topology.atomic

topology.atomic

Atomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc. The order of the fields comes from the gromacs topology file format. See gromacs manual

Classes

Name	Description
Angle	Information about one angle
AngleType	Information about one angletype
Atom	Information about one atom
AtomType	Information about one atom type
Bond	Information about one bond
BondType	Information about one bondtype
Dihedral	Information about one proper or improper dihedral
DihedralRestraint	Information about one dihedral restraint.
DihedralType	Information about one dihedraltype
Exclusion	Information about one exclusion
MultipleDihedralTypes	Multiple `DihedralTypes`s with the same ai, aj, ak, al
MultipleDihedrals	Multiple `Dihedral`s with the same ai, aj, ak, al
NonbondParamType	Information about one nonbonded parameterize
Pair	Information about one pair
PositionRestraint	Information about one position restraint.
ResidueAtomSpec	Information about one atom in a residue
ResidueBondSpec	Information about one bond in a residue
ResidueImproperSpec	Information about one improper dihedral in a residue
ResidueProperSpec	Information about one proper dihedral in a residue
ResidueType	Information about one residuetype from aminoacids.rtp
Settle	Information about one settles

Angle

topology.atomic.Angle(
    self,
    ai,
    aj,
    ak,
    funct,
    c0=None,
    c1=None,
    c2=None,
    c3=None,
    comment=None,
)

Information about one angle

A class containing angle information as in the angles section of the topology.

From gromacs topology: ; ai aj ak funct c0 c1 c2 c3 With aj < ai < ak

AngleType

topology.atomic.AngleType(
    self,
    i,
    j,
    k,
    id,
    id_sym,
    funct,
    c0=None,
    c1=None,
    c2=None,
    c3=None,
)

Information about one angletype

A class containing angle type information as in the angletypes section of the forcefield.

From gromacs version of the amber* ff: ; i j k func th0 cth

Atom

topology.atomic.Atom(
    self,
    nr,
    type,
    resnr,
    residue,
    atom,
    cgnr,
    charge,
    mass=None,
    typeB=None,
    chargeB=None,
    massB=None,
    bound_to_nrs=list(),
    is_radical=False,
    comment=None,
)

Information about one atom

A class containing atom information as in the atoms section of the topology. An atom keeps a list of which atoms it is bound to and its radical state.

From gromacs topology: ; nr type resnr residue atom cgnr charge mass typeB chargeB massB

AtomType

topology.atomic.AtomType(
    self,
    type,
    id,
    id_sym,
    at_num,
    mass,
    charge,
    ptype,
    sigma,
    epsilon,
)

Information about one atom type

A class containing atom type information as in the atomtypes section of the forcefield.

From gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon

Bond

topology.atomic.Bond(
    self,
    ai,
    aj,
    funct,
    c0=None,
    c1=None,
    c2=None,
    c3=None,
    c4=None,
    c5=None,
    comment=None,
)

Information about one bond

A class containing bond information as in the bonds section of the topology.

From gromacs topology: ; ai aj funct c0 c1 c2 c3 c4 c5 With ai < aj

BondType

topology.atomic.BondType(
    self,
    i,
    j,
    id,
    id_sym,
    funct,
    c0=None,
    c1=None,
    c2=None,
    c3=None,
)

Information about one bondtype

A class containing bond information as in the bondtype section of the forcefield.

From gromacs version of the amber* ff: ; i j func b0 kb Where i and j are atomtypes

Dihedral

topology.atomic.Dihedral(
    self,
    ai,
    aj,
    ak,
    al,
    funct,
    c0=None,
    c1=None,
    periodicity='',
    c3=None,
    c4=None,
    c5=None,
    comment=None,
)

Information about one proper or improper dihedral

A class containing dihedral information as in the dihedrals section of the topology. Improper dihedrals have funct 4. Proper dihedrals have funct != 4, mostly funct 9.

Note that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity.

From gromacs topology: ; ai aj ak al funct c0 c1 c2 c3 c4 c5 For proper dihedrals (funct 9): aj < ak

DihedralRestraint

topology.atomic.DihedralRestraint(self, ai, aj, ak, al, type, phi, dphi, fc)

Information about one dihedral restraint.

A class containing information as in the dihedral_restraints section of the topology.

From gromacs topology: ; ai aj ak al type phi dphi fc

DihedralType

topology.atomic.DihedralType(
    self,
    i,
    j,
    k,
    l,
    id,
    id_sym,
    funct,
    c0,
    c1,
    periodicity,
    c3=None,
    c4=None,
    c5=None,
)

Information about one dihedraltype

A class containing dihedral type information as in the dihedraltypes section of the forcefield. Improper dihedrals have funct 4. Proper dihedrals have funct 9.

Note that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity and part of the id.

From gromacs version of the amber* ff: ; i j k l func phase kd pn

Exclusion

topology.atomic.Exclusion(
    self,
    ai,
    aj=None,
    ak=None,
    al=None,
    am=None,
    an=None,
    ao=None,
    ap=None,
    comment=None,
)

Information about one exclusion

A class containing atom information as in the exclusions section of the topology.

It’s unlikey we need this many atomnumbers in a single exclusion, but just in case. Because the gromacs manuals just says

Each line should start with one atom index, followed by one or more atom indices. All non-bonded interactions between the first atom and the other atoms will be excluded. – https://manual.gromacs.org/current/reference-manual/topologies/molecule-definition.html#exclusions

From gromacs topology: ; ai aj ak al am an ao ap

MultipleDihedralTypes

topology.atomic.MultipleDihedralTypes(
    self,
    ai,
    aj,
    ak,
    al,
    funct,
    dihedral_types,
)

Multiple DihedralTypess with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedral_types dict is the periodicity (c2).

MultipleDihedrals

topology.atomic.MultipleDihedrals(self, ai, aj, ak, al, funct, dihedrals)

Multiple Dihedrals with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedrals dict is the periodicity (c2).

NonbondParamType

topology.atomic.NonbondParamType(
    self,
    i,
    j,
    id,
    id_sym,
    funct,
    c0=None,
    c1=None,
    c2=None,
)

Information about one nonbonded parameterize

typical in coarse grained models. A class containing nonbonded information as in the nonbond_params section of the forcefield.

From gromacs: ; Lennard jones between beads ; i j funda sigma(nm) epsilon (kmol/mol) Where i and j are atomtypes

Pair

topology.atomic.Pair(
    self,
    ai,
    aj,
    funct,
    c0=None,
    c1=None,
    c2=None,
    c3=None,
    comment=None,
)

Information about one pair

A class containing pair information as in the pair section of the topology.

From gromacs topology: ; ai aj funct c0 c1 c2 c3 ; comment

PositionRestraint

topology.atomic.PositionRestraint(self, ai, funct, fc, condition=None)

Information about one position restraint.

A class containing information as in the position_restraints section of the topology.

From gromacs topology: ; ai funct fc(x,y,z)

ResidueAtomSpec

topology.atomic.ResidueAtomSpec(self, name, type, charge, cgrp)

Information about one atom in a residue

; name type charge chargegroup

ResidueBondSpec

topology.atomic.ResidueBondSpec(self, atom1, atom2, b0=None, kb=None)

Information about one bond in a residue

; atom1 atom2 b0 kb

ResidueImproperSpec

topology.atomic.ResidueImproperSpec(
    self,
    atom1,
    atom2,
    atom3,
    atom4,
    c0,
    c1,
    c2,
)

Information about one improper dihedral in a residue

; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)

ResidueProperSpec

topology.atomic.ResidueProperSpec(self, atom1, atom2, atom3, atom4, c0, c1, c2)

Information about one proper dihedral in a residue

; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2

ResidueType

topology.atomic.ResidueType(
    self,
    residue,
    atoms,
    bonds,
    proper_dihedrals,
    improper_dihedrals,
)

Information about one residuetype from aminoacids.rtp

Settle

topology.atomic.Settle(self, nr, funct, doh, dhh)

Information about one settles

A class containing atom information as in the settle section of the topology.

From gromacs topology: ; nr funct doh dhh