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martini21p.py
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#!/usr/bin/env python
import sys
version = "1.1"
tag = "20120826-TAW"
# Martini Force Field Definition Generating Script - Polarizable water version
# Version 2012-02-19 TAW
# Dictionary of coarse grained bead types and masses
beads = { # Name: Mass
"P5": 72, "P4": 72, "P3": 72, "P2": 72, "P1": 72, # Polar
"Nda": 72, "Nd": 72, "Na": 72, "N0": 72, # Intermediate
"C5": 72, "C4": 72, "C3": 72, "C2": 72, "C1": 72, # Apolar
"Qda": 72, "Qd": 72, "Qa": 72, "Q0": 72, # Charged
"SP5": 45, "SP4": 45, "SP3": 45, "SP2": 45, "SP1": 45, # Ring type, polar
"SNda": 45, "SNd": 45, "SNa": 45, "SN0": 45, # Ring type, intermediate
"SC5": 45, "SC4": 45, "SC3": 45, "SC2": 45, "SC1": 45, # Ring type, apolar
"SQda": 45, "SQd": 45, "SQa": 45, "SQ0": 45, # Ring type, charged
"AC1": 72, "AC2": 72, # Amino acid side chains (Q-C interactions)
"POL": 24, "D": 24,
}
# Dictionary of hybrid particles and corresponding coarse grained types.
# The hybrid particles will have both atomistic and coarse grained
# interactions. In multiscaled simulations, they should form a specific
# energy group, for which no interactions need to be excluded explicitly.
# On the coarsegrained level, ions are treated coarsely, using simple Q types.
if len(sys.argv) > 1:
hybrid = {
"NA+": "Qd", "CA2+": "Qd", "MG2+": "Qd", "ZN2+": "Qd", "CU2+": "Qd", "CU1+": "Qd",
"CL-": "Qa",
}
else:
hybrid = {}
martini_v2_P ="""
; FORCEFIELD V2.1P - POLARIZABLE WATER .. VERSION 14-04-2010
;
; published online as supporting material for
;
; S.O. Yesylevskyy, L.V. Schafer, D. Sengupta, S.J. Marrink.
; "Polarizable water model for the coarse-grained Martini force field."
; PLoS Comp. Biol, 2010.
; This file contains all interaction parameters and topology for the
; polarizable water in combination with the Martini force field
; as implemented in Gromacs
; Polarizable water is compatible with all other
; molecules in Martini, both versions 2.0 and 2.1
; NOTE : if you use POL particles with peptides/proteins,
; change AC1 and AC2 type to regular C1 and C2 -
; AC1 and AC2 are obsolete in the polarizable force field.
[ defaults ]
1 1
[ atomtypes ]
; Currently eighteen particle types are defined, divided into four main categories
; (P, polar; N, intermediate; C, apolar; Q, charged)
; each of which has a number of sublevels (0,a,d, or ad)
; subtype 0 has no hydrogen bond forming capacities,
; subtype d has some hydrogen donor capacities,
; subtype a some hydrogen acceptor capacities,
; and subtype da has both donor and acceptor capacities
; or (1,2,3,4,5) where subtype 5 is more polar than 1.
; Two main classes of particles are furthermore distinguished, namely
; STANDARD particles which are mapped using a 4:1 mapping scheme, and
; RING particles which are used for ring compounds mapped 2-3:1.
; A special POL particle type is defined for the polarizable water,
; together with two D (dummy) particles for the associated particles
; that interact only through their charges.
; For reasons of computational efficiency, all particle masses are set to 72 amu,
; except for ring types which are set to 45 amu.
; For realistic dynamics, the particle masses should be adapted.
; This might require a reduction of the integration timestep, however.
; name mass charge ptype c6 c12
"""
# Epsilon: 5.60(A), 5.00(B), 4.50(C), 4.00(D), 3.50(E), 3.10(F), 2.70(G), 2.30(H), 2.00(I)
# Sigma: 0.00(0), 0.43(1), 0.47(2), 0.57(3), 0.62(4)
# Scaling: 1.00(a), 0.95(b), 0.90(c), 0.75(d), 0.71(e)
epsilon = {
"0":0.00, # no interaction
"A":5.60, # supra attractive
"B":5.00, # attractive
"C":4.50, # almost attractive
"D":4.00, # semi attractive
"E":3.50, # intermediate
"F":3.10, # almost intermediate
"G":2.70, # semi repulsive
"H":2.30, # almost repulsive
"I":2.00, # repulsive
"Z":0.25, # with sigma=1 yields c6=12=1
}
sigma = {
"0":0.00, # no interaction
"1":0.43, # ring bead type
"2":0.47, # default bead type
"3":0.57, # supra attractive bead type
"4":0.62, # super repulsive bead type
"5":1.00, # unity: c6/12 parity
}
scale = {
"a":1.00, # no scaling
"b":0.95, # 95%: interaction with polarizable water
"c":0.90, # 90%: S* - C1 interactions with BMW water
"d":0.75, # 75%: ring bead types (S*) and uncharged interactions with BMW for epsilon >=4.5
"e":0.71, # 71%: uncharged interactions with BMW for epsilon<4.5
}
# BEAD TYPES
# Default bead types; 4:1 mapping, 72 AMU
plain = {
"P5": 72, "P4": 72, "P3": 72, "P2": 72, "P1": 72, # Polar
"Nda": 72, "Nd": 72, "Na": 72, "N0": 72, # Intermediate
"C5": 72, "C4": 72, "C3": 72, "C2": 72, "C1": 72, # Apolar
"Qda": 72, "Qd": 72, "Qa": 72, "Q0": 72, # Charged
"AC1": 72, "AC2": 72, # Amino acid specific (Q-C interactions)
}
# Ring bead types; mapping 2:1 or 3:1, 45 AMU
small = {
"SP5": 45, "SP4": 45, "SP3": 45, "SP2": 45, "SP1": 45, # Ring type, polar
"SNda": 45, "SNd": 45, "SNa": 45, "SN0": 45, # Ring type, intermediate
"SC5": 45, "SC4": 45, "SC3": 45, "SC2": 45, "SC1": 45, # Ring type, apolar
"SQda": 45, "SQd": 45, "SQa": 45, "SQ0": 45, # Ring type, charged
}
# Virtual sites, plain type; mapping 4:1, no mass
vsite = {
"vP5": 0, "vP4": 0, "vP3": 0, "vP2": 0, "vP1": 0, # Polar
"vNda": 0, "vNd": 0, "vNa": 0, "vN0": 0, # Intermediate
"vC5": 0, "vC4": 0, "vC3": 0, "vC2": 0, "vC1": 0, # Apolar
"vQda": 0, "vQd": 0, "vQa": 0, "vQ0": 0, # Charged
"vAC1": 0, "vAC2": 0, # Amino acid specific (Q-C interactions)
}
# Virtual sites, small type; mapping 2:1 or 3:1, no mass
svste = {
"vSP5": 0, "vSP4": 0, "vSP3": 0, "vSP2": 0, "vSP1": 0, # Ring type, polar
"vSNda": 0, "vSNd": 0, "vSNa": 0, "vSN0": 0, # Ring type, intermediate
"vSC5": 0, "vSC4": 0, "vSC3": 0, "vSC2": 0, "vSC1": 0, # Ring type, apolar
"vSQda": 0, "vSQd": 0, "vSQa": 0, "vSQ0": 0, # Ring type, charged
}
# Other: Special purpose types
other = {
"POL": 24, # Polarizable water main bead
"D": 24, # Polarizable water satellite
"BP4": 72, # Big water particle (antifreeze). Not used with BMW
}
classes = ("plain","small","vsite","svste","other")
# Dummy atom types. These will be given a repulsion "DUMMY_REPEL"
# with all atoms from the atomistic forcefield, if provided
dummy = ["D"]
# Gather all atom types
all,mass = zip(*[i for j in classes for i in eval(j).items()])
virtual = vsite.keys() + svste.keys()
rla = range(len(all))
cmb = [ (all[i],all[j]) for i in rla for j in rla[i:] ]
# Epsilon: 5.60(A), 5.00(B), 4.50(C), 4.00(D), 3.50(E), 3.10(F), 2.70(G), 2.30(H), 2.00(I)
# Sigma: 0.00(0), 0.43(1), 0.47(2), 0.57(3), 0.62(4)
# Scaling: 1.00(a), 0.95(b), 0.90(c), 0.75(d), 0.71(e)
#++++
table_plain = """
Qda Qd Qa Q0 P5 P4 P3 P2 P1 Nda Nd Na N0 C5 C4 C3 C2 C1 AC2 AC1
Qda Aa2 Ba2 Ba2 Ea2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
Qd Ba2 Ea2 Da2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
Qa Ba2 Da2 Ea2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
Q0 Ea2 Ha2 Ha2 Ea2 Aa2 Aa2 Aa2 Ba2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
P5 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ba2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
P4 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Da2 Da2 Da2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
P3 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Fa2 Ga2 Ha2 Ga2 Ha2
P2 Aa2 Aa2 Aa2 Ba2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ha2 Ga2 Ha2
P1 Aa2 Aa2 Aa2 Ca2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
Nda Aa2 Aa2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
Nd Aa2 Ca2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Da2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
Na Aa2 Aa2 Ca2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
N0 Da2 Da2 Da2 Da2 Ea2 Ea2 Ea2 Da2 Da2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
C5 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
C4 Fa2 Fa2 Fa2 Fa2 Ga2 Ga2 Fa2 Ea2 Ea2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
C3 Ga2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ga2 Ga2 Ga2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2
C2 Ha2 Ha2 Ha2 Ha2 Ha2 Ha2 Ga2 Ga2 Fa2 Ga2 Ga2 Ga2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
C1 Ha2 Ha2 Ha2 Ha2 Ia2 Ia2 Ha2 Ha2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
AC2 Ha2 Ha2 Ha2 Ha2 Ha2 Ha2 Ga2 Ga2 Fa2 Ga2 Ga2 Ga2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
AC1 Ha2 Ha2 Ha2 Ha2 Ia2 Ia2 Ha2 Ha2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
"""
table_small = """
SQda SQd SQa SQ0 SP5 SP4 SP3 SP2 SP1 SNda SNd SNa SN0 SC5 SC4 SC3 SC2 SC1
SQda Ad1 Bd1 Bd1 Ed1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
SQd Bd1 Ed1 Dd1 Hd1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Cd1 Ad1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
SQa Bd1 Dd1 Ed1 Hd1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Cd1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
SQ0 Ed1 Hd1 Hd1 Ed1 Bd1 Ad1 Ad1 Bd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
SP5 Ad1 Ad1 Ad1 Bd1 Ad1 Ad1 Ad1 Ad1 Ad1 Bd1 Bd1 Bd1 Ed1 Fd1 Gd1 Gd1 Hd1 Id1
SP4 Ad1 Ad1 Ad1 Ad1 Ad1 Bd1 Bd1 Cd1 Cd1 Dd1 Dd1 Dd1 Ed1 Fd1 Gd1 Gd1 Hd1 Id1
SP3 Ad1 Ad1 Ad1 Ad1 Ad1 Bd1 Bd1 Cd1 Cd1 Cd1 Cd1 Cd1 Ed1 Ed1 Fd1 Fd1 Gd1 Hd1
SP2 Ad1 Ad1 Ad1 Bd1 Ad1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Ed1 Fd1 Gd1 Hd1
SP1 Ad1 Ad1 Ad1 Cd1 Ad1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Ed1 Ed1 Fd1 Gd1
SNda Ad1 Ad1 Ad1 Cd1 Bd1 Dd1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Ed1 Ed1 Fd1 Gd1 Gd1 Gd1
SNd Ad1 Cd1 Ad1 Cd1 Bd1 Dd1 Cd1 Cd1 Cd1 Cd1 Dd1 Cd1 Ed1 Ed1 Fd1 Gd1 Gd1 Gd1
SNa Ad1 Ad1 Cd1 Cd1 Bd1 Dd1 Cd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Ed1 Fd1 Gd1 Gd1 Gd1
SN0 Dd1 Dd1 Dd1 Dd1 Ed1 Ed1 Ed1 Dd1 Dd1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Fd1 Gd1
SC5 Ed1 Ed1 Ed1 Ed1 Fd1 Fd1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Fd1 Fd1
SC4 Fd1 Fd1 Fd1 Fd1 Gd1 Gd1 Fd1 Ed1 Ed1 Fd1 Fd1 Fd1 Ed1 Ed1 Ed1 Ed1 Fd1 Fd1
SC3 Gd1 Gd1 Gd1 Gd1 Gd1 Gd1 Fd1 Fd1 Ed1 Gd1 Gd1 Gd1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1
SC2 Hd1 Hd1 Hd1 Hd1 Hd1 Hd1 Gd1 Gd1 Fd1 Gd1 Gd1 Gd1 Fd1 Fd1 Fd1 Ed1 Ed1 Ed1
SC1 Hd1 Hd1 Hd1 Hd1 Id1 Id1 Hd1 Hd1 Gd1 Gd1 Gd1 Gd1 Gd1 Fd1 Fd1 Ed1 Ed1 Ed1
"""
table_small_plain = """
Qda Qd Qa Q0 P5 P4 P3 P2 P1 Nda Nd Na N0 C5 C4 C3 C2 C1 AC2 AC1
SQda Aa2 Ba2 Ba2 Ea2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
SQd Ba2 Ea2 Da2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
SQa Ba2 Da2 Ea2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
SQ0 Ea2 Ha2 Ha2 Ea2 Aa2 Aa2 Aa2 Ba2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
SP5 Aa2 Aa2 Aa2 Ba2 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ba2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
SP4 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Da2 Da2 Da2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
SP3 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Fa2 Ga2 Ha2 Ga2 Ha2
SP2 Aa2 Aa2 Aa2 Ba2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ha2 Ga2 Ha2
SP1 Aa2 Aa2 Aa2 Ca2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
SNda Aa2 Aa2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
SNd Aa2 Ca2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Da2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
SNa Aa2 Aa2 Ca2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
SN0 Da2 Da2 Da2 Da2 Ea2 Ea2 Ea2 Da2 Da2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
SC5 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
SC4 Fa2 Fa2 Fa2 Fa2 Ga2 Ga2 Fa2 Ea2 Ea2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
SC3 Ga2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ga2 Ga2 Ga2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2
SC2 Ha2 Ha2 Ha2 Ha2 Ha2 Ha2 Ga2 Ga2 Fa2 Ga2 Ga2 Ga2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
SC1 Ha2 Ha2 Ha2 Ha2 Ia2 Ia2 Ha2 Ha2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
"""
table_vsite = """
vQda vQd vQa vQ0 vP5 vP4 vP3 vP2 vP1 vNda vNd vNa vN0 vC5 vC4 vC3 vC2 vC1 vAC2 vAC1
vQda Aa2 Ba2 Ba2 Ea2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vQd Ba2 Ea2 Da2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vQa Ba2 Da2 Ea2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vQ0 Ea2 Ha2 Ha2 Ea2 Aa2 Aa2 Aa2 Ba2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vP5 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ba2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
vP4 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Da2 Da2 Da2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
vP3 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Fa2 Ga2 Ha2 Ga2 Ha2
vP2 Aa2 Aa2 Aa2 Ba2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ha2 Ga2 Ha2
vP1 Aa2 Aa2 Aa2 Ca2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
vNda Aa2 Aa2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vNd Aa2 Ca2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Da2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vNa Aa2 Aa2 Ca2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vN0 Da2 Da2 Da2 Da2 Ea2 Ea2 Ea2 Da2 Da2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
vC5 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
vC4 Fa2 Fa2 Fa2 Fa2 Ga2 Ga2 Fa2 Ea2 Ea2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
vC3 Ga2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ga2 Ga2 Ga2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2
vC2 Ha2 Ha2 Ha2 Ha2 Ha2 Ha2 Ga2 Ga2 Fa2 Ga2 Ga2 Ga2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
vC1 Ha2 Ha2 Ha2 Ha2 Ia2 Ia2 Ha2 Ha2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
vAC2 Ha2 Ha2 Ha2 Ha2 Ha2 Ha2 Ga2 Ga2 Fa2 Ga2 Ga2 Ga2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
vAC1 Ha2 Ha2 Ha2 Ha2 Ia2 Ia2 Ha2 Ha2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
"""
table_vsite_plain = """
Qda Qd Qa Q0 P5 P4 P3 P2 P1 Nda Nd Na N0 C5 C4 C3 C2 C1 AC2 AC1
vQda Aa2 Ba2 Ba2 Ea2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vQd Ba2 Ea2 Da2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vQa Ba2 Da2 Ea2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vQ0 Ea2 Ha2 Ha2 Ea2 Aa2 Aa2 Aa2 Ba2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vP5 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ba2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
vP4 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Da2 Da2 Da2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
vP3 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Fa2 Ga2 Ha2 Ga2 Ha2
vP2 Aa2 Aa2 Aa2 Ba2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ha2 Ga2 Ha2
vP1 Aa2 Aa2 Aa2 Ca2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
vNda Aa2 Aa2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vNd Aa2 Ca2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Da2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vNa Aa2 Aa2 Ca2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vN0 Da2 Da2 Da2 Da2 Ea2 Ea2 Ea2 Da2 Da2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
vC5 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
vC4 Fa2 Fa2 Fa2 Fa2 Ga2 Ga2 Fa2 Ea2 Ea2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
vC3 Ga2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ga2 Ga2 Ga2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2
vC2 Ha2 Ha2 Ha2 Ha2 Ha2 Ha2 Ga2 Ga2 Fa2 Ga2 Ga2 Ga2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
vC1 Ha2 Ha2 Ha2 Ha2 Ia2 Ia2 Ha2 Ha2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
vAC2 Ha2 Ha2 Ha2 Ha2 Ha2 Ha2 Ga2 Ga2 Fa2 Ga2 Ga2 Ga2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
vAC1 Ha2 Ha2 Ha2 Ha2 Ia2 Ia2 Ha2 Ha2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
"""
table_vsite_small = """
SQda SQd SQa SQ0 SP5 SP4 SP3 SP2 SP1 SNda SNd SNa SN0 SC5 SC4 SC3 SC2 SC1
vQda Aa2 Ba2 Ba2 Ea2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2
vQd Ba2 Ea2 Da2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2
vQa Ba2 Da2 Ea2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2
vQ0 Ea2 Ha2 Ha2 Ea2 Ba2 Aa2 Aa2 Ba2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2
vP5 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ba2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2
vP4 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Da2 Da2 Da2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2
vP3 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Fa2 Ga2 Ha2
vP2 Aa2 Aa2 Aa2 Ba2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ha2
vP1 Aa2 Aa2 Aa2 Ca2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Ea2 Fa2 Ga2
vNda Aa2 Aa2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2
vNd Aa2 Ca2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Da2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2
vNa Aa2 Aa2 Ca2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2
vN0 Da2 Da2 Da2 Da2 Ea2 Ea2 Ea2 Da2 Da2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Ga2
vC5 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2
vC4 Fa2 Fa2 Fa2 Fa2 Ga2 Ga2 Fa2 Ea2 Ea2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2
vC3 Ga2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ga2 Ga2 Ga2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2
vC2 Ha2 Ha2 Ha2 Ha2 Ha2 Ha2 Ga2 Ga2 Fa2 Ga2 Ga2 Ga2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2
vC1 Ha2 Ha2 Ha2 Ha2 Ia2 Ia2 Ha2 Ha2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ea2 Ea2
vAC2 Ha2 Ha2 Ha2 Ha2 Ha2 Ha2 Ga2 Ga2 Fa2 Ga2 Ga2 Ga2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2
vAC1 Ha2 Ha2 Ha2 Ha2 Ia2 Ia2 Ha2 Ha2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ea2 Ea2
"""
table_svste = """
vSQda vSQd vSQa vSQ0 vSP5 vSP4 vSP3 vSP2 vSP1 vSNda vSNd vSNa vSN0 vSC5 vSC4 vSC3 vSC2 vSC1
vSQda Ad1 Bd1 Bd1 Ed1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
vSQd Bd1 Ed1 Dd1 Hd1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Cd1 Ad1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
vSQa Bd1 Dd1 Ed1 Hd1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Cd1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
vSQ0 Ed1 Hd1 Hd1 Ed1 Bd1 Ad1 Ad1 Bd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
vSP5 Ad1 Ad1 Ad1 Bd1 Ad1 Ad1 Ad1 Ad1 Ad1 Bd1 Bd1 Bd1 Ed1 Fd1 Gd1 Gd1 Hd1 Id1
vSP4 Ad1 Ad1 Ad1 Ad1 Ad1 Bd1 Bd1 Cd1 Cd1 Dd1 Dd1 Dd1 Ed1 Fd1 Gd1 Gd1 Hd1 Id1
vSP3 Ad1 Ad1 Ad1 Ad1 Ad1 Bd1 Bd1 Cd1 Cd1 Cd1 Cd1 Cd1 Ed1 Ed1 Fd1 Fd1 Gd1 Hd1
vSP2 Ad1 Ad1 Ad1 Bd1 Ad1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Ed1 Fd1 Gd1 Hd1
vSP1 Ad1 Ad1 Ad1 Cd1 Ad1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Ed1 Ed1 Fd1 Gd1
vSNda Ad1 Ad1 Ad1 Cd1 Bd1 Dd1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Ed1 Ed1 Fd1 Gd1 Gd1 Gd1
vSNd Ad1 Cd1 Ad1 Cd1 Bd1 Dd1 Cd1 Cd1 Cd1 Cd1 Dd1 Cd1 Ed1 Ed1 Fd1 Gd1 Gd1 Gd1
vSNa Ad1 Ad1 Cd1 Cd1 Bd1 Dd1 Cd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Ed1 Fd1 Gd1 Gd1 Gd1
vSN0 Dd1 Dd1 Dd1 Dd1 Ed1 Ed1 Ed1 Dd1 Dd1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Fd1 Gd1
vSC5 Ed1 Ed1 Ed1 Ed1 Fd1 Fd1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Fd1 Fd1
vSC4 Fd1 Fd1 Fd1 Fd1 Gd1 Gd1 Fd1 Ed1 Ed1 Fd1 Fd1 Fd1 Ed1 Ed1 Ed1 Ed1 Fd1 Fd1
vSC3 Gd1 Gd1 Gd1 Gd1 Gd1 Gd1 Fd1 Fd1 Ed1 Gd1 Gd1 Gd1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1
vSC2 Hd1 Hd1 Hd1 Hd1 Hd1 Hd1 Gd1 Gd1 Fd1 Gd1 Gd1 Gd1 Fd1 Fd1 Fd1 Ed1 Ed1 Ed1
vSC1 Hd1 Hd1 Hd1 Hd1 Id1 Id1 Hd1 Hd1 Gd1 Gd1 Gd1 Gd1 Gd1 Fd1 Fd1 Ed1 Ed1 Ed1
"""
table_svste_plain = """
Qda Qd Qa Q0 P5 P4 P3 P2 P1 Nda Nd Na N0 C5 C4 C3 C2 C1 AC2 AC1
vSQda Aa2 Ba2 Ba2 Ea2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vSQd Ba2 Ea2 Da2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vSQa Ba2 Da2 Ea2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vSQ0 Ea2 Ha2 Ha2 Ea2 Aa2 Aa2 Aa2 Ba2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vSP5 Aa2 Aa2 Aa2 Ba2 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ba2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
vSP4 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Da2 Da2 Da2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
vSP3 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Fa2 Ga2 Ha2 Ga2 Ha2
vSP2 Aa2 Aa2 Aa2 Ba2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ha2 Ga2 Ha2
vSP1 Aa2 Aa2 Aa2 Ca2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
vSNda Aa2 Aa2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vSNd Aa2 Ca2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Da2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vSNa Aa2 Aa2 Ca2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vSN0 Da2 Da2 Da2 Da2 Ea2 Ea2 Ea2 Da2 Da2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
vSC5 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
vSC4 Fa2 Fa2 Fa2 Fa2 Ga2 Ga2 Fa2 Ea2 Ea2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
vSC3 Ga2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ga2 Ga2 Ga2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2
vSC2 Ha2 Ha2 Ha2 Ha2 Ha2 Ha2 Ga2 Ga2 Fa2 Ga2 Ga2 Ga2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
vSC1 Ha2 Ha2 Ha2 Ha2 Ia2 Ia2 Ha2 Ha2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
"""
table_svste_small = """
SQda SQd SQa SQ0 SP5 SP4 SP3 SP2 SP1 SNda SNd SNa SN0 SC5 SC4 SC3 SC2 SC1
vSQda Ad1 Bd1 Bd1 Ed1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
vSQd Bd1 Ed1 Dd1 Hd1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Cd1 Ad1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
vSQa Bd1 Dd1 Ed1 Hd1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Ad1 Cd1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
vSQ0 Ed1 Hd1 Hd1 Ed1 Bd1 Ad1 Ad1 Bd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Fd1 Gd1 Hd1 Hd1
vSP5 Ad1 Ad1 Ad1 Bd1 Ad1 Ad1 Ad1 Ad1 Ad1 Bd1 Bd1 Bd1 Ed1 Fd1 Gd1 Gd1 Hd1 Id1
vSP4 Ad1 Ad1 Ad1 Ad1 Ad1 Bd1 Bd1 Cd1 Cd1 Dd1 Dd1 Dd1 Ed1 Fd1 Gd1 Gd1 Hd1 Id1
vSP3 Ad1 Ad1 Ad1 Ad1 Ad1 Bd1 Bd1 Cd1 Cd1 Cd1 Cd1 Cd1 Ed1 Ed1 Fd1 Fd1 Gd1 Hd1
vSP2 Ad1 Ad1 Ad1 Bd1 Ad1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Ed1 Fd1 Gd1 Hd1
vSP1 Ad1 Ad1 Ad1 Cd1 Ad1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Ed1 Ed1 Fd1 Gd1
vSNda Ad1 Ad1 Ad1 Cd1 Bd1 Dd1 Cd1 Cd1 Cd1 Cd1 Cd1 Cd1 Ed1 Ed1 Fd1 Gd1 Gd1 Gd1
vSNd Ad1 Cd1 Ad1 Cd1 Bd1 Dd1 Cd1 Cd1 Cd1 Cd1 Dd1 Cd1 Ed1 Ed1 Fd1 Gd1 Gd1 Gd1
vSNa Ad1 Ad1 Cd1 Cd1 Bd1 Dd1 Cd1 Cd1 Cd1 Cd1 Cd1 Dd1 Ed1 Ed1 Fd1 Gd1 Gd1 Gd1
vSN0 Dd1 Dd1 Dd1 Dd1 Ed1 Ed1 Ed1 Dd1 Dd1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Fd1 Gd1
vSC5 Ed1 Ed1 Ed1 Ed1 Fd1 Fd1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1 Fd1 Fd1
vSC4 Fd1 Fd1 Fd1 Fd1 Gd1 Gd1 Fd1 Ed1 Ed1 Fd1 Fd1 Fd1 Ed1 Ed1 Ed1 Ed1 Fd1 Fd1
vSC3 Gd1 Gd1 Gd1 Gd1 Gd1 Gd1 Fd1 Fd1 Ed1 Gd1 Gd1 Gd1 Ed1 Ed1 Ed1 Ed1 Ed1 Ed1
vSC2 Hd1 Hd1 Hd1 Hd1 Hd1 Hd1 Gd1 Gd1 Fd1 Gd1 Gd1 Gd1 Fd1 Fd1 Fd1 Ed1 Ed1 Ed1
vSC1 Hd1 Hd1 Hd1 Hd1 Id1 Id1 Hd1 Hd1 Gd1 Gd1 Gd1 Gd1 Gd1 Fd1 Fd1 Ed1 Ed1 Ed1
"""
table_svste_vsite = """
vQda vQd vQa vQ0 vP5 vP4 vP3 vP2 vP1 vNda vNd vNa vN0 vC5 vC4 vC3 vC2 vC1 vAC2 vAC1
vSQda Aa2 Ba2 Ba2 Ea2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vSQd Ba2 Ea2 Da2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Aa2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vSQa Ba2 Da2 Ea2 Ha2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Aa2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vSQ0 Ea2 Ha2 Ha2 Ea2 Aa2 Aa2 Aa2 Ba2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Fa2 Ga2 Ha2 Ha2 Ha2 Ha2
vSP5 Aa2 Aa2 Aa2 Ba2 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ba2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
vSP4 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Da2 Da2 Da2 Ea2 Fa2 Ga2 Ga2 Ha2 Ia2 Ha2 Ia2
vSP3 Aa2 Aa2 Aa2 Aa2 Aa2 Ba2 Ba2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Fa2 Ga2 Ha2 Ga2 Ha2
vSP2 Aa2 Aa2 Aa2 Ba2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ha2 Ga2 Ha2
vSP1 Aa2 Aa2 Aa2 Ca2 Aa2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
vSNda Aa2 Aa2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vSNd Aa2 Ca2 Aa2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Da2 Ca2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vSNa Aa2 Aa2 Ca2 Ca2 Ba2 Da2 Ca2 Ca2 Ca2 Ca2 Ca2 Da2 Ea2 Ea2 Fa2 Ga2 Ga2 Ga2 Ga2 Ga2
vSN0 Da2 Da2 Da2 Da2 Ea2 Ea2 Ea2 Da2 Da2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Ga2 Fa2 Ga2
vSC5 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
vSC4 Fa2 Fa2 Fa2 Fa2 Ga2 Ga2 Fa2 Ea2 Ea2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Fa2 Fa2 Fa2 Fa2
vSC3 Ga2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ga2 Ga2 Ga2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2 Ea2
vSC2 Ha2 Ha2 Ha2 Ha2 Ha2 Ha2 Ga2 Ga2 Fa2 Ga2 Ga2 Ga2 Fa2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
vSC1 Ha2 Ha2 Ha2 Ha2 Ia2 Ia2 Ha2 Ha2 Ga2 Ga2 Ga2 Ga2 Ga2 Fa2 Fa2 Ea2 Ea2 Ea2 Ea2 Ea2
"""
table_other = """
POL D
POL Da2 0
D 0 0
"""
table_other_plain = """
Qda Qd Qa Q0 P5 P4 P3 P2 P1 Nda Nd Na N0 C5 C4 C3 C2 C1 AC2 AC1
POL Aa2 Ba2 Ba2 Ca2 Ab2 Bb2 Bb2 Cb2 Cb2 Db2 Db2 Db2 Eb2 Fb2 Gb2 Gb2 Hb2 Ib2 Hb2 Ib2
D 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
"""
table_other_small = """
SQda SQd SQa SQ0 SP5 SP4 SP3 SP2 SP1 SNda SNd SNa SN0 SC5 SC4 SC3 SC2 SC1
POL Aa2 Ba2 Ba2 Ca2 Ab2 Bb2 Bb2 Cb2 Cb2 Db2 Db2 Db2 Eb2 Fb2 Gb2 Gb2 Hb2 Ib2
D 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
"""
table_other_vsite = """
vQda vQd vQa vQ0 vP5 vP4 vP3 vP2 vP1 vNda vNd vNa vN0 vC5 vC4 vC3 vC2 vC1 vAC2 vAC1
POL Aa2 Ba2 Ba2 Ca2 Ab2 Bb2 Bb2 Cb2 Cb2 Db2 Db2 Db2 Eb2 Fb2 Gb2 Gb2 Hb2 Ib2 Hb2 Ib2
D 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
"""
table_other_svste = """
vSQda vSQd vSQa vSQ0 vSP5 vSP4 vSP3 vSP2 vSP1 vSNda vSNd vSNa vSN0 vSC5 vSC4 vSC3 vSC2 vSC1
POL Aa2 Ba2 Ba2 Ca2 Ab2 Bb2 Bb2 Cb2 Cb2 Db2 Db2 Db2 Eb2 Fb2 Gb2 Gb2 Hb2 Ib2
D 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
"""
#++++++++++++++++++++++++++++++++
def table2pairs(x):
labels2 = x.pop(0)
return [((i[0],j),k) for i in x for j,k in zip(labels2,i[1:])]
def sigeps2c(eps=None,scl="a",sig="2"):
"""
Convert a string encoding for epsilon, sigma and scaling to C6 and C12 parameters
"""
if eps == None:
return None,None
if scl in sigma.keys():
sig, scl = scl, "2"
return 4*epsilon[eps]*scale[scl]*sigma[sig]**6, 4*epsilon[eps]*scale[scl]*sigma[sig]**12
tables = []
for i in classes:
tables.append(globals().get("table_%s"%i))
for j in classes:
tables.append(globals().get("table_%s_%s"%(i,j)))
tables = [[ j.split() for j in i.split("\n") if j not in ("","\n") ] for i in tables if i]
pairs = dict([j for i in tables for j in table2pairs(i)])
## -- Prepare the output
atomtypes = []
nonbond_params = []
pairtypes = []
## Read in atomistic stuff
# If a file with nonbonded parameters (atom types and interactions)
# is given on the command line, the output will be a merged forcefield
aa = len(sys.argv) > 1 and open(sys.argv[1]).readlines()
if len(sys.argv) > 1:
aa = open(sys.argv[1]).readlines()
key = ""
atomtypes.append("; Atomistic definitions\n")
nonbond_params.append("; Atomistic definitions\n")
pairtypes.append("; Atomistic definitions\n")
hk = hybrid.keys()
for line in aa:
s = line.strip()
if s and s[0] == "[":
key=line
elif "nonbond_params" in key:
nb = line.split()
# Have to exclude the hybrid atoms
# These (ions) should have CG self-interactions
if not (nb and nb[0] in hk and nb[1] in hk):
nonbond_params.append(line)
elif "atomtypes" in key:
atomtypes.append(line)
elif "pairtypes" in key:
pairtypes.append(line)
atomtypes.append("; End of atomistic definitions\n")
nonbond_params.append("; End of atomistic definitions\n")
pairtypes.append("; End of atomistic definitions\n")
# Note which atomtypes we have for defining interactions with dummy particles
aa_atomtypes = [i.split()[0] for i in atomtypes if i.strip() and not i.strip()[0] == ";"]
# Add coarsegrained stuff
typestr="%5s 0 %10.3f 0.000 %1s 0.0 0.0\n"
atomtypes.extend([typestr%(tp,ms,tp in virtual and 'V' or 'A') for tp,ms in zip(all,mass)])
# Reverse the hybrid stuff declared above
hv = hybrid.values()
mixed = {}
for k,v in hybrid.iteritems():
mixed.setdefault(v,[]).append(k)
for i,j in cmb:
c6,c12 = sigeps2c(*pairs.get((i,j),pairs.get((j,i),"")))
if c6 != None:
nonbond_params.append(" %7s %7s %2d %e %e\n"%(i,j,1,c6,c12))
mi = mixed.get(i,[])
mj = mixed.get(j,[])
for ki in mi:
nonbond_params.append(" %7s %7s %2d %e %e\n"%(ki,j,1,c6,c12))
for kj in mj:
nonbond_params.append(" %7s %7s %2d %e %e\n"%(ki,kj,1,c6,c12))
for kj in mj:
nonbond_params.append(" %7s %7s %2d %e %e\n"%(i,kj,1,c6,c12))
atomtypes.append("; End of coarsegrained definitions\n")
if nonbond_params:
nonbond_params.append("; End of coarsegrained definitions\n")
if pairtypes:
pairtypes.append("; End of coarsegrained definitions\n")
for i in dummy:
for j in aa_atomtypes:
if not j in hk:
nonbond_params.append(" %7s %7s %2d 0.0 DUMMY_REPEL\n"%(i,j,1))
## Print stuff:
print "; This file was created automagically by", sys.argv[0]
print "; (c)2012 Tsjerk A Wassenaar, University of Groningen"
print ";"
if len(sys.argv) > 1:
print "; This file contains a merged forcefield, combining %s with MARTINI" % sys.argv[1]
print ";"
print "#define DUMMY_REPEL 1e-7"
print ";"
print martini_v2_P
print "".join(atomtypes), "\n"
print "[ nonbond_params ]\n", "".join(nonbond_params), "\n"
if pairtypes:
print "[ pairtypes ]\n", "".join(pairtypes), "\n"
print
for i in sys.argv[2:]: print open(i).read()
# Also print water models:
print """
;;;;;; MARTINI WATER
[ moleculetype ]
; molname nrexcl
W 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 P4 1 W W 1 0
;;;;;; ANTIFREEZE (prevents freezing of water)
[ moleculetype ]
; molname nrexcl
WF 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 BP4 1 WF WF 1 0
;;;;;; POLARIZABLE WATER
[ moleculetype ]
; molname nrexcl
PW 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 POL 1 PW W 1 0
2 D 1 PW WP 1 0.46
3 D 1 PW WM 1 -0.46
#ifdef FLEXIBLE
; for minimization purposes replace constraints by stiff bonds:
[bonds]
; i j funct length force const.
1 2 1 0.14 50000
1 3 1 0.14 50000
#else
[constraints]
; i j funct length
1 2 1 0.14
1 3 1 0.14
#endif
[angles]
; i j k funct angle fc
2 1 3 2 0.0 4.2
[exclusions]
1 2 3
2 3
"""