Sign upLogin

xchem/XChemExplorer

View on GitHub
Star

Showing 640 of 1,077 total issues

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

    def StartGUI(self):
        self.window = gtk.Window(gtk.WINDOW_TOPLEVEL)
        self.window.connect("delete_event", gtk.main_quit)
        self.window.set_border_width(10)
        self.window.set_default_size(400, 800)
Severity: Major
Found in xce/lib/XChemCootTwin.py and 1 other location - About 1 mo to fix
xce/lib/XChemCootBuster.py on lines 179..608

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 3972.

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 2 locations. Consider refactoring.
Open

    def StartGUI(self):
        self.window = gtk.Window(gtk.WINDOW_TOPLEVEL)
        self.window.connect("delete_event", gtk.main_quit)
        self.window.set_border_width(10)
        self.window.set_default_size(400, 800)
Severity: Major
Found in xce/lib/XChemCootBuster.py and 1 other location - About 1 mo to fix
xce/lib/XChemCootTwin.py on lines 173..603

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 3972.

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

    def RefreshData(self):
        # reset spider plot image
        spider_plot_pic = gtk.gdk.pixbuf_new_from_file(
            os.path.join(
                os.getenv("XChemExplorer_DIR"),
Severity: Major
Found in xce/lib/XChemCootBuster.py and 1 other location - About 3 wks to fix
xce/lib/XChemCootTwin.py on lines 915..1296

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 2491.

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

    def RefreshData(self):
        # reset spider plot image
        spider_plot_pic = gtk.gdk.pixbuf_new_from_file(
            os.path.join(
                os.getenv("XChemExplorer_DIR"),
Severity: Major
Found in xce/lib/XChemCootTwin.py and 1 other location - About 3 wks to fix
xce/lib/XChemCootBuster.py on lines 924..1304

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 2491.

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

    def RefreshSiteData(self):
        if self.pandda_index == -1:
            self.merge_ligand_button.set_sensitive(True)
            self.place_ligand_here_button.set_sensitive(True)
        else:
Severity: Major
Found in xce/lib/XChemCootTwin.py and 2 other locations - About 1 wk to fix
xce/lib/XChemCootBuster.py on lines 749..873
xce/lib/XChemCootNew.py on lines 764..889

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 999.

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

    def RefreshSiteData(self):
        if self.pandda_index == -1:
            self.merge_ligand_button.set_sensitive(True)
            self.place_ligand_here_button.set_sensitive(True)
        else:
Severity: Major
Found in xce/lib/XChemCootBuster.py and 2 other locations - About 1 wk to fix
xce/lib/XChemCootNew.py on lines 764..889
xce/lib/XChemCootTwin.py on lines 744..869

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 999.

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

    def RefreshSiteData(self):
        if self.pandda_index == -1:
            self.merge_ligand_button.set_sensitive(True)
            self.place_ligand_here_button.set_sensitive(True)
        else:
Severity: Major
Found in xce/lib/XChemCootNew.py and 2 other locations - About 1 wk to fix
xce/lib/XChemCootBuster.py on lines 749..873
xce/lib/XChemCootTwin.py on lines 744..869

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 999.

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 2 locations. Consider refactoring.
Open

    def RefinementParams(self, RefmacParams):
        self.RefmacParams = RefmacParams
        self.window = gtk.Window(gtk.WINDOW_TOPLEVEL)
        self.window.connect("delete_event", gtk.main_quit)
        self.window.set_border_width(10)
Severity: Major
Found in xce/lib/XChemRefine.py and 1 other location - About 1 wk to fix
xce/lib/XChemRefine.py on lines 2170..2236

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 755.

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 2 locations. Consider refactoring.
Open

    def RefinementParams(self, RefmacParams):
        self.RefmacParams = RefmacParams
        self.window = gtk.Window(gtk.WINDOW_TOPLEVEL)
        self.window.connect("delete_event", gtk.main_quit)
        self.window.set_border_width(10)
Severity: Major
Found in xce/lib/XChemRefine.py and 1 other location - About 1 wk to fix
xce/lib/XChemRefine.py on lines 1197..1263

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 755.

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

    def merge_ligand_into_protein(self, widget):
        cpd = str(self.select_cpd_cb.get_active_text())
        for imol in coot_utils_XChem.molecule_number_list():
            if imol not in self.mol_dict["ligand_stereo"]:
                continue
Severity: Major
Found in xce/lib/XChemCootBuster.py and 2 other locations - About 5 days to fix
xce/lib/XChemCootNew.py on lines 1703..1780
xce/lib/XChemCootTwin.py on lines 1534..1611

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 596.

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

    def merge_ligand_into_protein(self, widget):
        cpd = str(self.select_cpd_cb.get_active_text())
        for imol in coot_utils_XChem.molecule_number_list():
            if imol not in self.mol_dict["ligand_stereo"]:
                continue
Severity: Major
Found in xce/lib/XChemCootTwin.py and 2 other locations - About 5 days to fix
xce/lib/XChemCootBuster.py on lines 1545..1622
xce/lib/XChemCootNew.py on lines 1703..1780

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 596.

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

    def merge_ligand_into_protein(self, widget):
        cpd = str(self.select_cpd_cb.get_active_text())
        for imol in coot_utils_XChem.molecule_number_list():
            if imol not in self.mol_dict["ligand_stereo"]:
                continue
Severity: Major
Found in xce/lib/XChemCootNew.py and 2 other locations - About 5 days to fix
xce/lib/XChemCootBuster.py on lines 1545..1622
xce/lib/XChemCootTwin.py on lines 1534..1611

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 596.

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

    def show_potential_link(self, *clicks):
        # first find imol of protein molecule
        # it's a prerequisite that the ligand is merged into the protein
        imol_protein = None
        for imol in coot_utils_XChem.molecule_number_list():
Severity: Major
Found in xce/lib/XChemCootTwin.py and 2 other locations - About 4 days to fix
xce/lib/XChemCootBuster.py on lines 1399..1469
xce/lib/XChemCootNew.py on lines 1557..1627

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 489.

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

    def show_potential_link(self, *clicks):
        # first find imol of protein molecule
        # it's a prerequisite that the ligand is merged into the protein
        imol_protein = None
        for imol in coot_utils_XChem.molecule_number_list():
Severity: Major
Found in xce/lib/XChemCootBuster.py and 2 other locations - About 4 days to fix
xce/lib/XChemCootNew.py on lines 1557..1627
xce/lib/XChemCootTwin.py on lines 1388..1458

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 489.

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

    def show_potential_link(self, *clicks):
        # first find imol of protein molecule
        # it's a prerequisite that the ligand is merged into the protein
        imol_protein = None
        for imol in coot_utils_XChem.molecule_number_list():
Severity: Major
Found in xce/lib/XChemCootNew.py and 2 other locations - About 4 days to fix
xce/lib/XChemCootBuster.py on lines 1399..1469
xce/lib/XChemCootTwin.py on lines 1388..1458

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 489.

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 2 locations. Consider refactoring.
Open

        for line in open(
            os.path.join(inital_model_directory, xtal, "validation_summary.txt")
        ):
            if "molprobity score" in line.lower():
                if len(line.split()) >= 4:
Severity: Major
Found in xce/helpers/update_data_source_after_refinement.py and 1 other location - About 4 days to fix
xce/lib/XChemUtils.py on lines 1160..1189

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 481.

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 2 locations. Consider refactoring.
Open

            for line in open(validation_summary):
                if "molprobity score" in line.lower():
                    if len(line.split()) >= 4:
                        db_dict["RefinementMolProbityScore"] = line.split()[3]
                        if float(line.split()[3]) < 2:
Severity: Major
Found in xce/lib/XChemUtils.py and 1 other location - About 4 days to fix
xce/helpers/update_data_source_after_refinement.py on lines 104..136

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 481.

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

    def GetRefinementHistory(self):
        RefinementCycle = []
        RcrystList = []
        RfreeList = []
Severity: Major
Found in xce/lib/XChemRefine.py and 2 other locations - About 4 days to fix
xce/lib/XChemRefine.py on lines 1398..1452
xce/lib/XChemRefine.py on lines 2336..2390

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 429.

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

    def GetRefinementHistory(self):
        RefinementCycle = []
        RcrystList = []
        RfreeList = []
Severity: Major
Found in xce/lib/XChemRefine.py and 2 other locations - About 4 days to fix
xce/lib/XChemRefine.py on lines 286..340
xce/lib/XChemRefine.py on lines 1398..1452

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 429.

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

    def GetRefinementHistory(self):
        RefinementCycle = []
        RcrystList = []
        RfreeList = []
Severity: Major
Found in xce/lib/XChemRefine.py and 2 other locations - About 4 days to fix
xce/lib/XChemRefine.py on lines 286..340
xce/lib/XChemRefine.py on lines 2336..2390

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 429.

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

Severity
Category
Status
Source
Language