//==============================
// MC-Sym 4.2 script generated by MC-Fold 1.0
// Please cite the following if you use MC-Sym:
// 	1) Major F et al. (1991) Science 253, 1255.
// 	2) Major F. (2003) Comp Sci Eng. 5, 44.


//========== Sequence ==========

sequence( r A1 GUGGUCUGAUGAGGCGAAAGCCGAAACUCGUAAGAGUCACCAC )
//             ((((((...(((((((..)))))))(((((..)))))))))))



//========== Relations ==========

relation(
	A25 A26 { adjacent_5p &&  stack } 10%
	A37 A38 { adjacent_5p && !stack } 10%
)



//========== Cycles ==========

ncm_03 = library(
	pdb( "MCSYM-DB/2_2/GCGC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A14:A15, A20:A21
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_04 = library(
	pdb( "MCSYM-DB/2_2/GGCC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A13:A14, A21:A22
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_05 = library(
	pdb( "MCSYM-DB/2_2/AGCG/*.pdb.gz" ) #1:#2, #3:#4 <- A12:A13, A22:A23
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_06 = library(
	pdb( "MCSYM-DB/2_2/GAGA/*.pdb.gz" ) #1:#2, #3:#4 <- A11:A12, A23:A24
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_07 = library(
	pdb( "MCSYM-DB/2_2/UGAA/*.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, A24:A25
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_08 = library(
	pdb( "MCSYM-DB/4/GUAA/*.pdb.gz" ) #1:#4 <- A30:A33
	rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) )
)

ncm_09 = library(
	pdb( "MCSYM-DB/2_2/CGAG/*.pdb.gz" ) #1:#2, #3:#4 <- A29:A30, A33:A34
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_10 = library(
	pdb( "MCSYM-DB/2_2/UCGA/*_s.pdb.gz" ) #1:#2, #3:#4 <- A28:A29, A34:A35
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_11 = library(
	pdb( "MCSYM-DB/2_2/CUAG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A27:A28, A35:A36
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_12 = library(
	pdb( "MCSYM-DB/2_2/ACGU/*_s.pdb.gz" ) #1:#2, #3:#4 <- A26:A27, A36:A37
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_13 = library(
	pdb( "MCSYM-DB/2_2/UCCA/*.pdb.gz" ) #1:#2, #3:#4 <- A5:A6, A38:A39
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_14 = library(
	pdb( "MCSYM-DB/2_2/GUAC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A39:A40
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_15 = library(
	pdb( "MCSYM-DB/2_2/GGCC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A40:A41
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_16 = library(
	pdb( "MCSYM-DB/2_2/UGCA/*_s.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A41:A42
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)

ncm_17 = library(
	pdb( "MCSYM-DB/2_2/GUAC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A42:A43
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
)



//=========== Backtrack ===========
// assemble the whole structure:

structure = backtrack(

	// stem_1
	ncm_03
	merge( ncm_04 2.0 )
	merge( ncm_05 2.0 )
	merge( ncm_06 2.0 )
	merge( ncm_07 2.0 )

	// stem_2
	place( A25 A26 ncm_12 )
	merge( ncm_11 2.0 )
	merge( ncm_10 2.0 )
	merge( ncm_09 2.0 )
	merge( ncm_08 2.0 )

	// stem_3
	place( A37 A38 ncm_13 )
	merge( ncm_14 2.0 )
	merge( ncm_15 2.0 )
	merge( ncm_16 2.0 )
	merge( ncm_17 2.0 )
)



// ========= Constraints / Restraints =========

clash                 ( structure 1.0 !( pse || lp || hydrogen ) )
ribose_rst            ( structure method = estimate, threshold = 2.0,
                        pucker = C3p_endo, glycosyl = anti )
backtrack_rst         ( structure method = probabilistic,
                        width_limit = 25%, height_limit = 100% )
implicit_phosphate_rst( structure sampling = 90% )



// ========= Exploration Initialization =========
explore(
	structure
	option( time_limit = 12h, seed = 3210 )
	reference( pdb( "1NYI01.pdb" ) )
	pdb( "1NYI" zipped )
)