| Files | Total | Priority 1 | Priority 2 | Priority 3 | Priority 4 | Priority 5 |
|---|---|---|---|---|---|---|
| 5 | 123 | 6 |
0 |
116 |
1 |
0 |
| Prio | File | Line | Description |
|---|---|---|---|
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 49-584 | The class 'AtomPlacer3D' has a Cyclomatic Complexity of 5 (Highest = 11). |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 84 | Avoid variables with short names like hc |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 104 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 117-184 | The method 'placeAliphaticHeavyChain' has a Cyclomatic Complexity of 11. |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 196-250 | The method 'zmatrixChainToCartesian' has a Cyclomatic Complexity of 11. |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 208 | Avoid variables with short names like cd |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 211 | Avoid variables with short names like bc |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 214 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 218 | Avoid variables with short names like n2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 226 | Avoid variables with short names like ba |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 264-266 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 292 | Avoid variables with short names like a |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 292 | Avoid variables with short names like b |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 292 | Avoid variables with short names like c |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 292 | Avoid variables with short names like d |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 296 | Avoid variables with short names like cb |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 297 | Avoid variables with short names like xT |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 314 | The String literal "bond" appears 4 times in this file; the first occurrence is on line 314 |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 335 | The String literal "angle" appears 12 times in this file; the first occurrence is on line 335 |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 366-368 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 371-373 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 392-394 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 397-399 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 418-420 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 423-425 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 438 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 443-446 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 545 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 576 | Avoid variables with short names like ac |
4 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 31 | Avoid unused imports such as 'java.io.IOException' |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 54-916 | The class 'AtomTetrahedralLigandPlacer3D' has a Cyclomatic Complexity of 4 (Highest = 13). |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 65 | Avoid variables with short names like XV |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 66 | Avoid variables with short names like YV |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 97-129 | The method 'add3DCoordinatesForSinglyBondedLigands' has a Cyclomatic Complexity of 10. |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 144 | Avoid variables with short names like d1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 145 | Avoid variables with short names like d2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 200-247 | The method 'get3DCoordinatesForLigands' has a Cyclomatic Complexity of 13. |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 214-216 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 251 | Avoid variables with short names like ca |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 370 | Avoid variables with short names like dx |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 406 | Avoid variables with short names like ba |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 415 | Avoid variables with short names like cb |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 431 | Avoid variables with short names like ax |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 438 | Avoid variables with short names like vx |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 440 | Avoid variables with short names like vy |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 442 | Avoid variables with short names like vz |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 477 | Avoid variables with short names like ba |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 479 | Avoid variables with short names like ca |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 484 | An empty statement (semicolon) not part of a loop |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 488 | Avoid variables with short names like ax |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 496 | Avoid variables with short names like ax |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 532 | Avoid variables with short names like bc |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 534 | Avoid variables with short names like dc |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 536 | Avoid variables with short names like ca |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 539 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 540 | Avoid variables with short names like n2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 546 | Avoid variables with short names like ax |
1 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 588-589 | Method names should not contain underscores |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 591 | Avoid variables with short names like ba |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 593 | Avoid variables with short names like ca |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 596 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 600 | Avoid variables with short names like n2 |
1 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 625 | Method names should not contain underscores |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 627 | Avoid variables with short names like ca |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 629 | Avoid variables with short names like ba |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 645 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 651 | Avoid variables with short names like n2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 670 | Avoid variables with short names like ab |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 671 | Avoid variables with short names like cr |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 709 | The String literal "bond" appears 4 times in this file; the first occurrence is on line 709 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 732 | The String literal "angle" appears 12 times in this file; the first occurrence is on line 732 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 769 | Avoid variables with short names like ax |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 771 | Avoid variables with short names like b |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 772 | Avoid variables with short names like c |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 773 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 774 | Avoid variables with short names like n2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 779-782 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 804 | Avoid variables with short names like a |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 804 | Avoid variables with short names like b |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 804 | Avoid variables with short names like c |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 818 | Avoid variables with short names like a |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 818 | Avoid variables with short names like b |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 818 | Avoid variables with short names like c |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 818 | Avoid variables with short names like d |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 819 | Avoid variables with short names like ab |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 820 | Avoid variables with short names like cb |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 821 | Avoid variables with short names like dc |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 822 | Avoid variables with short names like bc |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 823 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 824 | Avoid variables with short names like n2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 848 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 871 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 883 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 904 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 77-631 | The class 'ModelBuilder3D' has a Cyclomatic Complexity of 4 (Highest = 12). |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 156-246 | The method 'generate3DCoordinates' has a Cyclomatic Complexity of 12. |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 156-246 | The method generate3DCoordinates() has an NPath complexity of 960 |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 191 | The String literal "PlaceSubstitutensERROR: Cannot place substitutents due to:" appears 4 times in this file; the first occurrence is on line 191 |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 221 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 273 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 287-288 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 329 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 337 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 411-459 | The method 'setBranchAtom' has a Cyclomatic Complexity of 10. |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 450-452 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 508-511 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 524-528 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 549 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 567 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 569-570 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 570-571 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 584 | Avoid variables with short names like ac |
1 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 616 | Avoid throwing null pointer exceptions. |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 69-275 | The class 'TemplateHandler3D' has a Cyclomatic Complexity of 4 (Highest = 16). |
1 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 71 | Variables that are final and static should be in all caps. |
1 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 72-73 | Variables that are final and static should be in all caps. |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 132 | Avoid variables with short names like s |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 153 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 153 | Avoid variables with short names like st |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 198-254 | The method 'mapTemplates' has a Cyclomatic Complexity of 16. |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 198-254 | The method mapTemplates() has an NPath complexity of 404 |
1 |
org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor | 65 | Variables that are final and static should be in all caps. |
3 |
org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor | 129 | Avoid variables with short names like ac |
Generated by PMD 4.2.5 on 2009-11-18 - 21:34:20.