Tagged Data Manipulation

SD Tagged Data Manipulation

Meta information about a molecule is stored in what is known as ‘tagged data’. The most common example of this is the data fields found in SDF files. Since SD files are a common form of data storage and transfer from one system to another, OEChem TK provides several methods to manipulate this data. OEChem TK also provides round tripping SD data through the OEBinary, .oeb, and comma-separated-values, .csv file formats.

A simple class, OESDDataPair is used to set and retrieve SD data.

Data

Set method

Get method

tag

OESDDataPair.SetTag

OESDDataPair.GetTag

data

OESDDataPair.SetValue

OESDDataPair.GetValue

The following functions provide access to the SD data.

Functions to manipulate SD data

Function

Description

OEIsSDDataFormat

determines whether a file format support SD data

OESetSDData

set a tag and value data pair

OEAddSDData

add a tag and value data pair

OEHasSDData

determine whether a molecule has data with a given tag

OEGetSDData

get the value for the given tag

OEGetSDDataPairs

return an iterator over all the SD data pairs of the molecule

OECopySDData

copy the entire set of SD data from one molecule to another

OEDeleteSDData

delete all SD data items with the given tag

OEClearSDData

clear all SD data from a molecule

Since OESDDataPair stores SD data information in a string, numeric values have to be converted to a string with Java’s toString() method before storing a value with either OESetSDData or OEAddSDData functions.

oechem.OESetSDData(mol, "number of atoms", Integer.toString(mol.NumAtoms()));

Similarly the retrieved string can be converted to a numeric value with valueOf() methods.

if (oechem.OEHasSDData(mol,"weight")) {
    String str =  oechem.OEGetSDData(mol,"weight");
    float weight = Float.valueOf(str);
    System.out.println("weight= " + weight);
}

The following example shows how to manipulate SD tagged data.

Listing 1: SD data manipulation

package openeye.docexamples.oechem;

import openeye.oechem.*;

public class ManipulateSDData {

    private static void DumpSDData(OEMolBase mol) {
        System.out.println("SD data of " + mol.GetTitle());
        // loop over SD data
        for (OESDDataPair dp : oechem.OEGetSDDataPairs(mol))
            System.out.println(dp.GetTag() + " : " + dp.GetValue());
        System.out.println();
    }

    public static void main(String argv[]) {
        OEGraphMol mol = new OEGraphMol();
        oechem.OESmilesToMol(mol, "c1ccccc1");
        mol.SetTitle("benzene");

        // set some tagged data
        oechem.OESetSDData(mol, "color", "brown");
        oechem.OESetSDData(mol, new OESDDataPair("size", "small"));
        DumpSDData(mol);

        // check for existence of data, then delete it
        if (oechem.OEHasSDData(mol, "size"))
            oechem.OEDeleteSDData(mol, "size");
        DumpSDData(mol);

        // add additional color data
        oechem.OEAddSDData(mol, "color", "black");
        DumpSDData(mol);

        // remove all SD data
        oechem.OEClearSDData(mol);
        DumpSDData(mol);
    }
}

Note

If a data with the same tag already exists:

The output of the preceding program is the following:

SD data of benzene
color : brown
size : small

SD data of benzene
color : brown

SD data of benzene
color : brown
color : black

SD data of benzene

Note

Note that SD tagged data is specific to MDL’s SD file format. Any SD data added to a molecule will only be written out to SD files, OEBinary files, or CSV files. The SD data fields will only be filled when reading from SD files that contain SD tagged data, CSV data files, or from OEBinary files previously created to contain this data.

See also

CSV File Format

The CSV, comma-separated-values, file format is a comma file format used for data exchange in a wide variety of software. Other the years, the popularity of the format has out-stripped the robustness of many of its implementations leading to some subtle differences in how it is implemented between different software packages. This has led to creation and adoption of RFC 4180 as a standard for the CSV format. OEChem TK supports this standard as the base format for reading and writing molecules, OEMolBase objects, to .csv files. OEChem TK will read and write .csv files in the following layout:

  1. The first line can optionally contain a header to use as the SD tag.

    • OEChem TK decides if the first line is a header by trying to interpret the first column of the first line as SMILES. See the OEIFlavor.CSV.Header flavor.

  2. The first column is expected to be a SMILES string representing the molecule.

  3. The second column is the molecule title, as accessed through OEMolBase.GetTitle.

  4. Remaining columns will be read into SD data fields. The data is then accessible through OEGetSDData and OESetSDData.

    • If the file did not contain a header line, the SD tags will be named in the following pattern: OE_CSV_COLUMN_1, OE_CSV_COLUMN_2, …, OE_CSV_COLUMN_N.

  5. New-line characters are not supported inside a CSV record. They are round-tripped using the pipe character, |, instead.

Point #5 is a subtlety of meta-data interchange between SD files and CSV files. On the one hand, many CSV implementations do not support line-breaks inside CSV fields, Microsoft Excel does not and neither does OEChem TK. However, it is common to use multiple lines inside an SD data file like the following:

>  <activ_class>
Antiarthritic
Antiinflammatory
Cyclooxygenase-2 Inhibitor

OEChem TK implements a solution to this problem that ChemAxon has implemented and documented here. The solution is to use the pipe character, |, to represent line breaks inside a data field. For example, the previous example of a multi-line SD data field would look like the following:

SMILES,TITLE,active_class
...,...,Antiarthritic|Antiinflammatory|Cyclooxygenase-2 Inhibitor

This does cause a different problem for pipe characters inside data fields: how pipe characters are escaped? OEChem TK works around this problem by embedding the same semantics for CSV parsing to parse multi-line fields, just using the pipe character as the separator and the single quote character as the quoting escape character. Listing 2 demonstrates an example that writes out a tricky set of data to the OEFormat.CSV format.

Listing 2: Writing out SD data as CSV

package openeye.docexamples.oechem;

import openeye.oechem.*;

public class WriteCSV {
    public static void main(String argv[]) {
        oemolostream ofs = new oemolostream();
        ofs.SetFormat(OEFormat.CSV);

        OEGraphMol mol = new OEGraphMol();
        oechem.OESmilesToMol(mol, "O");
        mol.SetTitle("water");

        oechem.OESetSDData(mol, "phases", "gas,liquid,solid");
        oechem.OESetSDData(mol, "uses", "bathing\nwater guns\ntea|earl grey|hot");

        oechem.OEWriteMolecule(ofs, mol);
        
        ofs.close();
    }
}

The output of Listing 2 will look like the following:

SMILES,TITLE,phases,uses
O,water,"gas,liquid,solid",bathing|water guns|'tea|earl grey|hot'

Code Example

PDB Tagged Data Manipulation

The OEPDBDataPair class is used to set and retrieve PDB data pairs.

Data

Set method

Get method

tag

OEPDBDataPair.SetTag

OEPDBDataPair.GetTag

data

OEPDBDataPair.SetValue

OEPDBDataPair.GetValue

If you wish to store a numeric value, use Java’s .toString() method to convert it to a string (see examples in SD Tagged Data Manipulation).

The following functions provide access to the PDB data.

Functions to manipulate PDB data

Function

Description

OESetPDBData

set a tag and value data pair

OEAddPDBData

add a tag and value data pair

OEHasPDBData

determine whether a molecule has data with a given tag

OEGetPDBData

get the value for the given tag

OEGetPDBDataPairs

return an iterator over all the PDB data pairs of the molecule

OECopyPDBData

copy the entire set of PDB data from one molecule to another

OEDeletePDBData

delete all PDB data items with the given tag

OEClearPDBData

clear all PDB data from a molecule

Note

In case of PDB header items like REMARK, each line is treated as a separate instance, Therefore these multiple lines have to be added with OEAddPDBData and can be accessed via OEGetPDBDataPairs.

The following PDB fields are stored as tagged PDB data when OEIFlavor.PDB.DATA input flavor is set:

Imported PDB data fields

AUTHOR

CAVEAT

COMPND

CRYST1

DBREF

EXPDTA

FORMUL

HEADER

HELIX

HET

HETNAM

HETSYM

JRNL

KEYWDS

MODRES

MTRIX1

MTRIX2

MTRIX3

OBSLTE

ORIGX1

ORIGX2

ORIGX3

REMARK

REVDAT

SCALE1

SCALE2

SCALE3

SEQRES

SEQADV

SHEET

SITE

SOURCE

SPRSDE

SSBOND

TITLE

TURN

Warning

The tags of PDB data are always 6 characters long and space-padded (for example "HELIX " and not "HELIX" ).

The following example shows how to manipulate PDB tagged data.

Listing 3: PDB data manipulation

package openeye.docexamples.oechem;

import openeye.oechem.*;

public class ManipulatePDBData {

    public static void main(String argv[]) {
        if (argv.length != 1) {
            oechem.OEThrow.Usage("ManipulatePDBData <pdbfile>");
        }

        oemolistream ifs = new oemolistream();
        if (!ifs.open(argv[0])) {
            oechem.OEThrow.Fatal("Unable to open " + argv[0]);
        }
        // need to set input flavor to ensure PDB data is stored on molecule
        ifs.SetFlavor(OEFormat.PDB, OEIFlavor.Generic.Default |
                OEIFlavor.PDB.Default | OEIFlavor.PDB.DATA);
        OEGraphMol mol = new OEGraphMol();
        while (oechem.OEReadMolecule(ifs, mol)) {
            if (oechem.OEHasPDBData(mol,"COMPND")) {
                System.out.println("COMPND:");
                System.out.println(oechem.OEGetPDBData(mol,"COMPND"));
            }
            if (oechem.OEHasPDBData(mol,"HELIX ")) {
                System.out.println("HELIX:");
                System.out.println(oechem.OEGetPDBData(mol,"HELIX "));
            }
            if (oechem.OEHasPDBData(mol,"SSBOND")) {
                System.out.println("SSBOND:");
                for (OESDDataPair dp : oechem.OEGetPDBDataPairs(mol)) {
                    if (dp.GetTag().equals("SSBOND")) {
                        System.out.println(dp.GetValue());
                    }
                }
            }
        }
        ifs.close();
    }
}

The output of the preceding program for 1D1H is the following:

COMPND:
    MOL_ID: 1;
HELIX:
   1   1 THR A   11  ASP A   14  5
SSBOND:
   1 CYS A    2    CYS A   16                          1555   1555
   2 CYS A    9    CYS A   21                          1555   1555
   3 CYS A   15    CYS A   28                          1555   1555

Note

Note that PDB tagged data is specific to PDB file format. Any PDB data added to a molecule will only be written out to PDB files or OEBinary files.

See also

Multi-conformer molecules

See also

For using tag data with multi-conformer molecules, see Dude, where’s my SD data?.