MayaChemTools

Previous  TOC  NextDownloadPDBFiles.plCode | PDF | PDFGreen | PDFA4 | PDFA4Green

NAME

DownloadPDBFiles.pl - Download PDB files for PDB ID(s)

SYNOPSIS

DownloadPDBFiles.pl PDBID(s) or PDBIDsTextFile

DownloadPDBFiles.pl [-c, --colmode colnum | collabel] [-d, --dataLocationURL PDB URL] [-h, --help] [-d, --dataLocationURL PDB URL] [-e, --EDSMap yes | no] [--EDSMapLocationURL EDS Map URL] [-m, --mode <IDsOnCmdLine | IDsInFile>] [--PDBIDsCol number | string] [-w, --WorkingDir dirname] PDBID(s) or PDBIDsTextFile

DESCRIPTION

Download PDB files corresponding to PDB IDs specified in a column in a CSV/TSV text file or on the command line as space delimited parameters.

OPTIONS

-c, --colmode colnum | collabel

Specify how columns are identified in a TextFile containing PDB IDs: using column number or column label. Possible values: colnum or collabel. Default value: colnum.

-d, --dataLocationURL PDB URL

Specify location of PDB URL where data files are available for download. Default value: http://www.rcsb.org/pdb/files/.

-e, --EDSMap yes | no

Download Electron Density Map (EDS) in CCP4 format. Possible values: Yes or No. Default value: no.

--EDSMapLocationURL EDS Map URL

Specify location of EDS Map URL where data files are available for download. Default value: http://www.ebi.ac.uk/pdbe/coordinates/files/.

-h, --help

Print this help message.

--indelim comma | semicolon

Input delimiter for CSV TextFile containing PDB IDs. Possible values: comma or semicolon. Default value: comma. For TSV files, this option is ignored and tab is used as a delimiter.

-m, --mode <IDsOnCmdLine | IDsInFile>

Indicate how PDB IDs are specified: PDB IDs are either present as space delimited command line parameters or in a specific column in a CSV/TSV text file. Possible values: IDsOnCmdLine or IDsInFile. Default: IDsOnCmdLine.

-p, --PDBIDsCol number | string

Column used to identify PDB ID(s) in a text file. Default value: First column containing text string PDB_ID or <PDBID>.

For colnum value of -c, --colmode option, input value is a column number. Example: 1.

For collabel value of -c, --colmode option, input value is a column label. Example: PDB_ID.

This option is ignored during IDsOnCmdLine value of m, --mode option.

-w, --WorkingDir dirname

Location of working directory. Default: current directory.

EXAMPLES

To retrieve a PDB files for PDB ID 2HYY and generate a local 2HYY.pdb file, type:

% DownloadPDBFiles.pl 2HYY

To retrieve PDB files for multiple PDB IDs 2HYY and 1KV2 and generate corresponding local PDB files, type:

% DownloadPDBFiles.pl 2HYY 1KV2

To download PDB files for PDB IDs present in column name PDB_ID or PDBID in SamplePDBIDs.csv file and generate correponding PDB files, type

% DownloadPDBFiles.pl -m IDsInFile SamplePDBIDs.csv

To download PDB files for PDB IDs present in a specific column name in SamplePDBIDs.csv file and generate correponding PDB files, type

% DownloadPDBFiles.pl -m IDsInFile -c collabel -p PDB_ID SamplePDBIDs.csv

AUTHOR

Manish Sud

SEE ALSO

ExtractFromPDBFiles.pl, InfoPDBFiles.pl, ModifyPDBFiles.pl

COPYRIGHT

Copyright (C) 2018 Manish Sud. All rights reserved.

This file is part of MayaChemTools.

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

 

 

Previous  TOC  NextMay 15, 2018DownloadPDBFiles.pl