Previous TOC Next | InfoSDFiles.pl | Code | PDF | PDFGreen | PDFA4 | PDFA4Green

# NAME

InfoSDFiles.pl - List information about SDFile(s)

# SYNOPSIS

InfoSDFile.pl SDFile(s)...

InfoSDFile.pl [-a --all] [-c --count] [--chiral] [--datacheck] [-d --detail infolevel] [-e --empty] [-f, --fields] [-h, --help] [-i, --invalidatomnumbers] [-m, --mismatch] [-s, --salts] [-u, --unknownatoms] [-w, --workingdir dirname] SDFile(s)...

# DESCRIPTION

List information about SDFile(s) contents: number of compounds, empty records and so on. Multiple SDFile names are separated by spaces. The valid file extensions are .sdf and .sd. All other file names are ignored. All the SD files in a current directory can be specified either by *.sdf or the current directory name.

# OPTIONS

-a, --all

  List all the available information.

-c, --count

  List number of compounds. This is default behavior.

--chiral

  List number of empty atom/bond blocks for compounds with chiral flag set in count line.

-d, --detail infolevel

  Level of information to print. Default: 1. Possible values: 1, 2, or 3.

--datacheck

  List number of numerical and non-numerical values for each data field.

-e, --empty

  List number of empty atom/bond blocks and data fields for compounds.

-f, --fields

  List data field labels present for compounds.

-h, --help

  Print this help message.

-i, --invalidatomnumbers

  List number of bond blocks for compounds which contain invalid atom numbers.

-m, --mismatch

  List number of atom/bond blocks for compounds which don't match with counts line information in header block.

-s, --salts

  List number of atom blocks for compounds which contain salts identified as disconnected structural units.

-u, --unknownatoms

  List number of atom blocks for compounds which contain special atom symbols such as L, Q, * ,LP, X, R#, or any other non periodic table symbols.

-w, --workingdir dirname

  Location of working directory. Default: current directory.

# EXAMPLES

To count compounds in SD file(s), type:

% InfoSDFiles.pl Sample1.sdf
% InfoSDFiles.pl Sample1.sdf Sample2.sdf
% InfoSDFiles.pl *.sdf

To list all available information for SD file(s), type:

% InfoSDFiles.pl -a *.sdf

To list all data fields present in sample.sdf, type:

% InfoSDFiles.pl -f Sample.sdf

To count number of compounds which contain salts and list associated structural data, type:

% InfoSDFiles.pl -s -d 3 Sample.sdf

# AUTHOR

Manish Sud

# SEE ALSO

ExtractFromSDFiles.pl, FilterSDFiles.pl, MergeTextFilesWithSD.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 Next | October 25, 2018 | InfoSDFiles.pl