Topology parser (.itp) sensitive to underscores

[marcvdijk]

Parsing a GROMACS .itp topology file by the pyparsing itp_parser (lie_md.parsers.itp_parsing) fails when a filename in the .itp file contains an underscore.

Example .itp file content that fails:

; lig_30_GMX.itp created by acpype (Rev: 0) on Thu Mar 14 13:31:00 2019

[ atomtypes ]
;name   bond_type     mass     charge   ptype   sigma         epsilon       Amb
 oh       oh          0.00000  0.00000   A     3.06647e-01   8.80314e-01 ; 1.72  0.2104
 n2       n2          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ; 1.82  0.1700
 ce       ce          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860
 cc       cc          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860
 os       os          0.00000  0.00000   A     3.00001e-01   7.11280e-01 ; 1.68  0.1700
 cd       cd          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860
 ca       ca          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860
 nb       nb          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ; 1.82  0.1700
 ho       ho          0.00000  0.00000   A     0.00000e+00   0.00000e+00 ; 0.00  0.0000
 h4       h4          0.00000  0.00000   A     2.51055e-01   6.27600e-02 ; 1.41  0.0150
 ha       ha          0.00000  0.00000   A     2.59964e-01   6.27600e-02 ; 1.46  0.0150

[ moleculetype ]
;name            nrexcl
 lig_30           3

[ atoms ]
;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type
     1   oh     1   UNL     O    1    -0.360500     16.00000 ; qtot -0.361
     2   n2     1   UNL     N    2    -0.396200     14.01000 ; qtot -0.757
     3   ce     1   UNL     C    3     0.351200     12.01000 ; qtot -0.406
     4   cc     1   UNL    C1    4     0.189400     12.01000 ; qtot -0.216
     5   os     1   UNL    O1    5    -0.316800     16.00000 ; qtot -0.533
     6   cc     1   UNL    C2    6     0.325200     12.01000 ; qtot -0.208
     7   cd     1   UNL    C3    7    -0.234300     12.01000 ; qtot -0.442
     8   cd     1   UNL    C4    8    -0.176300     12.01000 ; qtot -0.618
     9   ca     1   UNL    C5    9    -0.238800     12.01000 ; qtot -0.857
    10   ca     1   UNL    C6   10    -0.048000     12.01000 ; qtot -0.905
    11   ca     1   UNL    C7   11    -0.215300     12.01000 ; qtot -1.120
    12   ca     1   UNL    C8   12     0.408200     12.01000 ; qtot -0.712
    13   nb     1   UNL    N1   13    -0.600001     14.01000 ; qtot -1.312
    14   ca     1   UNL    C9   14     0.417200     12.01000 ; qtot -0.895
    15   ho     1   UNL     H   15     0.418000      1.00800 ; qtot -0.477
    16   h4     1   UNL    H1   16    -0.007200      1.00800 ; qtot -0.484
    17   ha     1   UNL    H2   17     0.137000      1.00800 ; qtot -0.347
    18   ha     1   UNL    H3   18     0.142000      1.00800 ; qtot -0.205
    19   ha     1   UNL    H4   19     0.118000      1.00800 ; qtot -0.087
    20   ha     1   UNL    H5   20     0.117000      1.00800 ; qtot 0.030
    21   h4     1   UNL    H6   21    -0.016900      1.00800 ; qtot 0.013
    22   h4     1   UNL    H7   22    -0.012900      1.00800 ; qtot 0.000

The parser stops parsing when it encounters "lig_30" in [ moleculetype ] breaking follow up code that expects an [ atoms ] card. When replacing "lig_30" with the default ACPYPE file name "input" the parser continues parsing till the end of the file