Code
--[[
Band All Contacts Adaptive
original recipe "Band All Contacts Adaptive Strength",
by Susume, 2014/07/28
Places a band wherever there is a green dot on the contact map.
Dialog allows you to set different length and strength for
unmade vs. made contacts.
Use length multiplier greater than 1.0 for "push" bands.
revision history
----------------
Band All Contacts v0.1 - 2014/06/13 - Susume
Band All Contacts v0.2 - 2014/06/13 - Susume
Band All Contacts 2 Strengths - 2014/07/18 - Susume
Band All Contacts Adaptive Strength - 2014/07/28 - Susume
Band All Contacts Adaptive v2.0 - 2014/08/24 - Susume
v2.1 - 2014/09/21 - Susume
+ Added option to band to beta carbons instead of the default central carbons
Beta carbons are the first joint in the sidechains and can help twist the
backbone where needed to make more contacts.
v2.2 - 2015/07/16 - Susume
+ Added sliders to choose minimum contact weights to be banded.
+ Default minimum weight of 0 means all predicted contacts will be banded.
v2.2m - 2015/08/07 - Madde
+ Added option to set band strengths according to contact weights
+ Added option to band hydrophobics only to beta carbons
v2.3 2016/05/17 - LociOiling
+ Merged v2.2m
+ Added prune options from Band Pruner v0.2 - 2015/7/19 - Susume
+ Aerated code, restructured a bit
+ Splice in some Contact Cement stuff (Loci, Bruno Kestemont)
+ Added structure and parallel band logic based on
Helix Rebuild and Local Quake by spvincent
+ Threw in the print to a textbox thing from Print Protein 2.0
]]--
Recipe = "Band All Contacts Adaptive"
Version = "2.3"
ReVersion = Recipe .. " " .. Version
--defaults for dialog box
MinWeight = 0
MaxWeight = 4
MadeWeight = 0
UnmadeWeight = 0
MadeMult = .9
UnmadeMult = .75
MinMult = .1
MaxMult = 3
MadeStrength = 0.5
UnmadeStrength = 1.5
MinStrength = .1
MaxStrength = 5
MadeBeta = false
UnmadeBeta = false
MadeWrength = false
UnmadeWrength = false
MadePhobicsBeta = false
UnmadePhobicsBeta = false
-- Band Pruner
LongerThan = true
ShorterThan = false
MaxLength = 0
MinLength = 0
--
-- exclusions
--
noBandSelf = false -- don't band a structure to itself
DISALLOW_LL = false -- disallow bands parallel to helix
MAXANGLE = 30 --maximum deviation from perpendicular
--
-- constants
--
BETA_CARBON = 5
TERMINAL_BETA = 6
CENTER_CARBON = 2 --this is the default atom for bands to attach to
GLYCINE = "g"
--
-- custom list of hydrophobics
--
phobes = {
a = { "alanine", },
c = { "cysteine", },
f = { "phenylalanine", },
i = { "isoleucine", },
l = { "leucine", },
m = { "methionine", },
p = { "proline", },
v = { "valine", },
w = { "tryptophan", },
y = { "tyrosine", },
}
--
-- miscellaneous loose screws
--
bweight = 0 -- number of contacts skipped due to weight cutoff
bshort = 0 -- number of short contacts skipped
blong = 0 -- number of long contacts skipped
bunk = 0 -- number of bands skipped due to failed band.AddBetweenSegments
bsame = 0 -- number of bands skipped due to "don't band structure to self"
bpara = 0 -- number of bands skipped due to "disallow parallel to structure"
bcount = 0 -- number of bands made
VERBOSE = false
REPORT = false
segStart = 1
segEnd = structure.GetCount()
--
-- globals from Contact Cement
--
tContacts = 0
tHeat = 0
minHeat = 0.5
maxHeat = 0.9
meanHeat = 0.7
mediHeat = 0.7
madeTotal = 0
madePct = 0
unmadeTotal = 0
unmadePct = 0
minMadeDist = 99999
maxMadeDist = 0
minUnmadeDist = 99999
maxUnmadeDist = 0
tMadeDist = 0
tUnmadeDist = 0
variableHeat = false
singleEnd = false
--
-- structure table indexes
--
STRUTYPE = 1 -- structList [ 1 ] = type
STRUSEG1 = 2 -- structList [ 2 ] = start segment
STRUSEG2 = 3 -- structList [ 3 ] = end segment
STRUSLCT = 4 -- structList [ 4 ] = structure selected
STRUCONT = 5 -- structList [ 5 ] = # of contacts
--
-- contact map table indexes
--
MAPSEG1 = 1 -- contact [ 1 ] = seg1
MAPSEG2 = 2 -- contact [ 2 ] = seg2
MAPHEAT = 3 -- contact [ 3 ] = heat
MAPSS1 = 4 -- contact [ 4 ] = ss seg1
MAPSS2 = 5 -- contact [ 5 ] = ss seg2
MAPDIST = 6 -- contact [ 6 ] = dist
MAPCONT = 7 -- contact [ 7 ] = in contact
MAPBAND = 8 -- contact [ 8 ] = contact banded
MAPBLEN = 9 -- contact [ 9 ] = band goal length
MAPBSTR = 10 -- contact [ 10 ] = band strength
MAPATM1 = 11 -- contact [ 11 ] = band atom segment 1
MAPATM2 = 12 -- contact [ 12 ] = band atom segment 2
--
-- report
--
delim = "\t" -- tab delimiter
--
-- begin functions lifted from Contact Cement
--
function r3 ( i )
return i - i % 0.001
end
function GetStructs ()
local within_struct = false
local structList = {}
local structStart = 0
local structLast = 0
local structType = "?" -- not a valid structure type
for ii = 1, segEnd do
local currType = structure.GetSecondaryStructure ( ii )
if ( currType ~= structType ) then
if ( within_struct == true ) then
-- end of a struct
within_struct = false
structList [ #structList + 1 ] = { structType, structStart, structLast, false, 0 }
end
end
if ( within_struct == false ) then
-- start of a new struct
within_struct = true
structStart = ii
structType = currType
end
structLast = ii
end
if ( within_struct == true ) then
structList [ #structList + 1 ] = { structType, structStart, structLast, false, 0 }
end
return structList
end
function findContactStruct ( structList, segment )
for ii = 1, #structList do
if segment >= structList [ ii ] [ STRUSEG1 ]
and segment <= structList [ ii ] [ STRUSEG2 ] then
return ii
end
end
return nil
end
function SortByIndex ( tab, indx )
local ii
local jj
for ii = 1, #tab - 1 do
for jj = ii + 1, #tab do
local h1 = tab [ ii ] [ indx ]
local h2 = tab [ jj ] [ indx ]
if h2 > h1 then
tab [ ii ], tab [ jj ] = tab [ jj ], tab [ ii ]
end
end
end
return tab
end
function GetOnlyContacts()
tHeat = 0
local contacts = {}
for ii = segStart, segEnd - 1 do
for jj = ii + 1, segEnd do
if ( ii ~= jj ) then
local heat = contactmap.GetHeat ( ii, jj )
if ( heat > 0 ) then
local con = contactmap.IsContact ( ii, jj )
if con then
madeTotal = madeTotal + 1
else
unmadeTotal = unmadeTotal + 1
end
local ss1 = structure.GetSecondaryStructure ( ii )
local ss2 = structure.GetSecondaryStructure ( jj )
local dist = structure.GetDistance ( ii, jj )
local contact = { ii, jj, heat, ss1, ss2, dist, con, false, 0, 0, }
contacts [ #contacts + 1 ] = contact
tHeat = tHeat + heat
end
end
end
end
return contacts
end
function GetContacts( )
local ii
local jj
local contacts = GetOnlyContacts()
if ( #contacts > 0 ) then
print ( #contacts .. " predicted contacts found" )
madePct = r3 ( ( madeTotal / #contacts ) * 100 )
print ( madeTotal .. " made contacts (" .. madePct .. "%)" )
SortByIndex ( contacts, MAPHEAT )
minHeat = 9999999
maxHeat = 0
for ii = 1, #contacts do
if contacts [ ii ] [ MAPHEAT ] > maxHeat then
maxHeat = contacts [ ii ] [ MAPHEAT ]
end
if contacts [ ii ] [ MAPHEAT ] < minHeat then
minHeat = contacts [ ii ] [ MAPHEAT ]
end
if contacts [ ii ] [ MAPCONT ] then
tMadeDist = tMadeDist + contacts [ ii ] [ MAPDIST ]
if contacts [ ii ] [ MAPDIST ] > maxMadeDist then
maxMadeDist = contacts [ ii ] [ MAPDIST ]
end
if contacts [ ii ] [ MAPDIST ] < minMadeDist then
minMadeDist = contacts [ ii ] [ MAPDIST ]
end
else
tUnmadeDist = tUnmadeDist + contacts [ ii ] [ MAPDIST ]
if contacts [ ii ] [ MAPDIST ] > maxUnmadeDist then
maxUnmadeDist = contacts [ ii ] [ MAPDIST ]
end
if contacts [ ii ] [ MAPDIST ] < minUnmadeDist then
minUnmadeDist = contacts [ ii ] [ MAPDIST ]
end
end
end
if madeTotal > 0 then
print ( "minimum made contact distance = " .. r3 ( minMadeDist ) )
print ( "maximum made contact distance = " .. r3 ( maxMadeDist ) )
print ( "mean made contact distance = " .. r3 ( tMadeDist / madeTotal ) )
end
if unmadeTotal > 0 then
print ( "minimum unmade contact distance = " .. r3 ( minUnmadeDist ) )
print ( "maximum unmade contact distance = " .. r3 ( maxUnmadeDist ) )
print ( "mean unmade contact distance = " .. r3 ( tUnmadeDist / ( unmadeTotal ) ) )
end
if minHeat == maxHeat then
print ( "all contacts have heat = " .. r3 ( minHeat ) )
else
print ( "minimum contact heat = " .. r3 ( minHeat ) )
print ( "maximum contact heat = " .. r3 ( maxHeat ) )
meanHeat = tHeat / #contacts
print ( "mean contact heat = " .. r3 ( meanHeat ) )
ii = math.floor ( #contacts / 2 )
mediHeat = contacts [ ii ] [ MAPHEAT ]
if #contacts % 2 == 0 then -- even number of entries
ii = ii + 1
mediHeat = ( mediHeat + contacts [ ii ] [ MAPHEAT ] ) / 2 -- corrected BK 04/06/2014
end
print ( "median contact heat = " .. r3 ( mediHeat ) )
end
else
print ( "no predicted contacts found" )
end
return contacts
end
--
-- end functions lifted from Contact Cement
--
--
-- begin functions lifted and adapted from Spvincent's Helix Rebuild and Local Quake
--
--
-- BandAngleCheck - checks whether band is perpendicular to structure
--
-- returns true is band is within +/- perpendicular to structure it's in
--
-- adapted from spvincent's Local Quake
--
function BandAngleCheck ( band_a , band_b, structList, maxangle )
-- Tests the putative band to see,
-- should band_a lie on one of the structure,
-- whether the band is reasonably perpendicular to the structure.
for ii = 1, #structList do
--
-- ignore loops, check for beginning and ending segment in helix or loop
--
if structList [ ii ] [ STRUTYPE ] ~= "L"
and ( ( band_a >= structList [ ii ] [ STRUSEG1 ] )
and ( band_a <= structList [ ii ] [ STRUSEG2 ] ) ) then
-- Compute an approximate angle with the helix based on the cosine rule
local kindx
local a, b, c
if ( ( band_a - structList [ ii ] [ STRUSEG1 ] ) > ( structList [ ii ] [ STRUSEG2 ] - band_a ) ) then
-- The point lies closest to the helix end.
-- Compare against the start of the helix.
kindx = STRUSEG1
else
-- The point lies closest to the helix start.
-- Compare against the end of the helix.
kindx = STRUSEG2
end
a = structure.GetDistance ( band_a , structList [ ii ] [ kindx ] )
b = structure.GetDistance ( band_a , band_b )
c = structure.GetDistance ( structList [ ii ] [ kindx ], band_b )
local cos_angle = ( a * a + b * b - c * c ) / ( 2 * a * b )
-- We're looking for an angle of about 90 degrees
-- give or take a few: other angles will be rejected
local angle = math.deg ( math.acos ( cos_angle ) )
if ( ( angle < 90 - maxangle )
or ( angle > 90 + maxangle ) ) then
if VERBOSE then
print ( "BandAngleCheck: FAILED band "
.. band_a ..
" to "
.. band_b ..
", angle = "
.. r3 ( angle ) )
end
return false
else
if VERBOSE then
print ( "BandAngleCheck: OK band "
.. band_a ..
" to "
.. band_b ..
", angle = "
.. r3 ( angle ) )
end
return true
end
end
end
return true
end
--
-- end functions lifted and adapted from Spvincent's Helix Rebuild and Local Quake
--
function GetParams()
dlg = dialog.CreateDialog ( ReVersion )
dlg.l1a = dialog.AddLabel ( "-------- Bands on Made Contacts --------" )
-- dlg.l1b = dialog.AddLabel ( "Band if contact weight greater than" )
dlg.MadeWeight = dialog.AddSlider ( "Min Weight:", MadeWeight, MinWeight, MaxWeight, 1 )
-- dlg.l1c = dialog.AddLabel ( "Multiply current distance by" )
dlg.MadeMult = dialog.AddSlider ( "Dist. Multiplier:", MadeMult, MinMult, MaxMult, 2 )
dlg.MadeStrength = dialog.AddSlider ( "Strength:", MadeStrength, MinStrength, MaxStrength, 1 )
dlg.MadeWrength = dialog.AddCheckbox ( "Set strengths according to weights", MadeWrength )
-- dlg.l1d = dialog.AddLabel ( " (if checked, Strength slider acts as multiplier)" )
dlg.MadeBeta = dialog.AddCheckbox ( "Band beta carbons", MadeBeta )
dlg.MadePhobicsBeta = dialog.AddCheckbox ( "Band beta carbons (phobics only)", MadePhobicsBeta )
dlg.l2a = dialog.AddLabel ( "-------- Bands on Unmade Contacts --------" )
-- dlg.l2b = dialog.AddLabel ( "Band if contact weight greater than" )
dlg.UnmadeWeight = dialog.AddSlider ( "Min Weight:", UnmadeWeight, MinWeight, MaxWeight, 1 )
-- dlg.l2c = dialog.AddLabel ( "Multiply current distance by" )
dlg.UnmadeMult = dialog.AddSlider ( "Dist. Multiplier:", UnmadeMult, MinMult, MaxMult, 2 )
dlg.UnmadeStrength = dialog.AddSlider ( "Strength:", UnmadeStrength, MinStrength, MaxStrength, 1 )
dlg.UnmadeWrength = dialog.AddCheckbox ( "Set strengths according to weights", UnmadeWrength )
-- dlg.l2d = dialog.AddLabel ( "(if checked, Strength slider acts as multiplier)" )
dlg.UnmadeBeta = dialog.AddCheckbox ( "Band beta carbons", UnmadeBeta )
dlg.UnmadePhobicsBeta = dialog.AddCheckbox ( "Band beta carbons (phobics only)", UnmadePhobicsBeta )
dlg.l3a = dialog.AddLabel ( "-------- Exclusions --------" )
dlg.LongerThan = dialog.AddCheckbox ( "Skip distances longer than", LongerThan )
dlg.MaxLength = dialog.AddSlider ( "Max Length:", MaxLength, MinLength, MaxLength, 2 )
dlg.ShorterThan = dialog.AddCheckbox ( "Skip distances shorter than", ShorterThan )
dlg.MinLength = dialog.AddSlider ( "Min Length:", MinLength, MinLength, MaxLength, 2 )
dlg.noBandSelf = dialog.AddCheckbox ( "Don\'t band structure to itself", noBandSelf )
dlg.DISALLOW_LL = dialog.AddCheckbox ( "Don\'t band parallel to structure", DISALLOW_LL )
dlg.spc001 = dialog.AddLabel ( "" )
dlg.REPORT = dialog.AddCheckbox ( "Print contact report", REPORT )
dlg.ok = dialog.AddButton ( "OK", 1 )
dlg.cancel = dialog.AddButton ( "Cancel", 0 )
if dialog.Show ( dlg ) > 0 then
MadeWeight = dlg.MadeWeight.value
MadeMult = dlg.MadeMult.value
MadeStrength = dlg.MadeStrength.value
MadeWrength = dlg.MadeWrength.value
MadeBeta = dlg.MadeBeta.value
MadePhobicsBeta = dlg.MadePhobicsBeta.value
UnmadeWeight = dlg.UnmadeWeight.value
UnmadeMult = dlg.UnmadeMult.value
UnmadeStrength = dlg.UnmadeStrength.value
UnmadeWrength = dlg.UnmadeWrength.value
UnmadeBeta = dlg.UnmadeBeta.value
UnmadePhobicsBeta = dlg.UnmadePhobicsBeta.value
LongerThan = dlg.LongerThan.value
MaxLength = dlg.MaxLength.value
ShorterThan = dlg.ShorterThan.value
MinLength = dlg.MinLength.value
noBandSelf = dlg.noBandSelf.value
DISALLOW_LL = dlg.DISALLOW_LL.value
REPORT = dlg.REPORT.value
return true
else
print ( "Dialog cancelled" )
return false
end
end
function GetAtom ( seg, UseBeta, UsePhobicsBeta )
local atom
if UsePhobicsBeta then
local aa = structure.GetAminoAcid ( seg )
if seg == segEnd then
atom = TERMINAL_BETA
elseif phobes [ aa ] ~= nil then
atom = BETA_CARBON
else
atom = CENTER_CARBON
end
else
if UseBeta == false or structure.GetAminoAcid ( seg ) == GLYCINE then
atom = CENTER_CARBON
elseif ii == segEnd then
atom = TERMINAL_BETA
else
atom = BETA_CARBON
end
end
return atom
end
function MakeBands ( contactmap, structList )
for ii = 1, #contactmap do
local seg1 = contactmap [ ii ] [ MAPSEG1 ]
local seg2 = contactmap [ ii ] [ MAPSEG2 ]
local weight = contactmap [ ii ] [ MAPHEAT ]
local made = contactmap [ ii ] [ MAPCONT ]
local atom1 = CENTER_CARBON
local atom2 = CENTER_CARBON
local banded = false
local bandIt = false
local blen = 0
local bstr = 0
local UseBeta = false
local UsePhobicsBeta = false
if ( made and weight > MadeWeight )
or ( not made and weight > UnmadeWeight ) then
bandIt = true
if made then
UseBeta = MadeBeta
UsePhobicsBeta = MadePhobicsBeta
else
UseBeta = UnmadeBeta
UsePhobicsBeta = UnmadePhobicsBeta
end
else
bandIt = false
bweight = bweight + 1
end
if bandIt and noBandSelf then
local s1 = findContactStruct ( structList, contactmap [ ii ] [ MAPSEG1 ] )
local s2 = findContactStruct ( structList, contactmap [ ii ] [ MAPSEG2 ] )
if s1 == s2 then
bandIt = false
bsame = bsame + 1
end
end
if bandIt and DISALLOW_LL then
if not BandAngleCheck ( seg1, seg2, structList, MAXANGLE ) then
bandIt = false
bpara = bpara + 1
end
end
if bandIt then
atom1 = GetAtom ( seg1, UseBeta, UsePhobicsBeta )
atom2 = GetAtom ( seg2, UseBeta, UsePhobicsBeta )
local bnd = band.AddBetweenSegments ( seg1, seg2, atom1, atom2 )
if bnd ~= nil and bnd ~= 0 then
local bcur = band.GetLength ( bnd )
if LongerThan and bcur > MaxLength then
blong = blong + 1
elseif ShorterThan and bcur < MinLength then
bshort = bshort + 1
else
banded = true
if made then
blen = MadeMult * band.GetLength ( bnd )
bstr = MadeStrength
if MadeWrength then
bstr = MadeStrength * weight
else
bstr = MadeStrength
end
else
blen = UnmadeMult * band.GetLength ( bnd )
if UnmadeWrength then
bstr = UnmadeStrength * weight
else
bstr = UnmadeStrength
end
end
end
else
bunk = bunk + 1 -- band.AddBetweenSegments failed
print ( "ERROR: band.AddBetweenSegments ( "
.. seg1 .. ", "
.. seg2 .. ", "
.. atom1 .. ", "
.. atom2 .. " ) failed" )
end
if banded then
band.SetGoalLength ( bnd, blen )
band.SetStrength ( bnd, bstr )
contactmap [ ii ] [ MAPBAND ] = true
contactmap [ ii ] [ MAPBLEN ] = blen
contactmap [ ii ] [ MAPBSTR ] = bstr
contactmap [ ii ] [ MAPATM1 ] = atom1
contactmap [ ii ] [ MAPATM2 ] = atom2
bcount = bcount + 1
else
band.Delete ( bnd )
end
end
end
end
function PrintContacts ( contacts )
local tReport = ""
local headStr =
"seg1"
.. delim ..
"seg2"
.. delim ..
"weight"
.. delim ..
"ss1"
.. delim ..
"ss2"
.. delim ..
"distance"
.. delim ..
"contact"
.. delim ..
"banded"
.. delim ..
"goallen"
.. delim ..
"strength"
.. delim ..
"atom1"
.. delim ..
"atom2"
.. delim
print ( "--" )
print ( "\"contact map\"" )
print ( headStr )
tReport = tReport .. "\"contact map\"\n" .. headStr .. "\n"
for ii = 1, #contacts do
local kontact = ""
for jj = 1, #contacts [ ii ] do
kontact = kontact .. tostring ( contacts [ ii ] [ jj ] ) .. delim
end
print ( kontact )
tReport = tReport .. kontact .. "\n"
end
return tReport
end
function ShowReport ( tReport )
local ask = dialog.CreateDialog ( ReVersion .. " copy-and-paste" )
ask.l15 = dialog.AddLabel ( "Click inside the text box, then" )
ask.l16 = dialog.AddLabel ( "use ctrl+a (command+a on Mac) to select all," )
ask.l20 = dialog.AddLabel ( "and control+c or command+c to copy, then" )
ask.l30 = dialog.AddLabel ( "paste into spreadsheet" )
ask.rep = dialog.AddTextbox ( "contact map:", tReport )
ask.OK = dialog.AddButton ( "OK", 1 )
dialog.Show ( ask )
end
function NoContacts ()
local ask = dialog.CreateDialog ( ReVersion .. " no contacts" )
ask.l15 = dialog.AddLabel ( "No contacts found." )
ask.l16 = dialog.AddLabel ( "This recipe is for contact map puzzles." )
ask.OK = dialog.AddButton ( "OK", 1 )
dialog.Show ( ask )
end
function Cleanup ( error )
--
-- optionally, do not loop if cleanup causes an error
-- (any loop here is automatically terminated after a few iterations, however)
--
if CLEANUPENTRY ~= nil then
return
end
CLEANUPENTRY = true
print ( "---" )
local reason
local start, stop, line, msg
if error == nil then
reason = "complete"
else
--
-- model 120 - civilized error reporting,
-- thanks to Bruno K. and Jean-Bob
--
start, stop, line, msg = error:find ( ":(%d+):%s()" )
if msg ~= nil then
error = error:sub ( msg, #error )
end
if error:find ( "Cancelled" ) ~= nil then
reason = "cancelled"
else
reason = "error"
end
end
--
-- model 100 - print recipe name, puzzle, track, time, score, and gain
--
print ( ReVersion .. " " .. reason )
print ( "Puzzle: " .. puzzle.GetName () )
print ( "Track: " .. ui.GetTrackName () )
if reason == "error" then
print ( "Unexpected error detected" )
print ( "Error line: " .. line )
print ( "Error: \"" .. error .. "\"" )
end
--
-- model 130 - reset clash importance, clear selections, restore structures, etc.
--
local skips = 0
print ( "total contacts = " .. tContacts )
if bweight > 0 then
print ( "contacts skipped due to minimum weight = " .. bweight )
skips = skips + bweight
end
if bsame > 0 then
print ( "contacts skipped due \'band self\' = " .. bsame )
skips = skips + bsame
end
if bpara > 0 then
print ( "contacts skipped due to \'don\'t band parallel\' = " .. bpara )
skips = skips + bpara
end
if bunk > 0 then
print ( "bands failed due to unknown error = " .. bunk )
skips = skips + bunk
end
if bshort > 0 then
print ( "contacts skipped due to minimum distance = " .. bshort )
skips = skips + bshort
end
if blong > 0 then
print ( "contacts skipped due to maximum distance = " .. blong )
skips = skips + blong
end
if skips > 0 then
print ( "total contacts skipped = " .. skips )
end
print ( "contact bands created = " .. bcount )
print ( "total bands = " .. band.GetCount() )
end
function Main ()
print ( ReVersion )
print ( "Puzzle: " .. puzzle.GetName () )
print ( "Track: " .. ui.GetTrackName () )
print ( "Contact map statistics:" )
local structList = GetStructs ()
local contacts = GetContacts ()
tContacts = #contacts
if tContacts == 0 then
NoContacts ()
Cleanup ()
end
MinLength = math.min ( minMadeDist, minUnmadeDist )
MaxLength = math.max ( maxMadeDist, maxUnmadeDist )
if GetParams () then
print ( "options:" )
--print ( "Made Contacts: band current distance * " .. MadeMult .. ", strength " .. MadeStrength )
print ( "Made Contacts:" )
print ( " band if weight > " .. MadeWeight )
print ( " current distance * " .. MadeMult )
if MadeWrength then
print ( " strength according to weight * ".. MadeStrength )
else
print ( " strength " .. MadeStrength )
end
if MadePhobicsBeta then
print ( " band to beta carbons (hydrophobics only)" )
elseif MadeBeta then
print ( " band to beta carbons" )
else
print ( " normal band position" )
end
--print ( "Unmade Contacts: band current distance * " .. UnmadeMult .. ", strength " .. UnmadeStrength )
print ( "Unmade Contacts:" )
print ( " band if weight > " .. UnmadeWeight )
print ( " current distance * " .. UnmadeMult )
if UnmadeWrength then
print (" strength according to weight * " .. UnmadeStrength )
else
print ( " strength " .. UnmadeStrength )
end
if UnmadePhobicsBeta then
print (" band to beta carbons (hydrophobics only)" )
elseif UnmadeBeta then
print ( " band to beta carbons" )
else
print ( " normal band position" )
end
if LongerThan then
print ( "max band distance = " .. MaxLength )
end
if ShorterThan then
print ( "minimum band distance = " .. MinLength )
end
if noBandSelf then
print ( "don\'t band structures to themselves" )
end
if DISALLOW_LL then
print ( "don't allow bands parallel to a structure" )
end
print ( "--" )
MakeBands ( contacts, structList )
if REPORT then
local tReport = PrintContacts ( contacts )
ShowReport ( tReport )
end
end
Cleanup ()
end
xpcall ( Main, Cleanup )
