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HackaMol - HackaMol: Object-Oriented Library for Molecular Hacking
Citation: J. Chem. Inf. Model., 2015, 55, 721
Loading the HackaMol library in a script with
provides attributes and methods of a builder class. It also loads all the classes provided by the core so including them is not necessary, e.g.:
use HackaMol::Atom; use HackaMol::Bond; use HackaMol::Angle; use HackaMol::Dihedral; use HackaMol::AtomGroup; use HackaMol::Molecule;
The methods, described below, facilitate the creation of objects from files and other objects.
one argument: pdbid
This method will download the pdb, unless it exists, and load it into a HackaMol::Molecule object. For example,
my $mol = HackaMol->new->pdbid_mol('2cba');
one argument: filename.
This method parses the file (e.g. file.xyz, file.pdb) and returns an array of HackaMol::Atom objects.
one argument: filename.
This method parses the file (e.g. file.xyz, file.pdb) and returns a HackaMol::Molecule object.
two arguments: filename and a HackaMol::Molecule object.
This method reads the coordinates from a file and pushes them into the atoms contained in the molecule. Thus, the atoms in the molecule and the atoms in the file must be the same.
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
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
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
arguments are an atom attribute and then a list of atoms.
This method builds AtomGroup objects that are grouped by attribute.
The arguments are key_value pairs of bonding criteria (see example below).
This method returns bonds between bond_atoms and the candidates using the criteria (many of wich have defaults).
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($atj) ).
the argument is a list of atoms, e.g. '($mol->all_atoms)'.
this method returns disulfide bonds as bond objects.
name is a rw str provided by HackaMol::NameRole.
# simple example: load pdb file and extract the disulfide bonds use HackaMol; my $bldr = HackaMol->new( name => 'builder'); my $mol = $bldr->pdbid_mol('1kni'); my @disulfide_bonds = $bldr->find_disulfide_bonds( $mol->all_atoms ); print $_->dump foreach @disulfide_bonds;
See the above executed in this linked notebook
Demian Riccardi <email@example.com>
This software is copyright (c) 2015 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.