Demian Riccardi > HackaMol > HackaMol

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HackaMol-0.00_21.tar.gz

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NAME ^

HackaMol - HackaMol: Object-Oriented Library for Molecular Hacking

VERSION ^

version 0.00_21

SYNOPSIS ^

       use HackaMol;
       use Math::Vector::Real;

       my $hack = HackaMol->new( name => "hackitup" );

       # all coordinates from NMR ensemble are loaded into atoms
       my $mol  = $hack->read_file_mol("1L2Y.pdb");

       #recenter all coordinates to center of mass
       foreach my $t ( 0 .. $mol->tmax) {
           $mol->t($t);
           $mol->translate( -$mol->COM );
       }

       #create array of CA atoms with full occupancy

       my @CAs = grep {
                        $_->name    eq 'CA'  and
                        $_->occ == 1
                      } $mol->all_atoms;

       #print out the pdb with CA for several models from the NMR
       HackaMol::Molecule->new(
                                atoms=>[@CAs]
                              )-> print_pdb_ts([8,2,4,6,8,0], 'some.pdb');

       # print coordinates to trp-cage.xyz and return filehandle for future
       # writing
       my $fh = $mol->print_xyz( $mol->name . ".xyz" );
       foreach ( 1 .. 10 ) {
           $mol->rotate(
               V( 0, 0, 1 ),    # rotation vector
               36,              # rotate by 36 degrees
               V( 5, 0, 0 )     # origin of rotation
           );
           $mol->print_xyz($fh);
       }

       # translate/rotate method is provided by AtomGroupRole
       # populate groups byatom resid attr
       my @groups = $hack->group_by_atom_attr( 'resid', $mol->all_atoms );
       $mol->push_groups(@groups);

       foreach my $ang ( 1 .. 10 ) {
           $_->rotate( V( 1, 1, 1 ), 36, $_->COM ) foreach $mol->all_groups;
           $mol->print_xyz($fh);
       }

DESCRIPTION ^

The HackaMol library enables users to build simple, yet powerful scripts for carrying out computational work on molecules at multiple scales. The molecular object system organizes atoms within molecules using groups, bonds, angles, and dihedrals. HackaMol seeks to provide intuitive attributes and methods that may be harnessed to coerce molecular computation through a common core. The library is inspired by PerlMol, BioPerl, MMTSB, and my own experiences as a researcher.

The library is organized into two regions: HackaMol, the core (contained here) that has classes for atoms and molecules, and HackaMol::X, the extensions, such as HackaMol::X::Vina (an interface to Autodock Vina) or HackaMol::X::Calculator, a more general abstract calculator for coercing molecular computation through a common core. The three major goals of the core are for it to be well-tested, well-documented, and easy to install. The goal of the extensions is to provide a more flexible space for researchers to develop and share new methods that use the core.

HackaMol uses Math::Vector::Real (MVR) for all the vector operations. MVR is a lightweight solution with a fast XS dropin that overlaps very well with the desirables for working with atoms and coarse grained molecules. Extensions that treat much larger systems will definitely benefit from the capabilities PDL or Math::GSL.

The HackaMol class (loaded in Synopsis) uses the core classes to provide some object building utilities described below. This class consumes HackaMol::MolReadRole to provide structure readers for xyz and pdb coordinates. See Open Babel if other formats needed (All suggestions, contributions welcome!).

METHODS ^

build_bonds

takes a list of atoms and returns a list of bonds. The bonds are generated for "list neighbors" by simply stepping through the atom list one at a time. e.g.

  my @bonds = $hack->build_bonds(@atoms[1,3,5]);

will return two bonds: B13 and B35

build_angles

takes a list of atoms and returns a list of angles. The angles are generated analagously to build_bonds, e.g.

  my @angles = $hack->build_angles(@atoms[1,3,5]);

will return one angle: A135

build_dihedrals

takes a list of atoms and returns a list of dihedrals. The dihedrals are generated analagously to build_bonds, e.g.

  my @dihedral = $hack->build_dihedrals(@atoms[1,3,5]);

will croak! you need atleast four atoms.

  my @dihedral = $hack->build_dihedrals(@atoms[1,3,5,6,9]);

will return two dihedrals: D1356 and D3569

group_by_atom_attr

takes atom attribute and a list of atoms as arguments and builds AtomGroup objects by attribute. Grouping by graphical searches are needed!

find_bonds_brute

takes hash argument list and returns bonds. Find bonds between bond_atoms and the candidates.

  my @oxy_bonds = $hack->find_bonds_brute(
                                    bond_atoms => [$hg],
                                    candidates => [$mol->all_atoms],
                                    fudge      => 0.45,
                                    max_bonds  => 6,
  );

fudge is optional with Default is 0.45 (open babel uses same default); max_bonds is optional with default of 99. max_bonds is compared against the atom bond count, which are incremented during the search. Before returning the bonds, the bond_count are returned the values before the search. For now, molecules are responsible for setting the number of bonds in atoms. find_bonds_brute uses a bruteforce algorithm that tests the interatomic separation against the sum of the covalent radii + fudge. It will not test for bond between atoms if either atom has >= max_bonds. It does not return a self bond for an atom ( next if refaddr($ati) == refaddr($atj) ).

find_disulfide_bonds

takes a list of atoms and returns the disulfide bonds as bond objects.

ATTRIBUTES ^

name

name is a rw str provided by HackaMol::NameRole.

SEE ALSO ^

EXTENDS ^

CONSUMES ^

AUTHOR ^

Demian Riccardi <demianriccardi@gmail.com>

COPYRIGHT AND LICENSE ^

This software is copyright (c) 2014 by Demian Riccardi.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.

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