Provided by: libchemistry-mol-perl_0.39-1_all 
NAME
Chemistry::Tutorial - PerlMol Quick Tutorial
Introduction
The modules in the PerlMol toolkit are designed to simplify the handling of molecules from Perl programs
in a general and extensible way. These modules are object-oriented; however, this tries to assume little
or no knowledge of object-oriented programming in Perl. For a general introduction about how to use
object-oriented modules, see HTML::Tree::AboutObjects.
This document shows some of the more common methods included in the PerlMol toolkit, in a reasonable
order for a quick introduction. For more details see the perldoc pages for each module.
How to read a molecule from a file
The following code will read a PDB file:
use Chemistry::Mol;
use Chemistry::File::PDB;
my $mol = Chemistry::Mol->read("test.pdb");
The first two lines (which only need to be used once in a given program) tell Perl that you want to "use"
the specified modules The third line reads the file and returns a molecule object.
To read other formats such as MDL molfiles, you need to "use" the corresponding module, such as
Chemistry::File::MDLMol. Readers for several formats are under development.
The molecule object
"Chemistry::Mol->read" returns a Chemistry::Mol object. An object is a data structure of a given class
that has methods (i.e. subroutines) associated with it. To access or modify an object's properties, you
call the methods on the object through "arrow syntax":
my $name = $mol->name; # return the name of the molecule
$mol->name("water"); # set the name of the molecule to "water"
Note that these so-called accessor methods return the molecule object when they are used to set a
property. A consequence of that if you want, you can "chain" several methods to set several options in
one line:
$mol->name("water")->type("wet");
A Chemistry::Mol object contains essentially a list of atoms, a list of bonds, and a few generic
properties such as name, type, and id. The atoms and bonds themselves are also objects.
Writing a molecule file
To write a molecule to a file, just use the "write" method:
$mol->write("test.pdb");
Make sure you "use"d the right file I/O module. If you want to load all the available file I/O modules,
you can do it with
use Chemistry::File ':auto';
Selecting atoms in a molecule
You can get an array of all the atoms by calling the atoms method without parameters, or a specific atom
by giving its index:
@all_atoms = $mol->atoms;
$atom3 = $mol->atoms(3);
Note: Atom and bond indices are counted from 1, not from 0. This deviation from common Perl usage was
made to be consistent with the way atoms are numbered in most common file formats.
You can select atoms that match an arbitrary expression by using Perl's built-in "grep" function:
# get all oxygen atoms within 3.0 Angstroms of atom 37
@close_oxygens = grep {
$_->symbol eq 'O'
and $_->distance($mol->atoms(37)) < 3.0
} $mol->atoms;
The "grep" function loops through all the atoms returned by "$mol->atoms", aliasing each to $_ at each
iteration, and returns only those for which the expression in braces is true.
Using "grep" is a general way of finding atoms; however, since finding atoms by name is common, a
convenience method is available for that purpose.
$HB1 = $mol->atoms_by_name('HB1');
@H_atoms = $mol->atoms_by_name('H.*'); # name treated as a regex
Since the atom name is not generally unique, even the first example above might match more than one atom.
In that case, only the first one found is returned. In the second case, since you are assigning to an
array, all matching atoms are returned.
The atom object
Atoms are usually the most interesting objects in a molecule. Some of their main properties are Z,
symbol, and coords.
$atom->Z(8); # set atomic number to 8
$symbol = $atom->symbol;
$coords = $atom->coords;
Atom coordinates
The coordinates returned by "$atom->coords" are a Math::VectorReal object. You can print these objects
and use them to do vector algebra:
$c1 = $atom1->coords;
$c2 = $atom2->coords;
$dot_product = $c1 . $c2; # returns a scalar
$cross_product = $c1 x $c2; # returns a vector
$delta = $c2 - $c1; # returns a vector
$distance = $delta->length; # returns a scalar
($x, $y, $z) = $c1->array; # get the components of $c1
print $c1; # prints something like "[ 1.0E0 2.0E0 3.0E0 ]"
Since one is very often interested in calculating the distance between atoms, Atom objects provide a
"distance" method to save some typing:
$d = $atom1->distance($atom2);
$d2 = $atom1->distance($molecule2);
In the second case, the value obtained is the minimum distance between the atom and the molecule. This
can be useful for things such as finding the water molecules closest to a given atom.
Atoms may also have internal coordinates, which define the position of an atom relative to the positions
of other atoms by means of a distance, an angle, and a dihedral angle. Those coordinates can be accessed
through the $atom->internal_coords method, which uses Chemistry::InternalCoords objects.
The Bond object
A Chemistry::Bond object is a list of atoms with an associated bond order. In most cases, a bond has
exactly two atoms, but we don't want to exclude possibilities such as three-center bonds. You can get the
list of atoms in a bond by using the "atoms" method; the bond order is accessed trough the "order"
method;
@atoms_in_bond = $bond->atoms;
$bond_order = $bond->order;
The other interesting method for Bond objects is "length", which returns the distance between the two
atoms in a bond (this method requires that the bond have two atoms).
my $bondlength = $bond->length;
In addition to these properties, Bond objects have the generic properties described below. The most
important of these, as far as bonds are concerned, is "type".
Generic properties
There are three generic properties that all PerlMol objects have:
id Each object must have a unique ID. In most cases you don't have to worry about it, because it is
assigned automatically unless you specify it. You can use the "by_id" method to select an object
contained in a molecule:
$atom = $mol->by_id("a42");
In general, ids are preferable to indices because they don't change if you delete or move atoms or
other objects.
name
The name of the object does not have any meaning from the point of view of the core modules, but most
file types have the concept of molecule name, and some (such as PDB) have the concept of atom names.
type
Again, the meaning of type is not universally defined, but it would likely be used to specify atom
types and bond orders.
Besides these, the user can specify arbitrary attributes, as discussed in the next section.
User-specified attributes
The core PerlMol classes define very few, very generic properties for atoms and molecules. This was
chosen as a "minimum common denominator" because every file format and program has different ideas about
the names, values and meaning of these properties. For example, some programs only allow bond orders of
1, 2, and 3; some also have "aromatic" bonds; some use calculated non-integer bond orders. PerlMol tries
not to commit to any particular convention, but it allows you to specify whatever attributes you want for
any object (be it a molecule, an atom, or a bond). This is done through the "attr" method.
$mol->attr("melting point", "273.15"); # set m.p.
$color = $atom->attr("color"); # get atom color
The core modules store these values but they don't know what they mean and they don't care about them.
Attributes can have whatever name you want, and they can be of any type. However, by convention, non-core
modules that need additional attributes should prefix their name with a namespace, followed by a slash.
(This is done to avoid modules fighting over the same attribute name.) For example, atoms created by the
PDB reader module (Chemistry::File::PDB) have the "pdb/residue" attribute.
$mol = Chemistry::Mol->read("test.pdb");
$atom = $mol->atoms(1234);
print $atom->attr("pdb/residue_name"); # prints "ALA123"
Molecule subclasses
You can do lots of interesting thing with plain molecules. However, for some applications you may want to
extend the features of the main Chemistry::Mol class. There are several subclasses of Chemistry::Mol
available already:
Chemistry::MacroMol
Used for macromolecules.
Chemistry::Pattern
Used for substructure matching.
Chemistry::Ring
Used for representing rings (cycles) in molecules.
Chemistry::Reaction
Used for representing and applying chemical transformations.
As an example we'll discuss macromolecules. Future versions of this tutorial may also include a
discussion about patterns and rings.
Macromolecules
So far we have assumed that we are dealing with molecules of the Chemistry::Mol class. However, one of
the interesting things about object-oriented programming is that classes can be extended. For dealing
with macromolecules, we have the MacroMol class, which extends the Chemistry::Mol class. This means that
in practice you can use a Chemistry::MacroMol object exactly as you would use a Chemistry::Mol object,
but with some added functionality. In fact, the PDB reader can return Chemistry::MacroMol instead of
Chemistry::Mol objects just by changing the first example like this:
use Chemistry::MacroMol;
use Chemistry::File::PDB;
my $macromol = Chemistry::MacroMol->read("test.pdb");
Now the question is, what is the "added functionality" that MacroMol objects have on top of the original
Chemistry::Mol object?
The MacroMol object
For the purposes of this module, a macromolecule is considered to be a big molecule where atoms are
divided in Domains. A domain is just a subset of the atoms in the molecule; in a protein, a domain would
be just a residue.
You can select domains in a molecule in a way similar to that used for atoms and bonds, in this case
through the "domains" method:
my @all_domains = $macromol->domains;
my $domain = $macromol->domains(57);
The Domain object
A domain is a substructure of a larger molecule. Other than having a parent molecule, a domain is just
like a molecule. In other words, the Domain class extends the Chemistry::Mol class; it is basically a
collection of atoms and bonds.
my @atoms_in_domain = $domain->atoms;
my $atom5_in_domain = $domain->atoms(5);
If you want to get at a given atom in a given domain in a macromolecule, you can "chain" the method calls
without having to save the Domain object in a temporary variable:
my $domain57_atom5 = $macromol->domains(57)->atoms(5);
my $res233_HA = $macromol->domains(233)->atoms_by_name('HA');
The second example is a good way of selecting an atom from a PDB file when you know the residue number
and atom name.
VERSION
0.38
SOURCE CODE REPOSITORY
<https://github.com/perlmol/Chemistry-Mol>
SEE ALSO
Chemistry::Mol, Chemistry::Atom, Chemistry::Bond, Chemistry::File, Chemistry::MacroMol,
Chemistry::Domain.
AUTHOR
Ivan Tubert-Brohman <itub@cpan.org>
COPYRIGHT
Copyright (c) 2005 Ivan Tubert-Brohman. All rights reserved. This program is free software; you can
redistribute it and/or modify it under the same terms as Perl itself.