pysimm.forcefield

Submodules

• pysimm.forcefield.charmm
• pysimm.forcefield.dreiding
• pysimm.forcefield.forcefield
• pysimm.forcefield.gaff
• pysimm.forcefield.gaff2
• pysimm.forcefield.gasteiger
• pysimm.forcefield.pcff
• pysimm.forcefield.tip3p

Package Contents

Classes

Forcefield	pysimm.forcefield.Forcefield
Dreiding	pysimm.forcefield.Dreiding
Charmm	pysimm.forcefield.Charmm
Gaff	pysimm.forcefield.Gaff
Gaff2	pysimm.forcefield.Gaff2
Pcff	pysimm.forcefield.Pcff
Tip3p	pysimm.forcefield.Tip3p

Functions

__parse_charmm__()

Private method to read/convert CHARMM specific FF parameters from the form of GROMACS input format (.atp, .itp)

class pysimm.forcefield.Forcefield(file_=None, format=None)

Bases: object

pysimm.forcefield.Forcefield

Base Forcefield class definition. Initialize with force field xml file.

ff_class

force field class (1 or 2)

ff_name

force field name

particle_types

ItemContainer for particle_types

bond_types

ItemContainer for bond_types

angle_types

ItemContainer for angle_types

dihedral_types

ItemContainer for dihedral_types

improper_types

ItemContainer for improper_types

from_xml(self, file_)

from_json(self, json_file)

write_json(self, out)

write_xml(self, out)

pysimm.forcefield.Forcefield.write

Write Forcefield object to xml format.

Parameters

out – file name to write

Returns

None

class pysimm.forcefield.Dreiding(db_file=None)

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Dreiding

Forcefield object with typing rules for Dreiding model. By default reads data file in forcefields subdirectory.

ff_name

dreiding

pair_style

lj

ff_class

1

assign_ptypes(self, s)

pysimm.forcefield.Dreiding.assign_ptypes

Dreiding specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

Parameters

s – System

Returns

None

assign_btypes(self, s)

pysimm.forcefield.Dreiding.assign_btypes

Dreiding specific bond typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_atypes(self, s)

pysimm.forcefield.Dreiding.assign_atypes

Dreiding specific angle typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_dtypes(self, s)

pysimm.forcefield.Dreiding.assign_dtypes

Dreiding specific dihedral typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_itypes(self, s)

pysimm.forcefield.Dreiding.assign_itypes

Dreiding specific improper typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_charges(self, s, charges='gasteiger')

pysimm.forcefield.Dreiding.assign_charges

Charge assignment. Gasteiger is default for now.

Parameters

• s – System

• charges – gasteiger

Returns

None

class pysimm.forcefield.Charmm(db_file=None)

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Charmm

Forcefield object with typing rules for CHARMM model. By default reads data file in forcefields subdirectory.

ff_name

charmm

pair_style

lj/charmm

ff_class

1

assign_ptypes(self, s)

pysimm.forcefield.Charmm.assign_ptypes

Charmm specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

* Not entirely inclusive - some atom types not used *

Parameters

s – System

Returns

None

assign_extra_ljtypes(self, s)

pysimm.forcefield.Charmm.assign_extra_ljtypes

Addition to normal force field setup: filling up the non-diagonal interaction pair coefficients (coefficients for interaction of particles of different type).

Assumes that all ParticleType are defined for all particles in s

Parameters

s – System

Returns

None

assign_btypes(self, s)

pysimm.forcefield.Charmm.assign_btypes

Gaff specific bond typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_atypes(self, s)

pysimm.forcefield.Charmm.assign_atypes

Gaff specific boanglend typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_dtypes(self, s)

pysimm.forcefield.Charmm.assign_dtypes

CHARMM specific dihedral typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_itypes(self, s)

pysimm.forcefield.Charmm.assign_itypes

Gaff specific improper typing rules. There are none.

Parameters

s – System

Returns

None

assign_charges(self, s, charges='gasteiger')

pysimm.forcefield.Charmm.assign_charges

Charge assignment. Gasteiger is default for now.

Parameters

• s – System

• charges – gasteiger

Returns

None

__parse_add_file__(self, file)

Private method to read/convert CHARMM specific FF parameters from the native format (.prm) to add on top of currentely existing library of FF parameters. Will update this ForceField object with data from the file and will write the output ‘charmm_mod.json’ DB file

Parameters

file – (string) full (absolute or relative) path to an .prm file

Returns

none

pysimm.forcefield.__parse_charmm__()

Private method to read/convert CHARMM specific FF parameters from the form of GROMACS input format (.atp, .itp) to the PySIMM input format (.json).

Note: Because of the format specification, there are no sigma_{14} or epsilon_{14} parameters in the file as well as explicit non-diagonal LJ parameters (NBFIXes). They are read from a different file types (see charmm.__parse_add_file__())

Returns

None

class pysimm.forcefield.Gaff(db_file=None)

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Gaff

Forcefield object with typing rules for Gaff model. By default reads data file in forcefields subdirectory.

ff_name

gaff

pair_style

lj

ff_class

1

assign_ptypes(self, s)

pysimm.forcefield.Gaff.assign_ptypes

Gaff specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

* Not entirely inclusive - some atom types not used *

Parameters

s – System

Returns

None

assign_btypes(self, s)

pysimm.forcefield.Gaff.assign_btypes

Gaff specific bond typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_atypes(self, s)

pysimm.forcefield.Gaff.assign_atypes

Gaff specific boanglend typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_dtypes(self, s)

pysimm.forcefield.Gaff.assign_dtypes

Gaff specific dihedral typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_itypes(self, s)

pysimm.forcefield.Gaff.assign_itypes

Gaff specific improper typing rules. There are none.

Parameters

s – System

Returns

None

assign_charges(self, s, charges='gasteiger')

pysimm.forcefield.Gaff.assign_charges

Charge assignment. Gasteiger is default for now.

Parameters

• s – System

• charges – gasteiger

Returns

None

class pysimm.forcefield.Gaff2(db_file=None)

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Gaff2

Forcefield object with typing rules for Gaff2 model. By default reads data file in forcefields subdirectory.

ff_name

gaff2

pair_style

lj

bond_style

harmonic

angle_style

harmonic

dihedral_style

fourier

improper_style

cvff

ff_class

1

assign_ptypes(self, s)

pysimm.forcefield.Gaff2.assign_ptypes

Gaff2 specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

* Not entirely inclusive - some atom types not used *

Parameters

s – System

Returns

None

assign_btypes(self, s)

pysimm.forcefield.Gaff2.assign_btypes

Gaff2 specific bond typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_atypes(self, s)

pysimm.forcefield.Gaff2.assign_atypes

Gaff2 specific angle typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_dtypes(self, s)

pysimm.forcefield.Gaff2.assign_dtypes

Gaff2 specific dihedral typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_itypes(self, s)

pysimm.forcefield.Gaff2.assign_itypes

Gaff2 specific improper typing rules.

Parameters

s – System

Returns

None

assign_charges(self, s, charges='gasteiger')

pysimm.forcefield.Gaff.assign_charges

Charge assignment. Gasteiger is default for now.

Parameters

• s – System

• charges – gasteiger

Returns

None

class pysimm.forcefield.Pcff(db_file=None)

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Pcff

Forcefield object with typing rules for Pcff model. By default reads data file in forcefields subdirectory.

ff_name

pcff

pair_style

class2

ff_class

2

nb_mixing

sixth

assign_ptypes(self, s)

pysimm.forcefield.Pcff.assign_ptypes

Pcff specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

Parameters

s – System

Returns

None

assign_btypes(self, s)

pysimm.forcefield.Pcff.assign_btypes

Pcff specific bond typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_atypes(self, s)

pysimm.forcefield.Pcff.assign_atypes

Pcff specific angle typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_dtypes(self, s)

pysimm.forcefield.Pcff.assign_dtypes

Pcff specific dihedral typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_itypes(self, s)

pysimm.forcefield.Pcff.assign_itypes

Pcff specific improper typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_charges(self, s, charges='default')

pysimm.forcefield.Pcff.assign_charges

Default Pcff charge assignment. Gasteiger is also an option.

Parameters

• s – System

• charges – default

Returns

None

class pysimm.forcefield.Tip3p(db_file=None)

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Tip3p

Forcefield object with typing rules for Tip3p model. By default reads data file in forcefields subdirectory.

ff_name

tip3p

pair_style

lj

ff_class

1

assign_ptypes(self, s)

pysimm.forcefield.Tip3p.assign_ptypes

Tip3p specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

Parameters

s – System

Returns

None

assign_btypes(self, s)

pysimm.forcefield.Tip3p.assign_btypes

Tip3p specific bond typing rules. Requires System object Particle objects have type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_atypes(self, s)

pysimm.forcefield.Tip3p.assign_atypes

Tip3p specific angle typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters

s – System

Returns

None

assign_dtypes(self, s)

pysimm.forcefield.Tip3p.assign_dtypes

Tip3p specific dihedral typing rules. There are none.

Parameters

s – System

Returns

None

assign_itypes(self, s)

pysimm.forcefield.Tip3p.assign_itypes

Tip3p specific improper typing rules. There are none.

Parameters

s – System

Returns

None

assign_charges(self, s, charges='default')

pysimm.forcefield.Tip3p.assign_charges

Tip3p specific charge assignment. There are none.

Parameters

• s – System

• charges – default

Returns

None