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Perl module implements an object class for representing internal coordinates and provides methods for converting them to Cartesian coordinates.

Chemistry-MacroMol is a toolkit includes basic objects and methods to describe macromolecules, a macromolecule is just a molecule that consists of several "domains". For example, a protein consists of aminoacid residues, or a nucleic acid consists of bases. Therefore Chemistry::MacroMol is derived from Chemistry::Mol, with additional methods to handle the domains.

Select atoms in macromolecule

Perl molecular awk interpreter

Chemistr-Mol is a toolkit includes basic objects and methods to describe molecules. It consists of several modules: Chemistry::Mol, Chemistry::Atom, Chemistry::Bond, and Chemistry::File. They are the core modules of the PerlMol toolkit, see: http://www.perlmol.org/.

Paje is a graphical tool that displays traces produced during the execution of multithreaded programs. Other programs can also generate traces for this tool. Key Features * Supports multi threaded programs - each thread of the analysed program can be individually displayed, or multiple threads can be combined, to reduce screen space usage. * Interactivity - each entity represented on the screen can be interrogated for more information, - related entities are highlighted as mouse cursor passes over some representation LICENSE: LGPL2 or later

Perl module which implements basic pattern matching for molecules.

Explicit chemical reactions

Perl module which provides some basic methods for representing a ring.

FastHenry computes the frequency dependent self and mutual inductances and resistances between conductors of complex shape. The algorithm used in FastHenry is an acceleration of rge mesh formulation approach. The linear system resulting from the mesh formulation is solved using a generalized minimal residual algorithm with a fast multipole algorithm to efficiently compute the iterates. --------------------- Superconductivity Support ------------------------- This version of fasthenry has been modified to support superconducting segments and ground planes by Stephen R. Whiteley of Whitleley Research Inc. The analysis used is based on the London equations and the two-fluid model. Both reactive and lossy components of the superconductor complex conductivity are employed in obtaining the impedance matrix.