Source code for mdpy.core.particle

#!/usr/bin/env python
# -*- encoding: utf-8 -*-
"""
file : particle.py
created time : 2021/09/28
author : Zhenyu Wei
copyright : (C)Copyright 2021-present, mdpy organization
"""

from mdpy.utils import check_quantity_value
from mdpy.unit import *
from mdpy.error import *


class Particle:
    def __init__(
        self,
        particle_id=None,
        particle_type=None,
        particle_name=None,
        matrix_id=None,
        molecule_id=None,
        molecule_type=None,
        chain_id=None,
        mass=None,
        charge=None,
    ) -> None:
        # Compulsory attributes
        self._particle_id = particle_id
        self._particle_type = particle_type
        self._particle_name = particle_name
        self._matrix_id = matrix_id
        # Optional attributes
        self._molecule_id = molecule_id
        self._molecule_type = molecule_type
        self._chain_id = chain_id
        self._mass = check_quantity_value(mass, default_mass_unit)
        self._charge = check_quantity_value(charge, default_charge_unit)
        # Topology infomation
        self._excluded_particles = []
        self._num_excluded_particles = 0
        self._scaled_particles = []
        self._scaling_factors = []
        self._num_scaled_particles = 0

    def __repr__(self) -> str:
        return "<mdpy.core.Particle object: %s-%s-%d at %x>" % (
            self._molecule_type,
            self._particle_type,
            self._particle_id,
            id(self),
        )

    def __str__(self) -> str:
        return "%s-%s-%d" % (
            self._molecule_type,
            self._particle_type,
            self._particle_id,
        )

    def __eq__(self, o) -> bool:
        if id(self) == id(o):
            return True
        return False

    def change_matrix_id(self, matrix_id: int):
        # Only used by Topology
        self._matrix_id = matrix_id

    def add_excluded_particle(self, particle_matrix_id):
        if particle_matrix_id in self._excluded_particles:
            raise ParticleConflictError(
                "Particle %d has been added twice to the excluded_particles of Particle %d"
                % (particle_matrix_id, self._matrix_id)
            )
        if particle_matrix_id == self._matrix_id:
            raise ParticleConflictError(
                "Particle itself can not be added to the excluded_particles list."
            )
        self._excluded_particles.append(particle_matrix_id)
        self._num_excluded_particles += 1

    def del_excluded_particle(self, particle_matrix_id):
        if particle_matrix_id in self._excluded_particles:
            self._excluded_particles.remove(particle_matrix_id)
            self._num_excluded_particles -= 1

    def add_scaled_particle(self, particle_matrix_id: int, factor):
        # Benzene give two dihedral with same 1 4 particles
        if particle_matrix_id == self._matrix_id:
            raise ParticleConflictError(
                "Particle itself can not be added to the scaled_particles list."
            )
        elif not particle_matrix_id in self._scaled_particles:
            self._scaled_particles.append(particle_matrix_id)
            self._scaling_factors.append(factor)
            self._num_scaled_particles += 1

    def del_scaled_particle(self, particle_matrix_id):
        if particle_matrix_id in self._scaled_particles:
            self._scaling_factors.remove(
                self._scaling_factors[self._scaled_particles.index(particle_matrix_id)]
            )
            self._scaled_particles.remove(particle_matrix_id)
            self._num_scaled_particles -= 1

    @property
    def particle_id(self):
        return self._particle_id

    @property
    def particle_type(self):
        return self._particle_type

    @property
    def particle_name(self):
        return self._particle_name

    @property
    def matrix_id(self):
        return self._matrix_id

    @property
    def molecule_id(self):
        return self._molecule_id

    @property
    def molecule_type(self):
        return self._molecule_type

    @property
    def chain_id(self):
        return self._chain_id

    @property
    def mass(self):
        return self._mass

    @property
    def charge(self):
        return self._charge

    @property
    def excluded_particles(self):
        return self._excluded_particles

    @property
    def num_excluded_particles(self):
        return self._num_excluded_particles

    @property
    def scaled_particles(self):
        return self._scaled_particles

    @property
    def scaling_factors(self):
        return self._scaling_factors

    @property
    def num_scaled_particles(self):
        return self._num_scaled_particles