Mercurial > repos > deepakjadmin > mayatool3_test3

package Fingerprints::FingerprintsStringUtil;
#
# $RCSfile: FingerprintsStringUtil.pm,v $
# $Date: 2015/02/28 20:48:54 $
# $Revision: 1.24 $
#
# Author: Manish Sud <msud@san.rr.com>
#
# 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 Exporter;
use Carp;
use TextUtil ();
use Fingerprints::FingerprintsBitVector;
use Fingerprints::FingerprintsVector;

use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);

@ISA = qw(Exporter);
@EXPORT = qw();
@EXPORT_OK = qw(AreFingerprintsStringValuesValid GenerateFingerprintsString GenerateFingerprintsBitVectorString GenerateFingerprintsVectorString GetFingerprintsStringTypeAndDescription GetDefaultBitsOrder GetDefaultBitStringFormat GetDefaultVectorStringFormat GetFingeprintsStringDelimiter GetFingerprintsStringValues ParseFingerprintsString ParseFingerprintsBitVectorString ParseFingerprintsVectorString);

%EXPORT_TAGS = (all  => [@EXPORT, @EXPORT_OK]);

# Fingerprint string values delimiter...
my($FPStringDelim) = ';';

# Generate fingerprints string...
#
sub GenerateFingerprintsString {
  my($FingerprintsObject) = @_;
  my($VectorType);

  $VectorType = $FingerprintsObject->GetVectorType();

  VECTORTYPE : {
    if ($VectorType =~ /^FingerprintsBitVector$/i) { return GenerateFingerprintsBitVectorString(@_); last VECTORTYPE; }
    if ($VectorType =~ /^FingerprintsVector$/i) { return GenerateFingerprintsVectorString(@_); last VECTORTYPE; }
    croak "Error: FingerprintsStringUtil::GenerateFingerprintsString: Fingerprints object vector type, $VectorType, is not supported. Valid values: FingerprintsBitVector or FingerprintsVector...";
  }
  return '';
}

# Generate fingerprints bit vector string...
#
sub GenerateFingerprintsBitVectorString {
  my($FingerprintsObject, $BitStringFormat, $BitsOrder) = @_;
  my($FingerprintsString, $FingerprintsBitVector, @FingerprintsStringValues);

  if (!$BitStringFormat) { $BitStringFormat = GetDefaultBitStringFormat(); }
  if (!$BitsOrder) {$BitsOrder = GetDefaultBitsOrder(); }

  $FingerprintsString = '';
  $FingerprintsBitVector = Fingerprints::FingerprintsBitVector::IsFingerprintsBitVector($FingerprintsObject) ? $FingerprintsObject : $FingerprintsObject->GetFingerprintsBitVector();

  # Use specified size instead of size: it corresponds to actual size of the fingerprints bit vector;
  # size reflects actual internal size including any padding.
  #

  @FingerprintsStringValues = ();
  push @FingerprintsStringValues, ($FingerprintsObject->GetVectorType(), _GetFingerprintsDescription($FingerprintsObject), $FingerprintsBitVector->GetSpecifiedSize(), $BitStringFormat, $BitsOrder);

  $FingerprintsString = join("${FPStringDelim}",  @FingerprintsStringValues) . "${FPStringDelim}" . _GetFingerprintBitVectorString($FingerprintsBitVector, $BitStringFormat, $BitsOrder);

  return $FingerprintsString;
}

# Get fingerprint bit vector string...
#
sub _GetFingerprintBitVectorString {
  my($FingerprintsBitVector, $BitStringFormat, $BitsOrder) = @_;
  my($FingerprintBitString);

  if (!$BitStringFormat) { $BitStringFormat = GetDefaultBitStringFormat(); }
  if (!$BitsOrder) {$BitsOrder = GetDefaultBitsOrder(); }

  $FingerprintBitString = '';
  if (!$FingerprintsBitVector) {return $FingerprintBitString;}

  BITSTRINGFORMAT : {
    if ($BitStringFormat =~ /^(BinaryString|Binary|Bin)$/i) { return $FingerprintsBitVector->GetBitsAsBinaryString($BitsOrder); last BITSTRINGFORMAT; }
    if ($BitStringFormat =~ /^(HexadecimalString|Hexadecimal|Hex)$/i) { return $FingerprintsBitVector->GetBitsAsHexadecimalString($BitsOrder); last BITSTRINGFORMAT; }
    croak "Error: FingerprintsStringUtil::_GetFingerprintBitsAsString: Specified bit vector string format, $BitStringFormat, is not supported. Value values: Binary, Bin, BinaryString, Hexdecimal, Hex, HexadecimalString...";
  }
  return $FingerprintBitString;
}

# Generate fingerprints vector string...
#
sub GenerateFingerprintsVectorString {
  my($FingerprintsObject, $VectorStringFormat) = @_;
  my($FingerprintsString, $FingerprintsVector, @FingerprintsStringValues);

  $FingerprintsString = '';
  $FingerprintsVector = Fingerprints::FingerprintsVector::IsFingerprintsVector($FingerprintsObject) ? $FingerprintsObject : $FingerprintsObject->GetFingerprintsVector();

  if (!$VectorStringFormat) { $VectorStringFormat = _GetDefaultVectorStringFormat($FingerprintsVector); }

  @FingerprintsStringValues = ();
  push @FingerprintsStringValues, ($FingerprintsObject->GetVectorType(), _GetFingerprintsDescription($FingerprintsObject), $FingerprintsVector->GetNumOfValues(), $FingerprintsVector->GetType(), $VectorStringFormat);

  $FingerprintsString = join("${FPStringDelim}",  @FingerprintsStringValues) . "${FPStringDelim}" . _GetFingerprintVectorString($FingerprintsVector, $VectorStringFormat);

  return $FingerprintsString;
}

# Get fingerprint vector string...
#
sub _GetFingerprintVectorString {
  my($FingerprintsVector, $VectorStringFormat) = @_;
  my($FingerprintString);

  if (!$VectorStringFormat) { $VectorStringFormat = _GetDefaultVectorStringFormat($FingerprintsVector);}

  $FingerprintString = '';
  if (!$FingerprintsVector) {return $FingerprintString;}

  VECTORSTRINGFORMAT : {
    if ($VectorStringFormat =~ /^(IDsAndValuesString|IDsAndValues)$/i) { return $FingerprintsVector->GetIDsAndValuesString(); last VECTORSTRINGFORMAT; }
    if ($VectorStringFormat =~ /^(IDsAndValuesPairsString|IDsAndValuesPairs)$/i) { return $FingerprintsVector->GetIDsAndValuesPairsString(); last VECTORSTRINGFORMAT; }
    if ($VectorStringFormat =~ /^(ValuesAndIDsString|ValuesAndIDs)$/i) { return $FingerprintsVector->GetValuesAndIDsString(); last VECTORSTRINGFORMAT; }
    if ($VectorStringFormat =~ /^(ValuesAndIDsPairsString|ValuesAndIDsPairs)$/i) { return $FingerprintsVector->GetValuesAndIDsPairsString(); last VECTORSTRINGFORMAT; }
    if ($VectorStringFormat =~ /^(ValuesString|Values)$/i) { return $FingerprintsVector->GetValuesString(); last VECTORSTRINGFORMAT; }
    croak "Error: FingerprintsStringUtil::_GetFingerprintVectorString: Specified vector string format, $VectorStringFormat, is not supported. Value values: IDsAndValuesString, IDsAndValues, IDsAndValuesPairsString, IDsAndValuesPairs, ValuesAndIDsString, ValuesAndIDs, ValuesAndIDsPairsString, ValuesAndIDsPairs, ValuesString, Values...";
  }
  return $FingerprintString;
}

# Get fingerprints string type and description...
sub GetFingerprintsStringTypeAndDescription {
  my($FingerprintsString) = @_;
  my($Type, $Description);

  ($Type, $Description) = _ParseFingerprintsStringValues($FingerprintsString);

  return ($Type, $Description);
}

# Get all fingerprints string values...
sub GetFingerprintsStringValues {
  my($FingerprintsString) = @_;

  return _ParseFingerprintsStringValues($FingerprintsString);
}

# Parse fingerprints string and return FingerprintsBitVector or FingerprintsVector object...
#
sub ParseFingerprintsString {
  my($FingerprintsString) = @_;

  VECTORTYPE : {
    if ($FingerprintsString =~ /^FingerprintsBitVector/i) { return ParseFingerprintsBitVectorString(@_); last VECTORTYPE; }
    if ($FingerprintsString =~ /^FingerprintsVector/i) { return ParseFingerprintsVectorString(@_); last VECTORTYPE; }
    croak "Error: FingerprintsStringUtil::ParseFingerprintsString: Fingerprints string vector type is not supported. Valid values: FingerprintsBitVector or FingerprintsVector...";
  }
  return undef;
}

# Parse fingerprints bit vector string and retrun bit vector...
#
sub ParseFingerprintsBitVectorString {
  my($FingerprintsString, $ValidateValues) = @_;
  my($ErrorMsgPrefix, $VectorType, $Description, $Size, $BitStringFormat, $BitsOrder, $BitVectorString);

  $ErrorMsgPrefix = "Error: ParsePathLengthFingerprintsBitVectorString";
  ($VectorType, $Description, $Size, $BitStringFormat, $BitsOrder, $BitVectorString) = _ParseFingerprintsStringValues($FingerprintsString);
  if ($ValidateValues) {
    _ValidateFingerprintsStringValues($ErrorMsgPrefix, $VectorType, $Size, $BitStringFormat, $BitsOrder, $BitVectorString);
  }

  return _GenerateFingerprintBitVector($VectorType, $Description, $Size, $BitStringFormat, $BitsOrder, $BitVectorString);
}

# Generate fingerints bit vector...
#
sub _GenerateFingerprintBitVector {
  my($VectorType, $Description, $Size, $BitStringFormat, $BitsOrder, $BitVectorString) = @_;
  my($FingerprintsBitVector);

  $FingerprintsBitVector = undef;

  BITSTRINGFORMAT : {
    if ($BitStringFormat =~ /^(BinaryString|Binary|Bin)$/i) {
      $FingerprintsBitVector = Fingerprints::FingerprintsBitVector::NewFromBinaryString($BitVectorString, $BitsOrder);
      last BITSTRINGFORMAT;
    }
    if ($BitStringFormat =~ /^(HexadecimalString|Hexadecimal|Hex)$/i) {
      $FingerprintsBitVector = Fingerprints::FingerprintsBitVector::NewFromHexadecimalString($BitVectorString, $BitsOrder);
      last BITSTRINGFORMAT;
    }
    croak "Error: FingerprintsStringUtil::_GenerateFingerprintBitVector: Specified bit vector string format, $BitStringFormat, is not supported. Value values: Binary, Bin, BinaryString, Hexdecimal, Hex, HexadecimalString...";
  }

  if (defined $FingerprintsBitVector) {
    # Set fingerints vector type and description...
    $FingerprintsBitVector->SetVectorType($VectorType);
    $FingerprintsBitVector->SetDescription($Description);

    # Set specified size which might be different from the bit string size due to padding
    # used by Perl vec function to handle bit vectors in BitVectot class...
    #
    $FingerprintsBitVector->SetSpecifiedSize($Size);
  }

  return $FingerprintsBitVector;
}

# Parse fingerprints vector string and retrun vector...
#
sub ParseFingerprintsVectorString {
  my($FingerprintsString, $ValidateValues) = @_;
  my($ErrorMsgPrefix, $VectorType, $Description, $NumOfValues, $VectorValuesType, $VectorStringFormat, $VectorString1, $VectorString2);

  $ErrorMsgPrefix = "Error: ParseFingerprintsVectorString";
  ($VectorType, $Description, $NumOfValues, $VectorValuesType, $VectorStringFormat, $VectorString1, $VectorString2) = _ParseFingerprintsStringValues($FingerprintsString);

  # No need to check $VectorString1 and $VectorString2 values as they would be
  # checked later during the creation of FingerprintsVector...
  #
  if ($ValidateValues) {
    _ValidateFingerprintsStringValues($ErrorMsgPrefix, $VectorType, $NumOfValues, $VectorValuesType, $VectorStringFormat);
  }

  return _GenerateFingerprintVector($VectorType, $Description, $VectorValuesType, $VectorStringFormat, $VectorString1, $VectorString2);
}

# Generate fingerints vector...
#
sub _GenerateFingerprintVector {
  my($VectorType, $Description, $VectorValuesType, $VectorStringFormat, $VectorString1, $VectorString2) = @_;
  my($FingerprintsVector, $VectorString);

  $VectorString = TextUtil::IsEmpty($VectorString2) ? $VectorString1 : "${VectorString1};${VectorString2}";
  $FingerprintsVector = undef;

  VECTORSTRINGFORMAT : {
    if ($VectorStringFormat =~ /^(ValuesString|Values)$/i) {
      $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesString($VectorValuesType, $VectorString);
      last VECTORSTRINGFORMAT;
    }
    if ($VectorStringFormat =~ /^(IDsAndValuesString|IDsAndValues)$/i) {
      $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesString($VectorValuesType, $VectorString);
      last VECTORSTRINGFORMAT;
    }
    if ($VectorStringFormat =~ /^(IDsAndValuesPairsString|IDsAndValuesPairs)$/i) {
      $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesPairsString($VectorValuesType, $VectorString);
      last VECTORSTRINGFORMAT;
    }
    if ($VectorStringFormat =~ /^(ValuesAndIDsString|ValuesAndIDs)$/i) {
      $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsString($VectorValuesType, $VectorString);
      last VECTORSTRINGFORMAT;
    }
    if ($VectorStringFormat =~ /^(ValuesAndIDsPairsString|ValuesAndIDsPairs)$/i) {
      $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsPairsString($VectorValuesType, $VectorString);
      last VECTORSTRINGFORMAT;
    }
    croak "Error: FingerprintsStringUtil::_GenerateFingerprintVector: Specified vector string format, $VectorStringFormat, is not supported. Value values: IDsAndValuesString, IDsAndValues, IDsAndValuesPairsString, IDsAndValuesPairs, ValuesAndIDsString, ValuesAndIDs, ValuesAndIDsPairsString, ValuesAndIDsPairs, ValuesString, Values...";
  }

  if (defined $FingerprintsVector) {
    # Set fingerints vector type and description...
    $FingerprintsVector->SetVectorType($VectorType);
    $FingerprintsVector->SetDescription($Description);
  }

  return $FingerprintsVector;
}

# Validate fingerint string values...
#
sub AreFingerprintsStringValuesValid {
  my($FingerprintsString) = @_;
  my($Value);

  for $Value (_ParseFingerprintsStringValues($FingerprintsString)) {
    if (TextUtil::IsEmpty($Value)) {
      return 0;
    }
  }
  return 1;
}

# Get fingerprints description...
#
sub _GetFingerprintsDescription {
  my($FingerprintsObject) = @_;
  my($Description);

  $Description = $FingerprintsObject->GetDescription();

  return TextUtil::IsEmpty($Description) ? 'No description available for fingerprints' : $Description;
}

# Parse fingerprints string values...
#
sub _ParseFingerprintsStringValues {
  my($FingerprintsString) = @_;

  return split "${FPStringDelim}", $FingerprintsString;
}

# Check to make sure already parsed fingerprints string values are valid....
#
sub _ValidateFingerprintsStringValues {
  my($ErrorMsgPrefix, @Values) = @_;
  my($Value);

  for $Value (@Values) {
    if (TextUtil::IsEmpty($Value)) {
      croak("${ErrorMsgPrefix}: _ValidateFingerprintsStringValues: Fingerprints string format is not valid: An empty value found...");
    }
  }
}

# Default bit string format...
#
sub GetDefaultBitStringFormat {
  return 'HexadecimalString';
}

# Default bit order...
#
sub GetDefaultBitsOrder {
  return 'Ascending';
}

# Default vector string format using fingerprints or fingerprints vector object...
#
sub GetDefaultVectorStringFormat {
  my($FingerprintsObject) = @_;
  my($FingerprintsVector);

  $FingerprintsVector = Fingerprints::FingerprintsVector::IsFingerprintsVector($FingerprintsObject) ? $FingerprintsObject : $FingerprintsObject->GetFingerprintsVector();

  return _GetDefaultVectorStringFormat($FingerprintsVector);
}

# Default vector string format using fingerprits vector object...
#
sub _GetDefaultVectorStringFormat {
  my($FingerprintsVector) = @_;
  my($Type);

  $Type = $FingerprintsVector->GetType();

  return ($Type =~ /^NumericalValues$/i) ? 'IDsAndValuesString' : 'ValuesString';
}

# Fingerprints string delimiter...
#
sub GetFingeprintsStringDelimiter {
  return $FPStringDelim;
}

1;

__END__

=head1 NAME

FingerprintsStringUtil

=head1 SYNOPSIS

use Fingerprints::FingerprintsStringUtil;

use Fingerprints::FingerprintsStringUtil qw(:all);

=head1 DESCRIPTION

B<FingerprintsStringUtil> module provides the following functions:

AreFingerprintsStringValuesValid, GenerateFingerprintsBitVectorString,
GenerateFingerprintsString, GenerateFingerprintsVectorString,
GetDefaultBitStringFormat, GetDefaultBitsOrder, GetDefaultVectorStringFormat,
GetFingeprintsStringDelimiter, GetFingerprintsStringTypeAndDescription,
GetFingerprintsStringValues, ParseFingerprintsBitVectorString,
ParseFingerprintsString, ParseFingerprintsVectorString

The current release of MayaChemTools supports the following types of fingerprint
bit-vector and vector strings:

    FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
    us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
    C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
    1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
    TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
    -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...

    FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
    ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
    .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
    O.X1.BO2;2 4 14 3 10 1 1 1 3 2

    FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
    ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
    N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1

    FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
    umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
    12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
    2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
    O9 O10 O11 O12 OS F Cl Br I Hal P S1 S2 S3 Me1 Me2;5 0 0 0 2 0 0 0 0 1
    1 0 0 1 0 0 0 14 0 4 2 1 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0...

    FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
    AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
    H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
    .024 -2.270

    FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
    ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
    4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
    4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
    0 0 0 0 0 0 0 0 0 0 0 0 0 0

    FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
    us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
    666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
    08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
    5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
    532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...

    FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
    :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
    13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
    2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
    3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
    1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1

    FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
    es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
    0000000001010000000110000011000000000000100000000000000000000000100001
    1000000110000000000000000000000000010011000000000000000000000000010000
    0000000000000000000000000010000000000000000001000000000000000000000000
    0000000000010000100001000000000000101000000000000000100000000000000...

    FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
    s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
    62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
    1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
    7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
    632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...

    FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
    haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
    926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
    44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
    1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
    1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...

    FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
    0000000000000000000000000000000001001000010010000000010010000000011100
    0100101010111100011011000100110110000011011110100110111111111111011111
    11111111111110111000

    FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
    1110011111100101111111000111101100110000000000000011100010000000000000
    0000000000000000000000000000000000000000000000101000000000000000000000
    0000000000000000000000000000000000000000000000000000000000000000000000
    0000000000000000000000000000000000000011000000000000000000000000000000
    0000000000000000000000000000000000000000

    FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
    ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
    0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0
    0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0
    5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1
    3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1

    FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
    ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0
    0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0
    0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
    0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
    0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...

    FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
    th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
    0100010101011000101001011100110001000010001001101000001001001001001000
    0010110100000111001001000001001010100100100000000011000000101001011100
    0010000001000101010100000100111100110111011011011000000010110111001101
    0101100011000000010001000011000010100011101100001000001000100000000...

    FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
    1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
    C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
    2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
    2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
    4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....

    FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
    h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
    8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N
    5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
    CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
    OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...

    FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
    istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
    .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
    H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
    2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
    1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...

    FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
    stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
    Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
    BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
    23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
    1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...

    FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
    3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
    C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
    2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
    2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1

    FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
    lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
    H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
    ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
    4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2

    FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
    inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
    .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
    0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
    -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
    1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
    2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...

    FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
    :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
    .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
    D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
    -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
    3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...

    FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
    Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
    -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
    HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
    BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
    18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
    3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1

    FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
    ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
    0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
    0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
    0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
    0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...

    FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
    MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
    Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
    -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
    HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
    46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
    28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
    119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...

    FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
    istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
    8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
    0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
    14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
    0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...

=head1 FUNCTIONS

=over 4

=item B<AreFingerprintsStringValuesValid>

    $Status = AreFingerprintsStringValuesValid($FPString);

Returns 0 or 1 based on whether I<FingerprintsString> contains valid values.

=item B<GetDefaultBitStringFormat>

    $BitStringFormat = GetDefaultBitStringFormat();

Returns default B<BitStringFormat> for fingerprints bit-vector strings.

=item B<GetDefaultBitsOrder>

    $BitsOrder = GetDefaultBitsOrder();

Returns default B<BitsOrder> for fingerprints bit-vector fingerprints.

=item B<GetDefaultVectorStringFormat>

    $StringFormat = GetDefaultVectorStringFormat();

Returns default B<VectorStringFormat> for fingerprints vector strings.

=item B<GetFingeprintsStringDelimiter>

    $Delimiter = GetFingeprintsStringDelimiter();

Returns string B<Delimiter> used to generate fingerprints bit-vector and vector strings.

=item B<GenerateFingerprintsBitVectorString>

    $FPString = GenerateFingerprintsBitVectorString($FPBitVectorObject,
                [$BitStringFormat, $BitsOrder]);

Returns a B<FingerprintsString> generated using I<FingerprintsBitVectorObject> and
optionally specified I<BitStringFormat> and I<BitsOrder> values.

Possible I<BitStringFormat> values: I<BinaryString, Binary, Bin, HexadecimalString,
Hexadecimal, or Hex>. Default I<BitStringFormat> value: I<BinaryString>.

Possible I<BitsOrder> values: I<Ascending or Descending>. Default I<BitsOrder> value:
I<Ascending>.

=item B<GenerateFingerprintsVectorString>

    $FPString = GenerateFingerprintsVectorString($FPVectorObject,
                [$VectorStringFormat]);

Returns a B<FingerprintsString> generated using I<FingerprintsVectorObject> and optionally
specified I<VectorStringFormat>.

Possible I<VectorStringFormat> values: I<IDsAndValuesString, IDsAndValues,
IDsAndValuesPairsString, IDsAndValuesPairs, ValuesAndIDsString, ValuesAndIDs,
ValuesAndIDsPairsString, ValuesAndIDsPairs, ValuesString, Values>.

Default I<VectorStringFormat> value: for I<NumericalValues> I<FPVectorType> -
I<IDsAndValuesString>; for all other I<FPVectorType>s - I<ValuesString>.

=item B<GenerateFingerprintsString>

    $FPString = GenerateFingerprintsBitVectorString($FPBitVectorObject,
                [$BitStringFormat, $BitsOrder]);

    $FPString = GenerateFingerprintsVectorString($FPVectorObject,
                [$VectorStringFormat]);

Returns a B<FingerprintsString> generated using I<FingerprintsBitVectorObject> or
I<FingerprintsVectorObject> and optionally specified parameters.

=item B<GetFingerprintsStringTypeAndDescription>

    ($FPType, $FPDescription) = GetFingerprintsStringTypeAndDescription(
                                $FPString);

Returns B<FingerprintsStringType> and I<FingerprintsStringDescription> strings for
B<FingerprintsString> corresponding to B<FingerprintsBitVectorObject> or
B<FingerprintsVectorObject>.

=item B<GetFingerprintsStringValues>

    @FPStringValues = GetFingerprintsStringValues($FPString);

Parses B<FingerprintsString> corresponding to B<FingerprintsBitVectorObject> or
B<FingerprintsVectorObject> and returns its individual component values as an
array.

=item B<ParseFingerprintsBitVectorString>

    $FPBitVectorObject = ParseFingerprintsBitVectorString($FPBitVectorString,
                         [$ValidateValues]);

Returns B<FingerprintsBitVectorObject> generated by parsing I<FingerprintsBitVectorString>
with optional validation of its component values.

=item B<ParseFingerprintsString>

    $FPBitVectorObject = ParseFingerprintsBitVectorString($FPBitVectorString,
                         [$ValidateValues]);

    $FPVectorObject = ParseFingerprintsVectorString($FPVectorString,
                      [$ValidateValues]);

Returns B<FingerprintsBitVectorObject> or I<B<FingerprintsVectorObject>> generated
by parsing I<FingerprintsBitVectorString> or I<FingerprintsVectorString> with
optional validation of its component values.

=item B<ParseFingerprintsVectorString>

    $FPVectorObject = ParseFingerprintsVectorString($FPVectorString,
                      [$ValidateValues]);

Returns B<FingerprintsVectorObject> generated by parsing I<FingerprintsVectorString>
with optional validation of its component values.

=back

=head1 AUTHOR

Manish Sud <msud@san.rr.com>

=head1 SEE ALSO

BitVector.pm, FingerprintsBitVector.pm, FingerprintsVector.pm, Vector.pm

=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
author	deepakjadmin
date	Wed, 20 Jan 2016 12:15:15 -0500
parents	73ae111cf86f
children