cmp.parse1: Parsing an SDF file and calculate the descriptor for one...

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Parsing an SDF file and calculate the descriptor for one compound

Description

Read SDF information from an SDF file or connection, parse the first compound, and calculate the descriptor for that compound. The returned descriptor can be added to database returned by 'cmp.parse' or be used as the query structure when calling 'search'. This function will only parse one compound and return only the descriptor. To parse all compounds in an SDF file, use 'cmp.parse'.

Usage

cmp.parse1(filename)

Arguments

filename

The file name of the SDF file or a URL or a connection.

Details

'cmp.parse1' can take a file name or a URL or a connection. When a connection is used, the current line must be the first line of SDF of the compound to be parsed. 'cmp.parse1' will skip the header and parse from the 4th line. Therefore, the compound ID information will be skipped. After the parsing is done, if 'filename' is a connection, it will then point to the line after the connection table of SDF. You can use some other procedure to parse the annotation block.

Value

Return the descriptor, which is encoded as a vector.

Author(s)

Y. Eddie Cao, Li-Chang Cheng

References

Chen X and Reynolds CH (2002). "Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficients", in J Chem Inf Comput Sci.

See Also

cmp.parse, cmp.search, cmp.cluster, cmp.similarity

Examples

# load an SDF file from web and parse it
## Not run: structure <- cmp.parse1("http://bioweb.ucr.edu/ChemMineV2/compound/Aurora/b32:NNQS2MBRHAZTI===/sdf")

girke-lab/ChemmineR documentation built on July 28, 2023, 10:36 a.m.