Skip to content

Commit

Permalink
documentation (#164)
Browse files Browse the repository at this point in the history
  • Loading branch information
@MTLehner
MTLehner committed Jan 20, 2022
1 parent 8fc070f commit b0461a0
Showing 1 changed file with 161 additions and 0 deletions.
161 changes: 161 additions & 0 deletions pygromos/files/topology/top.py
View file
Expand Up @@ -403,6 +403,15 @@ def get_num_atomtypes(self) -> int:
return int(self.ATOMTYPENAME.content[0][0])

def add_new_atomtype(self, name:str, verbose=False):
"""add a atomtype to ATOMTYPENAME block
Parameters
----------
name : str
new atomtype name
verbose : bool, optional
by default False
"""
if not hasattr(self, "ATOMTYPENAME"):
defaultContent=['0', 'Dummy']
self.add_block(blocktitle="ATOMTYPENAME", content=defaultContent, verbose=verbose)
Expand All @@ -415,6 +424,15 @@ def add_new_atomtype(self, name:str, verbose=False):
self.ATOMTYPENAME.content[0][0] = str(int(self.ATOMTYPENAME.content[0][0])+1)

def add_new_resname(self, name:str, verbose=False):
"""add a resname to the RESNAME block
Parameters
----------
name : str
resname name
verbose : bool, optional
by default False
"""
if not hasattr(self, "RESNAME"):
defaultContent=['0', 'Dummy']
self.add_block(blocktitle="RESNAME", content=defaultContent, verbose=verbose)
Expand All @@ -427,6 +445,8 @@ def add_new_resname(self, name:str, verbose=False):
self.RESNAME.content[0][0] = str(int(self.RESNAME.content[0][0])+1)

def add_new_soluteatom(self, ATNM:int=0, MRES:int=0, PANM:str="", IAC:int=0, MASS:float=0, CG:float=0, CGC:int=0, INE:list=[], INE14:list=[], verbose=False):
"""add a soluteatom to the SOLUTEATOM block
"""
if not hasattr(self, "SOLUTEATOM"):
self.add_block(blocktitle="SOLUTEATOM", content=[], verbose=verbose)
self.SOLUTEATOM.NRP = 0
Expand All @@ -445,6 +465,21 @@ def add_new_soluteatom(self, ATNM:int=0, MRES:int=0, PANM:str="", IAC:int=0, MAS


def add_new_bond(self, k:float, b0:float, atomI:int, atomJ:int, includesH:bool = False, verbose=False):
"""add a bond between atom I and J to the BOND block
Parameters
----------
k : float
force konstant
b0 : float
distance at which the force is 0
atomI : int
atom I
atomJ : int
atom J
includesH : bool, optional
wheter it should be added to BOND or BONDH, by default False
"""
#check if all classes are ready, if not create
if not hasattr(self, "BONDSTRETCHTYPE"):
self.add_block(blocktitle="BONDSTRETCHTYPE", content=list(), verbose=verbose)
Expand Down Expand Up @@ -484,6 +519,27 @@ def add_new_bond(self, k:float, b0:float, atomI:int, atomJ:int, includesH:bool =
self.BOND.NBON += 1

def add_new_angle(self, k:float, kh:float, b0:float, atomI:int, atomJ:int, atomK:int, includesH:bool = False, verbose=False, convertToQuartic=False):
"""add a angle between atom I, J and K to the ANGLE block
Parameters
----------
k : float
force konstant
kh : float
force konstant harmonic
b0 : float
angle at which the force is 0
atomI : int
atom I
atomJ : int
atom J
atomK : int
atom K
includesH : bool, optional
ANGLE or ANGLEH, by default False
convertToQuartic : bool, optional
auto convert, by default False
"""
#check if all classes are ready, if not create
if not hasattr(self, "BONDANGLEBENDTYPE"):
self.add_block(blocktitle="BONDANGLEBENDTYPE", content=[], verbose=verbose)
Expand Down Expand Up @@ -547,6 +603,27 @@ def harmonic2quarticAngleConversion(self, kh, b0):
return 2*kbT/(term1 + term2)

def add_new_torsiondihedral(self, CP:float, PD:float, NP:int, atomI:int, atomJ:int, atomK:int, atomL:int, includesH:bool = False, verbose=False):
"""add a torsiondihedral between atom I, J, K and L to the TORSIONDIHEDRAL block
Parameters
----------
CP : float
force constant
PD : float
phase
NP : int
multiplicity
atomI : int
atom I
atomJ : int
atom J
atomK : int
atom K
atomL : int
atom L
includesH : bool, optional
DIHEDRAL or DIHEDRALH, by default False
"""
#check if all classes are ready, if not create
if not hasattr(self, "TORSDIHEDRALTYPE"):
self.add_block(blocktitle="TORSDIHEDRALTYPE", content=[], verbose=verbose)
Expand Down Expand Up @@ -581,6 +658,15 @@ def add_new_torsiondihedral(self, CP:float, PD:float, NP:int, atomI:int, atomJ:i


def add_new_impdihedral_type(self, CQ:float, Q0:float, verbose=False):
"""add a new impodihedraltype
Parameters
----------
CQ : float
force constant
Q0 : float
Q0
"""
#check if all classes are ready, if not create
if not hasattr(self, "IMPDIHEDRALTYPE"):
self.add_block(blocktitle="IMPDIHEDRALTYPE", content=[], verbose=verbose)
Expand All @@ -590,6 +676,25 @@ def add_new_impdihedral_type(self, CQ:float, Q0:float, verbose=False):


def add_new_impdihedral(self, CQ:float, Q0:float, atomI:int, atomJ:int, atomK:int, atomL:int, includesH:bool = False, verbose=False):
"""add a new impdihedral
Parameters
----------
CQ : float
force constant
Q0 : float
Q0
atomI : int
atom I
atomJ : int
atom J
atomK : int
atom K
atomL : int
atom L
includesH : bool, optional
IMPDIHEDRALH or IMPDIHEDRAL, by default False
"""
#check if all classes are ready, if not create
if not hasattr(self, "IMPDIHEDRALTYPE"):
self.add_block(blocktitle="IMPDIHEDRALTYPE", content=[], verbose=verbose)
Expand Down Expand Up @@ -626,6 +731,21 @@ def add_new_crossdihedral(self, verbose=False):
raise NotImplementedError("Who needs this???? Could you plox implement it. UwU")

def add_new_LJparameter(self, C6:float, C12:float, CS6:float=0, CS12:float=0, combination_rule:str="geometric", verbose=False, AddATOMTYPENAME:str=None, lowerBound:float=1e-100):
"""add a LJ entry to the LJ parameter block
Parameters
----------
C6 : float
C12 : float
CS6 : float, optional
CS12 : float, optional
combination_rule : str, optional
no other options supported rigth now, by default "geometric"
AddATOMTYPENAME : str, optional
if not None a new atomtype is made, by default None
lowerBound : float, optional
saftey, by default 1e-100
"""
if not hasattr(self, "LJPARAMETERS"):
self.add_block(blocktitle="LJPARAMETERS", content=[], verbose=verbose)
self.LJPARAMETERS.NRATT2 = 0
Expand Down Expand Up @@ -667,6 +787,7 @@ def add_new_LJparameter(self, C6:float, C12:float, CS6:float=0, CS12:float=0, co


def find_LJparameterNumber(self, C12:float, C6:float) -> int:
"""find the LJ parameter number"""
if not hasattr(self, "LJPARAMETERS"):
return 0
elif self.LJPARAMETERS.NRATT2 < 1:
Expand All @@ -678,6 +799,13 @@ def find_LJparameterNumber(self, C12:float, C6:float) -> int:
return 0 # LJ parameter not found

def get_LJparameter_from_IAC(self, IAC:int):
"""get the LJ parameter from the IAC number
Parameters
----------
IAC : int
[description]
"""
if not hasattr(self, "LJPARAMETERS"):
raise Exception("no LJPARAMETERS block to search in")
if (IAC**2 - 1) > self.LJPARAMETERS.NRATT2:
Expand All @@ -686,6 +814,39 @@ def get_LJparameter_from_IAC(self, IAC:int):


def add_new_atom(self, ATNM:int=0, MRES:int=0, PANM:str='_', IAC:int=1, MASS:float=1.0, CG:int=0, CGC:int=1, INE:list=[], INE14:list=[], verbose=False, C6:float=None, C12:float=None, CS6:float=0, CS12:float=0, IACname:str=None):
"""add a atom to a system (with creating a new atomtype if needed and adding LJ parameters if needed)
Parameters
----------
ATNM : int, optional
number of the atom in the system, by default 0
MRES : int, optional
residue number, by default 0
PANM : str, optional
name of the atom, by default '_'
IAC : int, optional
atomtype number of the atom, by default 1
MASS : float, optional
mass of the atom, by default 1.0
CG : int, optional
charge of the atom, by default 0
CGC : int, optional
charge group bool, by default 1
INE : list, optional
INE list, by default []
INE14 : list, optional
INE14 list, by default []
C6 : float, optional
C6 value, by default None
C12 : float, optional
C12 value, by default None
CS6 : float, optional
CS6 value, by default 0
CS12 : float, optional
CS12 value, by default 0
IACname : str, optional
new IACname if NONE PANM is used, by default None
"""
if IACname is None:
IACname = PANM

Expand Down

0 comments on commit b0461a0

Please sign in to comment.