Bases: object
Class to manage ligands databases (sdf). Ligands are stored as moleculekit.smallmol.smallmol.SmallMol objects and fields type in the sdf are stored in a list
Example
>>> import os
>>> from moleculekit.home import home
>>> lib = SmallMolLib(os.path.join(home(dataDir='test-smallmol'), 'fda_drugs_light.sdf'))
>>> lib.numMols
100
Methods
Attributes
Merge two moleculekit.smallmol.smallmol.SmallMolLib objects
smallLib (moleculekit.smallmol.smallmol.SmallMolLib) – The new SmallMolLib to merge
Adds a new moleculekit.smallmol.smallmol.SmallMol object in the current SmallMolLib object
smallmol (moleculekit.smallmol.smallmol.SmallMol) – The SmallMol object to add
Returns a copy of the SmallMolLib object
Depicts the molecules into a grid. It is possible to save it into an svg file and also generates a jupiter-notebook rendering
ids (list) – The index of the molecules to depict
sketch (bool) – Set to True for 2D depiction
filename (str) – Set the filename for the svg file
ipython (bool) – Set to True to return the jupiter-notebook rendering
optimize (bool) – Set to True to optimize the conformation. Works only with 3D.
optimizemode (['std', 'mmff']) – Set the optimization mode for 3D conformation
removeHs (bool) – Set to True to hide hydrogens in the depiction
legends (str) – The name to used for each molecule. Can be ‘names’:the name of themselves; or ‘items’: a incremental id
highlightAtoms (list) – A List of atom to highligh for each molecule. It can be also a list of atom list, in this case different colors will be used
mols_perrow (int) – The number of molecules to depict per row of the grid
ipython_svg
SVG object if ipython is set to True
Returns the SmallMol objects that corresponds ot the indexes of the list passed
ids (list) – The index list of the molecules to return
smallmollist – The list of SmallMol objects
Example
>>> lib2 = lib.getMols([1,2,3])
>>> len(lib2)
3
Returns the number of molecules
Removes the moleculekit.smallmol.smallmol.SmallMol object based on the indexes in the list
ids (list) – The list of molecules index to remove from the SmallMolLib
Returns a pandas.DataFrame of the SmallMolLib object.
Writes an sdf file with molecules stored. Is it possible also to manage which field will be written
Writes a smi file with molecules stored. Is it possible to specify the header of the smi file. The name of the ligands can be their ligand name or a sequential ID.