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NAME

FingerprintsFPFileIO

SYNOPSIS

use FileIO::FingerprintsFPFileIO;

use FileIO::FingerprintsFPFileIO qw(:all);

DESCRIPTION

FingerprintsFPFileIO class provides the following methods:

new, GetFingerprints, GetFingerprintsString, GetHeaderDataKeyValue, GetHeaderDataKeys, GetHeaderDataKeysAndValues, GetPartialFingerprintsString, GetRequiredHeaderDataKeys, GetRequiredHeaderDataKeysAndValues, IsFingerprintsDataValid, IsFingerprintsFPFile, IsFingerprintsFileDataValid, IsHeaderDataKeyPresent, Next, Read, SetBitStringFormat, SetBitsOrder, SetCompoundID, SetDetailLevel, SetFingerprints, SetFingerprintsString, SetFingerprintsStringMode, SetPartialFingerprintsString, SetVectorStringFormat, WriteFingerprints, WriteFingerprintsString

The following methods can also be used as functions:

IsFingerprintsFPFile

FingerprintsFPFileIO class is derived from FileIO class and uses its methods to support generic file related functionality.

The MayaChemTools fingerprints file (FP) format with .fpf or .fp file extensions supports two types of fingerprints data: fingerprints bit-vectors and fingerprints vectors.

Example of FP file format containing fingerprints bit-vector string data:

Example of FP file format containing fingerprints vector string data:

FP file data format consists of two main sections: header section and fingerprints string data section. The header section lines start with # and the first line not starting with # represents the start of fingerprints string data section. The header section contains both the required and optional information which is specified as key = value pairs. The required information describes fingerprints bit-vector and vector strings and used to generate fingerprints objects; the optional information is ignored during generation of fingerpints objects.

The key = value data specification in the header section and its processing follows these rules:

The default optional header data section key = value pairs are:

The FingerprintsStringType key is required data header key for both fingerprints bit-vector and vector strings. Possible key values: FingerprintsBitVector or FingerprintsVector. For example:

The required data header keys for fingerprints bit-vector string are: Description, Size, BitStringFormat, and BitsOrder. Possible values for BitStringFormat: HexadecimalString or BinaryString. Possible values for BitsOrder: Ascending or Descending. The Description key contains information about various parameters used to generate fingerprints bit-vector string. The Size corresponds to number of fingerprints bits and is always less than or equal to number of bits in bit-vetor string which might contain extra bits at the end to round off the size to make it multiple of 8. For example:

The required data header keys for fingerprints vector string are: Description, VectorStringFormat, and VectorValuesType. Possible values for VectorStringFormat: DsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString or ValuesString. Possible values for VectorValuesType: NumericalValues, OrderedNumericalValues or AlphaNumericalValues. The Description keys contains information various parameters used to generate fingerprints vector string. For example:

The fingerprints data section for fingerprints bit-vector string contains data in the following format:

For example:

The fingerprints data section for fingerprints vector string contains data in the following format:

For example:

Unlike fingerprints bit-vector string, Size is specified for each partial fingerprints vector string: It may change from molecule to molecule for same type of fingerprints.

Values IDs are optional for fingerprints vector string containing OrderedNumericalValues or AlphaNumericalValues; however, they must be present for for NumericalValues. Due to various possible values for VectorStringFormat, the fingerprints data section for fingerprints vector string supports following type of data formats:

However, all the fingerprints vector string data present in FP file must correspond to only one of the formats shown above; multiple data formats in the same file are not allowed.

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

METHODS

new

$NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(%IOParameters);

Using specified IOParameters names and values hash, new method creates a new object and returns a reference to a newly created FingerprintsFPFileIO object. By default, the following properties are initialized during Read mode:

Name = '';
Mode = 'Read';
Status = 0;
FingerprintsStringMode = 'AutoDetect';
ValidateData = 1;
DetailLevel = 1;

During Write mode, the following properties get initialize by default:

FingerprintsStringMode = undef;

BitStringFormat = HexadecimalString;
BitsOrder = Ascending;

VectorStringFormat = NumericalValuesString or ValuesString;

Examples:

$NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO( 'Name' => 'Sample.fpf', 'Mode' => 'Read', 'FingerprintsStringMode' => 'AutoDetect');

$NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO( 'Name' => 'Sample.fpf', 'Mode' => 'Write', 'FingerprintsStringMode' => 'FingerprintsBitVectorString', 'Overwrite' => 1, 'BitStringFormat' => 'HexadecimalString', 'BitsOrder' => 'Ascending');

$NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO( 'Name' => 'Sample.fp', 'Mode' => 'Write', 'FingerprintsStringMode' => 'FingerprintsVectorString', 'Overwrite' => 1, 'VectorStringFormat' => 'IDsAndValuesString');

GetFingerprints

$FingerprintsObject = $FingerprintsFPFileIO->GetFingerprints();

Returns FingerprintsObject generated for current data line using fingerprints bit-vector or vector string data. The fingerprints object corresponds to any of the supported fingerprints such as PathLengthFingerprints, ExtendedConnectivity, and so on.

GetFingerprintsString

$FingerprintsString = $FingerprintsFPFileIO->GetFingerprintsString();

Returns FingerprintsString for current data line.

GetHeaderDataKeyValue

$KeyValue = $FingerprintsFPFileIO->GetHeaderDataKeyValue($Key);

Returns KeyValue of a data header Key.

GetHeaderDataKeys

@Keys = $FingerprintsFPFileIO->GetHeaderDataKeys();
$NumOfKeys = $FingerprintsFPFileIO->GetHeaderDataKeys();

Returns an array of data header Keys retrieved from data header section of fingerprints file. In scalar context, it returns number of keys.

GetHeaderDataKeysAndValues

%KeysAndValues = $FingerprintsFPFileIO->GetHeaderDataKeysAndValues();

Returns a hash of data header keys and values retrieved from data header section of fingerprints file.

GetPartialFingerprintsString

$FingerprintsString = $FingerprintsFPFileIO->GetPartialFingerprintsString();

Returns partial FingerprintsString for current data line. It corresponds to fingerprints string specified present in a line.

GetRequiredHeaderDataKeys

@Keys = $FingerprintsFPFileIO->GetRequiredHeaderDataKeys();
$NumOfKeys = $FingerprintsFPFileIO->GetRequiredHeaderDataKeys();

Returns an array of required data header Keys for a fingerprints file containing bit-vector or vector strings data. In scalar context, it returns number of keys.

GetRequiredHeaderDataKeysAndValues

%KeysAndValues = $FingerprintsFPFileIO-> GetRequiredHeaderDataKeysAndValues();

Returns a hash of required data header keys and values for a fingerprints file containing bit-vector or vector strings data

IsFingerprintsDataValid

$Status = $FingerprintsFPFileIO->IsFingerprintsDataValid();

Returns 1 or 0 based on whether FingerprintsObject is valid.

IsFingerprintsFPFile

$Status = $FingerprintsFPFileIO->IsFingerprintsFPFile($FileName);
$Status = FileIO::FingerprintsFPFileIO::IsFingerprintsFPFile($FileName);

Returns 1 or 0 based on whether FileName is a FP file.

IsFingerprintsFileDataValid

$Status = $FingerprintsFPFileIO->IsFingerprintsFileDataValid();

Returns 1 or 0 based on whether fingerprints file contains valid fingerprints data.

IsHeaderDataKeyPresent

$Status = $FingerprintsFPFileIO->IsHeaderDataKeyPresent($Key);

Returns 1 or 0 based on whether data header Key is present in data header section of a FP file.

Next or Read

$FingerprintsFPFileIO = $FingerprintsFPFileIO->Next();
$FingerprintsFPFileIO = $FingerprintsFPFileIO->Read();

Reads next available fingerprints line in FP file, processes the data, generates appropriate fingerprints object, and returns FingerprintsFPFileIO. The generated fingerprints object is available using method GetFingerprints.

SetBitStringFormat

$FingerprintsFPFileIO->SetBitStringFormat($Format);

Sets bit string Format for fingerprints bit-vector string data in a FP file and returns FingerprintsFPFileIO. Possible values for BitStringFormat: BinaryString or HexadecimalString.

SetBitsOrder

$FingerprintsFPFileIO->SetBitsOrder($BitsOrder);

Sets BitsOrder for fingerprints bit-vector string data in a FP file and returns FingerprintsFPFileIO. Possible values for BitsOrder: Ascending or Descending.

SetCompoundID

$FingerprintsFPFileIO->SetCompoundID($ID);

Sets compound ID for current data line and returns FingerprintsFPFileIO. Spaces are not allowed in compound IDs.

SetDetailLevel

$FingerprintsFPFileIO->SetDetailLevel($Level);

Sets details Level for generating diagnostics messages during FP file processing and returns FingerprintsFPFileIO. Possible values: Positive integers.

SetFingerprints

$FingerprintsFPFileIO->SetFingerprints($FingerprintsObject);

Sets FingerprintsObject for current data line and returns FingerprintsFPFileIO.

SetFingerprintsString

$FingerprintsFPFileIO->SetFingerprintsString($FingerprintsString);

Sets FingerprintsString for current data line and returns FingerprintsFPFileIO.

SetFingerprintsStringMode

$FingerprintsFPFileIO->SetFingerprintsStringMode($Mode);

Sets FingerprintsStringMode for FP file and returns FingerprintsFPFileIO. Possible values: AutoDetect, FingerprintsBitVectorString, or FingerprintsVectorString

SetPartialFingerprintsString

$FingerprintsFPFileIO->SetPartialFingerprintsString($PartialString);

Sets PartialFingerprintsString for current data line and returns FingerprintsFPFileIO.

SetVectorStringFormat

$FingerprintsFPFileIO->SetVectorStringFormat($Format);

Sets VectorStringFormat for FP file and returns FingerprintsFPFileIO. Possible values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString.

WriteFingerprints

$FingerprintsFPFileIO->WriteFingerprints($FingerprintsObject,
                                         $CompoundID);

Writes fingerprints string generated from FingerprintsObject object and other data including CompoundID to FP file and returns FingerprintsFPFileIO.

WriteFingerprintsString

$FingerprintsFPFileIO->WriteFingerprints($FingerprintsString,
                                         $CompoundID);

Writes FingerprintsString and other data including CompoundID to FP file and returns FingerprintsFPFileIO.

Caveats:

o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat values are ignored during writing of fingerprints and it's written to the file as it is.
o FingerprintsString is a regular fingerprints string as oppose to a partial fingerprints string.

AUTHOR

Manish Sud

SEE ALSO

FingerprintsSDFileIO.pm, FingerprintsTextFileIO.pm

COPYRIGHT

Copyright (C) 2024 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.