Chemistry::File - Molecule file I/O base class
# As a convenient interface for several mol readers:
use Chemistry::File qw(PDB MDLMol); # load PDB and MDL modules
# or try to use every file I/O module installed in the system:
use Chemistry::File ':auto';
my $mol1 = Chemistry::Mol->read("file.pdb");
my $mol2 = Chemistry::Mol->read("file.mol");
# as a base for a mol reader:
package Chemistry::File::Myfile;
use base qw(Chemistry::File);
use Chemistry::Mol;
Chemistry::Mol->register_format("myfile", __PACKAGE__);
# override the read_mol method
sub read_mol {
my ($self, $fh, %opts) = shift;
my $mol_class = $opts{mol_class} || "Chemistry::Mol";
my $mol = $mol_class->new;
# ... do some stuff with $fh and $mol ...
return $mol;
}
# override the write_mol method
sub write_mol {
my ($self, $fh, $mol, %opts) = shift;
print $fh $mol->name, "\n";
# ... do some stuff with $fh and $mol ...
}
The main use of this module is as a base class for other molecule file I/O
modules (for example, Chemistry::File::PDB). Such modules should override and
extend the Chemistry::File methods as needed. You only need to care about the
methods here if if you are writing a file I/O module or if you want a finer
degree of control than what is offered by the simple read and write methods in
the Chemistry::Mol class.
From the user's point of view, this module can also be used as shorthand for
using several Chemistry::File modules at the same time.
use Chemistry::File qw(PDB MDLMol);
is exactly equivalent to
use Chemistry::File::PDB;
use Chemistry::File::MDLMol;
If you use the :auto keyword, Chemistry::File will autodetect and load all the
Chemistry::File::* modules installed in your system.
use Chemistry::File ':auto';
Before version 0.30, file I/O modules typically used only parse_string,
write_string, parse_file, and write_file, and they were generally used as
class methods. A file could contain one or more molecules and only be read or
written whole; reading it would return every molecule on the file. This was
problematic when dealing with large multi-molecule files (such as SDF files),
because all the molecules would have to be loaded into memory at the same
time.
While version 0.30 retains backward compatibility with that simple model, it
also allows a more flexible interface that allows reading one molecule at a
time, skipping molecules, and reading and writing file-level information that
is not associated with specific molecules. The following diagram shows the
global structure of a file according to the new model:
+-----------+
| header |
+-----------+
| molecule |
+-----------+
| molecule |
+-----------+
| ... |
+-----------+
| footer |
+-----------+
In cases where the header and the footer are empty, the model reduces to the
pre-0.30 version. The low-level steps to read a file are the following:
$file = Chemistry::File::MyFormat->new(file => 'xyz.mol');
$file->open('<');
$file->read_header;
while (my $mol = $self->read_mol($file->fh, %opts)) {
# do something with $mol...
}
$self->read_footer;
The "read" method does all the above automatically, and it stores all
the molecules read in the mols property.
All the methods below include a list of options %opts at the end of the
parameter list. Each class implementing this interface may have its own
particular options. However, the following options should be recognized by all
classes:
- mol_class
- A class or object with a "new" method that
constructs a molecule. This is needed when the user want to specify a
molecule subclass different from the default. When this option is not
defined, the module may use Chemistry::Mol or whichever class is
appropriate for that file format.
- format
- The name of the file format being used, as registered by
Chemistry::Mol->register_format.
- fatal
- If true, parsing errors should throw an exception; if
false, they should just try to recover if possible. True by default.
The class methods in this class (or rather, its derived classes) are usually not
called directly. Instead, use Chemistry::Mol->read, write, print, parse,
and file. These methods also work if called as instance methods.
- $class->parse_string($s, %options)
- Parse a string $s and return one or more molecule objects.
This is an abstract method, so it should be provided by all derived
classes.
- $class->write_string($mol, %options)
- Convert a molecule to a string. This is an abstract method,
so it should be provided by all derived classes.
- $class->parse_file($file, %options)
- Reads the file $file and returns one or more molecules. The
default method slurps the whole file and then calls parse_string, but
derived classes may choose to override it. $file can be a filehandle, a
filename, or a scalar reference. See "new" for details.
- $class->write_file($mol, $file, %options)
- Writes a file $file containing the molecule $mol. The
default method calls write_string first and then saves the string to a
file, but derived classes may choose to override it. $file can be either a
filehandle or a filename.
- $class->name_is($fname, %options)
- Returns true if a filename is of the format corresponding
to the class. It should look at the filename only, because it may be
called with non-existent files. It is used to determine with which format
to save a file. For example, the Chemistry::File::PDB returns true if the
file ends in .pdb.
- $class->string_is($s, %options)
- Examines the string $s and returns true if it has the
format of the class.
- $class->file_is($file, %options)
- Examines the file $file and returns true if it has the
format of the class. The default method slurps the whole file and then
calls string_is, but derived classes may choose to override it.
- $class->slurp
- Reads a file into a scalar. Automatic decompression of
gzipped files is supported if the Compress::Zlib module is installed.
Files ending in .gz are assumed to be compressed; otherwise it is possible
to force decompression by passing the gzip => 1 option (or no
decompression with gzip => 0).
- $class->new(file => $file, opts => \%opts)
- Create a new file object. This method is usually called
indirectly via the Chemistry::Mol->file method. $file may be a scalar
with a filename, an open filehandle, or a reference to a scalar. If a
reference to a scalar is used, the string contained in the scalar is used
as an in-memory file.
Chemistry::File objects are derived from Chemistry::Obj and have the same
properties (name, id, and type), as well as the following ones:
- file
- The "file" as described above under
"new".
- fh
- The filehandle used for reading and writing molecules. It
is opened by "open".
- opts
- A hashref containing the options that are passed through to
the old-style class methods. They are also passed to the instance method
to keep a similar interface, but they could access them via $self->opts
anyway.
- mode
- '>' if the file is open for writing, '<' for reading,
and false if not open.
- mols
- "read" stores all the molecules that were read in
this property as an array reference. "write" gets the molecules
to write from here.
These methods should be overridden, because they don't really do much by
default.
- $file->read_header
- Read whatever information is available in the file before
the first molecule. Does nothing by default.
- $file->read_footer
- Read whatever information is available in the file after
the last molecule. Does nothing by default.
- $self->slurp_mol($fh)
- Reads from the input string until the end of the current
molecule and returns the "slurped" string. It does not parse the
string. It returns undefined if there are no more molecules in the file.
This method should be overridden if needed; by default, it slurps until
the end of the file.
- $self->skip_mol($fh)
- Similar to slurp_mol, but it doesn't need to return
anything except true or false. It should also be overridden if needed; by
default, it just calls slurp_mol.
- $file->read_mol($fh, %opts)
- Read the next molecule in the input stream. It returns
false if there are no more molecules in the file. This method should be
overridden by derived classes; otherwise it will call slurp_mol and
parse_string (for backwards compatibility; it is recommended to override
read_mol directly in new modules).
Note: some old file I/O modules (written before the 0.30 interface) may
return more than one molecule anyway, so it is recommended to call
read_mol in list context to be safe:
($mol) = $file->read_mol($fh, %opts);
- $file->write_header
- Write whatever information is needed before the first
molecule. Does nothing by default.
- $file->write_footer
- Write whatever information is needed after the last
molecule. Does nothing by default.
- $self->write_mol($fh, $mol, %opts)
- Write one molecule to $fh. By default and for backward
compatibility, it just calls "write_string" and prints its
return value to $self->fh. New classes should override it.
- $self->open($mode)
- Opens the file (held in $self->file) for reading by
default, or for writing if $mode eq '>'. This method sets $self->fh
transparently regardless of whether $self->file is a filename
(compressed or not), a scalar reference, or a filehandle.
- $self->close
- Close the file. For regular files this just closes the
filehandle, but for gzipped files it does some additional postprocessing.
This method is called automatically on object destruction, so it is not
mandatory to call it explicitly.
- $file->read
- Read the whole file. This calls open, read_header, read_mol
until there are no more molecules left, read_footer, and close. Returns a
list of molecules if called in list context, or the first molecule in
scalar context.
- $self->write
- Write all the molecules in $self->mols. It just calls
open, write_header, write_mol (per each molecule), write_footer, and
close.
The :auto feature may not be entirely portable, but it is known to work under
Unix and Windows (either Cygwin or ActiveState).
<
https://github.com/perlmol/Chemistry-Mol>
Chemistry::Mol
Ivan Tubert-Brohman-Brohman <
[email protected]>
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.