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Changes for version 0.046 - 2017-10-10

  • add selection hash attribute to manage selections (todo, use it or lose it!).
  • fix model read bug where number of atoms grows between models (see the unusual 2d6b)
  • add x_flag to aa321 default 1, replaces unknown 3-letter code with X
  • protein backbone/sidechain selection fix for the bb carbonyl oxygen
  • sidechains selection -> sidechain (watch out for OXT)
  • changed fudge from 0.45 to 0.15 for find_disulfide_bonds
  • HackaMol.pm consumes NERFRole

Modules

HackaMol: Object-Oriented Library for Molecular Hacking
Angle class for HackaMol
HackaMol Atom Class
HackaMol AtomGroup class
HackaMol Bond class
Dihedral Angle class for HackaMol
Molecule class for HackaMol
package for period table data... needs to change
Role for a group of atoms
Array traits for containers of HackaMol Bonds, Angles, Dihedrals.
Role for using LWP::Simple to fetch files from www
Read files with molecular information
Role providing Natural extension reference frame implementation for molecular building
provides name attribute
PdbRole of lazy attributes for HackaMol atoms
Provides the core of HackaMol Atom and Molecule classes.
simple role that provides attributes needed for setting up quantum chemistry calculations
provides attributes needed for quantum chemistry calculations
Read files with molecular information
Read files with molecular information
Read files with molecular information
Read files with molecular information
Read files with molecular information
Atom selections in molecules