moleculekit.writers module

moleculekit.writers.BCIFwrite(mol, filename, explicitbonds=None, chemcomp=None)

moleculekit.writers.BINCOORwrite(mol, filename)

moleculekit.writers.BINPOSwrite(mol, filename)

moleculekit.writers.CIFwrite(mol, filename, explicitbonds=None, chemcomp=None, return_data=False, writebonds=True, fp_precision=3)

Write mol to an mmCIF file.

Parameters:

• mol (moleculekit.molecule.Molecule) – The molecule to write.

• filename (str) – Output path. Unused when return_data is True.

• explicitbonds (tuple or None) – (bonds, bondtype) to write instead of mol.bonds / mol.bondtype.

• chemcomp (bool or None) – Force treating the molecule as a single chemical component (True) or as a structure (False). By default a molecule with a single resname is treated as a component.

• return_data (bool) – Return the assembled data containers instead of writing a file. Used by BCIFwrite() to encode the same content as binary mmCIF.

• writebonds (bool) – Whether to write connectivity at all.

• fp_precision (int) – Number of decimals for the coordinates.

moleculekit.writers.DCDwrite(mol, filename)

moleculekit.writers.GROwrite(mol, filename)

moleculekit.writers.INPCRDwrite(mol, filename)

moleculekit.writers.JSONwrite(mol, filename)

moleculekit.writers.MDTRAJwrite(mol, filename)

moleculekit.writers.MMTFwrite(mol, filename)

moleculekit.writers.MOL2write(mol, filename, explicitbonds=None)

moleculekit.writers.NETCDFwrite(mol, filename)

moleculekit.writers.PDBQTwrite(mol, filename, frames=None, writebonds=True)

moleculekit.writers.PDBwrite(mol, filename, frames=None, writebonds=True, mode='pdb')

moleculekit.writers.PSFwrite(mol, filename, explicitbonds=None)

moleculekit.writers.SDFwrite(mol, filename)

moleculekit.writers.TRRwrite(mol, filename)

moleculekit.writers.XSCwrite(mol, filename, frames=None)

moleculekit.writers.XTCwrite(mol, filename)

moleculekit.writers.XYZwrite(mol, filename)

moleculekit.writers.checkTruncations(mol)