NAME
HackaMol::Molecule - Molecule class for HackaMol
VERSION
version 0.00_19
SYNOPSIS
use HackaMol;
use Math::Vector::Real;
my $hack = HackaMol->new(name => "hackitup");
my @atoms = $hack->read_file_atoms("t/lib/1L2Y.pdb");
my $mol = HackaMol::Molecule->new(name=> 'trp-cage', atoms=>[@atoms]);
$mol->translate(-$mol->COM);
$mol->rotate(V(1,0,0), 180, V(10,10,10));
$mol->print_xyz;
# see examplesDESCRIPTION
The Molecule class provides methods and attributes for collections of atoms that may be divided into groups, placed into bonds, angles, and dihedrals. The Molecule class extends the AtomGroup parent class, which consumes the AtomGroupRole, and consumes PhysVecMVRRole, QmRole, and BondsAnglesDihedralsRole. See the documentation of those classes and roles for details.
In addition to Bonds, Angles, and Dihedrals, which also consume the AtomGroupRole, the Molecule class has the atomgroups attr. The atomgroups attr is an ArrayRef[AtomGroup] with native array traits that allows all the atoms in the Molecule to be grouped and regroup at will. Thus, the Molecule class provides a suite of methods and attributes that is very powerful. For example, a HackaMolX extension for proteins could group the atoms by sidechains and backbones, populate bonds, and then use Math::Vector::Real objects to sample alternative conformations of the sidechains and backbone.
METHODS
t
t is the same attr as before. Molecule modifies t. the $mol->t accessor behaves as before. The $mol->(1) setter $self->gt(1) to set t for all atoms in the molecule.
push_groups_by_atom_attr
takes atom attribute as argument. pushes the atoms into the atomgroup array by attribute
all_bonds_atoms
takes array of atoms as argument, returns array of bonds that includes 1 or more of those atoms
all_angles_atoms
takes array of atoms as argument, returns array of angles that includes 1 or more of those atoms
all_dihedrals_atoms
takes array of atoms as argument, returns array of dihedrals that includes 1 or more of those atoms
bond_stretch_atoms
takes Bond object, a distance (angstroms, typically), and active atoms as arguments. translates the active atoms along the bond_vector by the distance and stores coordinates in place ($atom->set_coords($mol->t,$translated_coors)).
bond_stretch_groups
takes Bond object, a distance (angstroms, typically), and active groups as arguments. translates the atoms in the active groups along the bond_vector by the distance and stores coordinates in place.
angle_bend_atoms
takes Angle object, an angle (degress), and active atoms as arguments. rotates the active atoms about the vector normal to be angle and stores rotated coordinates in place ($atom->set_coords($mol->t,$rotated_coor)).
angle_bend_groups
takes Angle object, an angle (degress), and active groups as arguments. rotates the atoms in the active groups about the vector normal to be angle and stores rotated coordinates in place ($atom->set_coords($mol->t,$rotated_coor)).
dihedral_rotate_atoms
takes Dihedral object, an angle (degress), and active atoms as arguments. rotates the active atoms about the dihedral and stores rotated coordinates in place ($atom->set_coords($mol->t,$rotated_coor)).
dihedral_rotate_groups
takes Dihedral object, an angle (degress), and active groups as arguments. rotates atoms in groups about the dihedral and stores rotated coordinates in place ($atom->set_coords($mol->t,$rotated_coor)).
ARRAY METHODS
push_groups, get_groups, set_groups, all_groups, count_groups, delete_groups, clear_groups
ARRAY traits for the groups attribute, respectively: push, get, set, elements, count, delete, clear
push_groups
push bond on to groups array
$group->push_groups($bond1, $bond2, @othergroups);
all_groups
returns array of all elements in groups array
print $_->bond_order, "\n" foreach $group->all_groups;
get_groups
return element by index from groups array
print $group->get_groups(1); # returns $bond2 from that pushed above
set_groups
set groups array by index
$group->set_groups(1, $bond1);
count_groups
return number of groups in the array
print $group->count_groups;
has_groups
same as count_groups, allows clearer conditional code. i.e. doing something if $mol->has_groups;
push_bonds, set_bonds, delete_bonds, clear_bonds
MODIFIED ARRAY traits for the bonds attribute provided by BondsAnglesDihedralsRole
push_bonds
before push_bonds, bond_count is incremented for all atoms in all bonds to be pushed.
set_bonds
around set_bonds, bound_count decremented for all atoms in bond being replaced. Then, bond_count is incremented for all atoms in new bond
delete_bonds
before deleting bond, bond_count decremented for all atoms in bond.
clear_bonds
before clearing bonds, bond_count decremented for all atoms in all bonds.
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.