本文整理汇总了Python中FUNC.spl方法的典型用法代码示例。如果您正苦于以下问题：Python FUNC.spl方法的具体用法？Python FUNC.spl怎么用？Python FUNC.spl使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类FUNC的用法示例。
在下文中一共展示了FUNC.spl方法的5个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: __init__
# 需要导入模块: import FUNC [as 别名]
# 或者: from FUNC import spl [as 别名]
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)]],
#.........这里部分代码省略.........
示例2: __init__
# 需要导入模块: import FUNC [as 别名]
# 或者: from FUNC import spl [as 别名]
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)]],
#.........这里部分代码省略.........
示例3: __init__
# 需要导入模块: import FUNC [as 别名]
# 或者: from FUNC import spl [as 别名]
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)]],
#.........这里部分代码省略.........
示例4: naming
# 需要导入模块: import FUNC [as 别名]
# 或者: from FUNC import spl [as 别名]
##########################
## 4 # FG -> CG MAPPING ## -> @MAP <-
##########################
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 ]
)示例5: structure
# 需要导入模块: import FUNC [as 别名]
# 或者: from FUNC import spl [as 别名]
# dihedral definitions, which are not present for coil and termini
#
ss_names = {
"F": "Collagenous Fiber", #@#
"E": "Extended structure (beta sheet)", #@#
"H": "Helix structure", #@#
"1": "Helix start (H-bond donor)", #@#
"2": "Helix end (H-bond acceptor)", #@#
"3": "Ambivalent helix type (short helices)", #@#
"T": "Turn", #@#
"S": "Bend", #@#
"C": "Coil", #@#
}
bbss = ss_names.keys()
bbss = FUNC.spl(" F E H 1 2 3 T S C") # SS one letter
# The following dictionary contains secondary structure types as assigned by
# different programs. The corresponding Martini secondary structure types are
# listed in cgss
#
# NOTE:
# Each list of letters in the dictionary ss should exactly match the list
# in cgss.
#
ssdefs = {
"dssp": list(".HGIBETSC~"), # DSSP one letter secondary structure code #@#
"pymol": list(".H...S...L"), # Pymol one letter secondary structure code #@#
"gmx": list(".H...ETS.C"), # Gromacs secondary structure dump code #@#
"self": list("FHHHEETSCC") # Internal CG secondary structure codes #@#