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 provides several methods to manipulate this data. 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
OESetSDData	set a tag and value data pair
OEAddSDData	add a tag and value data pair
OEHasSDData	determine whether a molecule has an 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 an other
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 Python’s str() method before storing a value with either OESetSDData or OEAddSDData functions.

OESetSDData(mol,"number of atoms",str(mol.NumAtoms()))

Similarly the retrieved string can be converted to a numeric value with int() or float() functions.

if OEHasSDData(mol,"weight"):
    weight = float(OEGetSDData(mol,"weight"))
    print "weight=",weight

The following example shows how to manipulate SD tagged data.

Listing 1: SD data manipulation

#!/usr/bin/env python
from openeye.oechem import *
import os, sys

def DumpSDData(mol):
   print "SD data of",mol.GetTitle()
   #loop over SD data
   for dp in OEGetSDDataPairs(mol):
      print dp.GetTag(),':',dp.GetValue()
   print
   
mol = OEGraphMol()
OEParseSmiles(mol, "c1ccccc1")
mol.SetTitle("benzene")

# set some tagged data
OESetSDData(mol,'color','brown')
OESetSDData(mol,OESDDataPair('size','small'))
DumpSDData(mol)

# check for existence of data, then delete it
if OEHasSDData(mol,'size'):
    OEDeleteSDData(mol,'size')
DumpSDData(mol)

# add additional color data
OEAddSDData(mol,'color','black')
DumpSDData(mol)

# remove all SD data
OEClearSDData(mol)
DumpSDData(mol)

Note

If a data with the same tag already exists:

• it is replaced, when using OESetSDData function
• it is added, when using OEAddSDData function

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 or OEBinary files. The SD data fields will only be filled when reading from SD files that contain SD tagged data or from OEBinary files previously created to contain this data.

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 Python’s str() method to convert it to a string and then use int() or float() on the value when retrieving the data (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 an 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 an other
OEDeletePDBData	delete all PDB data items with the given tag
OEClearSDData	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 character long ans space-padded (for example "HELIX " and not "HELIX" ).

The following example shows how to manipulate PDB tagged data.

Listing 2: PDB data manipulation

#!/usr/bin/env python
from openeye.oechem import *
import os, sys

if len(sys.argv) != 2:
   OEThrow.Usage("%s <pdbfile>"%sys.argv[0])

ifs = oemolistream()    
if not ifs.open(sys.argv[1]):
   OEThrow.Fatal("Unable to open %s"%sys.argv[1])

# 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)

mol = OEGraphMol()
while OEReadMolecule(ifs,mol):
   if OEHasPDBData(mol,"COMPND"):
      print "COMPND:"
      print OEGetPDBData(mol,"COMPND")
      
   if OEHasPDBData(mol,"HELIX "):
      print "HELIX:" 
      print OEGetPDBData(mol,"HELIX ")

   if OEHasPDBData(mol,"SSBOND"):
      print "SSBOND:" 
      for dp in OEGetPDBDataPairs(mol):
         if dp.GetTag() == "SSBOND":
            print dp.GetValue()

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.

Multi-conformer molecules

See also

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