def __init__(self,tpr,symtab=None):
self.position = tpr.tell()
ngrps = versions.ngrps(tpr)
self.extend([
("nameidx", Integer(tpr) if tpr.version >= 57 else None), # Symtab index for Moleculetype Name
("natoms", Integer(tpr)), # Number of atoms in Moleculetype
("nres", Integer(tpr)), # Number of residues in Moleculetype
("ngroupname", Integer(tpr) if tpr.version < 57 else None), # Number of group names in Moleculetype.
# Kept in struct starting with version 57.
])
self.extend([
("atoms", Tuple(tpr, self.natoms, Atom)),
("atomnameidx", Tuple(tpr, self.natoms, Integer)),
("atomtypeidx", Tuple(tpr, self.natoms, Integer) if tpr.version > 20 else []),
("atomtypeBidx", Tuple(tpr, self.natoms, Integer) if tpr.version > 20 else []),
("residues", Tuple(tpr, self.nres, (Integer,Integer,Char) if tpr.version >= 63 else (Integer,))),
("groupnameidx", Tuple(tpr, self.ngroupname, Integer) if tpr.version < 57 else []),
("groups", Tuple(tpr, ngrps, Group) if tpr.version < 57 else []),
("ilists", Ilist(tpr) if tpr.version >= 57 else None),
("cgs", Block(tpr) if tpr.version >= 57 else None),
("excls", BlockA(tpr)),
])
if symtab:
self.setnames(symtab)
def __init__(self,tpr):
ngrps = versions.ngrps(tpr)
self.extend([
("symtab", Strings(tpr)),
("symstridx", Integer(tpr)),
])
self.extend([
("symstr", self.symtab[self.symstridx]),
("ffparam", FFParam(tpr,self.symtab) if tpr.version >= 57 else None),
("moltypes", Group(tpr, Moltype) if tpr.version >= 57 else None),
("molblocks", Group(tpr, Molblock) if tpr.version >= 57 else None),
("topnatoms", Integer(tpr) if tpr.version >= 57 else None),
("atomtypes", AtomTypes(tpr) if tpr.version > 25 else None),
# For earlier versions (<57), there should be one moltype, and
# this set of ffparam/ilists should be set as attribute to that
("ffparam", FFParam(tpr,self.symtab) if tpr.version < 57 else None),
("ilists", Ilist(tpr) if tpr.version < 57 else None),
("cmapN", Integer(tpr) if tpr.version >= 65 else None),
("cmapGridSize", Integer(tpr) if tpr.version >= 65 else None),
])
self.extend([
("cmap", [ Tuple(tpr, self.cmapGridSize**2, (Real, Real, Real, Real)) for i in range(self.cmapN) ] if tpr.version >= 65 else None ),
("groupids", [ Group(tpr, Integer) for i in range(ngrps) ] if tpr.version >= 57 else None ),
("groupnameidx", Group(tpr, Integer) if tpr.version >= 57 else None),
("groups", [ Group(tpr, Unsigned) for i in range(ngrps) ] if tpr.version >= 57 else None ),
("cgs", Block(tpr) if tpr.version < 57 else None),
("mol", Block(tpr) if tpr.version < 57 else None),
("shake", BlockA(tpr) if tpr.version < 51 else None),
])
def __init__(self, tpr):
self.position = tpr.tell()
ngrps = versions.ngrps(tpr)
self.extend([
("m", Real(tpr)), ("q", Real(tpr)), ("mB", Real(tpr)),
("qB", Real(tpr)), ("type", Unsigned(tpr)),
("typeB", Unsigned(tpr)), ("ptype", Integer(tpr)),
("resind", Integer(tpr)),
("atomnumber", Integer(tpr) if tpr.version >= 52 else 0),
("groups",
Tuple(tpr, ngrps, Unsigned) if tpr.version < 57 else None)
])
def __init__(self,tpr):
self.position = tpr.tell()
ngrps = versions.ngrps(tpr)
self.extend([
("m", Real(tpr)),
("q", Real(tpr)),
("mB", Real(tpr)),
("qB", Real(tpr)),
("type", Unsigned(tpr)),
("typeB", Unsigned(tpr)),
("ptype", Integer(tpr)),
("resind", Integer(tpr)),
("atomnumber", Integer(tpr) if tpr.version >= 52 else 0),
("groups", Tuple(tpr, ngrps, Unsigned) if tpr.version < 57 else None)
])
def __init__(self, tpr):
ngrps = versions.ngrps(tpr)
self.extend([
("symtab", Strings(tpr)),
("symstridx", Integer(tpr)),
])
self.extend([
("symstr", self.symtab[self.symstridx]),
("ffparam",
FFParam(tpr, self.symtab) if tpr.version >= 57 else None),
("moltypes", Group(tpr, Moltype) if tpr.version >= 57 else None),
("molblocks", Group(tpr, Molblock) if tpr.version >= 57 else None),
("topnatoms", Integer(tpr) if tpr.version >= 57 else None),
("atomtypes", AtomTypes(tpr) if tpr.version > 25 else None),
# For earlier versions (<57), there should be one moltype, and
# this set of ffparam/ilists should be set as attribute to that
("ffparam", FFParam(tpr, self.symtab) if tpr.version < 57 else None
),
("ilists", Ilist(tpr) if tpr.version < 57 else None),
("cmapN", Integer(tpr) if tpr.version >= 65 else None),
("cmapGridSize", Integer(tpr) if tpr.version >= 65 else None),
])
self.extend([
("cmap", [
Tuple(tpr, self.cmapGridSize**2, (Real, Real, Real, Real))
for i in range(self.cmapN)
] if tpr.version >= 65 else None),
("groupids",
[Group(tpr, Integer)
for i in range(ngrps)] if tpr.version >= 57 else None),
("groupnameidx",
Group(tpr, Integer) if tpr.version >= 57 else None),
("groups", [Group(tpr, Unsigned)
for i in range(ngrps)] if tpr.version >= 57 else None),
("cgs", Block(tpr) if tpr.version < 57 else None),
("mol", Block(tpr) if tpr.version < 57 else None),
("shake", BlockA(tpr) if tpr.version < 51 else None),
])
def __init__(self, tpr, symtab=None):
self.position = tpr.tell()
ngrps = versions.ngrps(tpr)
self.extend([
("nameidx", Integer(tpr) if tpr.version >= 57 else
None), # Symtab index for Moleculetype Name
("natoms", Integer(tpr)), # Number of atoms in Moleculetype
("nres", Integer(tpr)), # Number of residues in Moleculetype
("ngroupname", Integer(tpr) if tpr.version < 57 else
None), # Number of group names in Moleculetype.
# Kept in struct starting with version 57.
])
self.extend([
("atoms", Tuple(tpr, self.natoms, Atom)),
("atomnameidx", Tuple(tpr, self.natoms, Integer)),
("atomtypeidx",
Tuple(tpr, self.natoms, Integer) if tpr.version > 20 else []),
("atomtypeBidx",
Tuple(tpr, self.natoms, Integer) if tpr.version > 20 else []),
("residues",
Tuple(tpr, self.nres,
(Integer, Integer, Char) if tpr.version >= 63 else
(Integer, ))),
("groupnameidx",
Tuple(tpr, self.ngroupname, Integer) if tpr.version < 57 else []),
("groups", Tuple(tpr, ngrps, Group) if tpr.version < 57 else []),
("ilists", Ilist(tpr) if tpr.version >= 57 else None),
("cgs", Block(tpr) if tpr.version >= 57 else None),
("excls", BlockA(tpr)),
])
if symtab:
self.setnames(symtab)
