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Convert to python3 and work with dssp version 4 #18

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Convert to python3 and work with dssp version 4 #18

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d2ffd2d
Initial conversion to python3
dkoes Nov 2, 2022
ab97aec
dssp versions
dkoes Nov 2, 2022
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12 changes: 6 additions & 6 deletions DOC.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ def __init__(self, func=str, num=1, default=None, description=""):
self.value = default
self.description = description

def __nonzero__(self):
def __bool__(self):
if self.func == bool:
return self.value != False
return bool(self.value)
Expand All @@ -30,11 +30,11 @@ def setvalue(self, v):

# Parameters can be defined for multiple forcefields
# We look for them within the script...
forcefields = [str(ff).split('.')[-1] for ff in globals().values() if (type(ff) == types.ClassType and hasattr(ff,"ff"))]
forcefields = [str(ff).split('.')[-1] for ff in list(globals().values()) if (type(ff) == type and hasattr(ff,"ff"))]
# ... in the local directory, ....
forcefields += [ff[:-3] for ff in os.listdir(".") if ff[-6:] == "_ff.py"]
# ... and in the GMXDATA dir.
if os.environ.has_key("GMXDATA"):
if "GMXDATA" in os.environ:
forcefields += [ff[:-3] for ff in os.listdir(os.environ["GMXDATA"]+"/top/") if ff[-6:] == "_ff.py"]

# Lists for gathering arguments to options that can be specified
Expand Down Expand Up @@ -238,9 +238,9 @@ def help():
import sys
for item in options:
if type(item) == str:
print item
print(item)
for item in options:
if type(item) != str:
print "%10s %s" % (item[0], item[1].description)
print
print("%10s %s" % (item[0], item[1].description))
print()
sys.exit()
2 changes: 1 addition & 1 deletion FUNC.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ def nsplit(*x):

# Make a dictionary from two lists
def hash(x, y):
return dict(zip(x, y))
return dict(list(zip(x, y)))


# Function to reformat pattern strings
Expand Down
14 changes: 7 additions & 7 deletions ForceFields/elnedyn22_BBbonds_ff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -195,26 +195,26 @@ def __init__(self):
# 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()])
self.bbBeadDictS = dict([(i,FUNC.hash(SS.bbss,self.bbtyp[i])) for i in list(self.bbtyp.keys())])

## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = FUNC.hash(SS.bbss,zip(self.bbldef,self.bbkb))
self.bbBondDictD = FUNC.hash(SS.bbss,list(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()])
self.bbBondDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbltyp[i],self.bbkbtyp[i])))) for i in list(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))
self.bbAngleDictD = FUNC.hash(SS.bbss,list(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()])
self.bbAngleDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbatyp[i],self.bbkatyp[i])))) for i in list(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))
self.bbDihedDictD = FUNC.hash(SS.bbss,list(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()])
self.bbDihedDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbdtyp[i],self.bbkdtyp[i])))) for i in list(self.bbdtyp.keys())])

# The following function returns the backbone bead for a given residue and
# secondary structure type.
Expand Down
14 changes: 7 additions & 7 deletions ForceFields/elnedyn22_BBconstr_ff.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -195,26 +195,26 @@ def __init__(self):
# 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()])
self.bbBeadDictS = dict([(i,FUNC.hash(SS.bbss,self.bbtyp[i])) for i in list(self.bbtyp.keys())])

## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = FUNC.hash(SS.bbss,zip(self.bbldef,self.bbkb))
self.bbBondDictD = FUNC.hash(SS.bbss,list(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()])
self.bbBondDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbltyp[i],self.bbkbtyp[i])))) for i in list(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))
self.bbAngleDictD = FUNC.hash(SS.bbss,list(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()])
self.bbAngleDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbatyp[i],self.bbkatyp[i])))) for i in list(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))
self.bbDihedDictD = FUNC.hash(SS.bbss,list(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()])
self.bbDihedDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbdtyp[i],self.bbkdtyp[i])))) for i in list(self.bbdtyp.keys())])

# The following function returns the backbone bead for a given residue and
# secondary structure type.
Expand Down
14 changes: 7 additions & 7 deletions ForceFields/elnedyn22_ff.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -194,26 +194,26 @@ def __init__(self):
# 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()])
self.bbBeadDictS = dict([(i,FUNC.hash(SS.bbss,self.bbtyp[i])) for i in list(self.bbtyp.keys())])

## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = FUNC.hash(SS.bbss,zip(self.bbldef,self.bbkb))
self.bbBondDictD = FUNC.hash(SS.bbss,list(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()])
self.bbBondDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbltyp[i],self.bbkbtyp[i])))) for i in list(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))
self.bbAngleDictD = FUNC.hash(SS.bbss,list(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()])
self.bbAngleDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbatyp[i],self.bbkatyp[i])))) for i in list(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))
self.bbDihedDictD = FUNC.hash(SS.bbss,list(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()])
self.bbDihedDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbdtyp[i],self.bbkdtyp[i])))) for i in list(self.bbdtyp.keys())])

# The following function returns the backbone bead for a given residue and
# secondary structure type.
Expand Down
14 changes: 7 additions & 7 deletions ForceFields/elnedyn22p_BBbonds_ff.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -200,26 +200,26 @@ def __init__(self):
# 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()])
self.bbBeadDictS = dict([(i,FUNC.hash(SS.bbss,self.bbtyp[i])) for i in list(self.bbtyp.keys())])

## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = FUNC.hash(SS.bbss,zip(self.bbldef,self.bbkb))
self.bbBondDictD = FUNC.hash(SS.bbss,list(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()])
self.bbBondDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbltyp[i],self.bbkbtyp[i])))) for i in list(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))
self.bbAngleDictD = FUNC.hash(SS.bbss,list(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()])
self.bbAngleDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbatyp[i],self.bbkatyp[i])))) for i in list(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))
self.bbDihedDictD = FUNC.hash(SS.bbss,list(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()])
self.bbDihedDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbdtyp[i],self.bbkdtyp[i])))) for i in list(self.bbdtyp.keys())])

# The following function returns the backbone bead for a given residue and
# secondary structure type.
Expand Down
14 changes: 7 additions & 7 deletions ForceFields/elnedyn22p_BBconstr_ff.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -200,26 +200,26 @@ def __init__(self):
# 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()])
self.bbBeadDictS = dict([(i,FUNC.hash(SS.bbss,self.bbtyp[i])) for i in list(self.bbtyp.keys())])

## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = FUNC.hash(SS.bbss,zip(self.bbldef,self.bbkb))
self.bbBondDictD = FUNC.hash(SS.bbss,list(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()])
self.bbBondDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbltyp[i],self.bbkbtyp[i])))) for i in list(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))
self.bbAngleDictD = FUNC.hash(SS.bbss,list(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()])
self.bbAngleDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbatyp[i],self.bbkatyp[i])))) for i in list(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))
self.bbDihedDictD = FUNC.hash(SS.bbss,list(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()])
self.bbDihedDictS = dict([(i,FUNC.hash(SS.bbss,list(zip(self.bbdtyp[i],self.bbkdtyp[i])))) for i in list(self.bbdtyp.keys())])

# The following function returns the backbone bead for a given residue and
# secondary structure type.
Expand Down
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