annotate tools/rdock/data/scripts/dock.prm @ 0:bc03dbb6eb37 draft

planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty

RBT_PARAMETER_FILE_V1.00
TITLE Free docking (indexed VDW)

SECTION SCORE
	INTER	 RbtInterIdxSF.prm
    	INTRA    RbtIntraSF.prm
	SYSTEM   RbtTargetSF.prm
END_SECTION

SECTION SETSLOPE_1
	TRANSFORM           		RbtNullTransform
	[e-mail]	5.0	# Dock with a high penalty for leaving the cavity
	[e-mail]	0.1	# Gradually ramp up dihedral weight from 0.1->0.5
	[e-mail]		1.0	# Gradually ramp up energy cutoff for switching to quadratic
	[e-mail]		TRUE	# Start docking with a 4-8 vdW potential
	[e-mail]	180.0	# Broader angular dependence
	[e-mail]	180.0	# Broader angular dependence
	[e-mail]	1.5	# Broader distance range
END_SECTION

SECTION RANDOM_POP
        TRANSFORM                       RbtRandPopTransform
        POP_SIZE                        50
	SCALE_CHROM_LENGTH		TRUE
END_SECTION

SECTION GA_SLOPE1
	TRANSFORM			RbtGATransform	
	PCROSSOVER			0.4	# Prob. of crossover
	XOVERMUT			TRUE	# Cauchy mutation after each crossover
	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
	STEP_SIZE			1.0	# Max translational mutation
END_SECTION

SECTION SETSLOPE_3
	TRANSFORM           		RbtNullTransform
	[e-mail]	0.2
	[e-mail]		5.0
	[e-mail]	140.0
	[e-mail]	140.0
	[e-mail]	1.2
END_SECTION

SECTION GA_SLOPE3
	TRANSFORM			RbtGATransform	
	PCROSSOVER			0.4	# Prob. of crossover
	XOVERMUT			TRUE	# Cauchy mutation after each crossover
	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
	STEP_SIZE			1.0	# Max torsional mutation
END_SECTION

SECTION SETSLOPE_5
	TRANSFORM           		RbtNullTransform
	[e-mail]	0.3
	[e-mail]		25.0
	[e-mail]		FALSE	# Now switch to a convential 6-12 for final GA, MC, minimisation
	[e-mail]	120.0
	[e-mail]	120.0
	[e-mail]	0.9
END_SECTION

SECTION GA_SLOPE5
	TRANSFORM			RbtGATransform	
	PCROSSOVER			0.4	# Prob. of crossover
	XOVERMUT			TRUE	# Cauchy mutation after each crossover
	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
	STEP_SIZE			1.0	# Max torsional mutation
END_SECTION

SECTION SETSLOPE_10
	TRANSFORM           		RbtNullTransform
	[e-mail]	0.5	# Final dihedral weight matches SF file
	[e-mail]		120.0	# Final ECUT matches SF file
	[e-mail]	80.0
	[e-mail]	100.0
	[e-mail]	0.6
END_SECTION

SECTION MC_10K
	TRANSFORM           		RbtSimAnnTransform
	START_T             		10.0
	FINAL_T             		10.0
	NUM_BLOCKS          		5
	STEP_SIZE          		0.1
	MIN_ACC_RATE            	0.25
	PARTITION_DIST          	8.0
	PARTITION_FREQ          	50
	HISTORY_FREQ            	0
END_SECTION

SECTION SIMPLEX
	TRANSFORM			RbtSimplexTransform
	MAX_CALLS			200
	NCYCLES				20
	STOPPING_STEP_LENGTH		10e-4
	PARTITION_DIST			8.0
        STEP_SIZE			1.0
	CONVERGENCE			0.001
END_SECTION

SECTION FINAL
	TRANSFORM           		RbtNullTransform
	[e-mail]	1.0	# revert to standard cavity penalty
END_SECTION