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Similar blocks of code found in 2 locations. Consider refactoring.
Open

        for monomer in alphabet.monomers.values():
            if monomer in monomer.base_monomers:
                monomer.base_monomers.remove(monomer)
Severity: Minor
Found in bpforms/alphabet/protein.py and 1 other location - About 45 mins to fix
bpforms/alphabet/protein.py on lines 141..143

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 35.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

for code in monomer_freq.keys():
    monomer_freq[code] *= (1. + doubling_time / half_life)
Severity: Minor
Found in examples/modomics_analysis.py and 1 other location - About 45 mins to fix
examples/modomics_analysis.py on lines 46..47

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 35.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

                monomer.r_bond_atoms = [Atom(Monomer, element='O', position=monomers[monomer.id]['r_bond_atom'])]
Severity: Major
Found in bpforms/alphabet/dna.py and 2 other locations - About 40 mins to fix
bpforms/alphabet/dna.py on lines 318..318
bpforms/alphabet/dna.py on lines 322..322

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

                monomer.r_displaced_atoms = [Atom(Monomer, element='H', position=monomers[monomer.id]['r_bond_atom'])]
Severity: Major
Found in bpforms/alphabet/dna.py and 2 other locations - About 40 mins to fix
bpforms/alphabet/dna.py on lines 318..318
bpforms/alphabet/dna.py on lines 321..321

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

can_monomers = [bpforms.rna_alphabet.monomers.A, 
                bpforms.rna_alphabet.monomers.C,
                bpforms.rna_alphabet.monomers.G,
                bpforms.rna_alphabet.monomers.U]
Severity: Minor
Found in examples/homo_sapiens_rna/curate.py and 1 other location - About 40 mins to fix
examples/modomics_analysis.py on lines 10..14

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 3 locations. Consider refactoring.
Open

@bpforms.core.cache.memoize(typed=False, expire=30 * 24 * 60 * 60)
Severity: Major
Found in bpforms/rest.py and 2 other locations - About 40 mins to fix
bpforms/rest.py on lines 227..227
bpforms/rest.py on lines 269..269

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        if atom_b_idx:
            monomer.backbone_bond_atoms = [Atom(Monomer, 'O', atom_b_idx)]
            monomer.backbone_displaced_atoms = [Atom(Monomer, 'H', atom_b_idx)]
Severity: Minor
Found in bpforms/alphabet/rna.py and 1 other location - About 40 mins to fix
bpforms/alphabet/rna.py on lines 919..921

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 3 locations. Consider refactoring.
Open

@bpforms.core.cache.memoize(typed=False, expire=30 * 24 * 60 * 60)
Severity: Major
Found in bpforms/rest.py and 2 other locations - About 40 mins to fix
bpforms/rest.py on lines 227..227
bpforms/rest.py on lines 312..312

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

                monomer.l_bond_atoms = [Atom(Monomer, element='P', position=monomers[monomer.id]['l_bond_atom'])]
Severity: Major
Found in bpforms/alphabet/dna.py and 2 other locations - About 40 mins to fix
bpforms/alphabet/dna.py on lines 321..321
bpforms/alphabet/dna.py on lines 322..322

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 3 locations. Consider refactoring.
Open

@bpforms.core.cache.memoize(typed=False, expire=30 * 24 * 60 * 60)
Severity: Major
Found in bpforms/rest.py and 2 other locations - About 40 mins to fix
bpforms/rest.py on lines 269..269
bpforms/rest.py on lines 312..312

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        atom_n_neighbors = set((atom.GetIdx(), atom.GetAtomicNum()) for atom in openbabel.OBAtomAtomIter(atom_n))
Severity: Minor
Found in bpforms/alphabet/protein.py and 1 other location - About 40 mins to fix
bpforms/alphabet/protein.py on lines 826..826

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        if atom_r_idx:
            monomer.r_bond_atoms = [Atom(Monomer, 'O', atom_r_idx)]
            monomer.r_displaced_atoms = [Atom(Monomer, 'H', atom_r_idx)]
Severity: Minor
Found in bpforms/alphabet/rna.py and 1 other location - About 40 mins to fix
bpforms/alphabet/rna.py on lines 916..918

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

canonical_monomers = [
    bpforms.rna_alphabet.monomers.A,
    bpforms.rna_alphabet.monomers.C,
    bpforms.rna_alphabet.monomers.G,
    bpforms.rna_alphabet.monomers.U,
Severity: Minor
Found in examples/modomics_analysis.py and 1 other location - About 40 mins to fix
examples/homo_sapiens_rna/curate.py on lines 21..24

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        atom_c_neighbors = set((atom.GetIdx(), atom.GetAtomicNum()) for atom in openbabel.OBAtomAtomIter(atom_c))
Severity: Minor
Found in bpforms/alphabet/protein.py and 1 other location - About 40 mins to fix
bpforms/alphabet/protein.py on lines 825..825

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 34.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Function build_dnamod has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def build_dnamod(self, alphabet, ph=None, major_tautomer=False, dearomatize=False):
Severity: Minor
Found in bpforms/alphabet/dna.py - About 35 mins to fix

    Function build_repairtoire has 5 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def build_repairtoire(self, alphabet, ph=None, major_tautomer=False, dearomatize=False):
    Severity: Minor
    Found in bpforms/alphabet/dna.py - About 35 mins to fix

      Function build_rna_mod_db has 5 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def build_rna_mod_db(self, alphabet, session, ph=None, major_tautomer=False, dearomatize=False):
      Severity: Minor
      Found in bpforms/alphabet/rna.py - About 35 mins to fix

        Function build_alphabets has 5 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def build_alphabets(ph=None, major_tautomer=False, dearomatize=False, _max_monomers=float('inf'), alphabets=None):
        Severity: Minor
        Found in bpforms/util.py - About 35 mins to fix

          Function __init__ has 5 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def __init__(self, id=None, uniprot_id=None, org_taxid=None, exp_org_taxid=None, het=None):
          Severity: Minor
          Found in examples/pdb_analysis.py - About 35 mins to fix

            Function get_resid_monomer_structure has 5 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                def get_resid_monomer_structure(self, name, pdb_filename, ph=None, major_tautomer=False, dearomatize=False):
            Severity: Minor
            Found in bpforms/alphabet/protein.py - About 35 mins to fix
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