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Remove label in adjlist before detecting cutting label #2519

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hwpang merged 1 commit into from
Aug 8, 2023
+10 −1
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Remove label in adjlist before detecting cutting label #2519

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11 changes: 10 additions & 1 deletion rmgpy/species.py
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Original file line number Diff line number Diff line change
Expand Up @@ -365,8 +365,17 @@ def from_adjacency_list(self, adjlist, raise_atomtype_exception=True, raise_char
list in the `molecule` attribute. Does not generate resonance isomers
of the loaded molecule.
"""
lines = adjlist.splitlines()

if len(lines[0].split()) == 1:
label = lines.pop(0) # remove the first line if it is a label before detecting cutting label
adjlist_no_label = '\n'.join(lines)
else:
adjlist_no_label = adjlist

# detect if it contains cutting label
_ , cutting_label_list = Fragment().detect_cutting_label(adjlist)
_ , cutting_label_list = Fragment().detect_cutting_label(adjlist_no_label)

@rwest rwest Aug 4, 2023

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detect_cutting_label is designed to work on SMILES-like strings, and looks quite complex.
what does a cutting label in an adjacency list look like? there might be a much faster way to just see if it's present in the adjacency list (which seems to be all you need to know here?)

@lily90502 lily90502 Aug 4, 2023 •
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An example of fragment RCC adjacency list:
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} 2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S} 3 R u0 p0 c0 {1,S} 4 H u0 p0 c0 {1,S} 5 H u0 p0 c0 {1,S} 6 H u0 p0 c0 {2,S} 7 H u0 p0 c0 {2,S} 8 H u0 p0 c0 {2,S}

I think another way is to check the atom type to see if it is Atom or Cuttinglabel. But I guess this will be slower?

@hwpang hwpang Aug 4, 2023

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Yeah, there are definitely better ways to do this. I'm not familiar with the detect_cutting_label function, so this PR is a quick fix, but someone should work on improving detect_cutting_label to specialize in adjacency list.


if cutting_label_list == []:
self.molecule = [Molecule().from_adjacency_list(adjlist, saturate_h=False,
raise_atomtype_exception=raise_atomtype_exception,
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