diff mayachemtools/lib/AtomicDescriptors/AtomicDescriptors.pm @ 0:73ae111cf86f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayachemtools/lib/AtomicDescriptors/AtomicDescriptors.pm	Wed Jan 20 11:55:01 2016 -0500
@@ -0,0 +1,305 @@
+package AtomicDescriptors::AtomicDescriptors;
+#
+# $RCSfile: AtomicDescriptors.pm,v $
+# $Date: 2015/02/28 20:47:48 $
+# $Revision: 1.17 $
+#
+# Author: Manish Sud <[e-mail]>
+#
+# Copyright (C) 2015 Manish Sud. All rights reserved.
+#
+# This file is part of MayaChemTools.
+#
+# MayaChemTools is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3 of the License, or (at your option) any
+# later version.
+#
+# MayaChemTools is distributed in the hope that it will be useful, but without
+# any warranty; without even the implied warranty of merchantability of fitness
+# for a particular purpose.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
+# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
+# Boston, MA, 02111-1307, USA.
+#
+
+use strict;
+use Carp;
+use Exporter;
+use Scalar::Util ();
+use ObjectProperty;
+use TextUtil ();
+
+use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
+
+@ISA = qw(ObjectProperty Exporter);
+@EXPORT = qw();
+@EXPORT_OK = qw();
+
+%EXPORT_TAGS = (all  => [@EXPORT, @EXPORT_OK]);
+
+# Setup class variables...
+my($ClassName);
+_InitializeClass();
+
+# Class constructor...
+sub new {
+  my($Class, %PropertyNamesAndValues) = @_;
+
+  # Initialize object...
+  my $This = {};
+  bless $This, ref($Class) || $Class;
+  $This->_InitializeAtomicDescriptors();
+
+  $This->_InitializeAtomicDescriptorsProperties(%PropertyNamesAndValues);
+
+  return $This;
+}
+
+# Initialize object data...
+#
+sub _InitializeAtomicDescriptors {
+  my($This) = @_;
+
+  # Molecule object...
+  $This->{Molecule} = '';
+
+  # Type of atomic descriptors...
+  $This->{Type} = '';
+
+  # By default, atomic decriptor values are also calculated for hydrogens...
+  $This->{IgnoreHydrogens} = 0;
+
+  # Calculated atomic descriptor values hash. Instead of assigning the calculated values to Atom
+  # objects, these values are stored in the current object in a hash with atom ID and atomic descriptor
+  # values as key/value pairs.
+  #
+  # Unlike molecular descriptors, no descriptor names are assigned to individual atomic descriptor
+  # values.
+  #
+  %{$This->{DescriptorValues}} = ();
+}
+
+# Initialize class ...
+sub _InitializeClass {
+  #Class name...
+  $ClassName = __PACKAGE__;
+}
+
+# Initialize object properties....
+sub _InitializeAtomicDescriptorsProperties {
+  my($This, %PropertiesNamesAndValues) = @_;
+
+  my($Name, $Value, $MethodName);
+  while (($Name, $Value) = each  %PropertiesNamesAndValues) {
+    $MethodName = "Set${Name}";
+    $This->$MethodName($Value);
+  }
+
+  return $This;
+}
+
+# Initialize descriptor values for all atoms in a molecule...
+#
+sub _InitializeDescriptorValues {
+  my($This) = @_;
+
+  if (!$This->{Molecule}) {
+    return $This;
+  }
+
+  # Assign 'None' to all atomic descriptor values...
+  #
+  my($Atom, $AtomID);
+
+  ATOM: for $Atom ($This->{Molecule}->GetAtoms()) {
+    $AtomID = $Atom->GetID();
+    $This->{DescriptorValues}{$AtomID} = 'None';
+  }
+
+  return $This;
+}
+
+# Set molecule object and make sure it's not already set...
+#
+sub SetMolecule {
+  my($This, $Molecule) = @_;
+
+  if ($This->{Molecule}) {
+    croak "Error: ${ClassName}->SetMolecule: Can't change molecule object:  It's already set...";
+  }
+  $This->{Molecule} = $Molecule;
+
+  # Weaken the reference to disable increment of reference count...
+  Scalar::Util::weaken($This->{Molecule});
+
+  return $This;
+}
+
+# Set type and make sure it's not already set...
+#
+sub SetType {
+  my($This, $Type) = @_;
+
+  if ($This->{Type}) {
+    croak "Error: ${ClassName}->SetType: Can't change AtomicDescriptors type:  It's already set...";
+  }
+  $This->{Type} = $Type;
+
+  return $This;
+}
+
+# Set specific atomic descriptor value...
+#
+sub SetDescriptorValue {
+  my($This, $Atom, $AtomicDescriptor) = @_;
+  my($AtomID);
+
+  $AtomID = $Atom->GetID();
+  $This->{DescriptorValues}{$AtomID} = $AtomicDescriptor;
+
+  return $This;
+}
+
+# Get specific atomic descriptor value...
+#
+sub GetDescriptorValue {
+  my($This, $Atom) = @_;
+  my($AtomID);
+
+  $AtomID = $Atom->GetID();
+
+  return exists $This->{DescriptorValues}{$AtomID} ? $This->{DescriptorValues}{$AtomID} : 'None';
+}
+
+# Get calculated atomic descriptor values as a  hash with atom ID and atomic descriptor
+# values as key/value pairs...
+#
+sub GetDescriptorValues {
+  my($This) = @_;
+
+  return %{$This->{DescriptorValues}};
+}
+
+# Are all atomic descriptor values successfully calculated?
+#
+# Notes:
+#   . Dynamic checking of calculated descriptor values for atoms eliminates the need
+#     to check and synchronize valid descriptor values during SetDescriptorValue.
+#
+sub IsDescriptorsGenerationSuccessful {
+  my($This) = @_;
+  my($Atom, $DescriptorValue, @Atoms);
+
+  ATOM: for $Atom ($This->{Molecule}->GetAtoms()) {
+    if ($This->{IgnoreHydrogens} && $Atom->IsHydrogen()) {
+      next ATOM;
+    }
+    $DescriptorValue = $This->GetDescriptorValue($Atom);
+    if ($DescriptorValue =~ /^None$/i) {
+      return 0;
+    }
+  }
+
+  return 1;
+}
+
+1;
+
+__END__
+
+=head1 NAME
+
+AtomicDescriptors - AtomicDescriptors class
+
+=head1 SYNOPSIS
+
+use AtomicDescriptors::AtomicDescriptors;
+
+use AtomicDescriptors::AtomicDescriptors qw(:all);
+
+=head1 DESCRIPTION
+
+B<AtomicDescriptors> base class used to derive all other atomic descriptors classes provides the following methods:
+
+new, GetDescriptorValue, GetDescriptorValues,
+IsDescriptorsGenerationSuccessful, SetDescriptorValue
+
+B<AtomicDescriptors> class is  derived from B<ObjectProperty> base class which provides methods not
+explicitly defined in B<Fingerprints> or B<ObjectProperty> classes using Perl's AUTOLOAD functionality.
+These methods are generated on-the-fly for a specified object property:
+
+    Set<PropertyName>(<PropertyValue>);
+    $PropertyValue = Get<PropertyName>();
+    Delete<PropertyName>();
+
+=head2 METHODS
+
+=over 4
+
+=item B<new>
+
+    $NewAtomicDescriptors = new AtomicDescriptors::
+                            AtomicDescriptors(%NamesAndValues);
+
+Using specified I<AtomicDescriptors> property names and values hash, B<new> method creates a new object
+and returns a reference to newly created B<AtomicDescriptors> object. By default, following properties are
+initialized:
+
+    Molecule = '';
+    Type = '';
+    IgnoreHydrogens = 0;
+
+=item B<GetDescriptorValue>
+
+    $Value = $AtomicDescriptors->GetDescriptorValue($Atom);
+
+Returns calculated atomic descriptor I<Value> for specified I<Atom>.
+
+=item B<GetDescriptorValues>
+
+    %Values = $AtomicDescriptors->GetDescriptorValues();
+
+Returns calculated atomic descriptor values for all atoms as a hash with atom ID
+and atomic descriptor values as key/value pairs.
+
+=item B<IsDescriptorsGenerationSuccessful>
+
+    $Status = $AtomicDescriptors->
+              IsDescriptorsGenerationSuccessful();
+
+Returns 1 or 0 based on whether atomic desctiptors calculations was successful.
+For a successful atomic descriptors calculation, all atoms must have a value of other
+than a string I<None>.
+
+=item B<SetDescriptorValue>
+
+    $AtomicDescriptors->SetDescriptorValue($Atom, $Value);
+
+Sets specified atomic descriptor I<Value> for I<Atom> and returns I<$AtomicDescriptors>.
+
+=back
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+demo
+
+=head1 COPYRIGHT
+
+Copyright (C) 2015 Manish Sud. All rights reserved.
+
+This file is part of MayaChemTools.
+
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.
+
+=cut