depth. Default is 6.
size	The length of the fingerprint bit string. Default is 1024.
silent	Logical. Whether the calculating process should be shown or not, default is TRUE.

Details

Calculate the extended molecular fingerprints. Considers paths of a given length, similar to the standard type, but takes rings and atomic properties into account into account. This is hashed fingerprints, with a default length of 1024.

Value

A list, each component represents one of the molecules, each element in the component represents the index of which element in the fingerprint is 1. Each component's name is the length of the fingerprints.

Author(s)

Nan Xiao <https://nanx.me>

See Also

extractDrugExtendedComplete

Examples

smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')

mol = readMolFromSmi(smi, type = 'mol')
fp  = extractDrugExtended(mol)
head(fp)

Example output

OpenJDK 64-Bit Server VM warning: Can't detect primordial thread stack location - find_vma failed
$`1024`
  [1]   10   15   29   42   54   59   62   65   66   69   76   77   79   86   89
 [16]  100  110  113  118  119  123  130  134  141  147  157  160  165  167  171
 [31]  176  179  184  188  191  196  223  225  236  245  252  253  260  272  280
 [46]  283  289  297  302  303  305  326  331  335  345  351  361  389  400  402
 [61]  405  407  408  417  424  439  441  447  451  454  456  460  468  474  478
 [76]  482  508  521  542  545  548  566  577  579  580  589  591  597  598  606
 [91]  607  610  611  613  622  645  652  654  661  672  679  687  691  704  705
[106]  713  718  724  728  729  738  742  746  753  760  762  766  773  777  782
[121]  785  788  794  797  811  813  819  827  834  841  843  846  849  855  862
[136]  869  872  874  877  926  927  928  935  939  950  953  955  968  970  973
[151]  977  990  996 1010 1011 1012 1014 1015

$`1024`
 [1]   26   54   79  103  123  147  184  188  202  227  228  260  339  368  402
[16]  451  478  482  520  542  545  572  582  606  613  705  713  718  791  811
[31]  813  908  926  927  950  977  980  996 1010 1014

$`1024`
 [1]   26   54   79  147  184  188  227  228  260  339  368  402  478  520  542
[16]  572  582  606  613  705  713  718  791  813  908  926  927  950  977  980
[31]  996 1010 1014

$`1024`
 [1]   17   21   23   32   63   76  103  129  135  145  147  159  170  172  184
[16]  191  196  202  225  228  239  251  255  258  260  265  282  283  290  307
[31]  313  326  327  331  332  341  347  360  361  383  384  399  400  404  407
[46]  416  437  446  471  478  488  506  513  520  526  535  545  551  575  582
[61]  591  606  613  616  618  619  676  704  713  727  728  755  772  810  812
[76]  819  827  828  833  858  878  903  908  910  924  950  954  955  976  980
[91]  982  992  996 1010 1014

$`1024`
 [1]    5   23   33   42   54   62   63   69   70   76   79   87   92  112  147
[16]  151  170  174  184  188  199  217  228  260  265  268  273  285  313  322
[31]  364  372  387  394  424  437  467  468  478  504  506  510  520  542  551
[46]  567  578  606  607  611  613  617  623  641  650  672  702  705  713  718
[61]  723  742  750  753  765  776  787  788  805  810  829  833  835  841  851
[76]  858  903  910  919  927  929  941  944  950  962  964  970  977  980  988
[91]  990  996 1010 1011 1014

$`1024`
 [1] 147 228 260 304 321 389 439 520 606 613 713 950 996

Rcpi documentation built on Nov. 8, 2020, 8:23 p.m.