set the maximum rmsd cutoff to be applied during alignment optimization . default : 99 = unlimited concode_field_sep double rmsdThrJoin concode_elem_sep int maxGapSize concode_elem_sep double DEFAULT_GAP_OPEN concode_elem_sep double DISTANCE_INCREMENT concode_elem_sep int SIDE_CHAIN_ANGLE_SCORING concode_elem_sep double distanceIncrement concode_elem_sep int sideChainScoringType concode_elem_sep double oRmsdThr concode_elem_sep int maxNrIterationsForOptimization concode_elem_sep int CA_AND_SIDE_CHAIN_ANGLE_SCORING concode_elem_sep double DEFAULT_GAP_EXTENSION concode_elem_sep int scoringStrategy concode_elem_sep double maxOptRMSD concode_elem_sep String SCORING_STRATEGY concode_elem_sep SubstitutionMatrix<AminoAcidCompound> substitutionMatrix concode_elem_sep int DEFAULT_SCORING_STRATEGY concode_elem_sep boolean showAFPRanges concode_elem_sep double DEFAULT_oRmsdThr concode_elem_sep double gapOpen concode_elem_sep double gapExtension concode_elem_sep int SIDE_CHAIN_SCORING concode_elem_sep int winSize concode_elem_sep double rmsdThr concode_elem_sep double seqWeight concode_field_sep int getMaxNrIterationsForOptimization concode_elem_sep Double getMaxOptRMSD concode_elem_sep void setShowAFPRanges concode_elem_sep void setGapOpen concode_elem_sep Double getRmsdThr concode_elem_sep Double getGapOpen concode_elem_sep void setORmsdThr concode_elem_sep void setSubstitutionMatrix concode_elem_sep void setRmsdThr concode_elem_sep List<String> getUserConfigParameterNames concode_elem_sep double getSeqWeight concode_elem_sep void setSeqWeight concode_elem_sep Integer getMaxGapSize concode_elem_sep Double getGapExtension concode_elem_sep void setWinSize concode_elem_sep Integer getScoringStrategy concode_elem_sep List<String> getUserConfigHelp concode_elem_sep SubstitutionMatrix<AminoAcidCompound> getSubstitutionMatrix concode_elem_sep void setMaxGapSize concode_elem_sep List<Class> getUserConfigTypes concode_elem_sep void setRmsdThrJoin concode_elem_sep void setGapExtension concode_elem_sep Double getORmsdThr concode_elem_sep void setScoringStrategy concode_elem_sep boolean isShowAFPRanges concode_elem_sep Integer getWinSize concode_elem_sep void setMaxNrIterationsForOptimization concode_elem_sep Double getRmsdThrJoin concode_elem_sep Double getDistanceIncrement concode_elem_sep List<String> getUserConfigParameters concode_elem_sep void reset concode_elem_sep String toString concode_elem_sep void setDistanceIncrement
void function ( Double arg0 ) { if ( arg0 == null ) arg0 = 99d ; maxOptRMSD = arg0 ; }