Molecule¶

This class stores arrays of atoms. It is also used for residues within polymers, such as amino acids within a protein. As such, a Molecule instance has id, resname, and atoms attributes.

API Reference¶

class pmx.molecule.Molecule(**kwargs)¶

Class for storing molecule/residue data.

resname¶

residue/molecule name

Type: str

id¶

residue ID

Type: int

natoms¶

number of atoms in the Molecule

Type: int

atoms¶

list of atoms in Molecule

Type: list

chain¶

the Chain instance the Molecule is part of

Type: Chain

chain_id¶

ID of the chain the residue is part of

Type: int

moltype¶

the type of molecule/residue (protein, dna, rna, ion, water, or unknown).

Type: str

Methods

`set_resname`(resname)	Set the residue name.
`set_resid`(resid)	Set the residue ID.
`insert_atom`(pos, atom[, id])	Insert an atom at a certain position.
`append`(atom)	Append an atom to the Molecule.
`remove_atom`(atom)	Delete an atom from Molecule.
`fetch`(key[, how, wildcard])	Fetch atoms.
`fetchm`(keys[, how])	Fetch multiple atoms.
`is_hybrid`()	Checks whether the molecule/residue is a pmx hybrid.
`rename_atoms_to_gmx`()	Renames atoms to comply with Gromacs syntax.