diff docs/modules/txt/MolecularDescriptorsGenerator.txt @ 0:4816e4a8ae95 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/modules/txt/MolecularDescriptorsGenerator.txt	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,334 @@
+NAME
+    MolecularDescriptorsGenerator
+
+SYNOPSIS
+    use MolecularDescriptors::MolecularDescriptorsGenerator;
+
+    use MolecularDescriptors::MolecularDescriptorsGenerator qw(:all);
+
+DESCRIPTION
+    MolecularDescriptorsGenerator class provides the following methods:
+
+    new, GenerateDescriptors, GetAvailableClassAndDescriptorNames,
+    GetAvailableClassNameForDescriptorName,
+    GetAvailableDescriptorClassNames, GetAvailableDescriptorNames,
+    GetAvailableDescriptorNamesForDescriptorClass,
+    GetDescriptorClassParameters, GetDescriptorNames,
+    GetDescriptorNamesAndValues, GetDescriptorValueByName,
+    GetDescriptorValues, GetRuleOf3DescriptorNames,
+    GetRuleOf5DescriptorNames, IsDescriptorClassNameAvailable,
+    IsDescriptorNameAvailable, IsDescriptorsGenerationSuccessful,
+    SetDescriptorClassParameters, SetDescriptorNames, SetMode, SetMolecule,
+    StringifyMolecularDescriptorsGenerator
+
+    MolecularDescriptorsGenerator is derived from is derived from
+    ObjectProperty base class that provides methods not explicitly defined
+    in MolecularDescriptorsGenerator or 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>();
+
+    MolecularDescriptorsGenerator is designed to provide a plug-in
+    environment for molecular descriptors development. The molecular
+    descriptor class modules available in MolecularDescriptors directory
+    under MayaChemTools/lib directory are automatically detected and loaded
+    into the system. The descriptor names provided by each descriptor class
+    module through its GetDescriptorNames function are retrieved and are
+    made available for calculations of their values for a specified
+    molecule.
+
+    Any combination of available descriptor names can be specified during
+    calculation of descriptor values using GenerateDescriptors method. The
+    current release of MayaChemTools supports generation of four sets of
+    descriptors: All available descriptors, rule of 5 or 3 descriptors, or a
+    specified set of descriptor names.
+
+    RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight,
+    HydrogenBondDonors, HydrogenBondAcceptors, SLogP. RuleOf5 states:
+    MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors
+    <= 10, and logP <= 5.
+
+    RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight,
+    RotatableBonds, HydrogenBondDonors, HydrogenBondAcceptors, SLogP, TPSA.
+    RuleOf3 states: MolecularWeight <= 300, RotatableBonds <= 3,
+    HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and TPSA
+    <= 60.
+
+    Before calculation of a specified set of descriptors by
+    GenerateDescriptors method, a set of descriptor calculation control
+    parameters for a specific descriptor class name can be set using
+    SetDescriptorClassParameters method. The specified control parameter
+    names and values are simply passed on to specified descriptor class
+    during instantiation of descriptor class object without performing any
+    validation of parameter names and associated values. It's up to the
+    appropriate descriptor class methods to validate these parameters and
+    values. In addition to specified parameter names and values, the
+    parameter hash must also contain descriptor class name as key and value
+    pair with DescriptorClassName as key with class name as value.
+
+  METHODS
+    new
+            $NewMolecularDescriptorsGenerator = new MolecularDescriptors::
+                                                MolecularDescriptorsGenerator(
+                                                %NamesAndValues);
+
+        Using specified *MolecularDescriptorsGenerator* property names and
+        values hash, new method creates a new object and returns a reference
+        to newly created MolecularDescriptorsGenerator object. By default,
+        the following properties are initialized:
+
+            Mode = 'All'
+            @{$This->{DescriptorNames}} = ()
+            %{$This->{DescriptorClassParameters}} = ()
+            @{$This->{DescriptorClassNames}} = ()
+            %{$This->{DescriptorClassObjects}} = ()
+            @{$This->{DescriptorValues}} = ()
+
+        Examples:
+
+            $MolecularDescriptorsGenerator = new MolecularDescriptors::
+                                             MolecularDescriptorsGenerator(
+                                      'Molecule' => $Molecule);
+
+            @DescriptorNames = qw(MolecularWeight HydrogenBondDonors Fsp3Carbons)
+            $MolecularDescriptorsGenerator = new MolecularDescriptors::
+                                             MolecularDescriptorsGenerator(
+                                      'Mode' => 'Specify',
+                                      'DescriptorNames' => \@DescriptorNames);
+
+            $MolecularDescriptorsGenerator->SetDescriptorClassParameters(
+                                      'DescriptorClassName' => 'WeightAndMassDescriptors',
+                                      'WeightPrecision' => 2,
+                                      'MassPrecision' => 2);
+
+            $MolecularDescriptorsGenerator->SetDescriptorClassParameters(
+                                      'DescriptorClassName' => 'HydrogenBondsDescriptors',
+                                      'HydrogenBondsType' => 'HBondsType1');
+
+            $MolecularDescriptorsGenerator->SetMolecule($Molecule);
+            $MolecularDescriptorsGenerator->GenerateDescriptors();
+            print "MolecularDescriptorsGenerator: $MolecularDescriptorsGenerator\n";
+
+    GenerateDescriptors
+            $MolecularDescriptorsGenerator->GenerateDescriptors();
+
+        Calculates descriptor values for specified descriptors and returns
+        *MolecularDescriptorsGenerator*.
+
+        Descriptor class objects are instantiated only once at first
+        invocation. During subsequent calls to GenerateDescriptors method,
+        descriptor values are initialized and GenerateDescriptors method
+        provided by descriptor class is used to calculate descriptor values
+        for specified descriptors.
+
+    GetAvailableClassAndDescriptorNames
+            %ClassAndDescriptorNames = $MolecularDescriptorsGenerator->
+                                      GetAvailableClassAndDescriptorNames();
+            %ClassAndDescriptorNames = MolecularDescriptors::
+                                       MolecularDescriptorsGenerator::
+                                       GetAvailableClassAndDescriptorNames();
+
+        Returns available descriptors class and descriptors names as a hash
+        containing key and value pairs corresponding to class name and an
+        array of descriptor names available for the class.
+
+    GetAvailableClassNameForDescriptorName
+            $DescriptorClassName = $MolecularDescriptorsGenerator->
+                              GetAvailableClassNameForDescriptorName($DescriptorName);
+
+            $DescriptorClassName = MolecularDescriptors::MolecularDescriptorsGenerator::
+                              GetAvailableClassNameForDescriptorName($DescriptorName);
+
+        Returns available descriptor class name for a descriptor name.
+
+    GetAvailableDescriptorClassNames
+            $Return = $MolecularDescriptorsGenerator->GetAvailableDescriptorClassNames();
+
+            @DescriptorClassNames = $MolecularDescriptorsGenerator->
+                                      GetAvailableDescriptorClassNames();
+            @DescriptorClassNames = MolecularDescriptors::
+                                      MolecularDescriptorsGenerator::
+                                      GetAvailableDescriptorClassNames();
+
+        Returns available descriptor class names as an array or number of
+        available descriptor class names in scalar context.
+
+    GetAvailableDescriptorNames
+            @DescriptorNames = $MolecularDescriptorsGenerator->
+                                      GetAvailableDescriptorNames();
+            @DescriptorNames = MolecularDescriptors::
+                                      MolecularDescriptorsGenerator::
+                                      GetAvailableDescriptorNames();
+
+        Returns available descriptor names as an array or number of
+        available descriptor names in scalar context.
+
+    GetAvailableDescriptorNamesForDescriptorClass
+            @DescriptorNames = $MolecularDescriptorsGenerator->
+                  GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);
+            @DescriptorNames = MolecularDescriptors::
+                               MolecularDescriptorsGenerator::
+                  GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);
+
+        Returns available descriptors names for a descriptor class as an
+        array or number of available descriptor names in scalar context.
+
+    GetDescriptorClassParameters
+            $DescriptorClassParametersRef = $MolecularDescriptorsGenerator->
+                                      GetDescriptorClassParameters();
+            $DescriptorClassParametersRef = MolecularDescriptors::
+                                            MolecularDescriptorsGenerator::
+                                            GetDescriptorClassParameters();
+
+        Returns descriptor name parameters as a reference to hash of hashes
+        with hash keys corresponding to class name and class parameter name
+        with hash value as class parameter value.
+
+    GetDescriptorNames
+            @DescriptorNames = $MolecularDescriptorsGenerator->GetDescriptorNames();
+            @DescriptorNames = MolecularDescriptors::MolecularDescriptorsGenerator::
+                               GetDescriptorNames();
+
+        Returns all available descriptor names as an array or number of
+        available descriptors in scalar context.
+
+    GetDescriptorNamesAndValues
+            %NamesAndValues = $MolecularDescriptorsGenerator->
+                                      GetDescriptorNamesAndValues();
+
+        Returns calculated molecular descriptor names and values as a hash
+        with descriptor names and values as hash key and value pairs.
+
+    GetDescriptorValueByName
+            $Value = $MolecularDescriptorsGenerator->
+                                      GetDescriptorValueByName($Name);
+
+        Returns calculated descriptor values for a specified descriptor
+        name.
+
+    GetDescriptorValues
+            @DescriptorValues = $MolecularDescriptorsGenerator->GetDescriptorValues();
+
+        Returns all calculated descriptor values as an array corresponding
+        to specified descriptor names.
+
+    GetRuleOf3DescriptorNames
+            @DescriptorNames = $MolecularDescriptorsGenerator->
+                               GetRuleOf3DescriptorNames();
+            @DescriptorNames = MolecularDescriptors::
+                               MolecularDescriptorsGenerator::
+                               GetRuleOf3DescriptorNames();
+
+        Returns rule of 3 descriptor names as an array or number of rule of
+        3 descriptors in scalar context.
+
+        RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight,
+        RotatableBonds, HydrogenBondDonors, HydrogenBondAcceptors, SLogP,
+        TPSA. RuleOf3 states: MolecularWeight <= 300, RotatableBonds <= 3,
+        HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and
+        TPSA <= 60.
+
+    GetRuleOf5DescriptorNames
+            @DescriptorNames = $MolecularDescriptorsGenerator->
+                                      GetRuleOf5DescriptorNames();
+            @DescriptorNames = $MolecularDescriptorsGenerator::
+                                     GetRuleOf5DescriptorNames();
+
+        Returns rule of 5 descriptor names as an array or number of rule of
+        4 descriptors in scalar context.
+
+        RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight,
+        HydrogenBondDonors, HydrogenBondAcceptors, SLogP. RuleOf5 states:
+        MolecularWeight <= 500, HydrogenBondDonors <= 5,
+        HydrogenBondAcceptors <= 10, and logP <= 5.
+
+    IsDescriptorClassNameAvailable
+            $Status = $MolecularDescriptorsGenerator->
+                                      IsDescriptorClassNameAvailable($ClassName);
+            $Status = MolecularDescriptors::
+                                      MolecularDescriptorsGenerator::
+                                      IsDescriptorClassNameAvailable($ClassName);
+
+        Returns 1 or 0 based on whether specified descriptor class name is
+        available.
+
+    IsDescriptorNameAvailable
+            $Status = $MolecularDescriptorsGenerator->
+                                      IsDescriptorNameAvailable($DescriptorName);
+            $Status = MolecularDescriptors::
+                                      MolecularDescriptorsGenerator::
+                                      IsDescriptorNameAvailable($DescriptorName);
+
+        Returns 1 or 0 based on whether specified descriptor name is
+        available.
+
+    IsDescriptorsGenerationSuccessful
+            $Status = $MolecularDescriptorsGenerator->
+                                      IsDescriptorsGenerationSuccessful();
+
+        Returns 1 or 0 based on whether descriptors generation is
+        successful.
+
+    SetDescriptorClassParameters
+            $MolecularDescriptorsGenerator->SetDescriptorClassParameters(
+                                      %NamesAndValues);
+
+        Sets descriptor calculation control parameters for a specified
+        descriptor class name and returns *MolecularDescriptorsGenerator*.
+
+        The specified parameter names and values are simply passed on to
+        specified descriptor class during instantiation of descriptor class
+        object without any performing any validation of parameter names and
+        associated values. It's up to the appropriate descriptor class
+        methods to validate these parameters and values.
+
+        In addition to specified parameter names and values, the parameter
+        hash must also contain descriptor class name as key and value pair
+        with DescriptorClassName as key with class name as value.
+
+    SetDescriptorNames
+            $MolecularDescriptorsGenerator->SetDescriptorNames(@Names);
+            $MolecularDescriptorsGenerator->SetDescriptorNames(\@Names);
+
+        Sets descriptor names to use for generating descriptor values using
+        an array or reference to an array and returns
+        *MolecularDescriptorsGenerator*.
+
+    SetMode
+            $MolecularDescriptorsGenerator->SetMode($Mode);
+
+        Sets descriptors generation mode and returns
+        *MolecularDescriptorsGenerator*. Possible *Mode* values: *All,
+        RuleOf5, RuleOf3, Specify*.
+
+    SetMolecule
+            $MolecularDescriptorsGenerator->SetMolecule($Molecule);
+
+        Sets molecule to use during calculation of molecular descriptors and
+        returns *MolecularDescriptorsGenerator*.
+
+    StringifyMolecularDescriptorsGenerator
+            $String = $MolecularDescriptorsGenerator->StringifyMolecularDescriptorsGenerator();
+
+        Returns a string containing information about
+        *MolecularDescriptorsGenerator* object.
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    MolecularDescriptors.pm
+
+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.
+