Can't use kwargs with mbuild.load when backend is gmso.

[umesh-timalsina]

I found an issue where, any kwargs that are provided to mbuild.load when using gmso as a backend, is not propagated. The issue stems from the following line in mbuild's conversion.py.

mbuild/mbuild/conversion.py

Line 431 in a1611f1

top = gmso.Topology.load(filename=filename)

Reproduce with non-atomistic mol2 files

@<TRIPOS>MOLECULE
PEN
    6    5    1    0    0
SMALL
NO_CHARGES
****
Energy = 0

@<TRIPOS>ATOM
      1  _CH3       0.0000    0.0000    0.0000    C    1  HEX        0.000000
      2  _CH2      -1.5000    0.0000    0.0000    C    1  HEX        0.000000
      3  _CH2      -2.2500    1.2990    0.0000    C    1  HEX        0.000000
      4  _CH2      -2.3176    2.1344    1.2440    C    1  HEX        0.000000
      5  _CH2      -2.4830    1.4760    2.5816    C    1  HEX        0.000000
      6  _CH3      -2.1676    0.0185    2.7441    C    1  HEX        0.000000
@<TRIPOS>BOND
    1     1     2  1
    2     2     3  1
    3     3     4  1
    4     4     5  1
    5     5     6  1

@<TRIPOS>SUBSTRUCTURE
1 ****        1 TEMP                        0 ****  **** 0 ROOT

#generated by VMD

Copy the content above and save it to a hexane.mol2 file.

from gmso.core.topology import Topology
from gmso.external.convert_mbuild import to_mbuild
import mbuild as mb

## With site_type='lj', elements are not inferred
gmso_top = Topology.load('hexane.mol2', site_type='lj')
mbuild_compound_using_gmso = to_mbuild(gmso_top)

print('Using gmso.Topology.load')
for particle in mbuild_compound_using_gmso.particles():
    print(particle.element)

print()
    
## Same with mbuild infers element
print('Using mbuild.load')
mbuild_compound_using_mbuild_dot_load = mb.load('hexane.mol2', site_type='lj', backend='gmso')
for particle in mbuild_compound_using_mbuild_dot_load.particles():
    print(particle.element)
print()

Using gmso.Topology.load
None
None
None
None
None
None

Using mbuild.load
Element: carbon, symbol: C, atomic number: 6, mass: 12.011
Element: carbon, symbol: C, atomic number: 6, mass: 12.011
Element: carbon, symbol: C, atomic number: 6, mass: 12.011
Element: carbon, symbol: C, atomic number: 6, mass: 12.011
Element: carbon, symbol: C, atomic number: 6, mass: 12.011
Element: carbon, symbol: C, atomic number: 6, mass: 12.011

Software versions

• Which version of mBuild are you using? (0.14.2)
• Which version of Python (3.9.7)?
• Which operating system? unix