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Fix align (#51)
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* Fix #48

* Fix #49
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@jmiller656
jmiller656 authored Dec 12, 2018
1 parent fefbf11 commit 363479b
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Showing 2 changed files with 3 additions and 765 deletions.
374 changes: 1 addition & 373 deletions src/main/java/org/moltimate/moltimatebackend/controller/MotifController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,6 @@ public ResponseEntity<Motif> findMotifByPdbId(@PathVariable String pdbId) {
@RequestMapping(value = "/debug", method = RequestMethod.GET)
public void createMotifs() {
motifService.saveMotif(make1a0j());
motifService.saveMotif(make1o2u());
motifService.saveMotif(make1rtf());
motifService.saveMotif(make2apr());
}
Expand All @@ -73,7 +72,7 @@ private Motif make1a0j() {
.chainName("A")
.build(),
Residue.builder()
.residueId("95")
.residueId("195")
.residueName("SER")
.chainName("A")
.build()
Expand Down Expand Up @@ -9292,375 +9291,4 @@ private Motif make2apr() {
.selectionQueries(selections)
.build();
}

private Motif make1o2u() {
String ecNumber = "3.4.21.4";

List<Residue> activeSite = Arrays.asList(
Residue.builder()
.residueId("57")
.residueName("HIS")
.chainName("A")
.build(),
Residue.builder()
.residueId("102")
.residueName("ASP")
.chainName("A")
.build()

);

HashMap<String, ResidueQuerySet> selections = new HashMap<>();

ArrayList<MotifSelection> asp = new ArrayList<MotifSelection>() {{
add(MotifSelection.builder()
.atom1Name("CB")
.residue1Name("ASP")
.atom2Name("CB")
.residue2Name("HIS")
.distance(7.92)
.build());
add(MotifSelection.builder()
.atom1Name("CB")
.residue1Name("ASP")
.atom2Name("CG")
.residue2Name("HIS")
.distance(7.90)
.build());
add(MotifSelection.builder()
.atom1Name("CB")
.residue1Name("ASP")
.atom2Name("ND1")
.residue2Name("HIS")
.distance(7.01)
.build());
add(MotifSelection.builder()
.atom1Name("CB")
.residue1Name("ASP")
.atom2Name("CD2")
.residue2Name("HIS")
.distance(9.14)
.build());
add(MotifSelection.builder()
.atom1Name("CB")
.residue1Name("ASP")
.atom2Name("CE1")
.residue2Name("HIS")
.distance(7.84)
.build());
add(MotifSelection.builder()
.atom1Name("CB")
.residue1Name("ASP")
.atom2Name("NE2")
.residue2Name("HIS")
.distance(9.05)
.build());
add(MotifSelection.builder()
.atom1Name("CG")
.residue1Name("ASP")
.atom2Name("CB")
.residue2Name("HIS")
.distance(6.54)
.build());
add(MotifSelection.builder()
.atom1Name("CG")
.residue1Name("ASP")
.atom2Name("CG")
.residue2Name("HIS")
.distance(6.40)
.build());
add(MotifSelection.builder()
.atom1Name("CG")
.residue1Name("ASP")
.atom2Name("ND1")
.residue2Name("HIS")
.distance(5.52)
.build());
add(MotifSelection.builder()
.atom1Name("CG")
.residue1Name("ASP")
.atom2Name("CD2")
.residue2Name("HIS")
.distance(7.62)
.build());
add(MotifSelection.builder()
.atom1Name("CG")
.residue1Name("ASP")
.atom2Name("CE1")
.residue2Name("HIS")
.distance(6.40)
.build());
add(MotifSelection.builder()
.atom1Name("CG")
.residue1Name("ASP")
.atom2Name("NE2")
.residue2Name("HIS")
.distance(7.57)
.build());
add(MotifSelection.builder()
.atom1Name("OD1")
.residue1Name("ASP")
.atom2Name("CB")
.residue2Name("HIS")
.distance(6.00)
.build());
add(MotifSelection.builder()
.atom1Name("OD1")
.residue1Name("ASP")
.atom2Name("CG")
.residue2Name("HIS")
.distance(6.11)
.build());
add(MotifSelection.builder()
.atom1Name("OD1")
.residue1Name("ASP")
.atom2Name("ND1")
.residue2Name("HIS")
.distance(5.51)
.build());
add(MotifSelection.builder()
.atom1Name("OD1")
.residue1Name("ASP")
.atom2Name("CD2")
.residue2Name("HIS")
.distance(7.39)
.build());
add(MotifSelection.builder()
.atom1Name("OD1")
.residue1Name("ASP")
.atom2Name("CE1")
.residue2Name("HIS")
.distance(6.55)
.build());
add(MotifSelection.builder()
.atom1Name("OD1")
.residue1Name("ASP")
.atom2Name("NE2")
.residue2Name("HIS")
.distance(7.55)
.build());
add(MotifSelection.builder()
.atom1Name("OD2")
.residue1Name("ASP")
.atom2Name("CB")
.residue2Name("HIS")
.distance(6.45)
.build());
add(MotifSelection.builder()
.atom1Name("OD2")
.residue1Name("ASP")
.atom2Name("CG")
.residue2Name("HIS")
.distance(5.96)
.build());
add(MotifSelection.builder()
.atom1Name("OD2")
.residue1Name("ASP")
.atom2Name("ND1")
.residue2Name("HIS")
.distance(4.85)
.build());
add(MotifSelection.builder()
.atom1Name("OD2")
.residue1Name("ASP")
.atom2Name("CD2")
.residue2Name("HIS")
.distance(7.03)
.build());
add(MotifSelection.builder()
.atom1Name("OD2")
.residue1Name("ASP")
.atom2Name("CE1")
.residue2Name("HIS")
.distance(5.53)
.build());
add(MotifSelection.builder()
.atom1Name("OD2")
.residue1Name("ASP")
.atom2Name("NE2")
.residue2Name("HIS")
.distance(6.77)
.build());
}};
ArrayList<MotifSelection> his = new ArrayList<MotifSelection>() {{
add(MotifSelection.builder()
.atom1Name("CB")
.residue1Name("HIS")
.atom2Name("CB")
.residue2Name("ASP")
.distance(7.92)
.build());
add(MotifSelection.builder()
.atom1Name("CB")
.residue1Name("HIS")
.atom2Name("CG")
.residue2Name("ASP")
.distance(6.54)
.build());
add(MotifSelection.builder()
.atom1Name("CB")
.residue1Name("HIS")
.atom2Name("OD1")
.residue2Name("ASP")
.distance(6.00)
.build());
add(MotifSelection.builder()
.atom1Name("CB")
.residue1Name("HIS")
.atom2Name("OD2")
.residue2Name("ASP")
.distance(6.45)
.build());
add(MotifSelection.builder()
.atom1Name("CG")
.residue1Name("HIS")
.atom2Name("CB")
.residue2Name("ASP")
.distance(7.90)
.build());
add(MotifSelection.builder()
.atom1Name("CG")
.residue1Name("HIS")
.atom2Name("CG")
.residue2Name("ASP")
.distance(6.40)
.build());
add(MotifSelection.builder()
.atom1Name("CG")
.residue1Name("HIS")
.atom2Name("OD1")
.residue2Name("ASP")
.distance(6.11)
.build());
add(MotifSelection.builder()
.atom1Name("CG")
.residue1Name("HIS")
.atom2Name("OD2")
.residue2Name("ASP")
.distance(5.96)
.build());
add(MotifSelection.builder()
.atom1Name("ND1")
.residue1Name("HIS")
.atom2Name("CB")
.residue2Name("ASP")
.distance(7.01)
.build());
add(MotifSelection.builder()
.atom1Name("ND1")
.residue1Name("HIS")
.atom2Name("CG")
.residue2Name("ASP")
.distance(5.52)
.build());
add(MotifSelection.builder()
.atom1Name("ND1")
.residue1Name("HIS")
.atom2Name("OD1")
.residue2Name("ASP")
.distance(5.51)
.build());
add(MotifSelection.builder()
.atom1Name("ND1")
.residue1Name("HIS")
.atom2Name("OD2")
.residue2Name("ASP")
.distance(4.85)
.build());
add(MotifSelection.builder()
.atom1Name("CD2")
.residue1Name("HIS")
.atom2Name("CB")
.residue2Name("ASP")
.distance(9.14)
.build());
add(MotifSelection.builder()
.atom1Name("CD2")
.residue1Name("HIS")
.atom2Name("CG")
.residue2Name("ASP")
.distance(7.62)
.build());
add(MotifSelection.builder()
.atom1Name("CD2")
.residue1Name("HIS")
.atom2Name("OD1")
.residue2Name("ASP")
.distance(7.39)
.build());
add(MotifSelection.builder()
.atom1Name("CD2")
.residue1Name("HIS")
.atom2Name("OD2")
.residue2Name("ASP")
.distance(7.03)
.build());
add(MotifSelection.builder()
.atom1Name("CE1")
.residue1Name("HIS")
.atom2Name("CB")
.residue2Name("ASP")
.distance(7.84)
.build());
add(MotifSelection.builder()
.atom1Name("CE1")
.residue1Name("HIS")
.atom2Name("CG")
.residue2Name("ASP")
.distance(6.40)
.build());
add(MotifSelection.builder()
.atom1Name("CE1")
.residue1Name("HIS")
.atom2Name("OD1")
.residue2Name("ASP")
.distance(6.55)
.build());
add(MotifSelection.builder()
.atom1Name("CE1")
.residue1Name("HIS")
.atom2Name("OD2")
.residue2Name("ASP")
.distance(5.53)
.build());
add(MotifSelection.builder()
.atom1Name("NE2")
.residue1Name("HIS")
.atom2Name("CB")
.residue2Name("ASP")
.distance(9.05)
.build());
add(MotifSelection.builder()
.atom1Name("NE2")
.residue1Name("HIS")
.atom2Name("CG")
.residue2Name("ASP")
.distance(7.57)
.build());
add(MotifSelection.builder()
.atom1Name("NE2")
.residue1Name("HIS")
.atom2Name("OD1")
.residue2Name("ASP")
.distance(7.55)
.build());
add(MotifSelection.builder()
.atom1Name("NE2")
.residue1Name("HIS")
.atom2Name("OD2")
.residue2Name("ASP")
.distance(6.77)
.build());
}};

selections.put("HIS 57", new ResidueQuerySet(his));
selections.put("ASP 102", new ResidueQuerySet(asp));

return Motif.builder()
.pdbId("1o2u")
.ecNumber(ecNumber)
.activeSiteResidues(activeSite)
.selectionQueries(selections)
.build();
}
}
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