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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.
- Function
- void print([arg1,...,argN])
- Description
- Print values to the output window and log file.
- V1 Function Name
- More Information
- Details
absolutebest.AreConditionsMet
- Function
- boolean absolutebest.AreConditionsMet()
- Description
- Return whether the absolute best pose satisfies all conditions.
- V1 Function Name
- New to V2
- More Information
- Details
absolutebest.GetEnergyScore
- Function
- number absolutebest.GetEnergyScore()
- Description
- Get the score for the absolute best pose.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
absolutebest.GetScore
- Function
- number absolutebest.GetScore()
- Description
- Get the score for the absolute best pose.
- V1 Function Name
- New to V2
- More Information
- Details
absolutebest.GetSegmentEnergyScore
- Function
- number absolutebest.GetSegmentEnergyScore(integer segmentIndex)
- Description
- Get the current score of the given segment.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
absolutebest.Restore
- Function
- void absolutebest.Restore()
- Description
- Load the absolute best pose.
- V1 Function Name
- restore_abs_best
- More Information
- Details
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
- More Information
- Details
band.Delete
- Function
- void band.Delete(integer bandIndex)
- Description
- Delete a band.
- V1 Function Name
- Similar to band_delete
- More Information
- Details
band.DeleteAll
- Function
- void band.DeleteAll()
- Description
- Delete all bands.
- V1 Function Name
- band_delete()
- More Information
- Details
band.Disable
- Function
- void band.Disable(integer bandIndex)
- Description
- Disable a band.
- V1 Function Name
- Similar to band_disable
- More Information
- Details
band.DisableAll
- Function
- void band.DisableAll()
- Description
- Disable all bands.
- V1 Function Name
- band_disable()
- More Information
- Details
band.Enable
- Function
- void band.Enable(integer bandIndex)
- Description
- Enable a band.
- V1 Function Name
- Similar to band_enable
- More Information
- Details
band.EnableAll
- Function
- void band.EnableAll()
- Description
- Enable all bands.
- V1 Function Name
- band_enable()
- More Information
- Details
band.GetCount
- Function
- number band.GetCount()
- Description
- Get the number of bands.
- V1 Function Name
- get_band_count
- More Information
- Details
band.GetGoalLength
- Function
- number band.GetGoalLength(integer bandIndex)
- Description
- Get the goal length of a band.
- V1 Function Name
- New to V2
- More Information
- Details
band.GetStrength
- Function
- number band.GetStrength(integer bandIndex)
- Description
- Get the strength of a band.
- V1 Function Name
- New to V2
- More Information
- Details
band.IsEnabled
- Function
- boolean band.IsEnabled(integer bandIndex)
- Description
- Return whether a band is enabled.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
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
- More Information
- Details
behavior.GetClashImportance
- Function
- void behavior.GetClashImportance()
- Description
- Get the clashing importance.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
creditbest.AreConditionsMet
- Function
- boolean creditbest.AreConditionsMet()
- Description
- Return whether the credit best pose satisfies all conditions.
- V1 Function Name
- New to V2
- More Information
- Details
creditbest.GetEnergyScore
- Function
- number creditbest.GetEnergyScore()
- Description
- Get the current energy score.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
creditbest.GetScore
- Function
- number creditbest.GetScore()
- Description
- Get the score for the credit best pose.
- V1 Function Name
- New to V2
- More Information
- Details
creditbest.GetSegmentEnergyScore
- Function
- number creditbest.GetSegmentEnergyScore(integer segmentIndex)
- Description
- Get the current score of the given segment.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
creditbest.Restore
- Function
- void creditbest.Restore()
- Description
- Load the credit best pose.
- V1 Function Name
- restore_credit_best
- More Information
- Details
current.AreConditionsMet
- Function
- boolean current.AreConditionsMet()
- Description
- Return whether the current pose satisfies all conditions.
- V1 Function Name
- are_conditions_met
- More Information
- Details
current.GetEnergyScore
- Function
- number current.GetEnergyScore()
- Description
- Get the current energy score.
- V1 Function Name
- get_score(true)
- More Information
- Details
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
- More Information
- Details
current.GetScore
- Function
- number current.GetScore()
- Description
- Get the current score.
- V1 Function Name
- get_ranked_score(true)
- More Information
- Details
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
- More Information
- Details
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
- More Information
- Details
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
- More Information
- Details
freeze.FreezeAll
- Function
- void freeze.FreezeAll()
- Description
- Freeze all segments. Freezes both the backbone and the sidechains.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
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
- More Information
- Details
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
- More Information
- Details
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
- More Information
- Details
freeze.UnfreezeAll
- Function
- void freeze.UnfreezeAll()
- Description
- Unfreeze all segments.
- V1 Function Name
- do_unfreeze_all
- More Information
- Details
puzzle.GetDescription
- Function
- string puzzle.GetDescription()
- Description
- Get the description of the puzzle.
- V1 Function Name
- New to V2
- More Information
- Details
puzzle.GetExpirationTime
- Function
- integer puzzle.GetExpirationTime()
- Description
- Get the date and time that the puzzle expires.
- V1 Function Name
- New to V2
- More Information
- Details
puzzle.GetName
- Function
- string puzzle.GetName()
- Description
- Get the name of the puzzle.
- V1 Function Name
- New to V2
- More Information
- Details
puzzle.GetPuzzleID
- Function
- string puzzle.GetPuzzleID()
- Description
- Get the ID Number of the puzzle.
- V1 Function Name
- New to V2
- More Information
- Details
puzzle.StartOver
- Function
- void puzzle.StartOver()
- Description
- Reset puzzle to the starting pose.
- V1 Function Name
- reset_puzzle
- More Information
- Details
recentbest.AreConditionsMet
- Function
- boolean recentbest.AreConditionsMet()
- Description
- Return whether the recent best pose satisfies all conditions.
- V1 Function Name
- New to V2
- More Information
- Details
recentbest.GetEnergyScore
- Function
- number recentbest.GetEnergyScore()
- Description
- Get the current energy score.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
recentbest.GetScore
- Function
- number recentbest.GetScore()
- Description
- Get the score for the recent best pose.
- V1 Function Name
- New to V2
- More Information
- Details
recentbest.GetSegmentEnergyScore
- Function
- number recentbest.GetSegmentEnergyScore(integer segmentIndex)
- Description
- Get the current score of the given segment.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
recentbest.Restore
- Function
- void recentbest.Restore()
- Description
- Load the recent best pose.
- V1 Function Name
- restore_recent_best
- More Information
- Details
recentbest.Save
- Function
- void recentbest.Save()
- Description
- Save the current pose as the recent best pose.
- V1 Function Name
- reset_recent_best
- More Information
- Details
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
- More Information
- Details
recipe.GetRandomSeed
- Function
- number recipe.GetRandomSeed()
- Description
- Returns a good seed for the math.randomseed() function.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
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
- More Information
- Details
recipe.SectionStart
- Function
- void recipe.SectionStart(string sectionName)
- Description
- Starts a reporting section.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
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
- More Information
- Details
save.LoadSecondaryStructure
- Function
- void save.LoadSecondaryStructure()
- Description
- Load previously saved structure assignment.
- V1 Function Name
- load_structure
- More Information
- Details
save.Quickload
- Function
- void save.Quickload(integer slot)
- Description
- Quickload from a slot.
- V1 Function Name
- quickload
- More Information
- Details
save.Quicksave
- Function
- void save.Quicksave(integer slot)
- Description
- Quicksave to a slot. (Range 1 to 100)
- V1 Function Name
- quicksave
- More Information
- Details
save.SaveSecondaryStructure
- Function
- void save.SaveSecondaryStructure()
- Description
- Save current structure assignment.
- V1 Function Name
- save_structure
- More Information
- Details
scoreboard.GetGroupRank
- Function
- integer scoreboard.GetGroupRank()
- Description
- Get the group rank.
- V1 Function Name
- New to V2
- More Information
- Details
scoreboard.GetGroupScore
- Function
- number scoreboard.GetGroupScore()
- Description
- Get the group score.
- V1 Function Name
- New to V2
- More Information
- Details
scoreboard.GetRank
- Function
- integer scoreboard.GetRank([scoretype])
- Description
- Get the rank.
- V1 Function Name
- New to V2
- More Information
- Details
scoreboard.GetScore
- Function
- number scoreboard.GetScore([scoretype])
- Description
- Get the score.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
selection.Deselect
- Function
- void selection.Deselect(integer segmentIndex)
- Description
- Deselect the segment at the given index
- V1 Function Name
- Similar to deselect_index
- More Information
- Details
selection.DeselectAll
- Function
- void selection.DeselectAll()
- Description
- Deselect all segments.
- V1 Function Name
- deselect_all
- More Information
- Details
selection.GetCount
- Function
- integer selection.GetCount()
- Description
- Get the number of selected segments.
- V1 Function Name
- New to V2
- More Information
- Details
selection.IsSelected
- Function
- boolean selection.IsSelected(integer segmentIndex)
- Description
- Returns whether a segment is selected.
- V1 Function Name
- New to V2
- More Information
- Details
selection.Select
- Function
- void selection.Select(integer segmentIndex)
- Description
- Select segment at the given index.
- V1 Function Name
- Similar to select_index
- More Information
- Details
selection.SelectAll
- Function
- void selection.SelectAll()
- Description
- Select all segments.
- V1 Function Name
- select_all
- More Information
- Details
selection.SelectRange
- Function
- void selection.SelectRange(integer segmentIndex1, integer segmentIndex2)
- Description
- Select segments from segmentIndex1 to segmentIndex2.
- V1 Function Name
- select_index_range
- More Information
- Details
structure.GetAminoAcid
- Function
- string structure.GetAminoAcid(integer segmentIndex)
- Description
- Get amino acid type.
- V1 Function Name
- Similar to get_aa
- More Information
- Details
structure.GetCount
- Function
- integer structure.GetCount()
- Description
- Return the number of segments.
- V1 Function Name
- get_segment_count
- More Information
- Details
structure.GetDistance
- Function
- number structure.GetDistance(integer segmentIndex1, integer segmentIndex2)
- Description
- Return distance between two segments.
- V1 Function Name
- get_segment_distance
- More Information
- Details
structure.GetNote
- Function
- string structure.GetNote(integer segmentIndex)
- Description
- Gets the note assigned to a segment.
- V1 Function Name
- New to V2
- More Information
- Details
structure.GetSecondaryStructure
- Function
- string structure.GetSecondaryStructure(integer segmentIndex)
- Description
- Get segment secondary structure type.
- V1 Function Name
- Similar to get_ss
- More Information
- Details
structure.IsHydrophobic
- Function
- boolean structure.IsHydrophobic(integer segmentIndex)
- Description
- Returns segment hydrophobicity.
- V1 Function Name
- Similar to is_hydrophobic
- More Information
- Details
structure.IsMutable
- Function
- boolean structure.IsMutable(integer segmentIndex)
- Description
- Returns whether a segment is mutable.
- V1 Function Name
- New to V2
- More Information
- Details
structure.LocalWiggleAll
- Function
- void structure.LocalWiggleAll(integer iterations[, backbone, sidechains])
- Description
- Local wiggle all segments.
- V1 Function Name
- New to V2
- More Information
- Details
structure.LocalWiggleSelected
- Function
- void structure.LocalWiggleSelected(integer iterations[, backbone, sidechains])
- Description
- Local wiggle selected segments.
- V1 Function Name
- Similar to do_global_wiggle_all
- More Information
- Details
structure.MutateSidechainsAll
- Function
- void structure.MutateSidechainsAll(integer iterations)
- Description
- Mutate all sidechains.
- V1 Function Name
- New to V2
- More Information
- Details
structure.MutateSidechainsSelected
- Function
- void structure.MutateSidechainsSelected(integer iterations)
- Description
- Mutate selected sidechains.
- V1 Function Name
- Similar to do_mutate
- More Information
- Details
structure.RebuildSelected
- Function
- void structure.RebuildSelected(integer iterations)
- Description
- Run rebuild on selection.
- V1 Function Name
- do_local_rebuild
- More Information
- Details
structure.SetAminoAcid
- Function
- void structure.SetAminoAcid(integer segmentIndex, string aminoAcid)
- Description
- Replace amino acid.
- V1 Function Name
- New to V2
- More Information
- Details
structure.SetAminoAcidSelected
- Function
- void structure.SetAminoAcidSelected(string aminoAcid)
- Description
- Changed the selected segments to the specified amino acid.
- V1 Function Name
- replace_aa
- More Information
- Details
structure.SetNote
- Function
- void structure.SetNote(integer segmentIndex, string note)
- Description
- Sets the not assigned to a segment.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
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
- More Information
- Details
structure.ShakeSidechainsAll
- Function
- void structure.ShakeSidechainsAll(integer iterations)
- Description
- Shake all sidechains.
- V1 Function Name
- New to V2
- More Information
- Details
structure.ShakeSidechainsSelected
- Function
- void structure.ShakeSidechainsSelected(integer iterations)
- Description
- Shake selected sidechains.
- V1 Function Name
- Similar to do_shake
- More Information
- Details
structure.WiggleAll
- Function
- void structure.WiggleAll(integer iterations[, boolean backbone, boolean sidechains])
- Description
- Global wiggle all segments.
- V1 Function Name
- New to V2
- More Information
- Details
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
- More Information
- Details
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
- More Information
- Details
ui.CenterViewport
- Function
- void ui.CenterViewport()
- Description
- Centers the viewport.
- V1 Function Name
- New to V2
- More Information
- Details
ui.GetTrackName
- Function
- string ui.GetTrackName()
- Description
- Gets the track name.
- V1 Function Name
- New to V2
- More Information
- Details
user.GetGroupID
- Function
- integer user.GetGroupID()
- Description
- Gets the group name.
- V1 Function Name
- New to V2
- More Information
- Details
user.GetGroupName
- Function
- string user.GetGroupName()
- Description
- Gets the group name.
- V1 Function Name
- New to V2
- More Information
- Details
user.GetPlayerID
- Function
- integer user.GetPlayerID()
- Description
- Gets the user name.
- V1 Function Name
- New to V2
- More Information
- Details
user.GetPlayerName
- Function
- string user.GetPlayerName()
- Description
- Gets the user name.
- V1 Function Name
- New to V2
- More Information
- Details