ptm (version 0.2.2)

get.hssp: Get a HSSP File

Description

Gets a HSSP file of the requested structure.

Usage

get.hssp(pdb, path, keepfiles = TRUE)

Arguments

pdb

the 4-letter identifier of the PDB file.

path

character string providing the path to the in-house HSSP database.

keepfiles

logical, if TRUE the dataframes will be saved in the working directory and we will keep the hssp file.

Value

Returns a dataframe corresponding to the profile.Rda described above.

Details

In order to use this function, you need to obtain a local copy of the HSSB database. This function will obtain and parse the requested HSSP file. When the argument <U+2018>keepfiles<U+2019> is set to TRUE, the get.hssp() function will build and save (in the working directory) the following 4 dataframes:

• id_seq_list.Rda: This block of information holds the metadata per sequence, and some alignment statistic. See https://swift.cmbi.umcn.nl/gv/hssp for a detailed description of the information that can be find in this block.

• id_aln.Rda This dataframe contains the alignment itself (each sequence is a column). Additional information such as secondary structure, SASA, etc., is also found in this block.

• id_profile.Rda This dataframe holds per amino acid type its percentage in the list of residues observed at that position. In addition, this dataframe also informs about the entropy at each position, as well as the number of sequences spanning this position (NOOC).

• id_insertions.Rda A dataframe with information regarding those sequences that contain insertions. See https://swift.cmbi.umcn.nl/gv/hssp for further details.

References

Touw et al (2015) Nucl. Ac. Res. 43:D364-368.

See Also

msa(), custom.aln(), list.hom(), parse.hssp(), shannon()

Examples

# NOT RUN {
get.hssp(file = './1u8f.hssp')
# }