| Files | Total | Priority 1 | Priority 2 | Priority 3 | Priority 4 | Priority 5 |
|---|---|---|---|---|---|---|
| 5 | 135 | 3 |
0 |
131 |
1 |
0 |
| Prio | File | Line | Description |
|---|---|---|---|
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 46-648 | The class 'AtomPlacer3D' has a Cyclomatic Complexity of 4 (Highest = 11). |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 81 | Avoid variables with short names like hc |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 101 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 115 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 115-182 | The method 'placeAliphaticHeavyChain' has a Cyclomatic Complexity of 11. |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 194-248 | The method 'zmatrixChainToCartesian' has a Cyclomatic Complexity of 11. |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 206 | Avoid variables with short names like cd |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 209 | Avoid variables with short names like bc |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 212 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 216 | Avoid variables with short names like n2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 224 | Avoid variables with short names like ba |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 262-264 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 291 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 291 | Avoid variables with short names like a |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 291 | Avoid variables with short names like b |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 291 | Avoid variables with short names like c |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 291 | Avoid variables with short names like d |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 295 | Avoid variables with short names like cb |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 296 | Avoid variables with short names like xT |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 312 | A method/constructor shouldn't explicitly throw java.lang.Exception |
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 | 334 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 336 | The String literal "angle" appears 12 times in this file; the first occurrence is on line 336 |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 367-369 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 372-374 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 393-395 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 398-400 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 419-421 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 424-426 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 439 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 444-447 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 609 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomPlacer3D | 640 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 53-915 | 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 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 97-131 | The method 'add3DCoordinatesForSinglyBondedLigands' has a Cyclomatic Complexity of 10. |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 144 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 146 | Avoid variables with short names like d1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 147 | Avoid variables with short names like d2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 202-249 | The method 'get3DCoordinatesForLigands' has a Cyclomatic Complexity of 13. |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 203 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 216-218 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 253 | Avoid variables with short names like ca |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 369 | Avoid variables with short names like dx |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 405 | Avoid variables with short names like ba |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 414 | Avoid variables with short names like cb |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 430 | Avoid variables with short names like ax |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 437 | Avoid variables with short names like vx |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 439 | Avoid variables with short names like vy |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 441 | Avoid variables with short names like vz |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 476 | Avoid variables with short names like ba |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 478 | Avoid variables with short names like ca |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 483 | An empty statement (semicolon) not part of a loop |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 487 | Avoid variables with short names like ax |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 495 | Avoid variables with short names like ax |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 531 | Avoid variables with short names like bc |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 533 | Avoid variables with short names like dc |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 535 | Avoid variables with short names like ca |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 538 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 539 | Avoid variables with short names like n2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 545 | Avoid variables with short names like ax |
1 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 587-588 | Method names should not contain underscores |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 590 | Avoid variables with short names like ba |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 592 | Avoid variables with short names like ca |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 595 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 599 | Avoid variables with short names like n2 |
1 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 624 | Method names should not contain underscores |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 626 | Avoid variables with short names like ca |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 628 | Avoid variables with short names like ba |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 644 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 650 | Avoid variables with short names like n2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 669 | Avoid variables with short names like ab |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 670 | Avoid variables with short names like cr |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 706 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 708 | The String literal "bond" appears 4 times in this file; the first occurrence is on line 708 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 729 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 731 | The String literal "angle" appears 12 times in this file; the first occurrence is on line 731 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 768 | Avoid variables with short names like ax |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 770 | Avoid variables with short names like b |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 771 | Avoid variables with short names like c |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 772 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 773 | Avoid variables with short names like n2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 778-781 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 803 | Avoid variables with short names like a |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 803 | Avoid variables with short names like b |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 803 | Avoid variables with short names like c |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 817 | Avoid variables with short names like a |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 817 | Avoid variables with short names like b |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 817 | Avoid variables with short names like c |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 817 | Avoid variables with short names like d |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 818 | Avoid variables with short names like ab |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 819 | Avoid variables with short names like cb |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 820 | Avoid variables with short names like dc |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 821 | Avoid variables with short names like bc |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 822 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 823 | Avoid variables with short names like n2 |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 847 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 870 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 882 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D | 903 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 83-691 | The class 'ModelBuilder3D' has a Cyclomatic Complexity of 4 (Highest = 12). |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 162 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 162-250 | The method 'generate3DCoordinates' has a Cyclomatic Complexity of 12. |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 162-250 | The method generate3DCoordinates() has an NPath complexity of 960 |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 195 | The String literal "PlaceSubstitutensERROR: Cannot place substitutents due to:" appears 4 times in this file; the first occurrence is on line 195 |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 225 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 280 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 282 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 296-297 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 339 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 347 | Avoid variables with short names like n1 |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 434 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 434-485 | The method 'setBranchAtom' has a Cyclomatic Complexity of 11. |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 476-478 | These nested if statements could be combined |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 497 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 542 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 547-550 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 563-567 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 588 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 627 | Avoid variables with short names like ac |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 629-630 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 630-631 | Avoid empty if statements |
3 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 644 | Avoid variables with short names like ac |
1 |
org.openscience.cdk.modeling.builder3d.ModelBuilder3D | 676 | Avoid throwing null pointer exceptions. |
4 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 45 | Avoid unused imports such as 'org.openscience.cdk.interfaces.IBond' |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 68-271 | The class 'TemplateHandler3D' has a Cyclomatic Complexity of 4 (Highest = 16). |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 129 | Avoid variables with short names like s |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 150 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 150 | Avoid variables with short names like st |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 194 | A method/constructor shouldn't explicitly throw java.lang.Exception |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 194-250 | The method 'mapTemplates' has a Cyclomatic Complexity of 16. |
3 |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D | 194-250 | The method mapTemplates() has an NPath complexity of 404 |
3 |
org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor | 129 | Avoid variables with short names like ac |
Generated by PMD 4.2.2 on 2008-11-20 - 12:29:05.