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There are four main poses (which are representations of the protein): absolutebest, creditbest, current, and recentbest. The current pose is what you are working with. You can save to the recentbest pose. The absolutebest, creditbest, and recentbest poses get updated automatically when the current pose beats their score. In the case of creditbest, this only happens when credit is received for the score.

print

Function
void print([arg1,...,argN])
Description
Print values to the output window and log file.
V1 Function Name
print
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absolutebest.AreConditionsMet

Function
boolean absolutebest.AreConditionsMet()
Description
Return whether the absolute best pose satisfies all conditions.
V1 Function Name
New to V2
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absolutebest.GetEnergyScore

Function
number absolutebest.GetEnergyScore()
Description
Get the score for the absolute best pose.
V1 Function Name
New to V2
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absolutebest.GetExplorationMultiplier

Function
number absolutebest.GetExplorationMultiplier()
Description
Get the Exploration multiplier. If the current puzzle is not an exploration puzzle, returns 0.
V1 Function Name
New to V2
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absolutebest.GetScore

Function
number absolutebest.GetScore()
Description
Get the score for the absolute best pose.
V1 Function Name
New to V2
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absolutebest.GetSegmentEnergyScore

Function
number absolutebest.GetSegmentEnergyScore(integer segmentIndex)
Description
Get the current score of the given segment.
V1 Function Name
New to V2
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absolutebest.GetSegmentEnergySubscore

Function
number absolutebest.GetSegmentEnergySubscore(integer segmentIndex, string scorePart)
Description
Get the current score part of the given segment.
V1 Function Name
New to V2
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absolutebest.Restore

Function
void absolutebest.Restore()
Description
Load the absolute best pose.
V1 Function Name
restore_abs_best
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band.AddBetweenSegments

Function
void band.AddBetweenSegments(integer segmentIndex1, integer segmentIndex2)
Description
Add a band between the two segments.
V1 Function Name
band_add_segment_segment
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band.Delete

Function
void band.Delete(integer bandIndex)
Description
Delete a band.
V1 Function Name
Similar to band_delete
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band.DeleteAll

Function
void band.DeleteAll()
Description
Delete all bands.
V1 Function Name
band_delete()
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band.Disable

Function
void band.Disable(integer bandIndex)
Description
Disable a band.
V1 Function Name
Similar to band_disable
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band.DisableAll

Function
void band.DisableAll()
Description
Disable all bands.
V1 Function Name
band_disable()
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band.Enable

Function
void band.Enable(integer bandIndex)
Description
Enable a band.
V1 Function Name
Similar to band_enable
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band.EnableAll

Function
void band.EnableAll()
Description
Enable all bands.
V1 Function Name
band_enable()
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band.GetCount

Function
number band.GetCount()
Description
Get the number of bands.
V1 Function Name
get_band_count
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band.GetGoalLength

Function
number band.GetGoalLength(integer bandIndex)
Description
Get the goal length of a band.
V1 Function Name
New to V2
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band.GetStrength

Function
number band.GetStrength(integer bandIndex)
Description
Get the strength of a band.
V1 Function Name
New to V2
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band.IsEnabled

Function
boolean band.IsEnabled(integer bandIndex)
Description
Return whether a band is enabled.
V1 Function Name
New to V2
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band.SetGoalLength

Function
void band.SetGoalLength(integer bandIndex, number length)
Description
Set the goal length of a band. (Range 0.0 to 10000.0)
V1 Function Name
band_set_length
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band.SetStrength

Function
void band.SetStrength(integer bandIndex, number strength)
Description
Set the strength of a band. (Range 0.0 to 10.0)
V1 Function Name
band_set_strength
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behavior.GetClashImportance

Function
void behavior.GetClashImportance()
Description
Get the clashing importance.
V1 Function Name
New to V2
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behavior.SetClashImportance

Function
void behavior.SetClashImportance(number importance)
Description
Set the clashing importance. (Range 0.0 to 1.0)
V1 Function Name
set_behavior_clash_importance
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creditbest.AreConditionsMet

Function
boolean creditbest.AreConditionsMet()
Description
Return whether the credit best pose satisfies all conditions.
V1 Function Name
New to V2
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creditbest.GetEnergyScore

Function
number creditbest.GetEnergyScore()
Description
Get the current energy score.
V1 Function Name
New to V2
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creditbest.GetExplorationMultiplier

Function
number creditbest.GetExplorationMultiplier()
Description
Get the Exploration multiplier. If the current puzzle is not an exploration puzzle, returns 0.
V1 Function Name
New to V2
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creditbest.GetScore

Function
number creditbest.GetScore()
Description
Get the score for the credit best pose.
V1 Function Name
New to V2
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creditbest.GetSegmentEnergyScore

Function
number creditbest.GetSegmentEnergyScore(integer segmentIndex)
Description
Get the current score of the given segment.
V1 Function Name
New to V2
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creditbest.GetSegmentEnergySubscore

Function
number creditbest.GetSegmentEnergySubscore(integer segmentIndex, string scorePart)
Description
Get the current score part of the given segment.
V1 Function Name
New to V2
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creditbest.Restore

Function
void creditbest.Restore()
Description
Load the credit best pose.
V1 Function Name
restore_credit_best
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current.AreConditionsMet

Function
boolean current.AreConditionsMet()
Description
Return whether the current pose satisfies all conditions.
V1 Function Name
are_conditions_met
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current.GetEnergyScore

Function
number current.GetEnergyScore()
Description
Get the current energy score.
V1 Function Name
get_score(true)
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current.GetExplorationMultiplier

Function
number current.GetExplorationMultiplier()
Description
Get the Exploration multiplier. If the current puzzle is not an exploration puzzle, returns 0.
V1 Function Name
get_exploration_score
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current.GetScore

Function
number current.GetScore()
Description
Get the current score.
V1 Function Name
get_ranked_score(true)
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current.GetSegmentEnergyScore

Function
number current.GetSegmentEnergyScore(integer segmentIndex)
Description
Get the current score of the given segment.
V1 Function Name
Similar to get_segment_score
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current.GetSegmentEnergySubscore

Function
number current.GetSegmentEnergySubscore(integer segmentIndex, string scorePart)
Description
Get the current score part of the given segment.
V1 Function Name
Similar to get_segment_score_part
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freeze.Freeze

Function
void freeze.Freeze(integer segmentIndex, boolean backbone, boolean sidechain)
Description
Freeze a segment's backbone and/or sidechain.
V1 Function Name
New to V2
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freeze.FreezeAll

Function
void freeze.FreezeAll()
Description
Freeze all segments. Freezes both the backbone and the sidechains.
V1 Function Name
New to V2
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freeze.FreezeSelected

Function
void freeze.FreezeSelected(boolean backbone, boolean sidechain)
Description
Freeze the selected segments. The backbone and sidechain arguments indicate which parts of the segment to freeze.
V1 Function Name
do_freeze
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freeze.GetCount

Function
integer,integer freeze.GetCount()
Description
Get the count of frozen segments. Returns backbone and sidechains counts.
V1 Function Name
New to V2
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freeze.IsFrozen

Function
boolean,boolean freeze.IsFrozen(integer segmentIndex)
Description
Returns whether the backbone and/or sidechain is frozen.
V1 Function Name
New to V2
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freeze.Unfreeze

Function
void freeze.Unfreeze(integer segmentIndex, boolean backbone, boolean sidechain)
Description
Unfreeze a segment's backbone and/or sidechain.
V1 Function Name
New to V2
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freeze.UnfreezeAll

Function
void freeze.UnfreezeAll()
Description
Unfreeze all segments.
V1 Function Name
do_unfreeze_all
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puzzle.GetDescription

Function
string puzzle.GetDescription()
Description
Get the description of the puzzle.
V1 Function Name
New to V2
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puzzle.GetExpirationTime

Function
integer puzzle.GetExpirationTime()
Description
Get the date and time that the puzzle expires.
V1 Function Name
New to V2
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puzzle.GetName

Function
string puzzle.GetName()
Description
Get the name of the puzzle.
V1 Function Name
New to V2
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puzzle.GetPuzzleID

Function
string puzzle.GetPuzzleID()
Description
Get the ID Number of the puzzle.
V1 Function Name
New to V2
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puzzle.StartOver

Function
void puzzle.StartOver()
Description
Reset puzzle to the starting pose.
V1 Function Name
reset_puzzle
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recentbest.AreConditionsMet

Function
boolean recentbest.AreConditionsMet()
Description
Return whether the recent best pose satisfies all conditions.
V1 Function Name
New to V2
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recentbest.GetEnergyScore

Function
number recentbest.GetEnergyScore()
Description
Get the current energy score.
V1 Function Name
New to V2
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recentbest.GetExplorationMultiplier

Function
number recentbest.GetExplorationMultiplier()
Description
Get the Exploration multiplier. If the current puzzle is not an exploration puzzle, returns 0.
V1 Function Name
New to V2
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recentbest.GetScore

Function
number recentbest.GetScore()
Description
Get the score for the recent best pose.
V1 Function Name
New to V2
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recentbest.GetSegmentEnergyScore

Function
number recentbest.GetSegmentEnergyScore(integer segmentIndex)
Description
Get the current score of the given segment.
V1 Function Name
New to V2
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recentbest.GetSegmentEnergySubscore

Function
number recentbest.GetSegmentEnergySubscore(integer segmentIndex, string scorePart)
Description
Get the current score part of the given segment.
V1 Function Name
New to V2
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recentbest.Restore

Function
void recentbest.Restore()
Description
Load the recent best pose.
V1 Function Name
restore_recent_best
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recentbest.Save

Function
void recentbest.Save()
Description
Save the current pose as the recent best pose.
V1 Function Name
reset_recent_best
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recipe.CompareNumbers

Function
boolean recipe.CompareNumbers(number num1, number num2)
Description
Returns true if the two real numbers are the same to the precision that Lua prints.
V1 Function Name
New to V2
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recipe.GetRandomSeed

Function
number recipe.GetRandomSeed()
Description
Returns a good seed for the math.randomseed() function.
V1 Function Name
New to V2
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recipe.ReportStatus

Function
number recipe.ReportStatus()
Description
Reports the current status to the recipe output window and log file. Returns the improvement to the score from the SectionStart call.
V1 Function Name
New to V2
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recipe.SectionEnd

Function
number recipe.SectionEnd()
Description
Ends a reporting section. Returns the improvement to the score from the SectionStart call.
V1 Function Name
New to V2
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recipe.SectionStart

Function
void recipe.SectionStart(string sectionName)
Description
Starts a reporting section.
V1 Function Name
New to V2
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rotamer.GetCount

Function
integer rotamer.GetCount(integer segmentIndex)
Description
Return the number of rotamers the sidechain at the given index can snap to. This number may change if the backbone moves.
V1 Function Name
get_sidechain_snap_count
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rotamer.SetRotamer

Function
void rotamer.SetRotamer(integer segmentIndex, integer position)
Description
Snap the sidechain at the given segment to a rotamer. (Range 1 to rotamer.GetCount()).
V1 Function Name
do_sidechain_snap
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save.LoadSecondaryStructure

Function
void save.LoadSecondaryStructure()
Description
Load previously saved structure assignment.
V1 Function Name
load_structure
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save.Quickload

Function
void save.Quickload(integer slot)
Description
Quickload from a slot.
V1 Function Name
quickload
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save.Quicksave

Function
void save.Quicksave(integer slot)
Description
Quicksave to a slot. (Range 1 to 100)
V1 Function Name
quicksave
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save.SaveSecondaryStructure

Function
void save.SaveSecondaryStructure()
Description
Save current structure assignment.
V1 Function Name
save_structure
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scoreboard.GetGroupRank

Function
integer scoreboard.GetGroupRank()
Description
Get the group rank.
V1 Function Name
New to V2
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scoreboard.GetGroupScore

Function
number scoreboard.GetGroupScore()
Description
Get the group score.
V1 Function Name
New to V2
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scoreboard.GetRank

Function
integer scoreboard.GetRank([scoretype])
Description
Get the rank.
V1 Function Name
New to V2
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scoreboard.GetScore

Function
number scoreboard.GetScore([scoretype])
Description
Get the score.
V1 Function Name
New to V2
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scoreboard.GetScoreType

Function
scoretype scoreboard.GetScoreType()
Description
Get the current type of score. Returns one of the scoretype enum values.
V1 Function Name
New to V2
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selection.Deselect

Function
void selection.Deselect(integer segmentIndex)
Description
Deselect the segment at the given index
V1 Function Name
Similar to deselect_index
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selection.DeselectAll

Function
void selection.DeselectAll()
Description
Deselect all segments.
V1 Function Name
deselect_all
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selection.GetCount

Function
integer selection.GetCount()
Description
Get the number of selected segments.
V1 Function Name
New to V2
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selection.IsSelected

Function
boolean selection.IsSelected(integer segmentIndex)
Description
Returns whether a segment is selected.
V1 Function Name
New to V2
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selection.Select

Function
void selection.Select(integer segmentIndex)
Description
Select segment at the given index.
V1 Function Name
Similar to select_index
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selection.SelectAll

Function
void selection.SelectAll()
Description
Select all segments.
V1 Function Name
select_all
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selection.SelectRange

Function
void selection.SelectRange(integer segmentIndex1, integer segmentIndex2)
Description
Select segments from segmentIndex1 to segmentIndex2.
V1 Function Name
select_index_range
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structure.GetAminoAcid

Function
string structure.GetAminoAcid(integer segmentIndex)
Description
Get amino acid type.
V1 Function Name
Similar to get_aa
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structure.GetCount

Function
integer structure.GetCount()
Description
Return the number of segments.
V1 Function Name
get_segment_count
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structure.GetDistance

Function
number structure.GetDistance(integer segmentIndex1, integer segmentIndex2)
Description
Return distance between two segments.
V1 Function Name
get_segment_distance
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structure.GetNote

Function
string structure.GetNote(integer segmentIndex)
Description
Gets the note assigned to a segment.
V1 Function Name
New to V2
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structure.GetSecondaryStructure

Function
string structure.GetSecondaryStructure(integer segmentIndex)
Description
Get segment secondary structure type.
V1 Function Name
Similar to get_ss
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structure.IsHydrophobic

Function
boolean structure.IsHydrophobic(integer segmentIndex)
Description
Returns segment hydrophobicity.
V1 Function Name
Similar to is_hydrophobic
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structure.IsMutable

Function
boolean structure.IsMutable(integer segmentIndex)
Description
Returns whether a segment is mutable.
V1 Function Name
New to V2
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structure.LocalWiggleAll

Function
void structure.LocalWiggleAll(integer iterations[, backbone, sidechains])
Description
Local wiggle all segments.
V1 Function Name
New to V2
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structure.LocalWiggleSelected

Function
void structure.LocalWiggleSelected(integer iterations[, backbone, sidechains])
Description
Local wiggle selected segments.
V1 Function Name
Similar to do_global_wiggle_all
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structure.MutateSidechainsAll

Function
void structure.MutateSidechainsAll(integer iterations)
Description
Mutate all sidechains.
V1 Function Name
New to V2
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structure.MutateSidechainsSelected

Function
void structure.MutateSidechainsSelected(integer iterations)
Description
Mutate selected sidechains.
V1 Function Name
Similar to do_mutate
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structure.RebuildSelected

Function
void structure.RebuildSelected(integer iterations)
Description
Run rebuild on selection.
V1 Function Name
do_local_rebuild
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structure.SetAminoAcid

Function
void structure.SetAminoAcid(integer segmentIndex, string aminoAcid)
Description
Replace amino acid.
V1 Function Name
New to V2
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structure.SetAminoAcidSelected

Function
void structure.SetAminoAcidSelected(string aminoAcid)
Description
Changed the selected segments to the specified amino acid.
V1 Function Name
replace_aa
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structure.SetNote

Function
void structure.SetNote(integer segmentIndex, string note)
Description
Sets the not assigned to a segment.
V1 Function Name
New to V2
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structure.SetSecondaryStructure

Function
void structure.SetSecondaryStructure(integer segmentIndex, string secondaryStructure)
Description
Set segments secondary structure. Valid values are e=sheet, h=helix, l=loop, m=molecule.
V1 Function Name
New to V2
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structure.SetSecondaryStructureSelected

Function
void structure.SetSecondaryStructureSelected(string secondaryStructure)
Description
Set the selected segments secondary structure. Valid values are e=sheet, h=helix, l=loop, m=molecule.
V1 Function Name
replace_ss
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structure.ShakeSidechainsAll

Function
void structure.ShakeSidechainsAll(integer iterations)
Description
Shake all sidechains.
V1 Function Name
New to V2
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structure.ShakeSidechainsSelected

Function
void structure.ShakeSidechainsSelected(integer iterations)
Description
Shake selected sidechains.
V1 Function Name
Similar to do_shake
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structure.WiggleAll

Function
void structure.WiggleAll(integer iterations[, boolean backbone, boolean sidechains])
Description
Global wiggle all segments.
V1 Function Name
New to V2
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structure.WiggleSelected

Function
void structure.WiggleSelected(integer iterations[, boolean backbone, boolean sidechains])
Description
Global wiggle selected segments.
V1 Function Name
Similar to do_global_wiggle_all
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ui.AlignGuide

Function
void ui.AlignGuide([integer segmentIndex])
Description
Aligns the guide. Aligns to a given segmentIndex if passed in.
V1 Function Name
New to V2
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ui.CenterViewport

Function
void ui.CenterViewport()
Description
Centers the viewport.
V1 Function Name
New to V2
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ui.GetTrackName

Function
string ui.GetTrackName()
Description
Gets the track name.
V1 Function Name
New to V2
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user.GetGroupID

Function
integer user.GetGroupID()
Description
Gets the group name.
V1 Function Name
New to V2
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user.GetGroupName

Function
string user.GetGroupName()
Description
Gets the group name.
V1 Function Name
New to V2
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user.GetPlayerID

Function
integer user.GetPlayerID()
Description
Gets the user name.
V1 Function Name
New to V2
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user.GetPlayerName

Function
string user.GetPlayerName()
Description
Gets the user name.
V1 Function Name
New to V2
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