This is a package for Python-parsers to process typical file formats used for Molecular Dynamics simulations. Currently supported modules and highlights:
Read GROMACS topology (.top) files and image them as a Python object or vice versa. The structure of the file is essentially captured in a doubly-linked list exposing it for easy manipulation. Common tasks like adding parts to a topology, merging topologies, retrieval of information, or checking the file for consistency can be performed.
Here is an example topology file from the GROMACS documentation:
;
; Example topology file (topol.top)
;
; The force-field files to be included
#include "amber99.ff/forcefield.itp"
[ moleculetype ]
; name nrexcl
Urea 3
[ atoms ]
1 C 1 URE C 1 0.880229 12.01000 ; amber C type
2 O 1 URE O 2 -0.613359 16.00000 ; amber O type
3 N 1 URE N1 3 -0.923545 14.01000 ; amber N type
4 H 1 URE H11 4 0.395055 1.00800 ; amber H type
5 H 1 URE H12 5 0.395055 1.00800 ; amber H type
6 N 1 URE N2 6 -0.923545 14.01000 ; amber N type
7 H 1 URE H21 7 0.395055 1.00800 ; amber H type
8 H 1 URE H22 8 0.395055 1.00800 ; amber H type
[ bonds ]
1 2
1 3
1 6
3 4
3 5
6 7
6 8
[ dihedrals ]
; ai aj ak al funct definition
2 1 3 4 9
2 1 3 5 9
2 1 6 7 9
2 1 6 8 9
3 1 6 7 9
3 1 6 8 9
6 1 3 4 9
6 1 3 5 9
[ dihedrals ]
3 6 1 2 4
1 4 3 5 4
1 7 6 8 4
[ position_restraints ]
; ai funct fc
1 1 1000 1000 1000 ; Restrain to a point
2 1 1000 0 1000 ; Restrain to a line (Y-axis)
3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane)
[ dihedral_restraints ]
; ai aj ak al type phi dphi fc
3 6 1 2 1 180 0 10
1 4 3 5 1 180 0 10
; Include TIP3P water topology
#include "amber99.ff/tip3p.itp"
[ system ]
Urea in Water
[ molecules ]
;molecule name nr.
Urea 1
SOL 1000
The file can be read for example like this:
from mdparser import topology as mdtop
from mdparser import tasks as mdtasks
parser = mdtop.GromacsTopParser(
include_shared=True, # Resolve include directives
include_blacklist=["forcefield.itp"] # Leave some includes untouched
)
with open("topol.top") as topfile:
top = parser.read(topfile)By default, comments (starting with ";") are ignored and conditional directives (#ifdef/#ifndef blocks) are resolved. Each element of the topology file is represented as a node in the top object. More specifically, a topology-element is translated into a specific type of node-value:
for node in top:
print(f"{node.value!r}")Include("amber99.ff/forcefield.itp")
MoleculetypeSection()
MoleculetypeEntry(molecule='Urea', nrexcl=3)
AtomsSubsection()
AtomsEntry(nr=1, type='C', resnr=1, residue='URE', atom='C', cgnr=1, charge=0.880229, mass=12.01, typeB=None, chargeB=None, massB=None)
AtomsEntry(nr=2, type='O', resnr=1, residue='URE', atom='O', cgnr=2, charge=-0.613359, mass=16.0, typeB=None, chargeB=None, massB=None)
AtomsEntry(nr=3, type='N', resnr=1, residue='URE', atom='N1', cgnr=3, charge=-0.923545, mass=14.01, typeB=None, chargeB=None, massB=None)
AtomsEntry(nr=4, type='H', resnr=1, residue='URE', atom='H11', cgnr=4, charge=0.395055, mass=1.008, typeB=None, chargeB=None, massB=None)
AtomsEntry(nr=5, type='H', resnr=1, residue='URE', atom='H12', cgnr=5, charge=0.395055, mass=1.008, typeB=None, chargeB=None, massB=None)
AtomsEntry(nr=6, type='N', resnr=1, residue='URE', atom='N2', cgnr=6, charge=-0.923545, mass=14.01, typeB=None, chargeB=None, massB=None)
AtomsEntry(nr=7, type='H', resnr=1, residue='URE', atom='H21', cgnr=7, charge=0.395055, mass=1.008, typeB=None, chargeB=None, massB=None)
AtomsEntry(nr=8, type='H', resnr=1, residue='URE', atom='H22', cgnr=8, charge=0.395055, mass=1.008, typeB=None, chargeB=None, massB=None)
BondsSubsection()
BondsEntry(i=1, j=2, funct=None, c=[])
BondsEntry(i=1, j=3, funct=None, c=[])
BondsEntry(i=1, j=6, funct=None, c=[])
BondsEntry(i=3, j=4, funct=None, c=[])
BondsEntry(i=3, j=5, funct=None, c=[])
BondsEntry(i=6, j=7, funct=None, c=[])
BondsEntry(i=6, j=8, funct=None, c=[])
DihedralsSubsection()
DihedralsEntry(i=2, j=1, k=3, l=4, funct=9, c=[])
DihedralsEntry(i=2, j=1, k=3, l=5, funct=9, c=[])
DihedralsEntry(i=2, j=1, k=6, l=7, funct=9, c=[])
DihedralsEntry(i=2, j=1, k=6, l=8, funct=9, c=[])
DihedralsEntry(i=3, j=1, k=6, l=7, funct=9, c=[])
DihedralsEntry(i=3, j=1, k=6, l=8, funct=9, c=[])
DihedralsEntry(i=6, j=1, k=3, l=4, funct=9, c=[])
DihedralsEntry(i=6, j=1, k=3, l=5, funct=9, c=[])
DihedralsSubsection()
DihedralsEntry(i=3, j=6, k=1, l=2, funct=4, c=[])
DihedralsEntry(i=1, j=4, k=3, l=5, funct=4, c=[])
DihedralsEntry(i=1, j=7, k=6, l=8, funct=4, c=[])
PositionRestraintsSubsection()
PositionRestraintsEntry(i=1, funct=1, c=[1000.0, 1000.0, 1000.0])
PositionRestraintsEntry(i=2, funct=1, c=[1000.0, 0.0, 1000.0])
PositionRestraintsEntry(i=3, funct=1, c=[1000.0, 0.0, 0.0])
DihedralRestraintsSubsection()
DihedralRestraintsEntry(i=3, j=6, k=1, l=2, funct=1, c=[180.0, 0.0, 10.0])
DihedralRestraintsEntry(i=1, j=4, k=3, l=5, funct=1, c=[180.0, 0.0, 10.0])
MoleculetypeSection()
MoleculetypeEntry(molecule='SOL', nrexcl=2)
AtomsSubsection()
AtomsEntry(nr=1, type='OW', resnr=1, residue='SOL', atom='OW', cgnr=1, charge=-0.834, mass=16.0, typeB=None, chargeB=None, massB=None)
AtomsEntry(nr=2, type='HW', resnr=1, residue='SOL', atom='HW1', cgnr=1, charge=0.417, mass=1.008, typeB=None, chargeB=None, massB=None)
AtomsEntry(nr=3, type='HW', resnr=1, residue='SOL', atom='HW2', cgnr=1, charge=0.417, mass=1.008, typeB=None, chargeB=None, massB=None)
SettlesSubsection()
SettlesEntry(i=1, funct=1, c=[0.09572, 0.15139])
ExclusionsSubsection()
ExclusionsEntry(indices=[1, 2, 3])
ExclusionsEntry(indices=[2, 1, 3])
ExclusionsEntry(indices=[3, 1, 2])
SystemSection()
SystemEntry(name='Urea in Water')
MoleculesSection()
MoleculesEntry(molecule='Urea', number=1)
MoleculesEntry(molecule='SOL', number=1000)The following figure illustrates, how these topology-elements are stored.
Nodes can be modified or deleted and new nodes can be inserted.