def __init__(self):
import SS,FUNC,IO
# parameters are defined here for the following (protein) forcefields:
self.name = 'elnedyn22'
# Charged types:
self.charges = {"Qd":1, "Qa":-1, "SQd":1, "SQa":-1, "RQd":1, "AQa":-1} #@#
#----+---------------------+
## A | BACKBONE PARAMETERS |
#----+---------------------+
#
# bbss lists the one letter secondary structure code
# bbdef lists the corresponding default backbone beads
# bbtyp lists the corresponding residue specific backbone beads
#
# bbd lists the structure specific backbone bond lengths
# bbkb lists the corresponding bond force constants
#
# bba lists the structure specific angles
# bbka lists the corresponding angle force constants
#
# bbd lists the structure specific dihedral angles
# bbkd lists the corresponding force constants
#
# -=NOTE=-
# if the secondary structure types differ between bonded atoms
# the bond is assigned the lowest corresponding force constant
#
# -=NOTE=-
# if proline is anywhere in the helix, the BBB angle changes for
# all residues
#
###############################################################################################
## BEADS ## #
# F E H 1 2 3 T S C # SS one letter
self.bbdef = FUNC.spl(" N0 Nda N0 Nd Na Nda Nda P5 P5") # Default beads #@#
self.bbtyp = { # #@#
"ALA": FUNC.spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4"), # ALA specific #@#
"PRO": FUNC.spl(" C5 N0 C5 N0 Na N0 N0 P4 P4"), # PRO specific #@#
"HYP": FUNC.spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4") # HYP specific #@#
} # #@#
## BONDS ## #
self.bbldef = (.365, .350, .350, .350, .350, .350, .350, .350, .350) # BB bond lengths #@#
self.bbkb = (1250, 1250, 1250, 1250, 1250, 1250, 500, 400, 400) # BB bond kB #@#
self.bbltyp = {} # #@#
self.bbkbtyp = {} # #@#
## ANGLES ## #
self.bbadef = (119.2, 134, 96, 96, 96, 96, 100, 130, 127) # BBB angles #@#
self.bbka = ( 150, 25, 700, 700, 700, 700, 25, 25, 25) # BBB angle kB #@#
self.bbatyp = { # #@#
"PRO": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127), # PRO specific #@#
"HYP": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127) # PRO specific #@#
} # #@#
self.bbkatyp = { # #@#
"PRO": ( 150, 25, 100, 100, 100, 100, 25, 25, 25), # PRO specific #@#
"HYP": ( 150, 25, 100, 100, 100, 100, 25, 25, 25) # PRO specific #@#
} # #@#
## DIHEDRALS ## #
self.bbddef = (90.7, 0, -120, -120, -120, -120) # BBBB dihedrals #@#
self.bbkd = ( 100, 10, 400, 400, 400, 400) # BBBB kB #@#
self.bbdmul = ( 1, 1, 1, 1, 1, 1) # BBBB mltplcty #@#
self.bbdtyp = {} # #@#
self.bbkdtyp = {} # #@#
#
###############################################################################################
# Some Forcefields use the Ca position to position the BB-bead (me like!)
self.ca2bb = True
# BBS angle, equal for all ss types
# Connects BB(i-1),BB(i),SC(i), except for first residue: BB(i+1),BB(i),SC(i)
# ANGLE Ka
self.bbsangle = [ 100, 25] #@#
# Bonds for extended structures (more stable than using dihedrals)
# LENGTH FORCE
self.ebonds = { #@#
'short': [ .640, 2500], #@#
'long' : [ .970, 2500] #@#
} #@#
#----+-----------------------+
## B | SIDE CHAIN PARAMETERS |
#----+-----------------------+
# Sidechain parameters for Elnedyn. (read from cg-2.1.dat).
# For HIS the order of bonds is changed and a bond with fc=0 is added.
# In the elnedyn2, TRP has an extra, cross-ring constraint
self.sidechains = {
#RES# BEADS BONDS ANGLES DIHEDRALS
'TRP': [FUNC.spl("SC4 SNd SC5 SC5"), [(0.255,73000), (0.220,None), (0.250,None), (0.280,None), (0.255,None), (0.35454,None)], [(142,30), (143,20), (104,50)], [(180,200)]],
'TYR': [FUNC.spl("SC4 SC4 SP1"), [(0.335, 6000), (0.335,6000), (0.240,None), (0.310,None), (0.310,None)], [(70,100), (130, 50)]],
'PHE': [FUNC.spl("SC5 SC5 SC5"), [(0.340, 7500), (0.340,7500), (0.240,None), (0.240,None), (0.240,None)], [(70,100), (125,100)]],
'HIS': [FUNC.spl("SC4 SP1 SP1"), [(0.195, None), (0.193,None), (0.295,None), (0.216,None)], [(135,100),(115, 50)]],
'HIH': [FUNC.spl("SC4 SP1 SP1"), [(0.195, None), (0.193,None), (0.295,None), (0.216,None)], [(135,100),(115, 50)]],
'ARG': [FUNC.spl("N0 Qd"), [(0.250,12500), (0.350,6200)], [(150,15)]],
'LYS': [FUNC.spl("C3 Qd"), [(0.250,12500), (0.300,9700)], [(150,20)]],
'CYS': [FUNC.spl("C5"), [(0.240, None)]],
'ASP': [FUNC.spl("Qa"), [(0.255, None)]],
'GLU': [FUNC.spl("Qa"), [(0.310, 2500)]],
'ILE': [FUNC.spl("C1"), [(0.225,13250)]],
'LEU': [FUNC.spl("C1"), [(0.265, None)]],
'MET': [FUNC.spl("C5"), [(0.310, 2800)]],
'ASN': [FUNC.spl("P5"), [(0.250, None)]],
'PRO': [FUNC.spl("C3"), [(0.190, None)]],
'GLN': [FUNC.spl("P4"), [(0.300, 2400)]],
'SER': [FUNC.spl("P1"), [(0.195, None)]],
'THR': [FUNC.spl("P1"), [(0.195, None)]],
'VAL': [FUNC.spl("C2"), [(0.200, None)]],
'GLY': [],
'ALA': [],
}
# Not all (eg Elnedyn) forcefields use backbone-backbone-sidechain angles and BBBB-dihedrals.
self.UseBBSAngles = False
self.UseBBBBDihedrals = False
# Martini 2.2p has polar and charged residues with seperate charges.
self.polar = []
self.charged = []
# If masses or charged diverge from standard (45/72 and -/+1) they are defined here.
self.mass_charge = {
#RES MASS CHARGE
}
# Defines the connectivity between between beads
# Connectivity records for Elnedyn (read from cg-2.1.dat).
# For HIS the order of bonds is changed and a bond with fc=0 is added.
self.connectivity = {
#RES BONDS ANGLES DIHEDRALS V-SITE
"TRP": [[(0, 1), (1, 2), (2, 4), (4, 3), (3, 1), (1, 4)],[(0, 1, 2), (0, 1, 4), (0, 1, 3)],[(1, 2, 3, 4)]],
"TYR": [[(0, 1), (0, 2), (1, 2), (1, 3), (2, 3)], [(0, 1, 2), (0, 1, 3)]],
"PHE": [[(0, 1), (0, 2), (1, 2), (1, 3), (2, 3)], [(0, 1, 2), (0, 1, 3)]],
"HIS": [[(0, 1), (1, 2), (1, 3), (2, 3)], [(0, 1, 2), (0, 1, 3)]],
"HIH": [[(0, 1), (1, 2), (1, 3), (2, 3)], [(0, 1, 2), (0, 1, 3)]],
"GLN": [[(0,1)]],
"ASN": [[(0,1)]],
"SER": [[(0,1)]],
"THR": [[(0,1)]],
"ARG": [[(0,1),(1,2)], [(0,1,2)]],
"LYS": [[(0,1),(1,2)], [(0,1,2)]],
"ASP": [[(0,1)]],
"GLU": [[(0,1)]],
"CYS": [[(0,1)]],
"ILE": [[(0,1)]],
"LEU": [[(0,1)]],
"MET": [[(0,1)]],
"PRO": [[(0,1)]],
"HYP": [[(0,1)]],
"VAL": [[(0,1)]],
"ALA": [],
"GLY": [],
}
#----+----------------+
## C | SPECIAL BONDS |
#----+----------------+
self.special = {
# Used for sulfur bridges
# ATOM 1 ATOM 2 BOND LENGTH FORCE CONSTANT
(("SC1","CYS"), ("SC1","CYS")): (0.24, None),
}
# By default use an elastic network
self.ElasticNetwork = True
# Elastic networks bond shouldn't lead to exclusions (type 6)
# But Elnedyn has been parametrized with type 1.
self.EBondType = 1
#----+----------------+
## D | INTERNAL STUFF |
#----+----------------+
## BACKBONE BEAD TYPE ##
# Dictionary of default bead types (*D)
self.bbBeadDictD = FUNC.hash(SS.bbss,self.bbdef)
# Dictionary of dictionaries of types for specific residues (*S)
self.bbBeadDictS = dict([(i,FUNC.hash(SS.bbss,self.bbtyp[i])) for i in self.bbtyp.keys()])
## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = FUNC.hash(SS.bbss,zip(self.bbldef,self.bbkb))
# Dictionary of dictionaries for specific types (*S)
self.bbBondDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbltyp[i],self.bbkbtyp[i]))) for i in self.bbltyp.keys()])
# This is tricky to read, but it gives the right bondlength/force constant
## BBB ANGLE TYPE ##
# Dictionary of default angle types (*D)
self.bbAngleDictD = FUNC.hash(SS.bbss,zip(self.bbadef,self.bbka))
# Dictionary of dictionaries for specific types (*S)
self.bbAngleDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbatyp[i],self.bbkatyp[i]))) for i in self.bbatyp.keys()])
## BBBB DIHEDRAL TYPE ##
# Dictionary of default dihedral types (*D)
self.bbDihedDictD = FUNC.hash(SS.bbss,zip(self.bbddef,self.bbkd,self.bbdmul))
# Dictionary of dictionaries for specific types (*S)
self.bbDihedDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbdtyp[i],self.bbkdtyp[i]))) for i in self.bbdtyp.keys()])
def __init__(self):
import SS,FUNC,IO
# parameters are defined here for the following (protein) forcefields:
self.name = 'martini22dna'
# Charged types:
self.charges = {"Qd":1, "Qa":-1, "SQd":1, "SQa":-1, "RQd":1, "AQa":-1} #@#
self.bbcharges = {"BB1":-1} #@#
#----+---------------------+
## A | BACKBONE PARAMETERS |
#----+---------------------+
#
# bbss lists the one letter secondary structure code
# bbdef lists the corresponding default backbone beads
# bbtyp lists the corresponding residue specific backbone beads
#
# bbd lists the structure specific backbone bond lengths
# bbkb lists the corresponding bond force constants
#
# bba lists the structure specific angles
# bbka lists the corresponding angle force constants
#
# bbd lists the structure specific dihedral angles
# bbkd lists the corresponding force constants
#
# -=NOTE=-
# if the secondary structure types differ between bonded atoms
# the bond is assigned the lowest corresponding force constant
#
# -=NOTE=-
# if proline is anywhere in the helix, the BBB angle changes for
# all residues
#
###############################################################################################
## BEADS ## #
# F E H 1 2 3 T S C # SS one letter
self.bbdef = FUNC.spl(" N0 Nda N0 Nd Na Nda Nda P5 P5") # Default beads #@#
self.bbtyp = { # #@#
"ALA": FUNC.spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4"), # ALA specific #@#
"PRO": FUNC.spl(" C5 N0 C5 N0 Na N0 N0 P4 P4"), # PRO specific #@#
"HYP": FUNC.spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4") # HYP specific #@#
} # #@#
## BONDS ## #
self.bbldef = (.365, .350, .310, .310, .310, .310, .350, .350, .350) # BB bond lengths #@#
self.bbkb = (1250, 1250, None, None, None, None, 1250, 1250, 1250) # BB bond kB #@#
self.bbltyp = {} # #@#
self.bbkbtyp = {} # #@#
## ANGLES ## #
self.bbadef = ( 119.2,134, 96, 96, 96, 96, 100, 130, 127) # BBB angles #@#
self.bbka = ( 150, 25, 700, 700, 700, 700, 20, 20, 20) # BBB angle kB #@#
self.bbatyp = { # #@#
"PRO": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127), # PRO specific #@#
"HYP": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127) # PRO specific #@#
} # #@#
self.bbkatyp = { # #@#
"PRO": ( 150, 25, 100, 100, 100, 100, 25, 25, 25), # PRO specific #@#
"HYP": ( 150, 25, 100, 100, 100, 100, 25, 25, 25) # PRO specific #@#
} # #@#
## DIHEDRALS ## #
self.bbddef = ( 90.7, 0, -120, -120, -120, -120) # BBBB dihedrals #@#
self.bbkd = ( 100, 10, 400, 400, 400, 400) # BBBB kB #@#
self.bbdmul = ( 1, 1, 1, 1, 1, 1) # BBBB mltplcty #@#
self.bbdtyp = {} # #@#
self.bbkdtyp = {} # #@#
#
###############################################################################################
# Some Forcefields use the Ca position to position the BB-bead (me like!)
# martini 2.1 doesn't
self.ca2bb = False
# BBS angle, equal for all ss types
# Connects BB(i-1),BB(i),SC(i), except for first residue: BB(i+1),BB(i),SC(i)
# ANGLE Ka
self.bbsangle = [ 100, 25] #@#
# Bonds for extended structures (more stable than using dihedrals)
# LENGTH FORCE
self.ebonds = { #@#
'short': [ .640, 2500], #@#
'long' : [ .970, 2500] #@#
} #@#
#----+-----------------------+
## B | SIDE CHAIN PARAMETERS |
#----+-----------------------+
# To be compatible with Elnedyn, all parameters are explicitly defined, even if they are double.
self.sidechains = {
#RES# BEADS BONDS ANGLES DIHEDRALS
# BB-SC SC-SC BB-SC-SC SC-SC-SC
"TRP": [FUNC.spl("SC4 SNd SC5 SC5"),[(0.300,5000)]+[(0.270,None) for i in range(5)], [(210,50),(90,50),(90,50)], [(0,50),(0,200)]],
"TYR": [FUNC.spl("SC4 SC4 SP1"), [(0.320,5000), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"PHE": [FUNC.spl("SC5 SC5 SC5"), [(0.310,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"HIS": [FUNC.spl("SC4 SP1 SP1"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"HIH": [FUNC.spl("SC4 SP1 SQd"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"ARG": [FUNC.spl("N0 Qd"), [(0.330,5000), (0.340,5000)], [(180,25)]],
"LYS": [FUNC.spl("C3 Qd"), [(0.330,5000), (0.280,5000)], [(180,25)]],
"CYS": [FUNC.spl("C5"), [(0.310,7500)]],
"ASP": [FUNC.spl("Qa"), [(0.320,7500)]],
"GLU": [FUNC.spl("Qa"), [(0.400,5000)]],
"ILE": [FUNC.spl("AC1"), [(0.310,None)]],
"LEU": [FUNC.spl("AC1"), [(0.330,7500)]],
"MET": [FUNC.spl("C5"), [(0.400,2500)]],
"ASN": [FUNC.spl("P5"), [(0.320,5000)]],
"PRO": [FUNC.spl("C3"), [(0.300,7500)]],
"HYP": [FUNC.spl("P1"), [(0.300,7500)]],
"GLN": [FUNC.spl("P4"), [(0.400,5000)]],
"SER": [FUNC.spl("P1"), [(0.250,7500)]],
"THR": [FUNC.spl("P1"), [(0.260,None)]],
"VAL": [FUNC.spl("AC2"), [(0.265,None)]],
"ALA": [],
"GLY": [],
}
# Not all (eg Elnedyn) forcefields use backbone-backbone-sidechain angles and BBBB-dihedrals.
self.UseBBSAngles = True
self.UseBBBBDihedrals = True
# Martini 2.2p has polar and charged residues with seperate charges.
self.polar = []
self.charged = []
# If masses or charged diverge from standard (45/72 and -/+1) they are defined here.
self.mass_charge = {
#RES MASS CHARGE
}
# Defines the connectivity between between beads
self.aa_connectivity = {
#RES BONDS ANGLES DIHEDRALS V-SITE
"TRP": [[(0,1),(1,2),(1,3),(2,3),(2,4),(3,4)], [(0,1,2),(0,1,3)], [(0,2,3,1),(1,2,4,3)]],
"TYR": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"PHE": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIS": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIH": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"GLN": [[(0,1)]],
"ASN": [[(0,1)]],
"SER": [[(0,1)]],
"THR": [[(0,1)]],
"ARG": [[(0,1),(1,2)], [(0,1,2)]],
"LYS": [[(0,1),(1,2)], [(0,1,2)]],
"ASP": [[(0,1)]],
"GLU": [[(0,1)]],
"CYS": [[(0,1)]],
"ILE": [[(0,1)]],
"LEU": [[(0,1)]],
"MET": [[(0,1)]],
"PRO": [[(0,1)]],
"HYP": [[(0,1)]],
"VAL": [[(0,1)]],
"ALA": [],
"GLY": [],
}
#----+----------------+
## C | DNA/RNA bases |
#----+----------------+
# DNA BACKBONE PARAMETERS
self.dna_bb = {
'atom' : FUNC.spl("Q0 SN0 SC2"),
'bond' : [(1, 0.360, 20000),
(1, 0.198, 80000),
(1, 0.353, 10000)],
'angle' : [(2, 110.0, 200),
(2, 102.0, 150),
(2, 106.0, 75)],
'dih' : [(2, 95.0, 25),
(1, 180.0, 2, 3),
(9, 85.0, 2, 2, 9, 160.0, 2, 3)],
'excl' : [(), (), ()],
'pair' : [],
}
# DNA BACKBONE CONNECTIVITY
self.dna_con = {
'bond' : [(0, 1),
(1, 2),
(2, 0)],
'angle' : [(0, 1, 2),
(1, 2, 0),
(2, 0, 1)],
'dih' : [(0, 1, 2, 0),
(1, 2, 0, 1),
(2, 0, 1, 2)],
'excl' : [(0, 2), (1, 0),(2, 1)],
'pair' : [],
}
## FOR PLOTTING ONLY
# # DNA BACKBONE PARAMETERS
# self.dna_bb = {
# 'atom' : FUNC.spl("Q0 SN0 SC2"),
# 'bond' : [(1, 0.360, 30000),
# (1, 0.400, 10000),
# (1, 0.200, 50000),
# (1, 0.355, 10000)],
# 'angle' : [(2, 115.0, 85),
# (2, 102.0, 105),
# (2, 110.0, 60)],
# 'dih' : [(2, 100.0, 1),
# (2, -120.0, 5),
# (2, 140.0, 5)],
# 'excl' : [(), (), ()],
# }
# # DNA BACKBONE CONNECTIVITY
# self.dna_con = {
# 'bond' : [(0, 1),
# (0, 2),
# (1, 2),
# (2, 0)],
# 'angle' : [(0, 1, 2),
# (1, 2, 0),
# (2, 0, 1)],
# 'dih' : [(0, 1, 2, 0),
# (1, 2, 0, 1),
# (2, 0, 1, 2)],
# 'excl' : [(0, 2), (1, 0), (2, 1)],
# }
# RNA BACKBONE PARAMETERS
self.rna_bb = {
'atom' : FUNC.spl("Q0 N0 C2"),
'bond' : [(0.120,5000),(0.220,5000),(0.320,5000)],
'angle' : [(10.0, 100), (20.0, 100), (30.0, 100)],
'dih' : [(100, 10), (100, 10), (100, 10),],
'excl' : [],
}
# RNA BACKBONE CONNECTIVITY
self.rna_con = {
'bond' : [(0,1),(1,2),(2,0)],
'angle' : [(0,1,2),(1,2,0),(2,0,1)],
'dih' : [(0,1,2,0),(1,2,0,1),(2,0,1,2)],
'excl' : [],
}
# For bonds, angles, and dihedrals the first parameter should always
# be the type. It is pretty annoying to check the connectivity from
# elsewhere so we update these one base at a time.
# ADENINE
self.bases = {
"DA": [FUNC.spl("TN0 TA2 TA3 TNa"),
# TYPE EQUIL OPTS TYPE EQUIL OPTS TYPE EQUIL OPTS
# [(1, 0.348, 20000), (1, 0.229, None), (1, 0.266, None), # BONDS BB3-SC1 bond lengthened by 0.048 nm.
[(1, 0.300, 30000), (1, 0.229, None), (1, 0.266, None), # BONDS BB3-SC1 bond lengthened by 0.048 nm.
(1, 0.326, 20000), (1, 0.288, None), (1, 0.162, None),],
[(2, 94.0, 250), (2, 160.0, 200), (2, 140.0, 200), # ANGLES
(1, 85.0, 200), (2, 158.0, 200), (1, 125.0, 200),
(1, 74.0, 200), (1, 98.0, 200)],
[(2, -90.0, 20), (2, -116.0, 0.5), (2, 98.0, 15)], # DIHEDRALS
[], # IMPROPERS
[], # VSITES
[(), (), (), (), (), (), (), (), (), (), (), (), (), ()], # EXCLUSIONS
[]], # PAIRS
}
self.base_connectivity = {
"DA": [[(2, 3), (3, 4), (4, 5), # BONDS
(4, 6), (5, 6), (6, 3)],
[(1, 2, 3), (2, 3, 4), (2, 3, 6), # ANGLES
(3, 4, 5), (3, 2, 7), (4, 3, 6),
(4, 5, 6), (5, 6, 3)],
[(0, 1, 2, 3), (1, 2, 3, 4), (1, 2, 3, 6),], # DIHEDRALS
[], # IMPROPERS
[], # VSITES
[(0, 3), (0, 4), (0, 5), # EXCLUSIONS
(0, 6), (1, 3), (1, 4),
(1, 5), (1, 6), (2, 3),
(2, 4), (2, 5), (2, 6),
(3, 5), (4, 6)],
[]], # PAIRS
}
# CYTOSINE
self.bases.update({
"DC": [FUNC.spl("TN0 TY2 TY3"),
# TYPE EQUIL OPTS TYPE EQUIL OPTS TYPE EQUIL OPTS
# [(1, 0.303, 20000), (1, 0.220, None), (1, 0.285, None), # BONDS BB3-SC1 bond lenghtened by 0.033 nm.
[(1, 0.270, 30000), (1, 0.220, None), (1, 0.285, None), # BONDS BB3-SC1 bond lenghtened by 0.033 nm.
(1, 0.268, None),],
[(2, 95.0, 210), (2, 95.0, 300), (1, 150.0, 500), # ANGLES
(1, 180.0, 30), (1, 61.0, 200), (1, 71.0, 200),
(1, 47.0, 200)],
[(2, -78.0, 25), (2, -90.0, 20), (2, -142.0, 50)], # DIHEDRALS
#[(2, -78.0, 25), (2, -108.0, 10), (2, 40.0, 15)], # DIHEDRALS
[], # IMPROPERS
[], # VSITES
[(), (), (), (), (), (), (), (), ()], # EXCLUSIONS
[]], # PAIRS
})
self.base_connectivity.update({
"DC": [[(2, 3), (3, 4), (4, 5), # BONDS
(5, 3)],
[(1, 2, 3), (2, 3, 4), (1, 3, 5), # ANGLES
(3, 2, 6), (3, 4, 5), (4, 3, 5),
(4, 5, 3)],
[(0, 1, 2, 3), (1, 2, 3, 4), (2, 1, 3, 5)], # DIHEDRALS
[], # IMPROPERS
[], # VSITES
[(0, 3), (0, 4), (0, 5), # EXCLUSIONS
(1, 3), (1, 4), (1, 5),
(2, 3), (2, 4), (2, 5)],
[]], # PAIRS
})
# GUANINE
self.bases.update({
"DG": [FUNC.spl("TN0 TG2 TG3 TNa"),
# TYPE EQUIL OPTS TYPE EQUIL OPTS TYPE EQUIL OPTS
# [(1, 0.353, 20000), (1, 0.295, None), (1, 0.295, None), # BONDS BB3-SC1 bond lengthened by 0.053 nm.
[(1, 0.300, 30000), (1, 0.295, None), (1, 0.295, None), # BONDS BB3-SC1 bond lengthened by 0.053 nm.
(1, 0.389, 20000), (1, 0.285, None), (1, 0.161, None),],
[(2, 94.5, 250), (2, 137.0, 300), (2, 130.0, 250), # ANGLES
(1, 69.5, 200), (2, 157.0, 150), (1, 125.0, 200),
(1, 84.0, 200), (1, 94.0, 200)],
[(2, -90.0, 20), (2, -117.0, 1), (2, 92.0, 15)], # DIHEDRALS
[], # IMPROPERS
[], # VSITES
[(), (), (), (), (), (), (), (), (), (), (), (), (), ()], # EXCLUSIONS
[]], # PAIRS
})
self.base_connectivity.update({
"DG": [[(2, 3), (3, 4), (4, 5), # BONDS
(4, 6), (5, 6), (6, 3)],
[(1, 2, 3), (2, 3, 4), (2, 3, 6), # ANGLES
(3, 4, 5), (3, 2, 7), (4, 3, 6),
(4, 5, 6), (5, 6, 3)],
[(0, 1, 2, 3), (1, 2, 3, 4), (1, 2, 3, 6),], # DIHEDRALS
[], # IMPROPERS
[], # VSITES
[(0, 3), (0, 4), (0, 5), # EXCLUSIONS
(0, 6), (1, 3), (1, 4),
(1, 5), (1, 6), (2, 3),
(2, 4), (2, 5), (2, 6),
(3, 5), (4, 6)],
[]], # PAIRS
})
# THYMINE
self.bases.update({
"DT": [FUNC.spl("TN0 TT2 TT3"),
# TYPE EQUIL OPTS TYPE EQUIL OPTS TYPE EQUIL OPTS
# [(1, 0.326, 20000), (1, 0.217, None), (1, 0.322, None), # BONDS BB3-SC1 bond lengthened by 0.056 nm.
[(1, 0.270, 30000), (1, 0.217, None), (1, 0.322, None), # BONDS BB3-SC1 bond lengthened by 0.056 nm.
(1, 0.265, None),],
[(2, 92.0, 220), (2, 107.0, 300), (1, 145.0, 400), # ANGLES
(1, 180.0, 30), (1, 55.0, 100), (1, 83.0, 100),
(1, 42.0, 100)],
[(2, -75.0, 40), (2, -110.0, 15), (2, -145.0, 65)], # DIHEDRALS
[], # IMPROPERS
[], # VSITES
[(), (), (), (), (), (), (), (), ()], # EXCLUSIONS
[]], # PAIRS
})
self.base_connectivity.update({
"DT": [[(2, 3), (3, 4), (4, 5), # BONDS
(5, 3)],
[(1, 2, 3), (2, 3, 4), (1, 3, 5), # ANGLES
(3, 2, 6), (3, 4, 5), (4, 3, 5),
(4, 5, 3)],
[(0, 1, 2, 3), (1, 2, 3, 4), (2, 1, 3, 5)], # DIHEDRALS
[], # IMPROPERS
[], # VSITES
[(0, 3), (0, 4), (0, 5), # EXCLUSIONS
(1, 3), (1, 4), (1, 5),
(2, 3), (2, 4), (2, 5)],
[]], # PAIRS
})
## FOR PLOTTING ONLY
# # ADENINE
# self.bases = {
# "DA": [FUNC.spl("TN0 TA2 TA3 TNa"),
# # TYPE EQUIL OPTS TYPE EQUIL OPTS TYPE EQUIL OPTS
# [(1, 0.330, 30000), (1, 0.229, 30000), (1, 0.266, 30000), # BONDS BB3-SC1 bond lengthened by 0.030 nm.
# (1, 0.325, 30000), (1, 0.288, 30000), (1, 0.162, 30000),],
# [(2, 93.0, 250), (2, 160.0, 200), (2, 140.0, 200), # ANGLES
# (2, 85.0, 200), (2, 148.0, 350), (2, 125.0, 200),
# (2, 74.0, 200), (2, 98.0, 200)],
# [(2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1)],
# [(2, 0.0, 500)], # IMPROPERS
# [], # VSITES
# [(), (), (), (), (), (), (), (), (), (), (), (), (), ()]], # EXCLUSIONS
# }
# self.base_connectivity = {
# "DA": [[(2, 3), (3, 4), (4, 5), # BONDS
# (4, 6), (5, 6), (6, 3)],
# [(1, 2, 3), (2, 3, 4), (2, 3, 6), # ANGLES
# (3, 4, 5), (3, 2, 7), (4, 3, 6),
# (4, 5, 6), (5, 6, 3)],
# [(0, 1, 2, 3), (0, 2, 3, 4), (0, 2, 3, 6), # DIHEDRALS
# (1, 2, 3, 4), (1, 2, 3, 6), (2, 8, 9,10),
# (3, 2, 7, 8), (3, 2, 7, 9), (3, 2, 7,10),
# (3, 7, 8,10), (3, 8, 9,10), (4, 2, 7, 8),
# (7, 2, 3, 4), (7, 2, 3, 6)],
# [(3, 4, 5, 6)], # IMPROPERS
# [], # VSITES
# [(0, 3), (0, 4), (0, 5), # EXCLUSIONS
# (0, 6), (1, 3), (1, 4),
# (1, 5), (1, 6), (2, 3),
# (2, 4), (2, 5), (2, 6),
# (3, 5), (4, 6)]],
# }
#
# # CYTOSINE
# self.bases.update({
# "DC": [FUNC.spl("TN0 TY2 TY3"),
# # TYPE EQUIL OPTS TYPE EQUIL OPTS TYPE EQUIL OPTS
# [(1, 0.290, 30000), (1, 0.220, 30000), (1, 0.285, 30000), # BONDS BB3-SC1 bond lenghtened by 0.020 nm.
# (1, 0.268, 30000),],
# [(2, 93.0, 200), (2, 108.0, 250), (2, 170.0, 350), # ANGLES
# (2, 180.0, 1), (2, 62.0, 200), (2, 71.0, 200),
# (2, 47.0, 200), (2, 100.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1)],
# [(2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1)],
# [], # IMPROPERS
# [], # VSITES
# [(), (), (), (), (), (), (), (), ()]], # EXCLUSIONS
# })
# self.base_connectivity.update({
# "DC": [[(2, 3), (3, 4), (4, 5), # BONDS
# (5, 3)],
# [(1, 2, 3), (2, 3, 4), (2, 3, 5), # ANGLES
# (3, 2, 6), (3, 4, 5), (4, 3, 5),
# (4, 5, 3), (1, 3, 5), (1, 5, 3),
# (2, 3, 6), (2, 1, 3), (2, 1, 5)],
# [(0, 1, 2, 3), (0, 2, 3, 4), (0, 2, 3, 5), # DIHEDRALS
# (1, 2, 3, 4), (1, 2, 3, 5), (2, 7, 8, 9),
# (3, 2, 6, 7), (3, 2, 6, 8), (3, 2, 6, 9),
# (3, 6, 7, 9), (3, 7, 8, 9), (4, 2, 6, 7),
# (6, 2, 3, 4), (6, 2, 3, 5), (2, 1, 3, 5),
# (2, 1, 5, 3)],
# [], # IMPROPERS
# [], # VSITES
# [(0, 3), (0, 4), (0, 5), # EXCLUSIONS
# (1, 3), (1, 4), (1, 5),
# (2, 3), (2, 4), (2, 5)]],
# })
#
# # GUANINE
# self.bases.update({
# "DG": [FUNC.spl("TN0 TG2 TG3 TNa"),
# # TYPE EQUIL OPTS TYPE EQUIL OPTS TYPE EQUIL OPTS
# [(1, 0.300, 30000), (1, 0.295, 30000), (1, 0.295, 30000), # BONDS BB3-SC1 bond stays the same.
# (1, 0.390, 30000), (1, 0.285, 30000), (1, 0.161, 30000),],
# [(2, 95.0, 250), (2, 137.0, 300), (2, 128.0, 250), # ANGLES
# (2, 69.0, 200), (2, 145.0, 350), (2, 125.0, 200),
# (2, 84.0, 200), (2, 94.0, 200)],
# [(2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1)],
# [(2, 0.0, 150)], # IMPROPERS
# [], # VSITES
# [(), (), (), (), (), (), (), (), (), (), (), (), (), ()]], # EXCLUSIONS
# })
# self.base_connectivity.update({
# "DG": [[(2, 3), (3, 4), (4, 5), # BONDS
# (4, 6), (5, 6), (6, 3)],
# [(1, 2, 3), (2, 3, 4), (2, 3, 6), # ANGLES
# (3, 4, 5), (3, 2, 7), (4, 3, 6),
# (4, 5, 6), (5, 6, 3)],
# [(0, 1, 2, 3), (0, 2, 3, 4), (0, 2, 3, 6), # DIHEDRALS
# (1, 2, 3, 4), (1, 2, 3, 6), (2, 8, 9,10),
# (3, 2, 7, 8), (3, 2, 7, 9), (3, 2, 7,10),
# (3, 7, 8,10), (3, 8, 9,10), (4, 2, 7, 8),
# (7, 2, 3, 4), (7, 2, 3, 6)],
# [(3, 4, 5, 6)], # IMPROPERS
# [], # VSITES
# [(0, 3), (0, 4), (0, 5), # EXCLUSIONS
# (0, 6), (1, 3), (1, 4),
# (1, 5), (1, 6), (2, 3),
# (2, 4), (2, 5), (2, 6),
# (3, 5), (4, 6)]],
# })
#
# # THYMINE
# self.bases.update({
# "DT": [FUNC.spl("TN0 TT2 TT3"),
# # TYPE EQUIL OPTS TYPE EQUIL OPTS TYPE EQUIL OPTS
# [(1, 0.310, 30000), (1, 0.217, 30000), (1, 0.322, 30000), # BONDS BB3-SC1 bond lengthened by 0.040 nm.
# (1, 0.265, 30000),],
# [(2, 93.0, 250), (2, 108.0, 350), (2, 165.0, 550), # ANGLES
# (2, 165.0, 400), (2, 55.0, 200), (2, 83.0, 200),
# (2, 42.0, 200), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1)],
# [(2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1),
# (2, 0.0, 1), (2, 0.0, 1), (2, 0.0, 1)],
# [], # IMPROPERS
# [], # VSITES
# [(), (), (), (), (), (), (), (), ()]], # EXCLUSIONS
# })
# self.base_connectivity.update({
# "DT": [[(2, 3), (3, 4), (4, 5), # BONDS
# (5, 3)],
# [(1, 2, 3), (2, 3, 4), (2, 3, 5), # ANGLES
# (3, 2, 6), (3, 4, 5), (4, 3, 5),
# (4, 5, 3), (2, 3, 6), (1, 3, 5),
# (2, 1, 3), (2, 1, 5)],
# [(0, 1, 2, 3), (0, 2, 3, 4), (0, 2, 3, 5), # DIHEDRALS
# (1, 2, 3, 4), (1, 2, 3, 5), (2, 7, 8, 9),
# (3, 2, 6, 7), (3, 2, 6, 8), (3, 2, 6, 9),
# (3, 6, 7, 9), (3, 7, 8, 9), (4, 2, 6, 7),
# (6, 2, 3, 4), (6, 2, 3, 5), (2, 1, 3, 5)],
# [], # IMPROPERS
# [], # VSITES
# [(0, 3), (0, 4), (0, 5), # EXCLUSIONS
# (1, 3), (1, 4), (1, 5),
# (2, 3), (2, 4), (2, 5)]],
# })
#----+----------------+
## D | SPECIAL BONDS |
#----+----------------+
self.special = {
# Used for sulfur bridges
# ATOM 1 ATOM 2 BOND LENGTH FORCE CONSTANT
(("SC1","CYS"), ("SC1","CYS")): (0.39, 5000),
}
# By default use an elastic network
self.ElasticNetwork = False
# Elastic networks bond shouldn't lead to exclusions (type 6)
# But Elnedyn has been parametrized with type 1.
self.EBondType = 6
#----+----------------+
## D | INTERNAL STUFF |
#----+----------------+
## BACKBONE BEAD TYPE ##
# Dictionary of default bead types (*D)
self.bbBeadDictD = FUNC.hash(SS.bbss,self.bbdef)
# Dictionary of dictionaries of types for specific residues (*S)
self.bbBeadDictS = dict([(i,FUNC.hash(SS.bbss,self.bbtyp[i])) for i in self.bbtyp.keys()])
# combine the connectivity records for different molecule types
self.connectivity = dict(self.base_connectivity.items() + self.aa_connectivity.items())
# XXX No need to do that, let's just use separate for DNA for now
## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = FUNC.hash(SS.bbss,zip(self.bbldef,self.bbkb))
# Dictionary of dictionaries for specific types (*S)
self.bbBondDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbltyp[i],self.bbkbtyp[i]))) for i in self.bbltyp.keys()])
# This is tricky to read, but it gives the right bondlength/force constant
## BBB ANGLE TYPE ##
# Dictionary of default angle types (*D)
self.bbAngleDictD = FUNC.hash(SS.bbss,zip(self.bbadef,self.bbka))
# Dictionary of dictionaries for specific types (*S)
self.bbAngleDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbatyp[i],self.bbkatyp[i]))) for i in self.bbatyp.keys()])
## BBBB DIHEDRAL TYPE ##
# Dictionary of default dihedral types (*D)
self.bbDihedDictD = FUNC.hash(SS.bbss,zip(self.bbddef,self.bbkd,self.bbdmul))
# Dictionary of dictionaries for specific types (*S)
self.bbDihedDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbdtyp[i],self.bbkdtyp[i]))) for i in self.bbdtyp.keys()])
## DNA DICTIONARIES ##
# Dictionary for the connectivities and parameters of bonds between DNA backbone beads
self.dnaBbBondDictC = dict(zip(self.dna_con['bond'],self.dna_bb['bond']))
# Dictionary for the connectivities and parameters of angles between DNA backbone beads
self.dnaBbAngleDictC = dict(zip(self.dna_con['angle'],self.dna_bb['angle']))
# Dictionary for the connectivities and parameters of dihedrals between DNA backbone beads
self.dnaBbDihDictC = dict(zip(self.dna_con['dih'],self.dna_bb['dih']))
# Dictionary for exclusions for DNA backbone beads
self.dnaBbExclDictC = dict(zip(self.dna_con['excl'],self.dna_bb['excl']))
# Dictionary for pairs for DNA backbone beads
self.dnaBbPairDictC = dict(zip(self.dna_con['pair'],self.dna_bb['pair']))
## RNA DICTIONARIES ##
# Dictionary for the connectivities and parameters of bonds between RNA backbone beads
self.rnaBbBondDictC = dict(zip(self.rna_con['bond'],self.rna_bb['bond']))
# Dictionary for the connectivities and parameters of angles between rna backbone beads
self.rnaBbAngleDictC = dict(zip(self.rna_con['angle'],self.rna_bb['angle']))
# Dictionary for the connectivities and parameters of dihedrals between rna backbone beads
self.rnaBbDihDictC = dict(zip(self.rna_con['dih'],self.rna_bb['dih']))
# Dictionary for exclusions for RNA backbone beads
self.rnaBbExclDictC = dict(zip(self.rna_con['excl'],self.rna_bb['excl']))
def __init__(self):
import SS,FUNC,IO
# parameters are defined here for the following (protein) forcefields:
self.name = 'martini22'
# Charged types:
self.charges = {"Qd":1, "Qa":-1, "SQd":1, "SQa":-1, "RQd":1, "AQa":-1} #@#
#----+---------------------+
## A | BACKBONE PARAMETERS |
#----+---------------------+
#
# bbss lists the one letter secondary structure code
# bbdef lists the corresponding default backbone beads
# bbtyp lists the corresponding residue specific backbone beads
#
# bbd lists the structure specific backbone bond lengths
# bbkb lists the corresponding bond force constants
#
# bba lists the structure specific angles
# bbka lists the corresponding angle force constants
#
# bbd lists the structure specific dihedral angles
# bbkd lists the corresponding force constants
#
# -=NOTE=-
# if the secondary structure types differ between bonded atoms
# the bond is assigned the lowest corresponding force constant
#
# -=NOTE=-
# if proline is anywhere in the helix, the BBB angle changes for
# all residues
#
###############################################################################################
## BEADS ## #
# F E H 1 2 3 T S C # SS one letter
self.bbdef = FUNC.spl(" N0 Nda N0 Nd Na Nda Nda P5 P5") # Default beads #@#
self.bbtyp = { # #@#
"ALA": FUNC.spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4"), # ALA specific #@#
"PRO": FUNC.spl(" C5 N0 C5 N0 Na N0 N0 P4 P4"), # PRO specific #@#
"HYP": FUNC.spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4") # HYP specific #@#
} # #@#
## BONDS ## #
self.bbldef = (.365, .350, .310, .310, .310, .310, .350, .350, .350) # BB bond lengths #@#
self.bbkb = (1250, 1250, None, None, None, None, 1250, 1250, 1250) # BB bond kB #@#
self.bbltyp = {} # #@#
self.bbkbtyp = {} # #@#
## ANGLES ## #
self.bbadef = ( 119.2,134, 96, 96, 96, 96, 100, 130, 127) # BBB angles #@#
self.bbka = ( 150, 25, 700, 700, 700, 700, 20, 20, 20) # BBB angle kB #@#
self.bbatyp = { # #@#
"PRO": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127), # PRO specific #@#
"HYP": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127) # PRO specific #@#
} # #@#
self.bbkatyp = { # #@#
"PRO": ( 150, 25, 100, 100, 100, 100, 25, 25, 25), # PRO specific #@#
"HYP": ( 150, 25, 100, 100, 100, 100, 25, 25, 25) # PRO specific #@#
} # #@#
## DIHEDRALS ## #
self.bbddef = ( 90.7, 0, -120, -120, -120, -120) # BBBB dihedrals #@#
self.bbkd = ( 100, 10, 400, 400, 400, 400) # BBBB kB #@#
self.bbdmul = ( 1, 1, 1, 1, 1, 1) # BBBB mltplcty #@#
self.bbdtyp = {} # #@#
self.bbkdtyp = {} # #@#
#
###############################################################################################
# Some Forcefields use the Ca position to position the BB-bead (me like!)
# martini 2.1 doesn't
self.ca2bb = False
# BBS angle, equal for all ss types
# Connects BB(i-1),BB(i),SC(i), except for first residue: BB(i+1),BB(i),SC(i)
# ANGLE Ka
self.bbsangle = [ 100, 25] #@#
# Bonds for extended structures (more stable than using dihedrals)
# LENGTH FORCE
self.ebonds = { #@#
'short': [ .640, 2500], #@#
'long' : [ .970, 2500] #@#
} #@#
#----+-----------------------+
## B | SIDE CHAIN PARAMETERS |
#----+-----------------------+
# To be compatible with Elnedyn, all parameters are explicitly defined, even if they are double.
self.sidechains = {
#RES# BEADS BONDS ANGLES DIHEDRALS
# BB-SC SC-SC BB-SC-SC SC-SC-SC
"TRP": [FUNC.spl("SC4 SNd SC5 SC5"),[(0.300,5000)]+[(0.270,None) for i in range(5)], [(210,50),(90,50),(90,50)], [(0,50),(0,200)]],
"TYR": [FUNC.spl("SC4 SC4 SP1"), [(0.320,5000), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"PHE": [FUNC.spl("SC5 SC5 SC5"), [(0.310,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"HIS": [FUNC.spl("SC4 SP1 SP1"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"HIH": [FUNC.spl("SC4 SP1 SQd"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"ARG": [FUNC.spl("N0 Qd"), [(0.330,5000), (0.340,5000)], [(180,25)]],
"LYS": [FUNC.spl("C3 Qd"), [(0.330,5000), (0.280,5000)], [(180,25)]],
"CYS": [FUNC.spl("C5"), [(0.310,7500)]],
"ASP": [FUNC.spl("Qa"), [(0.320,7500)]],
"PAS": [FUNC.spl("P3"), [(0.320,7500)]],
"GLU": [FUNC.spl("Qa"), [(0.400,5000)]],
"ILE": [FUNC.spl("AC1"), [(0.310,None)]],
"LEU": [FUNC.spl("AC1"), [(0.330,7500)]],
"MET": [FUNC.spl("C5"), [(0.400,2500)]],
"ASN": [FUNC.spl("P5"), [(0.320,5000)]],
"PRO": [FUNC.spl("C3"), [(0.300,7500)]],
"HYP": [FUNC.spl("P1"), [(0.300,7500)]],
"GLN": [FUNC.spl("P4"), [(0.400,5000)]],
"SER": [FUNC.spl("P1"), [(0.250,7500)]],
"THR": [FUNC.spl("P1"), [(0.260,None)]],
"VAL": [FUNC.spl("AC2"), [(0.265,None)]],
"ALA": [],
"GLY": [],
}
# Not all (eg Elnedyn) forcefields use backbone-backbone-sidechain angles and BBBB-dihedrals.
self.UseBBSAngles = True
self.UseBBBBDihedrals = True
# Martini 2.2p has polar and charged residues with seperate charges.
self.polar = []
self.charged = []
# If masses or charged diverge from standard (45/72 and -/+1) they are defined here.
self.mass_charge = {
#RES MASS CHARGE
}
# Defines the connectivity between between beads
self.connectivity = {
#RES BONDS ANGLES DIHEDRALS V-SITE
"TRP": [[(0,1),(1,2),(1,3),(2,3),(2,4),(3,4)], [(0,1,2),(0,1,3)], [(0,2,3,1),(1,2,4,3)]],
"TYR": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"PHE": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIS": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIH": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"GLN": [[(0,1)]],
"ASN": [[(0,1)]],
"SER": [[(0,1)]],
"THR": [[(0,1)]],
"ARG": [[(0,1),(1,2)], [(0,1,2)]],
"LYS": [[(0,1),(1,2)], [(0,1,2)]],
"ASP": [[(0,1)]],
"PAS": [[(0,1)]],
"GLU": [[(0,1)]],
"CYS": [[(0,1)]],
"ILE": [[(0,1)]],
"LEU": [[(0,1)]],
"MET": [[(0,1)]],
"PRO": [[(0,1)]],
"HYP": [[(0,1)]],
"VAL": [[(0,1)]],
"ALA": [],
"GLY": [],
}
#----+----------------+
## C | SPECIAL BONDS |
#----+----------------+
self.special = {
# Used for sulfur bridges
# ATOM 1 ATOM 2 BOND LENGTH FORCE CONSTANT
(("SC1","CYS"), ("SC1","CYS")): (0.24, None),
}
# By default use an elastic network
self.ElasticNetwork = False
# Elastic networks bond shouldn't lead to exclusions (type 6)
# But Elnedyn has been parametrized with type 1.
self.EBondType = 6
#----+----------------+
## D | INTERNAL STUFF |
#----+----------------+
## BACKBONE BEAD TYPE ##
# Dictionary of default bead types (*D)
self.bbBeadDictD = FUNC.hash(SS.bbss,self.bbdef)
# Dictionary of dictionaries of types for specific residues (*S)
self.bbBeadDictS = dict([(i,FUNC.hash(SS.bbss,self.bbtyp[i])) for i in self.bbtyp.keys()])
## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = FUNC.hash(SS.bbss,zip(self.bbldef,self.bbkb))
# Dictionary of dictionaries for specific types (*S)
self.bbBondDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbltyp[i],self.bbkbtyp[i]))) for i in self.bbltyp.keys()])
# This is tricky to read, but it gives the right bondlength/force constant
## BBB ANGLE TYPE ##
# Dictionary of default angle types (*D)
self.bbAngleDictD = FUNC.hash(SS.bbss,zip(self.bbadef,self.bbka))
# Dictionary of dictionaries for specific types (*S)
self.bbAngleDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbatyp[i],self.bbkatyp[i]))) for i in self.bbatyp.keys()])
## BBBB DIHEDRAL TYPE ##
# Dictionary of default dihedral types (*D)
self.bbDihedDictD = FUNC.hash(SS.bbss,zip(self.bbddef,self.bbkd,self.bbdmul))
# Dictionary of dictionaries for specific types (*S)
self.bbDihedDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbdtyp[i],self.bbkdtyp[i]))) for i in self.bbdtyp.keys()])
def __init__(self):
import SS, FUNC, IO
# parameters are defined here for the following (protein) forcefields:
self.name = 'elnedyn22p'
# Charged types:
self.charges = {
"Qd": 1,
"Qa": -1,
"SQd": 1,
"SQa": -1,
"RQd": 1,
"AQa": -1
} #@#
#----+---------------------+
## A | BACKBONE PARAMETERS |
#----+---------------------+
#
# bbss lists the one letter secondary structure code
# bbdef lists the corresponding default backbone beads
# bbtyp lists the corresponding residue specific backbone beads
#
# bbd lists the structure specific backbone bond lengths
# bbkb lists the corresponding bond force constants
#
# bba lists the structure specific angles
# bbka lists the corresponding angle force constants
#
# bbd lists the structure specific dihedral angles
# bbkd lists the corresponding force constants
#
# -=NOTE=-
# if the secondary structure types differ between bonded atoms
# the bond is assigned the lowest corresponding force constant
#
# -=NOTE=-
# if proline is anywhere in the helix, the BBB angle changes for
# all residues
#
###############################################################################################
## BEADS ## #
# F E H 1 2 3 T S C # SS one letter
self.bbdef = FUNC.spl(
" N0 Nda N0 Nd Na Nda Nda P5 P5"
) # Default beads #@#
self.bbtyp = { # #@#
"ALA":
FUNC.spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4"
), # ALA specific #@#
"PRO":
FUNC.spl(" C5 N0 C5 N0 Na N0 N0 P4 P4"
), # PRO specific #@#
"HYP":
FUNC.spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4"
) # HYP specific #@#
} # #@#
## BONDS ## #
self.bbldef = (.365, .350, .350, .350, .350, .350, .350, .350, .350
) # BB bond lengths #@#
self.bbkb = (1250, 1250, 1250, 1250, 1250, 1250, 500, 400, 400
) # BB bond kB #@#
self.bbltyp = {} # #@#
self.bbkbtyp = {} # #@#
## ANGLES ## #
self.bbadef = (119.2, 134, 96, 96, 96, 96, 100, 130, 127
) # BBB angles #@#
self.bbka = (150, 25, 700, 700, 700, 700, 25, 25, 25
) # BBB angle kB #@#
self.bbatyp = { # #@#
"PRO":
(119.2, 134, 98, 98, 98, 98, 100, 130, 127), # PRO specific #@#
"HYP":
(119.2, 134, 98, 98, 98, 98, 100, 130, 127) # PRO specific #@#
} # #@#
self.bbkatyp = { # #@#
"PRO":
(150, 25, 100, 100, 100, 100, 25, 25, 25), # PRO specific #@#
"HYP":
(150, 25, 100, 100, 100, 100, 25, 25, 25) # PRO specific #@#
} # #@#
## DIHEDRALS ## #
self.bbddef = (90.7, 0, -120, -120, -120, -120) # BBBB dihedrals #@#
self.bbkd = (100, 10, 400, 400, 400, 400) # BBBB kB #@#
self.bbdmul = (1, 1, 1, 1, 1, 1) # BBBB mltplcty #@#
self.bbdtyp = {} # #@#
self.bbkdtyp = {} # #@#
#
###############################################################################################
# Some Forcefields use the Ca position to position the BB-bead (me like!)
self.ca2bb = True
# BBS angle, equal for all ss types
# Connects BB(i-1),BB(i),SC(i), except for first residue: BB(i+1),BB(i),SC(i)
# ANGLE Ka
self.bbsangle = [100, 25] #@#
# Bonds for extended structures (more stable than using dihedrals)
# LENGTH FORCE
self.ebonds = { #@#
'short': [.640, 2500], #@#
'long': [.970, 2500] #@#
} #@#
#----+-----------------------+
## B | SIDE CHAIN PARAMETERS |
#----+-----------------------+
# Sidechain parameters for Elnedyn. (read from cg-2.1.dat).
# For HIS the order of bonds is changed and a bond with fc=0 is added.
# In the elnedyn2, TRP has an extra, cross-ring constraint
self.sidechains = {
#RES# BEADS BONDS ANGLES DIHEDRALS V-SITES
'TRP': [
FUNC.spl("SC4 SNd SC5 SC5"),
[(0.255, 73000), (0.220, None), (0.250, None), (0.280, None),
(0.255, None), (0.35454, None)],
[(142, 30), (143, 20), (104, 50)], [(180, 200)]
],
'TYR': [
FUNC.spl("SC4 SC4 SP1"),
[(0.335, 6000), (0.335, 6000), (0.240, None), (0.310, None),
(0.310, None)], [(70, 100), (130, 50)]
],
'PHE': [
FUNC.spl("SC5 SC5 SC5"),
[(0.340, 7500), (0.340, 7500), (0.240, None), (0.240, None),
(0.240, None)], [(70, 100), (125, 100)]
],
'HIS': [
FUNC.spl("SC4 SP1 SP1"),
[(0.195, 94000), (0.193, None), (0.295, None), (0.216, None)],
[(135, 100), (115, 50)]
],
'HIH': [
FUNC.spl("SC4 SP1 SQd"),
[(0.195, 94000), (0.193, None), (0.295, None), (0.216, None),
(0.11, None)], [(135, 100), (115, 50)]
],
'GLN': [
FUNC.spl("Nda D D"), [(0.300, 2400), (0.280, None)], [], [],
[(0.5, )]
],
'ASN': [
FUNC.spl("Nda D D"), [(0.250, 61000), (0.280, None)], [], [],
[(0.5, )]
],
'SER': [
FUNC.spl("N0 D D"), [(0.195, 94000), (0.280, None)], [], [],
[(0.5, )]
],
'THR': [
FUNC.spl("N0 D D"), [(0.195, 94000), (0.280, None)], [], [],
[(0.5, )]
],
'ARG': [
FUNC.spl("N0 Qd D"),
[(0.250, 12500), (0.350, 6200), (0.110, None)], [(150, 15)]
],
'LYS': [
FUNC.spl("C3 Qd D"),
[(0.250, 12500), (0.300, 9700), (0.110, None)], [(150, 20)]
],
'ASP': [FUNC.spl("Qa D"), [(0.255, None), (0.110, None)]],
'GLU': [FUNC.spl("Qa D"), [(0.310, 2500), (0.110, None)]],
'CYS': [FUNC.spl("C5"), [(0.240, None)]],
'ILE': [FUNC.spl("C1"), [(0.225, 13250)]],
'LEU': [FUNC.spl("C1"), [(0.265, None)]],
'MET': [FUNC.spl("C5"), [(0.310, 2800)]],
'PRO': [FUNC.spl("C3"), [(0.190, None)]],
'HYP': [FUNC.spl("P1"), [(0.190, None)]],
'VAL': [FUNC.spl("C2"), [(0.200, None)]],
'GLY': [],
'ALA': [],
}
# Not all (eg Elnedyn) forcefields use backbone-backbone-sidechain angles and BBBB-dihedrals.
self.UseBBSAngles = False
self.UseBBBBDihedrals = False
# Martini 2.2p has polar and charged residues with seperate charges.
self.polar = ["GLN", "ASN", "SER", "THR"]
self.charged = ["ARG", "LYS", "ASP", "GLU", "HIH"]
# If masses or charged diverge from standard (45/72 and -/+1) they are defined here.
self.mass_charge = {
#RES MASS CHARGE
"GLN": [[0, 36, 36], [0, 0.42, -0.42]],
"ASN": [[0, 36, 36], [0, 0.46, -0.46]],
"SER": [[0, 36, 36], [0, 0.40, -0.40]],
"THR": [[0, 36, 36], [0, 0.36, -0.36]],
"ARG": [[72, 36, 36], [0, 0, 1]],
"LYS": [[72, 36, 36], [0, 0, 1]],
"HIH": [[72, 72, 36, 36], [0, 0, 0, 1]],
"ASP": [[36, 36], [0, -1]],
"GLU": [[36, 36], [0, -1]],
}
# Defines the connectivity between between beads
# The polar sidechains have charged dummy beads, connected with a constraint
# The charged sidechains have a charged dummy bead.
self.connectivity = {
#RES BONDS ANGLES DIHEDRALS V-SITE
"TRP": [[(0, 1), (1, 2), (2, 4), (4, 3), (3, 1), (1, 4)],
[(0, 1, 2), (0, 1, 4), (0, 1, 3)], [(1, 2, 3, 4)]],
"TYR": [[(0, 1), (0, 2), (1, 2), (1, 3), (2, 3)],
[(0, 1, 2), (0, 1, 3)]],
"PHE": [[(0, 1), (0, 2), (1, 2), (1, 3), (2, 3)],
[(0, 1, 2), (0, 1, 3)]],
"HIS": [[(0, 1), (1, 2), (1, 3), (2, 3)], [(0, 1, 2), (0, 1, 3)]],
"HIH": [[(0, 1), (1, 2), (1, 3), (2, 3), (3, 4)],
[(0, 1, 2), (0, 1, 3)], [(0, 2, 3, 1)]],
"GLN": [[(0, 1), (2, 3)], [], [], [(1, 2, 3)]],
"ASN": [[(0, 1), (2, 3)], [], [], [(1, 2, 3)]],
"SER": [[(0, 1), (2, 3)], [], [], [(1, 2, 3)]],
"THR": [[(0, 1), (2, 3)], [], [], [(1, 2, 3)]],
"ARG": [[(0, 1), (1, 2), (2, 3)], [(0, 1, 2)]],
"LYS": [[(0, 1), (1, 2), (2, 3)], [(0, 1, 2)]],
"ASP": [[(0, 1), (1, 2)]],
"GLU": [[(0, 1), (1, 2)]],
"CYS": [[(0, 1)]],
"ILE": [[(0, 1)]],
"LEU": [[(0, 1)]],
"MET": [[(0, 1)]],
"PRO": [[(0, 1)]],
"HYP": [[(0, 1)]],
"VAL": [[(0, 1)]],
"ALA": [],
"GLY": [],
}
#----+----------------+
## C | SPECIAL BONDS |
#----+----------------+
self.special = {
# Used for sulfur bridges
# ATOM 1 ATOM 2 BOND LENGTH FORCE CONSTANT
(("SC1", "CYS"), ("SC1", "CYS")): (0.24, None),
}
# By default use an elastic network
self.ElasticNetwork = True
# Elastic networks bond shouldn't lead to exclusions (type 6)
# But Elnedyn has been parametrized with type 1.
self.EBondType = 1
#----+----------------+
## D | INTERNAL STUFF |
#----+----------------+
## BACKBONE BEAD TYPE ##
# Dictionary of default bead types (*D)
self.bbBeadDictD = FUNC.hash(SS.bbss, self.bbdef)
# Dictionary of dictionaries of types for specific residues (*S)
self.bbBeadDictS = dict([(i, FUNC.hash(SS.bbss, self.bbtyp[i]))
for i in self.bbtyp.keys()])
## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = FUNC.hash(SS.bbss, zip(self.bbldef, self.bbkb))
# Dictionary of dictionaries for specific types (*S)
self.bbBondDictS = dict([
(i, FUNC.hash(SS.bbss, zip(self.bbltyp[i], self.bbkbtyp[i])))
for i in self.bbltyp.keys()
])
# This is tricky to read, but it gives the right bondlength/force constant
## BBB ANGLE TYPE ##
# Dictionary of default angle types (*D)
self.bbAngleDictD = FUNC.hash(SS.bbss, zip(self.bbadef, self.bbka))
# Dictionary of dictionaries for specific types (*S)
self.bbAngleDictS = dict([
(i, FUNC.hash(SS.bbss, zip(self.bbatyp[i], self.bbkatyp[i])))
for i in self.bbatyp.keys()
])
## BBBB DIHEDRAL TYPE ##
# Dictionary of default dihedral types (*D)
self.bbDihedDictD = FUNC.hash(SS.bbss,
zip(self.bbddef, self.bbkd, self.bbdmul))
# Dictionary of dictionaries for specific types (*S)
self.bbDihedDictS = dict([
(i, FUNC.hash(SS.bbss, zip(self.bbdtyp[i], self.bbkdtyp[i])))
for i in self.bbdtyp.keys()
])
##########################
import FUNC
dnares3 = " DA DC DG DT"
dnares1 = " dA dC dG dT"
rnares3 = " A C G U"
rnares1 = " rA rC rG rU"
# Amino acid nucleic acid codes:
# The naming (AA and '3') is not strictly correct when adding DNA/RNA, but we keep it like this for consistincy.
AA3 = FUNC.spl("TRP TYR PHE HIS HIH ARG LYS CYS ASP GLU ILE LEU MET ASN PRO HYP GLN SER THR VAL ALA GLY"+dnares3+rnares3) #@#
AA1 = FUNC.spl(" W Y F H H R K C D E I L M N P O Q S T V A G"+dnares1+rnares1) #@#
# Dictionaries for conversion from one letter code to three letter code v.v.
AA123, AA321 = FUNC.hash(AA1, AA3), FUNC.hash(AA3, AA1)
# Residue classes:
protein = AA3[:-8] # remove eight to get rid of DNA/RNA here.
water = FUNC.spl("HOH SOL TIP")
lipids = FUNC.spl("DPP DHP DLP DMP DSP POP DOP DAP DUP DPP DHP DLP DMP DSP PPC DSM DSD DSS")
nucleic = FUNC.spl("DAD DCY DGU DTH ADE CYT GUA THY URA DA DC DG DT")
residueTypes = dict(
[(i, "Protein") for i in protein ] +
[(i, "Water") for i in water ] +
[(i, "Lipid") for i in lipids ] +
[(i, "Nucleic") for i in nucleic ]
)
def __init__(self):
import SS,FUNC,IO
# parameters are defined here for the following (protein) forcefields:
self.name = 'martini22p'
# Charged types:
self.charges = {"Qd":1, "Qa":-1, "SQd":1, "SQa":-1, "RQd":1, "AQa":-1} #@#
#----+---------------------+
## A | BACKBONE PARAMETERS |
#----+---------------------+
#
# bbss lists the one letter secondary structure code
# bbdef lists the corresponding default backbone beads
# bbtyp lists the corresponding residue specific backbone beads
#
# bbd lists the structure specific backbone bond lengths
# bbkb lists the corresponding bond force constants
#
# bba lists the structure specific angles
# bbka lists the corresponding angle force constants
#
# bbd lists the structure specific dihedral angles
# bbkd lists the corresponding force constants
#
# -=NOTE=-
# if the secondary structure types differ between bonded atoms
# the bond is assigned the lowest corresponding force constant
#
# -=NOTE=-
# if proline is anywhere in the helix, the BBB angle changes for
# all residues
#
###############################################################################################
## BEADS ## #
# F E H 1 2 3 T S C # SS one letter
self.bbdef = FUNC.spl(" N0 Nda N0 Nd Na Nda Nda P5 P5") # Default beads #@#
self.bbtyp = { # #@#
"ALA": FUNC.spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4"), # ALA specific #@#
"PRO": FUNC.spl(" C5 N0 C5 N0 Na N0 N0 P4 P4"), # PRO specific #@#
"HYP": FUNC.spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4") # HYP specific #@#
} # #@#
## BONDS ## #
self.bbldef = (.365, .350, .310, .310, .310, .310, .350, .350, .350) # BB bond lengths #@#
self.bbkb = (1250, 1250, None, None, None, None, 1250, 1250, 1250) # BB bond kB #@#
self.bbltyp = {} # #@#
self.bbkbtyp = {} # #@#
## ANGLES ## #
self.bbadef = ( 119.2,134, 96, 96, 96, 96, 100, 130, 127) # BBB angles #@#
self.bbka = ( 150, 25, 700, 700, 700, 700, 25, 25, 25) # BBB angle kB #@#
self.bbatyp = { # #@#
"PRO": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127), # PRO specific #@#
"HYP": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127) # PRO specific #@#
} # #@#
self.bbkatyp = { # #@#
"PRO": ( 150, 25, 100, 100, 100, 100, 25, 25, 25), # PRO specific #@#
"HYP": ( 150, 25, 100, 100, 100, 100, 25, 25, 25) # PRO specific #@#
} # #@#
## DIHEDRALS ## #
self.bbddef = ( 90.7, 0, -120, -120, -120, -120) # BBBB dihedrals #@#
self.bbkd = ( 100, 10, 400, 400, 400, 400) # BBBB kB #@#
self.bbdmul = ( 1, 1, 1, 1, 1, 1) # BBBB mltplcty #@#
self.bbdtyp = {} # #@#
self.bbkdtyp = {} # #@#
#
###############################################################################################
# Some Forcefields use the Ca position to position the BB-bead (me like!)
# martini 2.1 doesn't
self.ca2bb = False
# BBS angle, equal for all ss types
# Connects BB(i-1),BB(i),SC(i), except for first residue: BB(i+1),BB(i),SC(i)
# ANGLE Ka
self.bbsangle = [ 100, 25] #@#
# Bonds for extended structures (more stable than using dihedrals)
# LENGTH FORCE
self.ebonds = { #@#
'short': [ .640, 2500], #@#
'long' : [ .970, 2500] #@#
} #@#
#----+-----------------------+
## B | SIDE CHAIN PARAMETERS |
#----+-----------------------+
# To be compatible with Elnedyn, all parameters are explicitly defined, even if they are double.
self.sidechains = {
#RES# BEADS BONDS ANGLES DIHEDRALS V-SITES
# BB-SC SC-SC BB-SC-SC SC-SC-SC
"TRP": [FUNC.spl("SC4 SNd SC5 SC5"),[(0.300,5000)]+[(0.270,None) for i in range(5)], [(210,50),(90,50),(90,50)], [(0,50),(0,200)]],
"TYR": [FUNC.spl("SC4 SC4 SP1"), [(0.320,5000), (0.270,None), (0.270,None),(0.270,None)], [(150,50),(150,50)], [(0,50)]],
"PHE": [FUNC.spl("SC5 SC5 SC5"), [(0.310,7500), (0.270,None), (0.270,None),(0.270,None)], [(150,50),(150,50)], [(0,50)]],
"HIS": [FUNC.spl("SC4 SP1 SP1"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)], [(150,50),(150,50)], [(0,50)]],
"HIH": [FUNC.spl("SC4 SP1 SQd D"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None),(0.11,None)],[(150,50),(150,50)], [(0,50)]],
"GLN": [FUNC.spl("Nda D D"), [(0.400,5000), (0.280,None)], [], [], [(0.5,)]],
"ASN": [FUNC.spl("Nda D D"), [(0.320,5000), (0.280,None)], [], [], [(0.5,)]],
"SER": [FUNC.spl("N0 D D"), [(0.250,7500), (0.280,None)], [], [], [(0.5,)]],
"THR": [FUNC.spl("N0 D D"), [(0.260,9000), (0.280,None)], [], [], [(0.5,)]],
"ARG": [FUNC.spl("N0 Qd D"), [(0.330,5000), (0.340,5000), (0.110,None)], [(180,25)]],
"LYS": [FUNC.spl("C3 Qd D"), [(0.330,5000), (0.280,5000), (0.110,None)], [(180,25)]],
"ASP": [FUNC.spl("Qa D"), [(0.320,7500), (0.110,None)]],
"GLU": [FUNC.spl("Qa D"), [(0.400,5000), (0.110,None)]],
"CYS": [FUNC.spl("C5"), [(0.310,7500)]],
"ILE": [FUNC.spl("C1"), [(0.310,None)]],
"LEU": [FUNC.spl("C1"), [(0.330,7500)]],
"MET": [FUNC.spl("C5"), [(0.400,2500)]],
"PRO": [FUNC.spl("C3"), [(0.300,7500)]],
"HYP": [FUNC.spl("P1"), [(0.300,7500)]],
"VAL": [FUNC.spl("C2"), [(0.265,None)]],
"ALA": [],
"GLY": [],
}
# Not all (eg Elnedyn) forcefields use backbone-backbone-sidechain angles and BBBB-dihedrals.
self.UseBBSAngles = True
self.UseBBBBDihedrals = True
# Martini 2.2p has polar and charged residues with seperate charges.
self.polar = ["GLN","ASN","SER","THR"]
self.charged = ["ARG","LYS","ASP","GLU","HIH"]
# If masses or charged diverge from standard (45/72 and -/+1) they are defined here.
self.mass_charge = {
#RES MASS CHARGE
"GLN":[[0,36,36], [0,0.42,-0.42]],
"ASN":[[0,36,36], [0,0.46,-0.46]],
"SER":[[0,36,36], [0,0.40,-0.40]],
"THR":[[0,36,36], [0,0.36,-0.36]],
"ARG":[[72,36,36], [0,0,1]],
"LYS":[[72,36,36], [0,0,1]],
"HIH":[[45,45,36,36], [0,0,0,1]],
"ASP":[[36,36], [0,-1]],
"GLU":[[36,36], [0,-1]],
}
self.connectivity = {
#RES BONDS ANGLES DIHEDRALS V-SITE
"TRP": [[(0,1),(1,2),(1,3),(2,3),(2,4),(3,4)], [(0,1,2),(0,1,3)], [(0,2,3,1),(1,2,4,3)]],
"TYR": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"PHE": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIS": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIH": [[(0,1),(1,2),(1,3),(2,3),(3,4)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"GLN": [[(0,1),(2,3)], [], [], [(1,2,3)]],
"ASN": [[(0,1),(2,3)], [], [], [(1,2,3)]],
"SER": [[(0,1),(2,3)], [], [], [(1,2,3)]],
"THR": [[(0,1),(2,3)], [], [], [(1,2,3)]],
"ARG": [[(0,1),(1,2),(2,3)], [(0,1,2)]],
"LYS": [[(0,1),(1,2),(2,3)], [(0,1,2)]],
"ASP": [[(0,1),(1,2)]],
"GLU": [[(0,1),(1,2)]],
"CYS": [[(0,1)]],
"ILE": [[(0,1)]],
"LEU": [[(0,1)]],
"MET": [[(0,1)]],
"PRO": [[(0,1)]],
"HYP": [[(0,1)]],
"VAL": [[(0,1)]],
"ALA": [],
"GLY": [],
}
#----+----------------+
## C | SPECIAL BONDS |
#----+----------------+
self.special = {
# Used for sulfur bridges
# ATOM 1 ATOM 2 BOND LENGTH FORCE CONSTANT
(("SC1","CYS"), ("SC1","CYS")): (0.24, None),
}
# By default use an elastic network
self.ElasticNetwork = False
# Elastic networks bond shouldn't lead to exclusions (type 6)
# But Elnedyn has been parametrized with type 1.
self.EBondType = 6
#----+----------------+
## D | INTERNAL STUFF |
#----+----------------+
## BACKBONE BEAD TYPE ##
# Dictionary of default bead types (*D)
self.bbBeadDictD = FUNC.hash(SS.bbss,self.bbdef)
# Dictionary of dictionaries of types for specific residues (*S)
self.bbBeadDictS = dict([(i,FUNC.hash(SS.bbss,self.bbtyp[i])) for i in self.bbtyp.keys()])
## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = FUNC.hash(SS.bbss,zip(self.bbldef,self.bbkb))
# Dictionary of dictionaries for specific types (*S)
self.bbBondDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbltyp[i],self.bbkbtyp[i]))) for i in self.bbltyp.keys()])
# This is tricky to read, but it gives the right bondlength/force constant
## BBB ANGLE TYPE ##
# Dictionary of default angle types (*D)
self.bbAngleDictD = FUNC.hash(SS.bbss,zip(self.bbadef,self.bbka))
# Dictionary of dictionaries for specific types (*S)
self.bbAngleDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbatyp[i],self.bbkatyp[i]))) for i in self.bbatyp.keys()])
## BBBB DIHEDRAL TYPE ##
# Dictionary of default dihedral types (*D)
self.bbDihedDictD = FUNC.hash(SS.bbss,zip(self.bbddef,self.bbkd,self.bbdmul))
# Dictionary of dictionaries for specific types (*S)
self.bbDihedDictS = dict([(i,FUNC.hash(SS.bbss,zip(self.bbdtyp[i],self.bbkdtyp[i]))) for i in self.bbdtyp.keys()])
dnares3 = " DA DC DG DT"
dnares1 = " dA dC dG dT"
rnares3 = " A C G U"
rnares1 = " rA rC rG rU"
# Amino acid nucleic acid codes:
# The naming (AA and '3') is not strictly correct when adding DNA/RNA, but we keep it like this for consistincy.
AA3 = FUNC.spl(
"TRP TYR PHE HIS HIH ARG LYS CYS ASP GLU ILE LEU MET ASN PRO HYP GLN SER THR VAL ALA GLY"
+ dnares3 + rnares3) #@#
AA1 = FUNC.spl(
" W Y F H H R K C D E I L M N P O Q S T V A G"
+ dnares1 + rnares1) #@#
# Dictionaries for conversion from one letter code to three letter code v.v.
AA123, AA321 = FUNC.hash(AA1, AA3), FUNC.hash(AA3, AA1)
# Residue classes:
protein = AA3[:-8] # remove eight to get rid of DNA/RNA here.
water = FUNC.spl("HOH SOL TIP")
lipids = FUNC.spl(
"DPP DHP DLP DMP DSP POP DOP DAP DUP DPP DHP DLP DMP DSP PPC DSM DSD DSS")
nucleic = FUNC.spl("DAD DCY DGU DTH ADE CYT GUA THY URA DA DC DG DT")
residueTypes = dict([(i, "Protein") for i in protein] + [(i, "Water")
for i in water] +
[(i, "Lipid") for i in lipids] + [(i, "Nucleic")
for i in nucleic])
class CoarseGrained:
pattypes = {
"H": FUNC.pat(
".3. .33. .333. .3333. .13332. .113322. .1113222. .1111 2222.") #@#
}
#----+----------+
## C | INTERNAL |
#----+----------+
# Pymol Colors
# F E H 1 2 3 T S C
ssnum = (13, 4, 2, 2, 2, 2, 6, 22, 0) #@#
# Dictionary returning a number for a given type of secondary structure
# This can be used for setting the b-factor field for coloring
ss2num = FUNC.hash(bbss, ssnum)
# List of programs for which secondary structure definitions can be processed
programs = ssdefs.keys()
# Dictionaries mapping ss types to the CG ss types
ssd = dict([(i, FUNC.hash(ssdefs[i], cgss)) for i in programs])
# From the secondary structure dictionaries we create translation tables
# with which all secondary structure types can be processed. Anything
# not listed above will be mapped to C (coil).
# Note, a translation table is a list of 256 characters to map standard
# ascii characters to.
def tt(program):
return "".join([ssd[program].get(chr(i), "C") for i in range(256)])
"H": FUNC.pat(".3. .33. .333. .3333. .13332. .113322. .1113222. .1111 2222.") #@#
}
#----+----------+
## C | INTERNAL |
#----+----------+
# Pymol Colors
# F E H 1 2 3 T S C
ssnum = (13, 4, 2, 2, 2, 2, 6, 22, 0) #@#
# Dictionary returning a number for a given type of secondary structure
# This can be used for setting the b-factor field for coloring
ss2num = FUNC.hash(bbss, ssnum)
# List of programs for which secondary structure definitions can be processed
programs = ssdefs.keys()
# Dictionaries mapping ss types to the CG ss types
ssd = dict([(i, FUNC.hash(ssdefs[i], cgss)) for i in programs])
# From the secondary structure dictionaries we create translation tables
# with which all secondary structure types can be processed. Anything
# not listed above will be mapped to C (coil).
# Note, a translation table is a list of 256 characters to map standard
# ascii characters to.
