Molecule¶

class porems.molecule.Molecule(name='molecule', short='MOL', inp=None)¶

This class defines a molecule object, which is basically a list of Atom objects. Each atom object has a specific cartesian position and atom type, creating the construct of a molecule.

Functions have been provided for editing, moving and transforming the atom objects, either as a collective or specific part of the molecule.

Parameters:

namestring, optional: Molecule name
shortstring, optional: Molecule short name
inpNone, string, list, optional: None for empty Molecule, string to read a molecule from a specified file link or a list of either molecules to concatenate these into one object, or a list of atom objects

Examples

Following example generates a benzene molecule without hydrogen atoms

import porems as pms

mol = pms.Molecule("benzene", "BEN")
mol.add("C", [0,0,0])
mol.add("C", 0, r=0.1375, theta= 60)
mol.add("C", 1, r=0.1375, theta=120)
mol.add("C", 2, r=0.1375, theta=180)
mol.add("C", 3, r=0.1375, theta=240)
mol.add("C", 4, r=0.1375, theta=300)

Methods

`_box_size`()	Calculate the box size of the current molecule.
`_concat`(mol_list)	Concatenate a molecule list into one molecule object.
`_read`(file_path, file_type)	Read a molecule from a file.
`_temp`(atoms)	Create a temporary molecule of specified atom ids.
`_vector`(pos_a, pos_b)	Calculate the vector between to two positions as defined in `porems.geometry.vector` with the addition to define the inputs as atom indices.
`add`(atom_type, pos[, bond, r, theta, phi, ...])	Add a new atom in polar coordinates.
`append`(mol)	Append a given molecule to the current object.
`bond`(inp_a, inp_b)	Return the bond vector of a specified bond.
`centroid`()	Calculate the geometrical center of mass
`column_pos`()	Create column list of atom positions
`com`()	Calculate the center of mass
`delete`(atoms)	Delete specified atom from the molecule.
`get_atom_list`()	Return the atoms list.
`get_atom_type`(atom)	Return the atom type of the given atom id.
`get_box`()	Return the box size of the molecule.
`get_charge`()	Return the total charge of the molecule.
`get_mass`()	Return the molar mass of the molecule.
`get_masses`()	Return a list of masses of the atoms.
`get_name`()	Return the molecule name.
`get_num`()	Return the number of atoms.
`get_short`()	Return the molecule short name.
`move`(atom, pos)	Move whole the molecule to a new position, where the dragging point is a given atom that is moved to a specified position.
`overlap`([error])	Search for overlapping atoms.
`part_angle`(bond_a, bond_b, atoms, angle, zero)	Change the bond angle of two bond vectors.
`part_move`(bond, atoms, length[, vec])	Change the length of a specified bond.
`part_rotate`(bond, atoms, angle, zero)	Rotate a set of specified atoms around a given bond as the rotation axis.
`pos`(atom)	Get the position of an atom.
`put`(atom, pos)	Change the position of an atom to a given position vector \(\boldsymbol{a}\in\mathbb{R}^n\).
`rotate`(axis, angle[, is_deg])	Rotate data matrix \(\boldsymbol{D}\) around an axis \(\boldsymbol{a}\in\mathbb{R}^3\) with angle \(\alpha\in\mathbb{R}\) using rotation function `porems.geometry.rotate()`.
`set_atom_name`(atom, name)	Change the atom name of a specified atom.
`set_atom_residue`(atom, residue)	Change the residue index of a specified atom.
`set_atom_type`(atom, atom_type)	Change the atom type of a specified atom.
`set_box`(box)	Set the box size.
`set_charge`(charge)	Set the total charge of the molecule.
`set_mass`([mass])	Set the molar mass of the molecule.
`set_masses`([masses])	Set the molar masses of the atoms.
`set_name`(name)	Set the molecule name.
`set_short`(short)	Set the molecule short name.
`switch_atom_order`(atom_a, atom_b)	Switch atom order of two atoms.
`translate`(vec)	Translate the atoms data matrix \(\boldsymbol{D}\) along a vector \(\boldsymbol{a}\in\mathbb{R}^n\).
`zero`([pos])	Move whole the molecule, so that the minimal coordinate between all atoms is zero in all dimensions, or rather the values of the position variable `pos`.