comparison spring_package/Modeller.py @ 41:f316caf098a6 draft default tip

"planemo upload commit 685e1236afde7cf6bb0c9236de06998d2c211dd3"

40:06337927c198

            raise Exception("TMalign::Failed to retrieve TMalign results.")
    templateResidues = sorted(bioMolecule.calpha[templateChain].values(), key=lambda item: item["residueNumber"])
    templateIndex = 0
    for i in range(len(alignment)):
        t = templateAlign[i]
        if alignment[i] == ":":
            templateResidue = templateResidues[templateIndex]
            templateResidue["alignedResidue"] = modelAlign[i]
            aligned.append(templateResidue)
        if t != "-":
            templateIndex = templateIndex + 1

    print("Found %d templates." % len(templateList))
    for templateHit in templateList:
        if templateHit["score"] < minScore or maxTries == 0:
            break
        maxTries = maxTries - 1
        yield templateHit["templatePair"]


def createModel(args):
    print("SPRING - Complex Model Creation")
    aName = basename(args.a_hhr)

        return False
    maxScore = -9999
    maxInfo = None
    minScore = float(args.minscore)
    maxTries = int(args.maxtries)
    for [aTemplate, bTemplate] in getFrameworks(aTemplates, bTemplates, crossReference, minScore=minScore, maxTries=maxTries):
        print("Evaluating Complex Template: %s." % aTemplate)
        templateFile = "temp/template.pdb"
        createPDB(aTemplate, pdbDatabase, templateFile)
        templateMolecule = Molecule(templateFile)
        aTemplateChain = getChain(aTemplate)

                except Exception as e:
                    print("Warning: Failed TMalign [%s]." % bTemplateChain)
                    print(str(e))
                    continue
                biomolFound = True
                tmscore = min(coreScore, partnerScore)
                print("  tmscore:\t%5.2f" % tmscore)
                energy = -interfaceEnergy.get(coreAligned, partnerAligned)
                print("  energy:\t%5.2f" % energy)
                clashes = interfaceEnergy.getClashes(coreMolecule, partnerMolecule)
                print("  clashes:\t%5.2f" % clashes)
                springscore = tmscore + energy * args.wenergy
                print("  springscore:\t%5.2f" % springscore)
                if springscore > maxScore and clashes < args.maxclashes:
                    maxScore = springscore
                    maxInfo = dict(springscore=springscore, tmscore=tmscore, energy=energy, clashes=clashes)
                    coreMolecule.save(outputName, chainName="0")
                    partnerMolecule.save(outputName, chainName="1", append=True)
                    if args.showtemplate == "true":
                        bioMolecule.save(outputName, append=True)
            if biomolFound:
                break
    if maxInfo is not None:
        print("Final Model:")
        for key in maxInfo:
            print("  %s:\t%5.2f" % (key, maxInfo[key]))
        print("Completed.")
    else:
        print("Warning: Failed to determine model.")
    return maxInfo

41:f316caf098a6

            raise Exception("TMalign::Failed to retrieve TMalign results.")
    templateResidues = sorted(bioMolecule.calpha[templateChain].values(), key=lambda item: item["residueNumber"])
    templateIndex = 0
    for i in range(len(alignment)):
        t = templateAlign[i]
        if alignment[i] in [":", "."]:
            templateResidue = templateResidues[templateIndex]
            templateResidue["alignedResidue"] = modelAlign[i]
            aligned.append(templateResidue)
        if t != "-":
            templateIndex = templateIndex + 1

    print("Found %d templates." % len(templateList))
    for templateHit in templateList:
        if templateHit["score"] < minScore or maxTries == 0:
            break
        maxTries = maxTries - 1
        yield templateHit["templatePair"], templateHit["score"]


def createModel(args):
    print("SPRING - Complex Model Creation")
    aName = basename(args.a_hhr)

        return False
    maxScore = -9999
    maxInfo = None
    minScore = float(args.minscore)
    maxTries = int(args.maxtries)
    for [aTemplate, bTemplate], zscore in getFrameworks(aTemplates, bTemplates, crossReference, minScore=minScore, maxTries=maxTries):
        print("Evaluating Complex Template: %s." % aTemplate)
        templateFile = "temp/template.pdb"
        createPDB(aTemplate, pdbDatabase, templateFile)
        templateMolecule = Molecule(templateFile)
        aTemplateChain = getChain(aTemplate)

                except Exception as e:
                    print("Warning: Failed TMalign [%s]." % bTemplateChain)
                    print(str(e))
                    continue
                biomolFound = True
                print("  zscore:\t%5.2f" % zscore)
                tmscore = min(coreScore, partnerScore)
                print("  tmscore:\t%5.2f" % tmscore)
                energy = -interfaceEnergy.get(coreAligned, partnerAligned)
                print("  energy:\t%5.2f" % energy)
                clashes = interfaceEnergy.getClashes(coreMolecule, partnerMolecule)
                print("  clashes:\t%5.2f" % clashes)
                springscore = tmscore + energy * args.wenergy
                print("  springscore:\t%5.2f" % springscore)
                if springscore > maxScore and clashes < args.maxclashes:
                    maxScore = springscore
                    maxInfo = dict(aTemplate=aTemplate, bTemplate=bTemplate, springscore=springscore, tmscore=tmscore, energy=energy, clashes=clashes, zscore=zscore)
                    coreMolecule.save(outputName, chainName="0")
                    partnerMolecule.save(outputName, chainName="1", append=True)
                    if args.showtemplate == "true":
                        bioMolecule.save(outputName, append=True)
            if biomolFound:
                break
    if maxInfo is not None:
        print("Final Model:")
        for key in maxInfo:
            print("  %s:\t%s" % (key, maxInfo[key]))
        print("Completed.")
    else:
        print("Warning: Failed to determine model.")
    return maxInfo