import math
import time

predictedSecondary = '6TNA-SS.txt'
predictedTertiary = '6TNA-PT.txt'
knownStructure = ''
crystalStructure = ''
primarySequence = '6TNA-primary.txt'
ignoreList = ''

centerAtomName = 'C3*'

seed = 1
seed = int(time.time())

temp0=300
numRuns = 1
numSteps=100        # Number of iterations in a single run (absolute total)
numStepsVV=100      # Number of iterations done in C at a time without communicating with python
numStepsTemp=100    # Number of iterations between reasigning velocities to Boltzman distribution
numStepsPrint=100   # Number of iterations between prints
numStepsDumpPDB=100 # Number of iterations between pdb dumps
printEPArray=0      # EP = energy potential. Binary print EP array.
massDefault=325.0   # Residue mass
dt=0.005            # Time step in ps


cycles = 1500

#######
#BONDS#
#######

# ALL #
# Sequencial nucleotid bonds

B_K = 2.493*10.0**2/(2*0.4**2)              # kJ/nm^2
B_R = (1/10.0)*5.78              # nm

# HELICAL #
# base-pair bonds

Bh_K = 2.493*10.0**2/(2*1.6**2)               # kJ/nm^2
Bh_R = (1/10.0)*13.7

########
#ANGLES#
########

# NON-HELICAL #
# Three-sequential nucleotides
#splineDefFiles = ['angles_Energy.txt']

A_K = 2.493/(2*0.35**2)          # kJ/rad^2
A_R = 2.4                      # rad

# HELICAL #

# intra-strand, three-consecutive
Ah_K = 2.493*1/(2*0.25**2)        # kJ/rad^2
Ah_R = 2.6                      # rad

# inter-strand
Ah2_K = 2.493*1/(2*0.25**2)       # kJ/rad^2
Ah2_R = 1.50                     # rad


###########
#DIHEDRALS#
###########

# NON-HELICAL #

D_K1 = 5                       # kJ/rad^2
D_K2 = 0.0                     # kJ/rad^2
D_K3 = 0.0                     # kJ/rad^2
D_R = 0.3-math.pi                # rad

# HELICAL #

# intra-strand, four consecutive nucleotides

Dh_K1 = 50.0                      # kJ/rad^2
Dh_K2 = 0.0                        # kJ/rad^2
Dh_K3 = 0.0                        # kJ/rad^2
Dh_R = 0.3-math.pi               # rad

# inter-strand 1

Dh1_K1 = 100.0                    # kJ/rad^2
Dh1_K2 = 0.0                      # kJ/rad^2
Dh1_K3 = 0.0                       # kJ/rad^2
Dh1_R = -1.33-math.pi            # math.pi-1.33 rad

# inter-strand 2

Dh2_K1 = 100.0                     # kJ/rad^2
Dh2_K2 = 0.0                       # kJ/rad^2
Dh2_K3 = 0.0                       # kJ/rad^2
Dh2_R = 1.3-math.pi              # rad

############
#NON-BONDED#
############

#KR1 = (4.184/10)*332*q0*q1               # To use as coulombic, q0,q1 are charges of molecules
KR1=(4.184/10)*0.0 # change 0.0 to 1.0    # E = KR1/sqrt(wR1^2+R^2), reduces to standar coulombic if wR1=0
wR1=(1/100.0)*0.0 # change 0.0 to 1.0     # Not used (experimental)

# Van der Waal terms
# well depth for different energy functions
eR10R12 = 4.184*0.0                       #
eR6R12  = 4.184*0.0                       #
eR12  = 4.184*1.0     #0.5 # make small   # repulsive part of R1012 term
# dist of well bottom
sR10R12 = (1/10.0)*0.00
sR6R12  = (1/10.0)*0.00
HsR12  = (1/10.0)*1.00*8.0 # Van der Waals for any pair that includes a helical residue
NHsR12 = (1/10.0)*1.00*7.0 # Van der Waals for two non-helical residues

eps = (1/10.0)*0.0                        # offset for rounded nbi energy

#########
#HELICAL#
#########

pS_K=(4.184*100)*1 #.1                       # K for helix constraints (kJ/nm^2)
#helixResNumsFilename = 'helixLists.txt'   # File containing helical regions

##########
#TERTIARY#
##########

pT_K=2.493*10.0**2/(2*1.0**2)                       # K for known tertiary contacts (kJ/nm^2)
kS_K=(4.181*10)*10                       # K for predicted tertiary contacts (kJ/nm^2)
ptDist = 1.0                             # Predicted tertiary contact distance (nm)

#######
#OTHER#
#######

KSpread = (4.184*10)*(1/4.184)*0.0            # K for randy's spread function, like radius of gyration function

KR=0                                      # Constraint for atom positions to original (hooks law)
RR=(4.18*100)*0.0                         # Distance of min

startAtom = 1