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Pormake fragment #165

Merged
merged 4 commits into from
Jul 23, 2023
Merged

Pormake fragment #165

merged 4 commits into from
Jul 23, 2023

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gianmarco-terrones
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codecov bot commented Jul 23, 2023 •
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Codecov Report

Patch and project coverage have no change.

Comparison is base (d979f26) 25.65% compared to head (8f38386) 25.65%.

Additional details and impacted files 
@@           Coverage Diff           @@
##           master     #165   +/-   ##
=======================================
  Coverage   25.65%   25.65%           
=======================================
  Files         102      102           
  Lines       33827    33824    -3     
=======================================
  Hits         8678     8678           
+ Misses      25149    25146    -3
Flag Coverage Δ
unittests 25.65% <0.00%> (+<0.01%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
molSimplify/Informatics/MOF/MOF_descriptors.py 0.00% <0.00%> (ø)
molSimplify/Informatics/MOF/MOF_functionalizer.py 0.00% <0.00%> (ø)
molSimplify/Informatics/MOF/PBC_functions.py 0.00% <0.00%> (ø)
molSimplify/Informatics/MOF/cluster_extraction.py 0.00% <0.00%> (ø)
...plify/Informatics/MOF/fragment_MOFs_for_pormake.py 0.00% <0.00%> (ø)

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github-advanced-security[bot]
github-advanced-security bot found potential problems Jul 23, 2023
View reviewed changes
molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
@@ -289,8 +411,8 @@
X_string = ' '.join([str(val) for val in final_X_indices])
else:
X_string = ' '
coord_list, molgraph = returnXYZandGraph(xyzname, SBU_mol_atom_labels , cell , SBU_mol_fcoords_connected,SBU_mol_adj_mat)
SBU_mol.writexyz(xyzname,withgraph=True, specialheader=' '+X_string)
coord_list, molgraph = returnXYZandGraph(xyzname, SBU_mol_atom_labels, cell, SBU_mol_fcoords_connected, SBU_mol_adj_mat)

Check warning

Code scanning / CodeQL

Variable defined multiple times Warning

This assignment to 'coord_list' is unnecessary as it is
redefined
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before this value is used.
This assignment to 'coord_list' is unnecessary as it is
redefined
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before this value is used.
molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
@@ -289,8 +411,8 @@
X_string = ' '.join([str(val) for val in final_X_indices])
else:
X_string = ' '
coord_list, molgraph = returnXYZandGraph(xyzname, SBU_mol_atom_labels , cell , SBU_mol_fcoords_connected,SBU_mol_adj_mat)
SBU_mol.writexyz(xyzname,withgraph=True, specialheader=' '+X_string)
coord_list, molgraph = returnXYZandGraph(xyzname, SBU_mol_atom_labels, cell, SBU_mol_fcoords_connected, SBU_mol_adj_mat)

Check warning

Code scanning / CodeQL

Variable defined multiple times Warning

This assignment to 'molgraph' is unnecessary as it is
redefined
Loading
before this value is used.
This assignment to 'molgraph' is unnecessary as it is
redefined
Loading
before this value is used.
molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
@@ -373,24 +495,48 @@
X_string = ' '.join([str(val) for val in final_X_indices_linker])
else:
X_string = ' '
coord_list, molgraph = returnXYZandGraph(xyzname, linker_mol_atom_labels , cell , linker_mol_fcoords_connected,linker_mol_adj_mat)
linker_mol.writexyz(xyzname,withgraph=True, specialheader=' '+X_string)
coord_list, molgraph = returnXYZandGraph(xyzname, linker_mol_atom_labels , cell , linker_mol_fcoords_connected, linker_mol_adj_mat)

Check warning

Code scanning / CodeQL

Variable defined multiple times Warning

This assignment to 'coord_list' is unnecessary as it is
redefined
Loading
before this value is used.
molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
@@ -373,24 +495,48 @@
X_string = ' '.join([str(val) for val in final_X_indices_linker])
else:
X_string = ' '
coord_list, molgraph = returnXYZandGraph(xyzname, linker_mol_atom_labels , cell , linker_mol_fcoords_connected,linker_mol_adj_mat)
linker_mol.writexyz(xyzname,withgraph=True, specialheader=' '+X_string)
coord_list, molgraph = returnXYZandGraph(xyzname, linker_mol_atom_labels , cell , linker_mol_fcoords_connected, linker_mol_adj_mat)

Check warning

Code scanning / CodeQL

Variable defined multiple times Warning

This assignment to 'molgraph' is unnecessary as it is
redefined
Loading
before this value is used.
molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
tempgraph= molcif.graph[np.ix_(SBU_added,SBU_added)]
no_X_graph = molcif.graph[np.ix_(SBU_added_no_X,SBU_added_no_X)]
tempgraph = molcif.graph[np.ix_(SBU_added, SBU_added)]
no_X_graph = molcif.graph[np.ix_(SBU_added_no_X, SBU_added_no_X)]

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable no_X_graph is not used.
molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
write2file(logpath,"/%s.log"%name,tmpstr)
SBU_list , SBU_subgraphlist = include_extra_shells(SBU_list,SBU_subgraphlist,molcif ,adj_matrix)
write2file(logpath, "/%s.log"%name, tmpstr)
SBU_list , SBU_subgraphlist = include_extra_shells(SBU_list, SBU_subgraphlist, molcif, adj_matrix)

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable SBU_list is not used.
molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
write2file(logpath,"/%s.log"%name,tmpstr)
SBU_list , SBU_subgraphlist = include_extra_shells(SBU_list,SBU_subgraphlist,molcif ,adj_matrix)
write2file(logpath, "/%s.log"%name, tmpstr)
SBU_list , SBU_subgraphlist = include_extra_shells(SBU_list, SBU_subgraphlist, molcif, adj_matrix)

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable SBU_subgraphlist is not used.
molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list,SBU_subgraphlist,molcif ,adj_matrix)
SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list,SBU_subgraphlist,molcif ,adj_matrix)
SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list, SBU_subgraphlist, molcif, adj_matrix)
SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list, SBU_subgraphlist, molcif, adj_matrix)

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable SBU_list is not used.
molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list,SBU_subgraphlist,molcif ,adj_matrix)
SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list,SBU_subgraphlist,molcif ,adj_matrix)
SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list, SBU_subgraphlist, molcif, adj_matrix)
SBU_list, SBU_subgraphlist = include_extra_shells(SBU_list, SBU_subgraphlist, molcif, adj_matrix)

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable SBU_subgraphlist is not used.
@gianmarco-terrones gianmarco-terrones merged commit 6bec129 into master Jul 23, 2023
9 checks passed
@gianmarco-terrones gianmarco-terrones deleted the pormake_fragment branch July 23, 2023 17:51
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