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filter molecule for templates #339

Merged
merged 14 commits into from
Jun 21, 2024
Merged

filter molecule for templates #339

merged 14 commits into from
Jun 21, 2024

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fgrunewald
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@fgrunewald fgrunewald commented Aug 12, 2023 •
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This PR sets the stage for some important changes:

  • instead of matching templates by resnames each residue now requires a template_name attribute. This allows matching of non-identical residues that has the same resname
  • extract blocks now takes a template graph as input to extract the interactions, which is also used in PR Convert itp files to ff files #327

To Do

  • move ExtractBlock to separate file something like manipulate_molecules.py
  • speed up equivalence check or at least enable a bypass

@pckroon do you have any idea how to do the code below in faster?

polyply_1.0/polyply/src/generate_templates.py

Lines 295 to 314 in b97ba71

def group_by_isomorphism(meta_molecule, template_graphs={}):
"""
Extract all unique fragment graphs from meta_molecule
using the full subgraph isomorphism check.
"""
template_graphs = {}
for node in meta_molecule.nodes:
resname = meta_molecule.nodes[node]["resname"]
graph = meta_molecule.nodes[node]["graph"]
if resname in template_graphs and not nx.is_isomorphic(graph,
template_graphs[resname],
node_match=_atoms_match,
):
template_name = resname + str(len(template_graphs))
meta_molecule.nodes[node]["template"] = template_name
template_graphs[template_name] = graph
else:
meta_molecule.nodes[node]["template"] = resname
template_graphs[resname] = graph
return template_graphs

@fgrunewald
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note to self vf2pp from networkx 3 might speed up matching process also proper line by line benchmark is needed

@pckroon
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pckroon commented Aug 14, 2023

Not fundamentally, no. I'm also not sure what the goal you're trying to achieve is.

@fgrunewald
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Currently polyply assumes all residues are unique. That is mostly true but not quite at least at the all-atom level. For example, there might be a hydrogen extra or less depending on if a residue is located in the center or at the terminal. This functionality checks each residue against a collection of unique residues in order to find those that have the same resname but deviate as graphs. It makes generating the templates more robust for complicated AA structures

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pckroon commented Aug 15, 2023

Alright. I don't think there's really a faster way then. Unless you are willing to accept approximation, e.g. only check atom names.

@fgrunewald fgrunewald mentioned this pull request Jun 14, 2024
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@fgrunewald fgrunewald requested a review from pckroon June 14, 2024 13:36
@fgrunewald
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@csbrasnett this PR should fix the issue with the residue names; I think it is about time that we added this functionality

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pckroon requested changes Jun 14, 2024
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Small comments

polyply/src/backmap.py Outdated Show resolved Hide resolved
polyply/src/check_residue_equivalence.py Outdated Show resolved Hide resolved
polyply/src/check_residue_equivalence.py Outdated Show resolved Hide resolved
polyply/src/check_residue_equivalence.py Outdated Show resolved Hide resolved
polyply/src/check_residue_equivalence.py Outdated Show resolved Hide resolved
polyply/src/check_residue_equivalence.py Outdated Show resolved Hide resolved
polyply/src/generate_templates.py Show resolved Hide resolved
@fgrunewald fgrunewald requested a review from pckroon June 21, 2024 08:16
pckroon
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Small comments, mostly related to out-of-date docstrings

polyply/src/check_residue_equivalence.py Outdated Show resolved Hide resolved
polyply/src/check_residue_equivalence.py Show resolved Hide resolved
polyply/src/gen_coords.py Show resolved Hide resolved
polyply/src/generate_templates.py Show resolved Hide resolved
@fgrunewald fgrunewald requested a review from pckroon June 21, 2024 09:56
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Tiny nitpick, looks good otherwise!

polyply/tests/test_generate_templates.py Outdated Show resolved Hide resolved
@fgrunewald fgrunewald requested a review from pckroon June 21, 2024 10:45
@fgrunewald fgrunewald merged commit 160e970 into master Jun 21, 2024
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@fgrunewald fgrunewald deleted the master_copy branch June 21, 2024 11:09
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