def GromacsStructureFromPDB(pdbfile):
"""Take in a PDB file a GromacsStructure class."""
p = PDBStructure(filename=pdbfile)
gstruct = GromacsStructure(name=pdbfile, header="title" )
gatoms = GromacsAtoms()
for atom in p.atoms:
gatoms.append( GromacsAtom(resnum=atom["resSeq"], resname=atom["resName"], atomname=atom["name"], atomnum=atom["serial"],
x=(atom["x"]/10.), y=(atom["y"]/10.), z=(atom["z"]/10.), vx=0.0, vy=0.0, vz=0.0) )
gstruct.appendatoms( gatoms )
return gstruct
def PDBFromGrofile(grofile,
stripWaters=False,
stripIons=False,
stripDummy=False):
"""Take in a *.gro Grofile file and write it as a PDB file."""
gstruct = GromacsStructure(name=grofile, header="title")
gstruct.load(grofile)
p = PDBStructure()
for gatom in gstruct.atoms:
atom = {}
atom["serial"] = gatom.atomnum
atom["name"] = '%-4s' % (gatom.atomname.strip())
atom["altLoc"] = ' '
atom["resName"] = '%-4s' % (gatom.resname.strip())
atom["chainID"] = ' '
atom["resSeq"] = gatom.resnum
atom["iCode"] = ' '
atom["x"] = gatom.x * 10. # *.gro files are in nm
atom["y"] = gatom.y * 10.
atom["z"] = gatom.z * 10.
atom["occupancy"] = 1.0
atom["tempFactor"] = 0.0
atom["segID"] = ' '
atom["element"] = ' '
atom["charge"] = ' '
if (atom["resName"].count('HOH') > 0) or (atom["resName"].count('SOL')
> 0):
if not stripWaters:
atoms.append(atom)
elif (atom["resName"].count('Cl') > 0) or (atom["resName"].count('Na')
> 0):
if not stripIons:
atoms.append(atom)
elif (atom["resName"].count('DMM') > 0):
if not stripDummy:
p.atoms.append(atom)
else:
p.atoms.append(atom)
return p
def GromacsStructureFromPDB(pdbfile):
"""Take in a PDB file a GromacsStructure class."""
p = PDBStructure(filename=pdbfile)
gstruct = GromacsStructure(name=pdbfile, header="title")
gatoms = GromacsAtoms()
for atom in p.atoms:
gatoms.append(
GromacsAtom(resnum=atom["resSeq"],
resname=atom["resName"],
atomname=atom["name"],
atomnum=atom["serial"],
x=(atom["x"] / 10.),
y=(atom["y"] / 10.),
z=(atom["z"] / 10.),
vx=0.0,
vy=0.0,
vz=0.0))
gstruct.appendatoms(gatoms)
return gstruct
def PDBFromGrofile(grofile, stripWaters=False, stripIons=False, stripDummy=False):
"""Take in a *.gro Grofile file and write it as a PDB file."""
gstruct = GromacsStructure(name=grofile, header="title" )
gstruct.load(grofile)
p = PDBStructure()
for gatom in gstruct.atoms:
atom = { }
atom["serial"] = gatom.atomnum
atom["name"] = '%-4s'%(gatom.atomname.strip())
atom["altLoc"] = ' '
atom["resName"] = '%-4s'%(gatom.resname.strip())
atom["chainID"] = ' '
atom["resSeq"] = gatom.resnum
atom["iCode"] = ' '
atom["x"] = gatom.x*10. # *.gro files are in nm
atom["y"] = gatom.y*10.
atom["z"] = gatom.z*10.
atom["occupancy"] = 1.0
atom["tempFactor"] = 0.0
atom["segID"] = ' '
atom["element"] = ' '
atom["charge"] = ' '
if (atom["resName"].count('HOH')>0) or (atom["resName"].count('SOL')>0):
if not stripWaters:
atoms.append(atom)
elif (atom["resName"].count('Cl')>0) or (atom["resName"].count('Na')>0):
if not stripIons:
atoms.append(atom)
elif (atom["resName"].count('DMM')>0):
if not stripDummy:
p.atoms.append(atom)
else:
p.atoms.append(atom)
return p
def GromacsStructureFromGrofile(grofile):
"""Create a GromacsStructure objects from a grofile."""
gstruct = GromacsStructure(name=grofile, header="title")
gstruct.load(grofile)
return gstruct
def GromacsStructureFromGrofile(grofile):
"""Create a GromacsStructure objects from a grofile."""
gstruct = GromacsStructure(name=grofile, header="title" )
gstruct.load(grofile)
return gstruct
