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. Follow these instructions to build the compound library.

In general, compound libraries built with older versions of OST are compatible with newer version of OST, so it may not be necessary to rebuild a new one. However, some functionality may not be available. Currently, compound libraries built with OST 1.5.0 or later can be loaded.

GetDefaultLib()¶

Get the default compound library. This is set by SetDefaultLib().

If you obtained OpenStructure as a container or you compiled it with a specified COMPOUND_LIB flag, this function will return a compound library.

You can override the default compound library by pointing the OST_COMPOUNDS_CHEMLIB environment variable to a valid compound library file.

Returns:: Default compound library.
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(id, 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

FindCompounds(query, by, dialect='PDB')¶

Lookup one or more compound by SMILES string, InChI code, InChI key or formula.

The compound library is queried for exact string matches. Many SMILES strings can represent the same compound, so this function is only useful for SMILES strings coming from the PDB (or canonical SMILES from the OpenEye Toolkits). This is also the case for InChI codes, although to a lesser extent.

Obsolete compounds will be sorted at the back of the list. However, there is no guarantee that the first compound is active.

Parameters:

query (string) – the string to lookup.
by (string) – the key into which to lookup for the query. One of: “smiles”, “inchi_code”, “inchi_key” or “formula”.
dialect (string) – the dialect to select for (typically “PDB”, or “CHARMM” if your compound library was built with charmm support).

Returns:

A list of found compounds, or an empty list if no compound was found.

Return type:

list or 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, e.g ‘1S/H2O/h1H2’ for water, or an empty string if missing. Read-only.

Type:: str

inchi_key¶

The InChIKey of this compound, e.g. ‘XLYOFNOQVPJJNP-UHFFFAOYSA-N’ for water, or an empty string if missing. Read-only.

Type:: str

smiles¶

The SMILES string of this compound, e.g ‘O’ for water, or an empty string if missing. Read-only.

The string is read from the canonical SMILES produced by the OpenEye OEToolkits.

Type:: str

obsolete¶

Whether the component has been obsoleted by the PDB.

Type:: bool

replaced_by¶

If the component has been obsoleted by the PDB, this is the three-letter code of the compound that replaces it. This is not set for all obsolete compounds.

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.

charge¶: The charge of the atom.

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>

Notes:

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.
This also loads compounds which are reserved or obsoleted by the PDB to maximize compatibility with older PDB files. You can change that and skip obsolete entries with the -o flag, and reserved entries with the -i flag.

chemdict_tool create <components.cif> <compounds.chemlib> -i -o

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

The compound library¶

Example: Translating SEQRES entries¶

Creating a compound library¶

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