Free methods in molecular biology software for linux

Method::Declarative is a Perl module to create methods with declarative syntax.

SYNOPSIS

use Method::Declarative
(
--defaults =>
{
precheck =>
[
[ qw(precheck1 arg1 arg2) ],
# ...
],
postcheck =>
[
[ qw(postcheck1 arg3 arg4) ],
# ...
],
init =>
[
[ initcheck1 ],
# ...
],
end =>
[
[ endcheck1 ],
# ...
],
once =>
[
[ oncecheck1 ],
] ,
package => __CALLER__::internal,
},
method1 =>
{
ignoredefaults => [ qw(precheck end once) ],
code => __method1,
},
) ;

The Method::Declarative module creates methods in a using class namespace. The methods are created using a declarative syntax and building blocks provided by the using class. This class does not create the objects themselves.

The using class invokes Method::Declarative, passing it list of key-value pairs, where each key is the name of a method to declare (or the special key --default) and a hash reference of construction directives. The valid keys in the construction hash refs are:

code

The value corresponding to code key is a method name or code reference to be executed as the method. It is called like this:

$obj->$codeval(@args)

where $obj is the object or class name being used, $codeval is the coresponding reference or method name, and @args are the current arguments for the invocation. If $codeval is a method name, it needs to be reachable from $obj.

A code key in a method declaration will override any code key set in the --defaults section.

end

The value corresponding to the end key is an array reference, where each entry of the referenced array is another array ref. Each of the internally referenced arrays starts with a code reference or method name. The remaining elements of the array are used as arguments.
Each method declared by the arrays referenced from end are called on the class where the declared method resides in an END block when Method::Declarative unloads.

Each method is called like this:

$pkg->$codeval($name[, @args]);

where $pkg is the package or class name for the method, $name is the method name, and @args is the optional arguments that can be listed in each referenced list.

end blocks are run in the reverse order of method declaration (for example, if method1 is declared before method2, method2s end declaration will be run before method1s), and for each method they are run in the order in which they are declared.

Note that this is not an object destructor, and no objects of a particular class may still exist when these methods are run.

ignoredefaults

The value corresponding to the ignoredefaults key is an array reference pointing to a list of strings. Each string must corespond to a valid key, and indicates that any in-force defaults for that key are to be ignored. See the section on the special --defaults method for details.

init

The value corresponding to the init key is identical in structure to that corresponding to the end key. The only difference is that the declared methods/code refs are executed as soon as the method is available, rather than during an END block.

once

The value corresponding to the once key is identical in structure to that corresponding to the end key. The values are used when the method is invoked, however.

If the method is invoked on an object based on a hash ref, or on the class itself, and it has not been invoked before on that object or hash ref, the methods and code refs declared by this key are executed one at a time, like this:

$obj->$codeval($name, $isscalar, $argsref[, @args ]);

where $obj is the object or class on which the method is being invoked, $codeval is the method name or code reference supplied, $name is the name of the method, $isscalar is a flag to specify if the declared method itself is being executed in a scalar context, $argsref is a reference to the method arguments (@_, in other words), and @args are any optional arguments in the declaration.

The return value of each method or code reference call is used as the new arguments array for successive iterations or the declared method itself (including the object or class name). Yes, that means that these functions can change the the object or class out from under successive operations.

Any method or code ref returning an empty list will cause further processing for the method to abort, and an empty list or undefined value (as appropriate for the context) will be returned as the declared methods return value.

package

The value coresponding to the package key is a string that determines where the declared method is created (which is the callers package by default, unless modified with a --defaults section). The string __CALLER__ can be used to specify the callers namespace, so constructions like the one in the synopsis can be used to create methods in a namespace based on the calling package namespace.

postcheck

The value coresponding to the postcheck key is identical in structure to that coresponding to the end key. The postcheck operations are run like this:

$obj->$codeval($name, $isscalar, $vref[, @args ]);

where $obj is the underlying object or class, $codeval is the method or code ref from the list, $name is the name of the declared method, $isscalar is the flag specifying if the declared method was called in a scalar context, $vref is an array reference of the currently to-be-returned values, and @args is the optional arguments from the list.

Each method or code reference is expected to return the value(s) it wishes to have returned from the method. Returning a null list does NOT stop processing of later postcheck declarations.

precheck

The precheck phase operates similarly to the once phase, except that its triggered on all method calls (even if the underlying object is not a hash reference or a class name).
Any illegal or unrecognized key will cause a warning, and processing of the affected hashref will stop. This means a --defaults section will be ineffective, or a declared method wont be created.

Biomolecule Toolkit project is an Open Source library for the structural modeling of biological macromolecules. The toolkit provides a C++ interface for common tasks in computational structural biology, to facilitate the development of molecular modeling, design, and analysis tools.
Enhancements:
Documentation updates
- Addition of an extensive discussion of the leastsquares_superposition and RMSD-calculation methods, including a description of the mathematical theory behind their operation.
- Fully documented the rotation/translation methods
- Addition of a documented example program ("gyration_radius.cpp")
Bug fixes
- Fixed copy construction bug in PDBAtomDecorator that caused compilation errors in rare situations.
- Fixed a bug in PDBFileParser that caused a compilation error in the PDBSystem copy constructor.
- Fixed a const-conversion bug in GroupedElementIterator which prevented proper interoperation of const and non-const iterator types.
- Fixed a crash-producing bug in stream output for the TypeID class.
- Fixed a math error in RMSD and superposition methods that would corrupt molecule coordinates.
- Fixed a bug that caused all default-constructed PDBAtom objects to be treated as HETATMs.
Feature additions
- Added operator[] to AtomicStructure and PolymerStructure-derived classes.
- Added protected increment() and decrement() operators to TypeID class.
- PDBFileParser can now handle PDB files with ill-formed residue numbering (i.e. Files where residue numbers are repeated in successive chains).

Class::Method::hash is a Perl module that helps you create methods for handling a hash value.

SYNOPSIS

use Class::MethodMaker
[ hash => [qw/ x /] ];

$instance->x; # empty
$instance->x(a => 1, b => 2, c => 3);
$instance->x_count == 3; # true
$instance->x = (b => 5, d => 8); # Note this *replaces* the hash,
# not adds to it
$instance->x_index(b) == 5; # true
$instance->x_exists(c); # false
$instance->x_exists(d); # true

Creates methods to handle hash values in an object. For a component named x, by default creates methods x, x_reset, x_clear, x_isset, x_count, x_index, x_keys, x_values, x_each, x_exists, x_delete, x_set, x_get.

ExtUtils::ModuleMaker::StandardText are methods used within ExtUtils::ModuleMaker.

The methods described below are quasi-private methods which are called by the publicly available methods of ExtUtils::ModuleMaker and ExtUtils::ModuleMaker::Interactive. They are quasi-private in the sense that they are not intended to be called by the everyday user of ExtUtils::ModuleMaker. Nothing prevents a user from calling these methods, but they are documented here primarily so that users writing plug-ins for ExtUtils::ModuleMakers standard text will know what methods need to be subclassed.

The methods below are called in ExtUtils::ModuleMaker::complete_build() but not in that same packages new(). For methods called in new(), please see ExtUtils::ModuleMaker::Initializers.
The descriptions below are presented in hierarchical order rather than alphabetically. The order is that of how close to the surface can a particular method called?, where surface means being called within ExtUtils::ModuleMaker::complete_build().

So methods called within complete_build() are described before methods which are only called within other quasi-private methods. Some of the methods described are also called within ExtUtils::ModuleMaker::Interactive methods. And some quasi-private methods are called within both public and other quasi-private methods. Within each heading, methods are presented more or less as they are first called within the public or higher-order quasi-private methods.

Timestamp::Simple is a Perl module with simple methods for timestamping.

SYNOPSIS

use Timestamp::Simple qw(stamp);
print stamp, "n";

This module provides a simple method for returning a stamp to mark when an event occurs.

METHODS

stamp()

This method returns a timestamp in the form yyyymmddHHMMSS.

CAD::Drawing::Manipulate::Transform is a Perl module with Matrix methods for CAD::Drawing.

Provides 3D transformation methods (based on traditional matrix algorithms) for Drawing.pm objects.

Coordinate System

All of these methods assume a RIGHT-HANDED coordinate system. If you are using a left-handed coordinate system, you are going to have trouble, trouble, trouble. We arent making video games here!

Minnow is a Web-based PDF discussion engine for discussing and annotating documents in an online, multi-user environment.
Minnow was developed by the Mathematical Biology group at the Northwest Fisheries Science Center in Seattle, WA with support by NOAA/NMFS.
Enhancements:
- This release includes some major updates such as full-text extraction from PDFs, edit-in-place support for editing titles and descriptions of documents after theyve been imported, a progress meter for converting large PDFs to images, and user-level access control, allowing you to specify which users can view a document.