def set_segid(self, segid, new_segid):
"""
Renames a segment.
Args:
segid (str): Segment ID to change
new_segid (str): New segment ID
"""
_psfgen.set_atom_attr(psfstate=self._data,
segid=segid,
attribute="segid",
value=new_segid)
def set_resname(self, segid, resid, new_resname):
"""
Renames a residue
Args:
segid (str): Segment ID of residue to update
resid (str or int): Residue ID to update
new_resname (str): New residue name
"""
if isinstance(resid, int):
resid = str(resid)
_psfgen.set_atom_attr(psfstate=self._data,
segid=segid,
resid=resid,
attribute="resname",
value=new_resname)
def set_beta(self, segid, resid, atomname, beta):
"""
Updates the beta-factor of an atom
Args:
segid (str): Segment ID of atom to update
resid (str or int): Residue ID of atom to update
atomname (str): Name of atom to update
beta (float): New beta factor
"""
if isinstance(resid, int):
resid = str(resid)
_psfgen.set_atom_attr(psfstate=self._data,
segid=segid,
resid=resid,
aname=atomname,
attribute="beta",
value=beta)
def set_charge(self, segid, resid, atomname, charge):
"""
Updates the charge of an atom
Args:
segid (str): Segment ID of atom to update
resid (str or int): Residue ID of atom to update
atomname (str): Name of atom to update
charge (float): New charge
"""
if isinstance(resid, int):
resid = str(resid)
_psfgen.set_atom_attr(psfstate=self._data,
segid=segid,
resid=resid,
aname=atomname,
attribute="charge",
value=charge)
def set_mass(self, segid, resid, atomname, mass):
"""
Updates the mass of an atom
Args:
segid (str): Segment ID of atom to update
resid (str or int): Residue ID of atom to update
atomname (str): Name of atom to update
mass (float): New mass
"""
if isinstance(resid, int):
resid = str(resid)
_psfgen.set_atom_attr(psfstate=self._data,
segid=segid,
resid=resid,
aname=atomname,
attribute="mass",
value=mass)
def set_atom_name(self, segid, resid, atomname, new_atomname):
"""
Renames an atom
Args:
segid (str): Segment ID of atom to update
resid (str or int): Residue ID of atom to update
atomname (str): Name of atom to update
new_atomname (str): New atom name
"""
if isinstance(resid, int):
resid = str(resid)
_psfgen.set_atom_attr(psfstate=self._data,
segid=segid,
resid=resid,
aname=atomname,
attribute="name",
value=new_atomname)
def set_velocity(self, segid, resid, atomname, velocity):
"""
Sets the velocity of a given atom to new values
Args:
segid (str): Segment ID of atom
resid (str or int): Residue ID of atom
atomname (str): Atom name
velocity (3 membered list or tuple of double): New vx, vy, vz
velocities for atom
"""
if isinstance(resid, int):
resid = str(resid)
if isinstance(velocity, list):
velocity = tuple(velocity)
_psfgen.set_atom_attr(psfstate=self._data,
segid=segid,
resid=resid,
aname=atomname,
attribute="vel",
value=velocity)