The compound library

Compound libraries contain information on chemical compounds, such as their connectivity, chemical class and one-letter-code. The compound library has several uses, but the most important one is to provide the connectivy information for the rule-based processor.

The compound definitions for standard PDB files are taken from the components.cif dictionary provided by the PDB. The dictionary is updated with every PDB release and augmented with the compound definitions of newly crystallized compounds.

If you downloaded the bundle, a recent version of the compound library is already included. If you are compiling from source or want to incorporate the latest compound definitions, follow these instructions to build the compound library manually.

GetDefaultLib()

Returns:

Default compound library set by SetDefaultLib(). If you got OpenStructure as a bundle or you compiled it with a specified COMPOUND_LIB flag, this will return a compound library when executing scripts with ost.

Return type:

CompoundLib or None if no library set

SetDefaultLib(lib)

Parameters:

lib (CompoundLib) – Library to be set as default compound library.

class CompoundLib

static Load(database, readonly=True)

Load the compound lib from database with the given name.

Parameters:

readonly (bool) – Whether the library should be opened in read-only mode. It is important to note that only one program at the time has write access to compound library. If multiple programs try to open the compound library in write mode, the programs can deadlock.

Returns:

The loaded compound lib or None if it failed.

static Create(database)

Create a new compound library

FindCompound(tlc, dialect='PDB')

Lookup compound by its three-letter-code, e.g ALA. If no compound with that name exists, the function returns None. Compounds are cached after they have been loaded with FindCompound. To delete the compound cache, use ClearCache().

Returns:

The found compound

Return type:

Compound

Copy(dst_filename)

Copy database to dst_filename. The new library will be an exact copy of the database. The special name :memory: will create an in-memory version of the database. At the expense of memory, database lookups will become much faster.

Returns:

The copied compound library

Return type:

CompoundLib

ClearCache()

Clear the compound cache.

SetChemLibInfo()

When creating the new library the current date and the Version of OST used are stored into the table chemlib_info.

GetOSTVersionUsed()

Returns:

OST version (ost_version_used from the table chemlib_info)

Return type:

str

GetCreationDate()

Returns:

creation date (creation_date from the table chemlib_info)

Return type:

str

class Compound

Holds the description of a chemical compound, such as three-letter-code, and chemical class.

id

Alias for three_letter_code

three_letter_code

Three-letter code of the residue, e.g. ALA for alanine. The three-letter code is unique for each compound, always in uppercase letters and is between 1 and 3 characters long.

code is always uppercase.

one_letter_code

The one letter code of the residue, e.g. ‘G’ for glycine. If undefined, the one letter code of the residue is set to ‘?’

formula

The chemical composition, e.g. ‘H2 O’ for water. The elements are listed in alphabetical order.

dialect

The dialect of the compound.

atom_specs

The atom definitions of this compound. Read-only.

Type:

list of AtomSpec

bond_specs

The bond definitions of this compound. Read-only.

Type:

list of BondSpec

chem_class

The ChemClass of this compound. Read-only.

Type:

str

chem_type

The ChemType of this compound. Read-only.

Type:

str

inchi

The InChI code of this compound, without the ‘InChI=’ part, e.g ‘1S/H2O/h1H2’ for water. Read-only.

Type:

str

inchi

The InChIKey of this compound without the ‘InChIKey=’ part, e.g. ‘XLYOFNOQVPJJNP-UHFFFAOYSA-N’ for water. Read-only.

Type:

str

class AtomSpec

Definition of an atom

element

The element of the atom

name

The primary name of the atom

alt_name

Alternative atom name. If the atom has only one name, this is identical to name

is_leaving

Whether this atom is required for a residue to be complete. The best example of a leaving atom is the OXT atom of amino acids that gets lost when a peptide bond is formed.

class BondSpec

Definition of a bond

atom_one

The first atom of the bond, encoded as index into the Compound.atom_specs array.

atom_two

The second atom of the bond, encoded as index into the Compound.atom_specs array.

order

The bond order, 1 for single bonds, 2 for double-bonds and 3 for triple-bonds

Example: Translating SEQRES entries

In this example we will translate the three-letter-codes given in the SEQRES record to one-letter-codes. Note that this automatically takes care of modified amino acids such as selenium-methionine.

compound_lib=conop.CompoundLib.Load('compounds.chemlib')
seqres='ALA GLY MSE VAL PHE'
sequence=''
for tlc in seqres.split():
  compound=compound_lib.FindCompound(tlc)
  if compound:
     sequence+=compound.one_letter_code
print(sequence) # prints 'AGMVF'

Creating a compound library

The simplest way to create compound library is to use the chemdict_tool. The programs allows you to import the chemical description of the compounds from a mmCIF dictionary, e.g. the components.cif dictionary provided by the PDB. The latest dictionary for can be downloaded from the wwPDB site. The files are rather large, it is therefore recommended to download the gzipped version.

After downloading the file use chemdict_tool to convert the MMCIF dictionary into our internal format.

chemdict_tool create <components.cif> <compounds.chemlib>

Note that the chemdict_tool only understands .cif and .cif.gz files. If you have would like to use other sources for the compound definitions, consider writing a script by using the compound library API.

If you are working with CHARMM trajectory files, you will also have to add the definitions for CHARMM. Assuming your are in the top-level source directory of OpenStructure, this can be achieved by:

chemdict_tool update modules/conop/data/charmm.cif <compounds.chemlib> charmm

Once your library has been created, you need to tell cmake where to find it and make sure it gets staged.

cmake -DCOMPOUND_LIB=compounds.chemlib
make