marie_s Lv 1
parts can be useful on other recipe like find mutable.
Concatenation of recipes by spvincent, Ttaloc, Seagat, John McLeod, Crashguard303,Gary Forbis and authors on wiki
Profile
- Name
- print protein lua2 V0
- ID
- 31098
- Shared with
- Public
- Parent
- None
- Children
- Created on
- August 15, 2011 at 09:05 AM UTC
- Updated on
- August 15, 2011 at 09:05 AM UTC
- Description
all info on the protein
Best for
Code
--- info on the protein - concatenation of recipes , part of recipes or function by Tlaloc, spvincent, seagate, John McLeod, Crashguard303,Gary Forbis and authors on wiki
---- option for comma for delimitation of decimal number put y if your decimal point is not a point
comma='y'
if comma =='y' then separ=";" else separ="," end
----- count of segment, search of ligand
function GetSeCount ()
segCount = structure.GetCount()
isLigand =(structure.GetSecondaryStructure(segCount) == 'M') -- ligands have ss of 'M'
if isLigand then
print ('this puzzle is a ligand puzzle')
segCount = segCount - 1
end -- of isligand
return segCount
end -- of function GetSegCount
--- segments table without ligand
function tablesegment()
table={{}}
-- residues with -- in front (commented) are not in Foldit (as of Nov 15, 2010)
aminosLetterIndex=1
aminosShortIndex=2
aminosLongIndex=3
aminosPolarityIndex=4
aminosAcidityIndex=5
aminosHydropathyIndex=6
amino = {
{'a','Ala','Alanine', 'nonpolar','neutral', 1.8},
-- {'b','Asx','Asparagine or Aspartic acid' },
{'c','Cys','Cysteine', 'nonpolar','neutral', 2.5},
{'d','Asp','Aspartic acid', 'polar','negative', -3.5},
{'e','Glu','Glutamic acid', 'polar','negative', -3.5},
{'f','Phe','Phenylalanine','nonpolar','neutral', 2.8},
{'g','Gly','Glycine', 'nonpolar','neutral', -0.4},
{'h','His','Histidine', 'polar','neutral', -3.2},
{'i','Ile','Isoleucine', 'nonpolar','neutral', 4.5},
-- {'j','Xle','Leucine or Isoleucine' },
{'k','Lys','Lysine', 'polar','positive', -3.9},
{'l','Leu','Leucine', 'nonpolar','neutral', 3.8},
{'m','Met','Methionine ', 'nonpolar','neutral', 1.9},
{'n','Asn','Asparagine', 'polar','neutral', -3.5},
-- {'o','Pyl','Pyrrolysine' },
{'p','Pro','Proline', 'nonpolar','neutral', -1.6},
{'q','Gln','Glutamine', 'polar','neutral', -3.5},
{'r','Arg','Arginine', 'polar','positive', -4.5},
{'s','Ser','Serine', 'polar','neutral', -0.8},
{'t','Thr','Threonine', 'polar','neutral', -0.7},
-- {'u','Sec','Selenocysteine' },
{'v','Val','Valine', 'nonpolar','neutral', 4.2},
{'w','Trp','Tryptophan', 'nonpolar','neutral', -0.9},
-- {'x','Xaa','Unspecified or unknown amino acid' },
{'y','Tyr','Tyrosine', 'polar','neutral', -1.3},
-- {'z','Glx','Glutamine or glutamic acid' }
}
for i = 1, segCount do
table[i]={}
table[i][1]=structure.GetAminoAcid(i)
for j = 1, 20 do
if ( table[i][1]== amino[j][1] ) then
table[i][2]=amino[j][2]
table[i][3]=amino[j][3]
table[i][4]=amino[j][6]
end -- of if amino
end -- of loop onj
table[i][5]=structure.GetSecondaryStructure(i)
end -- of loop on i
return table
end -- function tablesegment
-- tlaloc functions to print sequence of letter
function BuildSequence(table)
string = ''
hydrostring=''
strucstring=''
for i=1, segCount do
string = string..table[i][1]
if structure.IsHydrophobic(i) then
hydrostring=hydrostring..'i'
else
hydrostring=hydrostring..'e' end
strucstring=strucstring..table[i][5]
end -- of loop on i
print('sequence with 1 letter by amino for searching in PDB')
print(string)
print('sequence with i if hydrophobic')
print(hydrostring)
print('sequence of structure')
print(strucstring)
end --function build sequence
---- find mutable segments
function FindMutable(table)
print("Finding Mutable Segments")
local mutable={}
mutablestring=''
local i
for i=1,segCount do
if structure.IsMutable(i) == true -- find the mutble segments
then mutable[#mutable + 1] = i
end -- of if mutable
end -- of loop on i
print(#mutable," mutables found")
for mut=1 ,#mutable do
print (mut,separ,mutable[mut],separ, table[mutable[mut]][1], separ,table[mutable[mut]][3])
mutablestring=mutablestring.."'"..table[mutable[mut]][1].."',"
end -- on loopon mut
print(mutablestring) --- for copy paste on other recipe
end --function finf mutable
-- function print score by spvincent
--Intended use.
-- 1) Run
-- 2) Open the script log (scriptlog.default.xml) in a text editor
-- 3) Strip off the start and end lines and save it as a text file with another name.
-- 4) Import that into Excel as a comma-delimited text file.
-- 5) Peruse, sort, compare against other solutions imported into a different sheet etc.
kNoTrunc = false
function t3 ( x )
-- Truncates a value to 3 decimal places unless kNoTrunc is set to true. Easier to read.
if ( kNoTrunc == true ) then
return x
else
if comma=="y" then x=1000*x return x - x% 1
else return x - x % 0.001 end -- on test on comma
end -- of test on trunc
end -- of function t3
function score(table)
print ( "n" , separ ,
"ID" , separ,
"SS" , separ ,
"Hyd",separ,
"score" , separ ,
"backbone" , separ,
"hiding" , separ ,
"packing" , separ ,
"bonding" , separ ,
"clashing" , separ ,
"sidechain" , separ,
"reference" )
for i = 1 , segCount do
print ( i , separ ,
table[i][1] , separ ,
table[i][5] , separ ,
t3(table[i][4] ), separ ,
t3 ( current.GetSegmentEnergyScore ( i ) ) , separ ,
t3 ( current.GetSegmentEnergySubscore ( i,"backbone" ) ) , separ ,
t3 ( current.GetSegmentEnergySubscore (i, "hiding" ) ) , separ,
t3 ( current.GetSegmentEnergySubscore ( i,"packing") ) , separ,
t3 ( current.GetSegmentEnergySubscore ( i,"bonding" ) ) , separ ,
t3 ( current.GetSegmentEnergySubscore (i, "clashing" ) ) , separ ,
t3 ( current.GetSegmentEnergySubscore (i, "sidechain" ) ) , separ ,
t3 ( current.GetSegmentEnergySubscore ( i,"reference" ) ) )
end -- of loop on i
end --- of function score
-- Table PuzzleStructsTab from Report on Structures, by John McLeod
function fstructure()
PuzzleStructsTab = {} -- consecutive elements are of the form { start_seg, end_seg, structure_code }
local PuzzleStructs_start_ind = 1
local PuzzleStructs_end_ind = 2
local PuzzleStructs_ss_ind = 3
PuzzleStructs_num_structs = 0
local current_struct = ''
local current_start_seg = 0
local current_struct_ind = 0
current_struct = structure.GetSecondaryStructure(1)
current_struct_ind = 1
current_start_seg = 1
PuzzleStructsTab[current_struct_ind] = {}
PuzzleStructsTab[current_struct_ind][PuzzleStructs_start_ind] = current_start_seg
PuzzleStructsTab[current_struct_ind][PuzzleStructs_ss_ind] = current_struct
for x=2, segCount do
if structure.GetSecondaryStructure(x) ~= current_struct then
current_struct = structure.GetSecondaryStructure(x)
current_struct_ind = current_struct_ind + 1
current_start_seg = x
PuzzleStructsTab[current_struct_ind] = {}
PuzzleStructsTab[current_struct_ind][PuzzleStructs_start_ind] = current_start_seg
PuzzleStructsTab[current_struct_ind][PuzzleStructs_ss_ind] = current_struct
PuzzleStructsTab[current_struct_ind - 1][PuzzleStructs_end_ind] = x - 1
end --if end struc
end--for x
PuzzleStructsTab[current_struct_ind][PuzzleStructs_end_ind] = segCount
PuzzleStructs_num_structs = current_struct_ind
return PuzzleStructsTab, PuzzleStructs_num_structs
end -- constructor for PuzzleStructsTab
---- function to print a litle contact table , has to be tested on the next free design puzzle
function contact()
head=separ..separ
first=1
for s=1 ,PuzzleStructs_num_structs do
if PuzzleStructsTab[s][3] =='H' or PuzzleStructsTab[s][3] == 'E' then
string=PuzzleStructsTab[s][3]..separ..PuzzleStructsTab[s][1]..separ..PuzzleStructsTab[s][2]
for s2=2,PuzzleStructs_num_structs do
if PuzzleStructsTab[s2][3] == 'H' or PuzzleStructsTab[s2][3] == 'E' then
if first then head=head..separ..PuzzleStructsTab[s2][3] end
mean= 0
nb=0
for i= PuzzleStructsTab[s][1],PuzzleStructsTab[s][2] do
min=999999
for j=PuzzleStructsTab[s2][1],PuzzleStructsTab[s2][2] do
dist=structure.GetDistance(i,j)
if dist<min then min=dist end
end --j
mean= mean+min
nb=nb+1
end --i
mean=mean/nb
if structure.GetDistance(PuzzleStructsTab[s][1],PuzzleStructsTab[s2][2] ) < structure.GetDistance(PuzzleStructsTab[s][1],PuzzleStructsTab[s2][1] ) then
if mean< 5 then c='X' else if mean<10 then c='x' else c=' ' end end
else
if mean< 5 then c='O' else if mean<10 then c='o' else c=' ' end end
end
string=string..separ..c
end--if
end --s2
if first==1 then print ('mini contact table') print(head) first=0 end
print(string)
end --- if
end -- s1
end -- function
----- count of segment and search of ligand
GetSeCount ()
print('number of segments : ',segCount)
tablesegment()
------ sequence of letters, hydrophobes, structures
BuildSequence(table)
----- find mutable segments and print them
FindMutable(table)
------ score of segments
score(table)
--- table des structures
fstructure()
-- mini contact table
contact()
--- end of recipe
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