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 DihedralTypess with the same ai, aj, ak, al |
| MultipleDihedrals | Multiple Dihedrals 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)
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)
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, mass, charge, ptype, sigma, epsilon, at_num=None)
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)
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)
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, ak=None, al=None)
Information about one exclusion
A class containing atom information as in the exclusions section of the topology.
From gromacs topology: ; ai aj ak al
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)
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
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