Free sdf software for linux

PerlPoint::Tags::SDF is a PerlPoint tag set used by pp2sdf.

SYNOPSIS

# declare tags used by pp2sdf
use PerlPoint::Tags::SDF;

This module declares PerlPoint tags used by pp2sdf. Tag declarations are used by the parser to determine if a used tag is valid, if it needs options, if it needs a body and so on. Please see PerlPoint::Tags for a detailed description of tag declaration.

Every PerlPoint translator willing to handle the tags of this module can declare this by using the module in the scope where it built the parser object.

# declare basic tags
use PerlPoint::Tags::SDF;

# load parser module
use PerlPoint::Parser;

...

# build parser
my $parser=new PerlPoint::Parser(...);

...

TAGS

PerlPoint::Tags::SDF declares all the tags of PerlPoint::Tags::Basic.

Additionally, the PerlPoint::Tags::HTML tags L, PAGEREF, SECTIONREF, U and XREF tags are supported. pp2sdf might interprete them slightly different to pp2html, please read its documentation for details.

PDL::IO::Misc is a Perl module with misc IO routines for PDL.

rcols()

Read ASCII whitespaced cols from a file into piddles and perl arrays (also see "rgrep()").

There are two calling conventions - the old version, where a pattern can be specified after the filename/handle, and the new version where options are given as as hash reference. This reference can be given as either the second or last argument.

The default behaviour is to ignore lines beginning with a # character and lines that only consist of whitespace. Options exist to only read from lines that match, or do not match, supplied patterns, and to set the types of the created piddles.
Can take file name or *HANDLE, and if no columns are specified, all are assumed. For the allowed types, see "Datatype_conversions" in PDL::Core.

Options:

EXCLUDE or IGNORE - ignore lines matching this pattern (default /^#/).
INCLUDE or KEEP - only use lines which match this pattern (default ).
LINES - which line numbers to use. Line numbers start at 0 and the syntax is a:b:c to use every cth matching line between a and b (default ).
DEFTYPE - default data type for stored data (if not specified, use the type stored in $PDL::IO::Misc::deftype, which starts off as double).
TYPES - reference to an array of data types, one element for each column to be read in. Any missing columns use the DEFTYPE value (default []).
PERLCOLS - an array of column numbers which are to be read into perl arrays rather than piddles. References to these arrays are returned after the requested piddles (default undef).

Usage:

($x,$y,...) = rcols( *HANDLE|"filename", { EXCLUDE => /^!/ },
$col1, $col2, ... )
($x,$y,...) = rcols( *HANDLE|"filename", $col1, $col2, ...,
{ EXCLUDE => /^!/ } )
($x,$y,...) = rcols( *HANDLE|"filename", "/foo/", $col1, $col2, ... )

e.g.,

$x = PDL->rcols file1;
($x,$y) = rcols *STDOUT;

# read in lines containing the string foo, where the first
# example also ignores lines that with a # character.
($x,$y,$z) = rcols file2, 0,4,5, { INCLUDE => /foo/ };
($x,$y,$z) = rcols file2, 0,4,5,
{ INCLUDE => /foo/, EXCLUDE => };

# ignore the first 27 lines of the file, reading in as ushorts
($x,$y) = rcols file3, { LINES => 27:-1, DEFTYPE => ushort };
($x,$y) = rcols file3,
{ LINES => 27:, TYPES => [ ushort, ushort ] };

# read in the first column as a perl array and the next two as piddles
($x,$y,$name) = rcols file4, 1, 2, { PERLCOLS => [ 0 ] };
printf "Number of names read in = %dn", 1 + $#$name;

Notes:

1. Quotes are required on patterns.
2. Columns are separated by whitespace by default, use $PDL::IO::Misc::colsep to specify an alternate separator.
3. For PDL-2.003, the meaning of the c value in the LINES option has changed: it now only counts matching lines rather than all lines as in previous versions of PDL.
4. LINES => -1:0:3 may not work as you expect, since lines are skipped when read in, then the whole array reversed.

wcols()

Write ASCII whitespaced cols into file from piddles efficiently.
If no columns are specified all are assumed. Will optionally only process lines matching a pattern. Can take file name or *HANDLE, and if no file/filehandle is given defaults to STDOUT.

Options:

HEADER - prints this string before the data. If the string is not terminated by a newline, one is added (default ).

Usage: wcols $piddle1, $piddle2,..., *HANDLE|"outfile", [%options];

e.g.,

wcols $x, $y+2, foo.dat;
wcols $x, $y+2, *STDERR;
wcols $x, $y+2, |wc;
wcols $a,$b,$c; # Orthogonal version of print $a,$b,$c :-)

wcols "%10.3f", $a,$b; # Formatted
wcols "%10.3f %10.5g", $a,$b; # Individual column formatting

wcols $a,$b, { HEADER => "# a b" };

Note: columns are separated by whitespace by default, use $PDL::IO::Misc::colsep to specify an alternate separator.

swcols()

generate string list from sprintf format specifier and a list of piddles
swcols takes an (optional) format specifier of the printf sort and a list of 1d piddles as input. It returns a perl array (or array reference if called in scalar context) where each element of the array is the string generated by printing the corresponding element of the piddle(s) using the format specified. If no format is specified it uses the default print format.

Usage: @str = swcols format, pdl1,pdl2,pdl3,...;

or

$str = swcols format, pdl1,pdl2,pdl3,...;

rgrep()

Read columns into piddles using full regexp pattern matching.

Options:

UNDEFINED: This option determines what will be done for undefined values. For instance when reading a comma-separated file of the type 1,2,,4 where the ,, indicates a missing value.

The default value is to assign $PDL::undefval to undefined values, but if UNDEFINED is set this is used instead. This would normally be set to a number, but if it is set to Bad and PDL is compiled with Badvalue support (see "" in PDL::Bad) then undefined values are set to the appropriate badvalue and the column is marked as bad.

DEFTYPE: Sets the default type of the columns - see the documentation for "rcols()"

TYPES: A reference to a Perl array with types for each column - see the documentation for "rcols()"

BUFFERSIZE: The number of lines to extend the piddle by. It might speed up the reading a little bit by setting this to the number of lines in the file, but in general "rasc()" is a better choice

Usage

($x,$y,...) = rgrep(sub, *HANDLE|"filename")

e.g.

($a,$b) = rgrep {/Foo (.*) Bar (.*) Mumble/} $file;

i.e. the vectors $a and $b get the progressive values of $1, $2 etc.

rdsa()

Read a FIGARO/NDF format file.

Requires non-PDL DSA module. Contact Frossie (frossie@jach.hawaii.edu) Usage:
([$xaxis],$data) = rdsa($file)
$a = rdsa file.sdf

Not yet tested with PDL-1.9X versions

isbigendian()

Determine endianness of machine - returns 0 or 1 accordingly

rasc()

Simple function to slurp in ASCII numbers quite quickly, although error handling is marginal (to nonexistent).

$pdl->rasc("filename"|FILEHANDLE [,$noElements]);
Where:
filename is the name of the ASCII file to read or
open file handle
$noElements is the optional number of elements in the file to read.
(If not present, all of the file will be read to fill up $pdl).
$pdl can be of type float or double for more precision.
# (test.num is an ascii file with 20 numbers. One number per line.)
$in = PDL->null;
$num = 20;
$in->rasc(test.num,20);
$imm = zeroes(float,20,2);
$imm->rasc(test.num);

rcube

Read list of files directly into a large data cube (for efficiency)

$cube = rcube &reader_function, @files;
$cube = rcube &rfits, glob("*.fits");

This IO function allows direct reading of files into a large data cube, Obviously one could use cat() but this is more memory efficient.

The reading function (e.g. rfits, readfraw) (passed as a reference) and files are the arguments.

The cube is created as the same X,Y dims and datatype as the first image specified. The Z dim is simply the number of images.

PerlPoint::Converters is a Perl module that contains a README and common functions for PerlPoint converters.

PerlPoint is a simple text format which allows easy typing of text with headlines, bullet lists, normal text paragraphs, indented paragraphs for code examples etc., from which slides for presentations can be generated by a script without the need of proprietary software.

Since there is a large variety of platforms which provide web browsers, HTML is a good choice for the output format. In principle, however, it is possible to generate each output format whose specification is known. At the moment there exist converters for HTML, LaTeX (alpha software) and SDF. The latter both may be used to generate printable output or to provide the basis for further processing.

Open Babel project is designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry.
Main features:
- A huge variety of common chemical file formats, including SDF/MOL, Mol2, PDB, SMILES, XYZ, CML... (details)
- Recognition of file type based on filename extension
- Chemical MIME support
- SMARTS matcher
- Flexible atom typer
- Flexible bond typer for perception of multiple bonds from atomic coordinates
- Gasteiger partial charge calculation
- Hydrogen addition and deletion
- Isotope support, calculation of average and exact masses
- Automatic feature perception (rings, bonds, hybridization, aromaticity)
- Multiple conformer storage within molecules
- Command line conversion for multiple molecules in one file
- Command line interface
- Bitvector class
- Vector and matrix transformations
- Molecular test suite
- Open-source/Free Software under the GNU General Public License
- Cross platform (Windows, Linux, Mac OS X, SGI, Solaris, Dreamcast...)
Version restrictions:
- Generate coordinates for SMILES strings. (Meaning all coordinates will be zero when converting from a SMILES string.)
- Handle 2D->3D conversion (or vice versa).
- Handle a variety of important file formats.
Whats New in 2.1.1 Development Release:
- Improved scripting support, including dictionary-support for OBGenericData in pybel, casting from OBUnitCell, etc. Improved access to OBRings from OBMol.GetSSSR().
- Added support for descriptors (e.g., PSA, logP) from scripting interfaces.
- Added support for reading all PDB records (beyond current atom and bond connections). Records not handled directly by Open Babel are added as key/value pairs through OBPairData.
- Added a new configure flag --with-pkglibdir to allow Linux package distributors to define version-specific directories for file format plugins.
- Fixed a bug which would not output chirality information for canonical SMILES with 3D files.
- Fixed problems with new line-ending code. Now correctly reads DOS and old Mac OS files with non-UNIX line endings.
- Correctly rejects SMILES with incorrect ring closures. Thanks to Craig James for the report.
- Fixed a crash when output to canonical SMILES.
- Fixed a crash when converting from SMILES to InChI.
- Fixed a crash when reading some PDB files on Windows.
- Fixed a crash when reading invalid MDL/SDF files.
- Fixed a bug which made it impossible to read some GAMESS files.
- Fixed a problem when reading ChemDraw CDX files on Mac OS X.
- A large number of additional fixes, including some rare crashes.

Photo Organizer is multi-user photo management tool that was designed for professional photographers.
It offers a searchable photo database that supports photo version control, client management, photo submission history, EXIF, IPTC, XML, and XMP, user quotas, a datebook, and printing labels and color brochures in PDF and PS formats.
Photo Organizer project uses PostgreSQL, features a Web interface, and uses DCRAW and ImageMagick to handle over a hundred image formats including several RAW formats.
Main features:
- Photo management: Naturally the main feature of the software is photo management. The system will allow you to store and retrieve photos in three sizes (original, midsize and thumbnail) For each photo detailed information is stored such as: Title, Caption, Keywords, Shooting location, Exposure Date, Equipment used, Equipment settings, Storage location and more. The system supports, photo version control, duplicates, and submission history, so tracking where the photo was submitted has been never easier. Photos can be ranked so that they can be displayed in the order of their relevance. Photos can be organized into folders and albums - kind of virtual folders.
Image files are stored in an image repository with automatic volume manager which makes Photo Organizer more secure (as access to the image files is permitted only via PO) and to ease the upload porcedure, a bulk upload mechanism was added with XML, XMP, IPTC and EXIF metadata import. Shooting data converters from NKN, TXT and SDF into XML provides compatibility with your exisiting database.
Thanks to Dave Coffins RAW image decoder Photo Organizer supports most RAW digital camera formats, enabling users to store original RAW files in the systems database.
- Client Management, Shop Module and Date book: The system has Client Management interface with onlineclient registration. Photos can be shared with Clients and non registered visitors. Access rights on Folder, Album or Photo level provides control over the visibility of each photo. Clients will be able to access protected photos, not visible for non registered visitors.
- Printing: Printing is one of the key features of Photo Organizer. You can create color brochures, including your photos in PDF and PS formats. Additionally you can print labelscontaining the shooting data and the bar coded photo identifier, which enables mass processing, easy data input and quick search of your photos. All this online from your browser.
- Search: A simple but powerful search engine is built into Photo Organizer. Supports basic logic operators (AND, OR and NOT) and allows the query of photos, folders & albums or users. It also implements stemming, to include related variations of your keywords.
Whats New in 2.34 RC4 Development Release:
- This release adds many minor bugfixes since -rc3, mostly relating to the localization framework and non-core features.
- This will hopefully be the final release candidate.
Whats New in 2.33e Stable Release:
- This bugfix release will be the final release of the old stable branch.
- Several import-related bugs have been fixed, and a problem deleting users via the admin interface has also been resolved.