groan_rs 0.11.3

--- # Parameters for default elements supported by the `groan_rs` library.
# Taken from Gromacs `atommass.dat` and `vdwradii.dat`. 
# Modified based on VMD's https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwtables.html#allatom.
# All fields are optional.
# When using `System::quess_elements` function, the elements are assigned to atoms based on the herein provided Groan Selection Language query.
# Higher placed elements have priority over the lower placed ones.
# Unknown fields and invalid queries, masses, van der Waals radii, min_bonds and max bonds will raise a parsing error.
# If you define multiple elements with the same name, only the last element with this name will be used!

dummy:
  query: name MN1 MN2 MNZ1 MNZ2 MW
  mass: 0.0
hydrogen:
  symbol: H
  query: name r'^[1-9]?[Hh].*'
  mass: 1.0079
  vdw: 0.1
  expected_max_bonds: 1
  expected_min_bonds: 1
carbon:
  symbol: C
  query: name r'^[Cc].*$' and not @ion
  mass: 12.0107
  vdw: 0.17
  expected_max_bonds: 4
  expected_min_bonds: 2
nitrogen:
  symbol: N
  query: name r'^[Nn].*$' and not @ion
  mass: 14.00670
  vdw: 0.1625
  expected_max_bonds: 4
  expected_min_bonds: 1
oxygen:
  symbol: O
  query: name r'^[Oo].*$'
  mass: 15.99940
  vdw: 0.15
  expected_max_bonds: 2
  expected_min_bonds: 1
phosphorus:
  symbol: P
  query: name r'^[Pp].*$'
  mass: 30.97380
  vdw: 0.1871
  expected_max_bonds: 5
  expected_min_bonds: 2
sulfur:
  symbol: S
  query: name r'^[Ss][^iI].*$' and not name SOD
  mass: 32.06500
  vdw: 0.1782
  expected_min_bonds: 1
sodium:
  symbol: Na
  query: name r'^[Nn][Aa]\+?$' SOD and @ion
  mass: 22.98970
chlorine:
  symbol: Cl
  query: name r'^[Cc][Ll]\-?$' CLA and @ion
  mass: 35.45300
potassium:
  symbol: K
  query: name r'^[Kk]\+?$'
  mass: 39.09830
calcium:
  symbol: Ca
  query: name r'^[Cc][Aa]2?\+?$' CAL Cal and @ion
  mass: 40.07800
magnesium:
  symbol: Mg
  query: name r'^[Mm][Gg]2?\+?$'
  mass: 24.30500
fluorine:
  symbol: F
  query: name r'^[Ff]\-?$'
  mass: 18.99840
  vdw: 0.156
iodine:
  symbol: I
  query: name r'^[Ii]\-?$'
  mass: 126.90450
silicon:
  symbol: Si
  query: name r'^[Ss][Ii].*$'
  mass: 28.08550
iron:
  symbol: Fe
  query: name r'^[Ff][Ee].*$'
  mass: 55.84500
gold:
  symbol: Au
  query: name r'^[Aa][Uu].*$'
  mass: 196.96650
aluminum:
  symbol: Al
  query: name r'^[Aa][Ll].*$'
  mass: 26.98150
lithium:
  symbol: Li
  query: name r'^[Ll][Ii].*$'
  mass: 6.94100
beryllium:
  symbol: Be
  query: name r'^[Bb][Ee].*$'
  mass: 9.01220
boron:
  symbol: B
  query: name r'^[Bb][^Ee].*$'
  mass: 10.81100
titanium:
  symbol: Ti
  query: name r'^[Tt][Ii].*$'
  mass: 47.86700
vanadium:
  symbol: V
  query: name r'^[Vv].*$'
  mass: 50.94150
chromium:
  symbol: Cr
  query: name r'^[Cc][Rr].*$'
  mass: 51.99610
manganese:
  symbol: Mn
  query: name r'^[Mm][Nn].*$'
  mass: 54.93800
cobalt:
  symbol: Co
  query: name r'^[Cc][Oo].*$'
  mass: 58.93320
nickel:
  symbol: Ni
  query: name r'^[Nn][Ii].*$'
  mass: 58.69340
copper:
  symbol: Cu
  query: name r'^[Cc][Uu].*$'
  mass: 63.54600
zinc:
  symbol: Zn
  query: name r'^[Zz][Nn].*$'
  mass: 65.39000
gallium:
  symbol: Ga
  query: name r'^[Gg][Aa].*$'
  mass: 69.72300
germanium:
  symbol: Ge
  query: name r'^[Gg][Ee].*$'
  mass: 72.64000
arsenic:
  symbol: As
  query: name r'^[Aa][Ss].*$'
  mass: 74.92160
selenium:
  symbol: Se
  query: name r'^[Ss][Ee].*$'
  mass: 78.96000
bromine:
  symbol: Br
  query: name r'^[Bb][Rr].*$'
  mass: 79.90400
silver:
  symbol: Ag
  query: name r'^[Aa][Gg].*$'
  mass: 107.86820
platinum:
  symbol: Pt
  query: name r'^[Pp][Tt].*$'
  mass: 195.07800
mercury:
  symbol: Hg
  query: name r'^[Hh][Gg].*$' and not @protein
  mass: 200.59000
lead:
  symbol: Pb
  query: name r'^[Pp][Bb].*$'
  mass: 207.20000
bismuth:
  symbol: Bi
  query: name r'^[Bb][Ii].*$'
  mass: 208.98040
...