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segfault in MaeMolSupplier #2881

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greglandrum opened this issue Jan 15, 2020 · 0 comments
Closed

segfault in MaeMolSupplier #2881

greglandrum opened this issue Jan 15, 2020 · 0 comments
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@greglandrum
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This MAE block (taken from $RDBASE/Data/templates.mae) generates a seg fault when it's being parsed:

f_m_ct { 
 s_m_title
 s_m_entry_id
 s_m_entry_name
 s_m_Source_Path
 s_m_Source_File
 i_m_Source_File_Index
 s_st_Chirality_1
 s_st_Chirality_2
 s_m_subgroup_title
 s_m_subgroupid
 b_m_subgroup_collapsed
 i_m_ct_format
 :::
 "Untitled Document-4" 
  17 
  newTemplates2.1 
  /Users/nicola/schrodinger/coordgen_standalone 
  templates.mae 
  17
  3_S_4_6_2 
  7_S_8_9_6_10 
  templates->templates->templates 
  templates->templates1->templates11 
  0
  2
 m_depend[2] { 
  # First column is dependency index #
  i_m_depend_dependency
  s_m_depend_property
  :::
  1 10 s_st_Chirality_1 
  2 10 s_st_Chirality_2 
  :::
 } 
 m_atom[15] { 
  # First column is atom index #
  i_m_mmod_type
  r_m_x_coord
  r_m_y_coord
  r_m_z_coord
  i_m_residue_number
  i_m_color
  i_m_atomic_number
  s_m_color_rgb
  s_m_atom_name
  :::
  1 5 1.186400 1.035900 0.000000 900 2 6 A0A0A0  C1 
  2 5 0.370300 1.157000 0.000000 900 2 6 A0A0A0  C2 
  3 4 -0.326500 0.715300 0.000000 900 2 6 A0A0A0  C3 
  4 5 0.085100 0.000400 0.000000 900 2 6 A0A0A0  C4 
  5 26 -0.328300 -0.713600 0.000000 900 43 7 5757FF  N5 
  6 5 -1.151500 0.716400 0.000000 900 2 6 A0A0A0  C6 
  7 5 -1.564900 0.002400 0.000000 900 2 6 A0A0A0  C7 
  8 5 -1.153300 -0.712600 0.000000 900 2 6 A0A0A0  C9 
  9 2 1.724800 0.410800 0.000000 900 2 6 A0A0A0  C12 
  10 2 1.723800 -0.414200 0.000000 900 2 6 A0A0A0  C13 
  11 5 1.183800 -1.037900 0.000000 900 2 6 A0A0A0  C14 
  12 5 0.367400 -1.157000 0.000000 900 2 6 A0A0A0  C15 
  13 7 2.508100 -0.670100 0.000000 900 2 6 A0A0A0  C16 
  14 7 2.993800 -0.003300 0.000000 900 2 6 A0A0A0  C17 
  15 29 2.509700 0.664800 0.000000 900 43 7 5757FF  N18 
  :::
 } 
 m_bond[17] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 2 1
  2 1 9 1
  3 2 3 1
  4 3 4 1
  5 3 6 1
  6 4 5 1
  7 5 8 1
  8 5 12 1
  9 6 7 1
  10 7 8 1
  11 9 10 2
  12 9 15 1
  13 10 11 1
  14 10 13 1
  15 11 12 1
  16 13 14 2
  17 14 15 1
  :::
 } 
} 

The problem is the chiral spec for atom 7, which specifies bonds that don't exist.

Aside from fixing the seg fault, the templates.mae file should be changed too.

@greglandrum greglandrum added this to the 2019_09_4 milestone Jan 15, 2020
greglandrum added a commit to greglandrum/rdkit that referenced this issue Jan 15, 2020
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