Index

_ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X

_

__repr__() (intermol.forces.abstract_type.AbstractType method)

A

a (intermol.forces.buckingham_nonbonded_type.BuckinghamNonbondedType attribute)
(intermol.forces.four_fdn_virtual_type.FourFdnVirtualType attribute)
(intermol.forces.three_fd_virtual_type.ThreeFdVirtualType attribute)
(intermol.forces.three_linear_virtual_type.ThreeLinearVirtualType attribute)
(intermol.forces.three_out_virtual_type.ThreeOutVirtualType attribute)
(intermol.forces.two_virtual_type.TwoVirtualType attribute)
Abstract2VirtualType (class in intermol.forces.abstract_2_virtual_type)
Abstract3VirtualType (class in intermol.forces.abstract_3_virtual_type)
Abstract4VirtualType (class in intermol.forces.abstract_4_virtual_type)
AbstractAngleType (class in intermol.forces.abstract_angle_type)
AbstractAtomType (class in intermol.forces.abstract_atom_type)
AbstractBondType (class in intermol.forces.abstract_bond_type)
AbstractDihedralType (class in intermol.forces.abstract_dihedral_type)
AbstractNonbondedType (class in intermol.forces.abstract_nonbonded_type)
AbstractPairType (class in intermol.forces.abstract_pair_type)
AbstractType (class in intermol.forces.abstract_type)
accepts() (in module intermol.decorators)
accepts_compatible_units() (in module intermol.decorators)
add() (intermol.orderedset.OrderedSet method)
add_atom() (intermol.molecule.Molecule method)
add_atomtype() (intermol.system.System method)
add_molecule() (intermol.moleculetype.MoleculeType method)
(intermol.system.System method)
add_molecule_type() (intermol.system.System method)
Atom (class in intermol.atom)
atom1 (intermol.forces.abstract_nonbonded_type.AbstractNonbondedType attribute)
atom2 (intermol.forces.abstract_nonbonded_type.AbstractNonbondedType attribute)
AtomCType (class in intermol.forces.atom_c_type)
atomic_number (intermol.atom.Atom attribute)
(intermol.forces.abstract_atom_type.AbstractAtomType attribute)
atoms (intermol.molecule.Molecule attribute)
(intermol.system.System attribute)
AtomSigepsType (class in intermol.forces.atom_sigeps_type)
atomtype (intermol.atom.Atom attribute)
(intermol.forces.abstract_atom_type.AbstractAtomType attribute)
atomtypes (intermol.system.System attribute)

B

b (intermol.forces.buckingham_nonbonded_type.BuckinghamNonbondedType attribute)
(intermol.forces.four_fdn_virtual_type.FourFdnVirtualType attribute)
(intermol.forces.three_linear_virtual_type.ThreeLinearVirtualType attribute)
(intermol.forces.three_out_virtual_type.ThreeOutVirtualType attribute)
B1 (intermol.forces.quartic_breakable_bond_type.QuarticBreakableBondType attribute)
B2 (intermol.forces.quartic_breakable_bond_type.QuarticBreakableBondType attribute)
beta (intermol.forces.morse_bond_type.MorseBondType attribute)
bondingtype (intermol.atom.Atom attribute)
bondingtype1 (intermol.forces.abstract_2_virtual_type.Abstract2VirtualType attribute)
(intermol.forces.abstract_3_virtual_type.Abstract3VirtualType attribute)
(intermol.forces.abstract_4_virtual_type.Abstract4VirtualType attribute)
(intermol.forces.abstract_angle_type.AbstractAngleType attribute)
(intermol.forces.abstract_bond_type.AbstractBondType attribute)
(intermol.forces.abstract_dihedral_type.AbstractDihedralType attribute)
(intermol.forces.abstract_pair_type.AbstractPairType attribute)
bondingtype2 (intermol.forces.abstract_2_virtual_type.Abstract2VirtualType attribute)
(intermol.forces.abstract_3_virtual_type.Abstract3VirtualType attribute)
(intermol.forces.abstract_4_virtual_type.Abstract4VirtualType attribute)
(intermol.forces.abstract_angle_type.AbstractAngleType attribute)
(intermol.forces.abstract_bond_type.AbstractBondType attribute)
(intermol.forces.abstract_dihedral_type.AbstractDihedralType attribute)
(intermol.forces.abstract_pair_type.AbstractPairType attribute)
bondingtype3 (intermol.forces.abstract_3_virtual_type.Abstract3VirtualType attribute)
(intermol.forces.abstract_4_virtual_type.Abstract4VirtualType attribute)
(intermol.forces.abstract_angle_type.AbstractAngleType attribute)
(intermol.forces.abstract_dihedral_type.AbstractDihedralType attribute)
bondingtype4 (intermol.forces.abstract_3_virtual_type.Abstract3VirtualType attribute)
(intermol.forces.abstract_4_virtual_type.Abstract4VirtualType attribute)
(intermol.forces.abstract_dihedral_type.AbstractDihedralType attribute)
bondtype (intermol.forces.abstract_atom_type.AbstractAtomType attribute)
box_vector (intermol.system.System attribute)
BuckinghamNonbonded (class in intermol.forces.buckingham_nonbonded_type)
BuckinghamNonbondedType (class in intermol.forces.buckingham_nonbonded_type)
build_paramlist() (in module intermol.forces.forcefunctions)
build_unitvars() (in module intermol.forces.forcefunctions)

C

c (intermol.forces.abstract_angle_type.AbstractAngleType attribute)
(intermol.forces.abstract_bond_type.AbstractBondType attribute)
(intermol.forces.connection_bond_type.ConnectionBondType attribute)
(intermol.forces.cosine_angle_type.CosineAngleType attribute)
(intermol.forces.cosine_squared_angle_type.CosineSquaredAngleType attribute)
(intermol.forces.cross_bond_angle_angle_type.CrossBondAngleAngleType attribute)
(intermol.forces.cross_bond_bond_angle_type.CrossBondBondAngleType attribute)
(intermol.forces.cubic_bond_type.CubicBondType attribute)
(intermol.forces.fene_bond_type.FeneBondType attribute)
(intermol.forces.fene_expandable_bond_type.FeneExpandableBondType attribute)
(intermol.forces.four_fdn_virtual_type.FourFdnVirtualType attribute)
(intermol.forces.g96_bond_type.G96BondType attribute)
(intermol.forces.harmonic_angle_type.HarmonicAngleType attribute)
(intermol.forces.harmonic_bond_type.HarmonicBondType attribute)
(intermol.forces.harmonic_potential_bond_type.HarmonicPotentialBondType attribute)
(intermol.forces.morse_bond_type.MorseBondType attribute)
(intermol.forces.nonlinear_bond_type.NonlinearBondType attribute)
(intermol.forces.quartic_angle_type.QuarticAngleType attribute)
(intermol.forces.quartic_bond_type.QuarticBondType attribute)
(intermol.forces.quartic_breakable_bond_type.QuarticBreakableBondType attribute)
(intermol.forces.three_out_virtual_type.ThreeOutVirtualType attribute)
(intermol.forces.urey_bradley_angle_type.UreyBradleyAngleType attribute)
C0 (intermol.forces.quartic_angle_type.QuarticAngleType attribute)
(intermol.forces.rb_dihedral_type.RbDihedralType attribute)
c1 (intermol.forces.fourier_dihedral_type.FourierDihedralType attribute)
C1 (intermol.forces.quartic_angle_type.QuarticAngleType attribute)
(intermol.forces.rb_dihedral_type.RbDihedralType attribute)
C12 (intermol.forces.lj_c_nonbonded_type.LjCNonbondedType attribute)
(intermol.forces.lj_c_pair_type.LjCPairType attribute)
(intermol.forces.ljq_c_pair_type.LjqCPairType attribute)
C2 (intermol.forces.cubic_bond_type.CubicBondType attribute)
c2 (intermol.forces.fourier_dihedral_type.FourierDihedralType attribute)
C2 (intermol.forces.quartic_angle_type.QuarticAngleType attribute)
(intermol.forces.quartic_bond_type.QuarticBondType attribute)
(intermol.forces.rb_dihedral_type.RbDihedralType attribute)
C3 (intermol.forces.cubic_bond_type.CubicBondType attribute)
c3 (intermol.forces.fourier_dihedral_type.FourierDihedralType attribute)
C3 (intermol.forces.quartic_angle_type.QuarticAngleType attribute)
(intermol.forces.quartic_bond_type.QuarticBondType attribute)
(intermol.forces.rb_dihedral_type.RbDihedralType attribute)
c4 (intermol.forces.fourier_dihedral_type.FourierDihedralType attribute)
C4 (intermol.forces.quartic_angle_type.QuarticAngleType attribute)
(intermol.forces.quartic_bond_type.QuarticBondType attribute)
(intermol.forces.rb_dihedral_type.RbDihedralType attribute)
c5 (intermol.forces.fourier_dihedral_type.FourierDihedralType attribute)
C5 (intermol.forces.rb_dihedral_type.RbDihedralType attribute)
C6 (intermol.forces.buckingham_nonbonded_type.BuckinghamNonbondedType attribute)
(intermol.forces.lj_c_nonbonded_type.LjCNonbondedType attribute)
(intermol.forces.lj_c_pair_type.LjCPairType attribute)
(intermol.forces.ljq_c_pair_type.LjqCPairType attribute)
(intermol.forces.rb_dihedral_type.RbDihedralType attribute)
canonical_angle() (intermol.gromacs.gromacs_parser.GromacsParser method)
(intermol.lammps.lammps_parser.LammpsParser method)
canonical_bond() (intermol.gromacs.gromacs_parser.GromacsParser method)
(intermol.lammps.lammps_parser.LammpsParser method)
canonical_dihedral() (intermol.gromacs.gromacs_parser.GromacsParser method)
(intermol.lammps.lammps_parser.LammpsParser method)
capifyname() (in module intermol.forces.forcefunctions)
cgnr (intermol.atom.Atom attribute)
charge (intermol.atom.Atom attribute)
(intermol.forces.abstract_atom_type.AbstractAtomType attribute)
choose_parameter_kwds_from_forces() (intermol.gromacs.gromacs_parser.GromacsParser method)
ConnectionBond (class in intermol.forces.connection_bond_type)
ConnectionBondType (class in intermol.forces.connection_bond_type)
convert_dihedral_from_fourier_to_trig() (in module intermol.forces.convert_dihedrals)
convert_dihedral_from_OPLS_to_RB() (in module intermol.forces.convert_dihedrals)
convert_dihedral_from_proper_to_trig() (in module intermol.forces.convert_dihedrals)
convert_dihedral_from_RB_to_OPLS() (in module intermol.forces.convert_dihedrals)
convert_dihedral_from_RB_to_trig() (in module intermol.forces.convert_dihedrals)
convert_dihedral_from_trig_to_fourier() (in module intermol.forces.convert_dihedrals)
convert_dihedral_from_trig_to_proper() (in module intermol.forces.convert_dihedrals)
convert_dihedral_from_trig_to_RB() (in module intermol.forces.convert_dihedrals)
convert_nothing() (in module intermol.forces.convert_dihedrals)
CosineAngle (class in intermol.forces.cosine_angle_type)
CosineAngleType (class in intermol.forces.cosine_angle_type)
CosineSquaredAngle (class in intermol.forces.cosine_squared_angle_type)
CosineSquaredAngleType (class in intermol.forces.cosine_squared_angle_type)
create_angle() (intermol.gromacs.gromacs_parser.GromacsParser method)
create_atom() (intermol.gromacs.gromacs_parser.GromacsParser method)
create_bond() (intermol.gromacs.gromacs_parser.GromacsParser method)
create_dihedral() (intermol.gromacs.gromacs_parser.GromacsParser method)
create_exclusion() (intermol.gromacs.gromacs_parser.GromacsParser method)
create_kwd_dict() (in module intermol.forces.forcefunctions)
create_kwds_from_entries() (in module intermol.forces.forcefunctions)
(intermol.gromacs.gromacs_parser.GromacsParser method)
(intermol.lammps.lammps_parser.LammpsParser method)
create_molecule() (intermol.gromacs.gromacs_parser.GromacsParser method)
create_moleculetype() (intermol.gromacs.gromacs_parser.GromacsParser method)
create_pair() (intermol.gromacs.gromacs_parser.GromacsParser method)
create_settle() (intermol.gromacs.gromacs_parser.GromacsParser method)
CrossBondAngleAngle (class in intermol.forces.cross_bond_angle_angle_type)
CrossBondAngleAngleType (class in intermol.forces.cross_bond_angle_angle_type)
CrossBondBondAngle (class in intermol.forces.cross_bond_bond_angle_type)
CrossBondBondAngleType (class in intermol.forces.cross_bond_bond_angle_type)
CubicBond (class in intermol.forces.cubic_bond_type)
CubicBondType (class in intermol.forces.cubic_bond_type)

D

D (intermol.forces.morse_bond_type.MorseBondType attribute)
d (intermol.forces.three_fad_virtual_type.ThreeFadVirtualType attribute)
(intermol.forces.three_fd_virtual_type.ThreeFdVirtualType attribute)
default_gromacs_include_dir() (in module intermol.gromacs.gromacs_parser)
delta (intermol.forces.fene_expandable_bond_type.FeneExpandableBondType attribute)
difference_update() (intermol.orderedset.OrderedSet method)
directive_before_moleculetype() (intermol.gromacs.gromacs_parser.GromacsParser method)
discard() (intermol.orderedset.OrderedSet method)

E

epsilon (intermol.atom.Atom attribute)
(intermol.forces.fene_expandable_bond_type.FeneExpandableBondType attribute)
(intermol.forces.lj_sigeps_nonbonded_type.LjSigepsNonbondedType attribute)
(intermol.forces.lj_sigeps_pair_type.LjSigepsPairType attribute)
(intermol.forces.ljq_sigeps_pair_type.LjqSigepsPairType attribute)
(intermol.forces.nonlinear_bond_type.NonlinearBondType attribute)

F

fc0 (intermol.forces.trig_dihedral_type.TrigDihedralType attribute)
fc1 (intermol.forces.trig_dihedral_type.TrigDihedralType attribute)
fc2 (intermol.forces.trig_dihedral_type.TrigDihedralType attribute)
fc3 (intermol.forces.trig_dihedral_type.TrigDihedralType attribute)
fc4 (intermol.forces.trig_dihedral_type.TrigDihedralType attribute)
fc5 (intermol.forces.trig_dihedral_type.TrigDihedralType attribute)
fc6 (intermol.forces.trig_dihedral_type.TrigDihedralType attribute)
FeneBond (class in intermol.forces.fene_bond_type)
FeneBondType (class in intermol.forces.fene_bond_type)
FeneExpandableBond (class in intermol.forces.fene_expandable_bond_type)
FeneExpandableBondType (class in intermol.forces.fene_expandable_bond_type)
find_dihedraltype() (intermol.gromacs.gromacs_parser.GromacsParser method)
find_forcetype() (intermol.gromacs.gromacs_parser.GromacsParser method)
find_match() (in module intermol.convert)
force (intermol.atom.Atom attribute)
FourFdnVirtual (class in intermol.forces.four_fdn_virtual_type)
FourFdnVirtualType (class in intermol.forces.four_fdn_virtual_type)
FourierDihedral (class in intermol.forces.fourier_dihedral_type)
FourierDihedralType (class in intermol.forces.fourier_dihedral_type)

G

G96Bond (class in intermol.forces.g96_bond_type)
G96BondType (class in intermol.forces.g96_bond_type)
get_diff() (in module intermol.convert)
get_force_atoms() (intermol.lammps.lammps_parser.LammpsParser method)
get_force_bondingtypes() (intermol.lammps.lammps_parser.LammpsParser method)
get_parameter_kwds_from_force() (in module intermol.forces.forcefunctions)
(intermol.gromacs.gromacs_parser.GromacsParser method)
(intermol.lammps.lammps_parser.LammpsParser method)
get_parameter_list_from_force() (in module intermol.forces.forcefunctions)
(intermol.gromacs.gromacs_parser.GromacsParser method)
(intermol.lammps.lammps_parser.LammpsParser method)
get_parameter_list_from_kwds() (in module intermol.forces.forcefunctions)
gromacs_angle_types (intermol.gromacs.gromacs_parser.GromacsParser attribute)
gromacs_angles (intermol.gromacs.gromacs_parser.GromacsParser attribute)
gromacs_bond_types (intermol.gromacs.gromacs_parser.GromacsParser attribute)
gromacs_bonds (intermol.gromacs.gromacs_parser.GromacsParser attribute)
gromacs_combination_rules (intermol.gromacs.gromacs_parser.GromacsParser attribute)
gromacs_dihedral_types (intermol.gromacs.gromacs_parser.GromacsParser attribute)
gromacs_dihedrals (intermol.gromacs.gromacs_parser.GromacsParser attribute)
gromacs_energies() (in module intermol.gromacs.gromacs_driver)
gromacs_pair_types (intermol.gromacs.gromacs_parser.GromacsParser attribute)
gromacs_pairs (intermol.gromacs.gromacs_parser.GromacsParser attribute)
GromacsGroParser (class in intermol.gromacs.grofile_parser)
GromacsParser (class in intermol.gromacs.gromacs_parser)
GromacsParser.TopMoleculeType (class in intermol.gromacs.gromacs_parser)

H

HarmonicAngle (class in intermol.forces.harmonic_angle_type)
HarmonicAngleType (class in intermol.forces.harmonic_angle_type)
HarmonicBond (class in intermol.forces.harmonic_bond_type)
HarmonicBondType (class in intermol.forces.harmonic_bond_type)
HarmonicPotentialBond (class in intermol.forces.harmonic_potential_bond_type)
HarmonicPotentialBondType (class in intermol.forces.harmonic_potential_bond_type)

I

improper (intermol.forces.abstract_dihedral_type.AbstractDihedralType attribute)
(intermol.forces.fourier_dihedral_type.FourierDihedralType attribute)
(intermol.forces.improper_harmonic_dihedral_type.ImproperHarmonicDihedralType attribute)
(intermol.forces.proper_periodic_dihedral_type.ProperPeriodicDihedralType attribute)
(intermol.forces.rb_dihedral_type.RbDihedralType attribute)
(intermol.forces.trig_dihedral_type.TrigDihedralType attribute)
ImproperHarmonicDihedral (class in intermol.forces.improper_harmonic_dihedral_type)
ImproperHarmonicDihedralType (class in intermol.forces.improper_harmonic_dihedral_type)
index (intermol.atom.Atom attribute)
intermol (module)
intermol.atom (module)
intermol.convert (module)
intermol.decorators (module)
intermol.forces (module)
intermol.forces.abstract_2_virtual_type (module)
intermol.forces.abstract_3_virtual_type (module)
intermol.forces.abstract_4_virtual_type (module)
intermol.forces.abstract_angle_type (module)
intermol.forces.abstract_atom_type (module)
intermol.forces.abstract_bond_type (module)
intermol.forces.abstract_dihedral_type (module)
intermol.forces.abstract_nonbonded_type (module)
intermol.forces.abstract_pair_type (module)
intermol.forces.abstract_type (module)
intermol.forces.atom_c_type (module)
intermol.forces.atom_sigeps_type (module)
intermol.forces.buckingham_nonbonded_type (module)
intermol.forces.connection_bond_type (module)
intermol.forces.convert_dihedrals (module)
intermol.forces.cosine_angle_type (module)
intermol.forces.cosine_squared_angle_type (module)
intermol.forces.cross_bond_angle_angle_type (module)
intermol.forces.cross_bond_bond_angle_type (module)
intermol.forces.cubic_bond_type (module)
intermol.forces.fene_bond_type (module)
intermol.forces.fene_expandable_bond_type (module)
intermol.forces.forcedata (module)
intermol.forces.forcefunctions (module)
intermol.forces.four_fdn_virtual_type (module)
intermol.forces.fourier_dihedral_type (module)
intermol.forces.g96_bond_type (module)
intermol.forces.harmonic_angle_type (module)
intermol.forces.harmonic_bond_type (module)
intermol.forces.harmonic_potential_bond_type (module)
intermol.forces.improper_harmonic_dihedral_type (module)
intermol.forces.lj_c_nonbonded_type (module)
intermol.forces.lj_c_pair_type (module)
intermol.forces.lj_default_pair_type (module)
intermol.forces.lj_sigeps_nonbonded_type (module)
intermol.forces.lj_sigeps_pair_type (module)
intermol.forces.ljq_c_pair_type (module)
intermol.forces.ljq_default_pair_type (module)
intermol.forces.ljq_sigeps_pair_type (module)
intermol.forces.make_forces (module)
intermol.forces.morse_bond_type (module)
intermol.forces.nonlinear_bond_type (module)
intermol.forces.proper_periodic_dihedral_type (module)
intermol.forces.quartic_angle_type (module)
intermol.forces.quartic_bond_type (module)
intermol.forces.quartic_breakable_bond_type (module)
intermol.forces.rb_dihedral_type (module)
intermol.forces.settles (module)
intermol.forces.three_fad_virtual_type (module)
intermol.forces.three_fd_virtual_type (module)
intermol.forces.three_linear_virtual_type (module)
intermol.forces.three_out_virtual_type (module)
intermol.forces.trig_dihedral_type (module)
intermol.forces.two_virtual_type (module)
intermol.forces.urey_bradley_angle_type (module)
intermol.gromacs (module)
intermol.gromacs.grofile_parser (module)
intermol.gromacs.gromacs_driver (module)
intermol.gromacs.gromacs_parser (module)
intermol.lammps (module)
intermol.lammps.lammps_driver (module)
intermol.lammps.lammps_parser (module)
intermol.molecule (module)
intermol.moleculetype (module)
intermol.orderedset (module)
intermol.system (module)
intersection_update() (intermol.orderedset.OrderedSet method)
invalid_line() (intermol.gromacs.gromacs_parser.GromacsParser method)

K

k (intermol.forces.cosine_angle_type.CosineAngleType attribute)
(intermol.forces.cosine_squared_angle_type.CosineSquaredAngleType attribute)
(intermol.forces.cross_bond_angle_angle_type.CrossBondAngleAngleType attribute)
(intermol.forces.cross_bond_bond_angle_type.CrossBondBondAngleType attribute)
(intermol.forces.fene_expandable_bond_type.FeneExpandableBondType attribute)
(intermol.forces.g96_bond_type.G96BondType attribute)
(intermol.forces.harmonic_angle_type.HarmonicAngleType attribute)
(intermol.forces.harmonic_bond_type.HarmonicBondType attribute)
(intermol.forces.harmonic_potential_bond_type.HarmonicPotentialBondType attribute)
(intermol.forces.improper_harmonic_dihedral_type.ImproperHarmonicDihedralType attribute)
(intermol.forces.proper_periodic_dihedral_type.ProperPeriodicDihedralType attribute)
(intermol.forces.quartic_breakable_bond_type.QuarticBreakableBondType attribute)
(intermol.forces.urey_bradley_angle_type.UreyBradleyAngleType attribute)
kb (intermol.forces.fene_bond_type.FeneBondType attribute)
kUB (intermol.forces.urey_bradley_angle_type.UreyBradleyAngleType attribute)

L

lamda (intermol.forces.nonlinear_bond_type.NonlinearBondType attribute)
lammps_angle_types (intermol.lammps.lammps_parser.LammpsParser attribute)
lammps_angles (intermol.lammps.lammps_parser.LammpsParser attribute)
lammps_bond_types (intermol.lammps.lammps_parser.LammpsParser attribute)
lammps_bonds (intermol.lammps.lammps_parser.LammpsParser attribute)
lammps_dihedral_types (intermol.lammps.lammps_parser.LammpsParser attribute)
lammps_dihedrals (intermol.lammps.lammps_parser.LammpsParser attribute)
lammps_energies() (in module intermol.lammps.lammps_driver)
lammps_improper_types (intermol.lammps.lammps_parser.LammpsParser attribute)
lammps_impropers (intermol.lammps.lammps_parser.LammpsParser attribute)
LammpsParser (class in intermol.lammps.lammps_parser)
length (intermol.forces.cubic_bond_type.CubicBondType attribute)
(intermol.forces.fene_bond_type.FeneBondType attribute)
(intermol.forces.fene_expandable_bond_type.FeneExpandableBondType attribute)
(intermol.forces.g96_bond_type.G96BondType attribute)
(intermol.forces.harmonic_bond_type.HarmonicBondType attribute)
(intermol.forces.harmonic_potential_bond_type.HarmonicPotentialBondType attribute)
(intermol.forces.morse_bond_type.MorseBondType attribute)
(intermol.forces.quartic_bond_type.QuarticBondType attribute)
LjCNonbonded (class in intermol.forces.lj_c_nonbonded_type)
LjCNonbondedType (class in intermol.forces.lj_c_nonbonded_type)
LjCPair (class in intermol.forces.lj_c_pair_type)
LjCPairType (class in intermol.forces.lj_c_pair_type)
LjDefaultPair (class in intermol.forces.lj_default_pair_type)
LjDefaultPairType (class in intermol.forces.lj_default_pair_type)
LjqCPair (class in intermol.forces.ljq_c_pair_type)
LjqCPairType (class in intermol.forces.ljq_c_pair_type)
LjqDefaultPair (class in intermol.forces.ljq_default_pair_type)
LjqDefaultPairType (class in intermol.forces.ljq_default_pair_type)
LjqSigepsPair (class in intermol.forces.ljq_sigeps_pair_type)
LjqSigepsPairType (class in intermol.forces.ljq_sigeps_pair_type)
LjSigepsNonbonded (class in intermol.forces.lj_sigeps_nonbonded_type)
LjSigepsNonbondedType (class in intermol.forces.lj_sigeps_nonbonded_type)
LjSigepsPair (class in intermol.forces.lj_sigeps_pair_type)
LjSigepsPairType (class in intermol.forces.lj_sigeps_pair_type)
load_gromacs() (in module intermol.gromacs.gromacs_parser)
load_lammps() (in module intermol.lammps.lammps_parser)
long (intermol.forces.abstract_pair_type.AbstractPairType attribute)
(intermol.forces.lj_c_pair_type.LjCPairType attribute)
(intermol.forces.lj_default_pair_type.LjDefaultPairType attribute)
(intermol.forces.lj_sigeps_pair_type.LjSigepsPairType attribute)
(intermol.forces.ljq_c_pair_type.LjqCPairType attribute)
(intermol.forces.ljq_default_pair_type.LjqDefaultPairType attribute)
(intermol.forces.ljq_sigeps_pair_type.LjqSigepsPairType attribute)
lookup_atom_atomtype() (intermol.gromacs.gromacs_parser.GromacsParser method)
lookup_atom_bondingtype() (intermol.gromacs.gromacs_parser.GromacsParser method)
lookup_gromacs_angles (intermol.gromacs.gromacs_parser.GromacsParser attribute)
lookup_gromacs_bonds (intermol.gromacs.gromacs_parser.GromacsParser attribute)
lookup_gromacs_combination_rules (intermol.gromacs.gromacs_parser.GromacsParser attribute)
lookup_gromacs_dihedrals (intermol.gromacs.gromacs_parser.GromacsParser attribute)
lookup_gromacs_pairs (intermol.gromacs.gromacs_parser.GromacsParser attribute)
lookup_lammps_angles (intermol.lammps.lammps_parser.LammpsParser attribute)
lookup_lammps_bonds (intermol.lammps.lammps_parser.LammpsParser attribute)
lookup_lammps_dihedrals (intermol.lammps.lammps_parser.LammpsParser attribute)
lookup_lammps_impropers (intermol.lammps.lammps_parser.LammpsParser attribute)

M

main() (in module intermol.convert)
mass (intermol.atom.Atom attribute)
(intermol.forces.abstract_atom_type.AbstractAtomType attribute)
Molecule (class in intermol.molecule)
molecule_types (intermol.system.System attribute)
MoleculeType (class in intermol.moleculetype)
MorseBond (class in intermol.forces.morse_bond_type)
MorseBondType (class in intermol.forces.morse_bond_type)
multiplicity (intermol.forces.proper_periodic_dihedral_type.ProperPeriodicDihedralType attribute)

N

n_atoms (intermol.system.System attribute)
name (intermol.atom.Atom attribute)
nonbonded_types (intermol.system.System attribute)
NonlinearBond (class in intermol.forces.nonlinear_bond_type)
NonlinearBondType (class in intermol.forces.nonlinear_bond_type)

O

optforceparams() (in module intermol.forces.forcefunctions)
optparamkeylookup() (in module intermol.forces.forcefunctions)
optparamlookup() (in module intermol.forces.forcefunctions)
order (intermol.forces.abstract_bond_type.AbstractBondType attribute)
(intermol.forces.connection_bond_type.ConnectionBondType attribute)
(intermol.forces.cubic_bond_type.CubicBondType attribute)
(intermol.forces.fene_bond_type.FeneBondType attribute)
(intermol.forces.fene_expandable_bond_type.FeneExpandableBondType attribute)
(intermol.forces.g96_bond_type.G96BondType attribute)
(intermol.forces.harmonic_bond_type.HarmonicBondType attribute)
(intermol.forces.harmonic_potential_bond_type.HarmonicPotentialBondType attribute)
(intermol.forces.morse_bond_type.MorseBondType attribute)
(intermol.forces.nonlinear_bond_type.NonlinearBondType attribute)
(intermol.forces.quartic_bond_type.QuarticBondType attribute)
(intermol.forces.quartic_breakable_bond_type.QuarticBreakableBondType attribute)
OrderedSet (class in intermol.orderedset)

P

paramlist (intermol.gromacs.gromacs_parser.GromacsParser attribute)
parse_angle_coeffs() (intermol.lammps.lammps_parser.LammpsParser method)
parse_angle_style() (intermol.lammps.lammps_parser.LammpsParser method)
parse_angles() (intermol.lammps.lammps_parser.LammpsParser method)
parse_args() (in module intermol.convert)
parse_atom_style() (intermol.lammps.lammps_parser.LammpsParser method)
parse_atoms() (intermol.lammps.lammps_parser.LammpsParser method)
parse_bond_coeffs() (intermol.lammps.lammps_parser.LammpsParser method)
parse_bond_style() (intermol.lammps.lammps_parser.LammpsParser method)
parse_bonded_style() (intermol.lammps.lammps_parser.LammpsParser method)
parse_bonds() (intermol.lammps.lammps_parser.LammpsParser method)
parse_boundary() (intermol.lammps.lammps_parser.LammpsParser method)
parse_box() (intermol.lammps.lammps_parser.LammpsParser method)
parse_dihedral_coeffs() (intermol.lammps.lammps_parser.LammpsParser method)
parse_dihedral_style() (intermol.lammps.lammps_parser.LammpsParser method)
parse_dihedrals() (intermol.lammps.lammps_parser.LammpsParser method)
parse_dimension() (intermol.lammps.lammps_parser.LammpsParser method)
parse_force() (intermol.lammps.lammps_parser.LammpsParser method)
parse_force_coeffs() (intermol.lammps.lammps_parser.LammpsParser method)
parse_improper_coeffs() (intermol.lammps.lammps_parser.LammpsParser method)
parse_improper_style() (intermol.lammps.lammps_parser.LammpsParser method)
parse_impropers() (intermol.lammps.lammps_parser.LammpsParser method)
parse_kspace_style() (intermol.lammps.lammps_parser.LammpsParser method)
parse_masses() (intermol.lammps.lammps_parser.LammpsParser method)
parse_pair_coeffs() (intermol.lammps.lammps_parser.LammpsParser method)
parse_pair_modify() (intermol.lammps.lammps_parser.LammpsParser method)
parse_pair_style() (intermol.lammps.lammps_parser.LammpsParser method)
parse_read_data() (intermol.lammps.lammps_parser.LammpsParser method)
parse_special_bonds() (intermol.lammps.lammps_parser.LammpsParser method)
parse_units() (intermol.lammps.lammps_parser.LammpsParser method)
parse_velocities() (intermol.lammps.lammps_parser.LammpsParser method)
phi (intermol.forces.proper_periodic_dihedral_type.ProperPeriodicDihedralType attribute)
(intermol.forces.trig_dihedral_type.TrigDihedralType attribute)
placeholder (intermol.forces.abstract_2_virtual_type.Abstract2VirtualType attribute)
(intermol.forces.abstract_3_virtual_type.Abstract3VirtualType attribute)
(intermol.forces.four_fdn_virtual_type.FourFdnVirtualType attribute)
(intermol.forces.three_fad_virtual_type.ThreeFadVirtualType attribute)
(intermol.forces.three_fd_virtual_type.ThreeFdVirtualType attribute)
(intermol.forces.three_linear_virtual_type.ThreeLinearVirtualType attribute)
(intermol.forces.three_out_virtual_type.ThreeOutVirtualType attribute)
(intermol.forces.two_virtual_type.TwoVirtualType attribute)
position (intermol.atom.Atom attribute)
process_angle() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_angletype() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_atom() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_atomtype() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_bond() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_bondtype() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_cmap() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_cmaptype() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_defaults() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_dihedral() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_dihedraltype() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_exclusion() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_file() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_forcetype() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_implicittype() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_line() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_molecule() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_moleculetype() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_nonbond_params() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_pair() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_pairtype() (intermol.gromacs.gromacs_parser.GromacsParser method)
process_settle() (intermol.gromacs.gromacs_parser.GromacsParser method)
ProperPeriodicDihedral (class in intermol.forces.proper_periodic_dihedral_type)
ProperPeriodicDihedralType (class in intermol.forces.proper_periodic_dihedral_type)
ptype (intermol.atom.Atom attribute)
(intermol.forces.abstract_atom_type.AbstractAtomType attribute)

Q

qi (intermol.forces.ljq_c_pair_type.LjqCPairType attribute)
(intermol.forces.ljq_sigeps_pair_type.LjqSigepsPairType attribute)
qj (intermol.forces.ljq_c_pair_type.LjqCPairType attribute)
(intermol.forces.ljq_sigeps_pair_type.LjqSigepsPairType attribute)
QuarticAngle (class in intermol.forces.quartic_angle_type)
QuarticAngleType (class in intermol.forces.quartic_angle_type)
QuarticBond (class in intermol.forces.quartic_bond_type)
QuarticBondType (class in intermol.forces.quartic_bond_type)
QuarticBreakableBond (class in intermol.forces.quartic_breakable_bond_type)
QuarticBreakableBondType (class in intermol.forces.quartic_breakable_bond_type)

R

r (intermol.forces.urey_bradley_angle_type.UreyBradleyAngleType attribute)
r0 (intermol.forces.nonlinear_bond_type.NonlinearBondType attribute)
r1 (intermol.forces.cross_bond_angle_angle_type.CrossBondAngleAngleType attribute)
(intermol.forces.cross_bond_bond_angle_type.CrossBondBondAngleType attribute)
r2 (intermol.forces.cross_bond_angle_angle_type.CrossBondAngleAngleType attribute)
(intermol.forces.cross_bond_bond_angle_type.CrossBondBondAngleType attribute)
r3 (intermol.forces.cross_bond_angle_angle_type.CrossBondAngleAngleType attribute)
RbDihedral (class in intermol.forces.rb_dihedral_type)
RbDihedralType (class in intermol.forces.rb_dihedral_type)
Rc (intermol.forces.quartic_breakable_bond_type.QuarticBreakableBondType attribute)
read() (intermol.gromacs.grofile_parser.GromacsGroParser method)
(intermol.gromacs.gromacs_parser.GromacsParser method)
(intermol.lammps.lammps_parser.LammpsParser method)
read_data() (intermol.lammps.lammps_parser.LammpsParser method)
read_file() (in module intermol.gromacs.gromacs_driver)
(in module intermol.lammps.lammps_driver)
read_input() (intermol.lammps.lammps_parser.LammpsParser method)
residue_index (intermol.atom.Atom attribute)
residue_name (intermol.atom.Atom attribute)
returns() (in module intermol.decorators)

S

SCALE_FROM (intermol.lammps.lammps_parser.LammpsParser attribute)
SCALE_INTO (intermol.lammps.lammps_parser.LammpsParser attribute)
scaleLJ (intermol.forces.abstract_pair_type.AbstractPairType attribute)
(intermol.forces.lj_c_pair_type.LjCPairType attribute)
(intermol.forces.lj_default_pair_type.LjDefaultPairType attribute)
(intermol.forces.lj_sigeps_pair_type.LjSigepsPairType attribute)
(intermol.forces.ljq_c_pair_type.LjqCPairType attribute)
(intermol.forces.ljq_default_pair_type.LjqDefaultPairType attribute)
(intermol.forces.ljq_sigeps_pair_type.LjqSigepsPairType attribute)
scaleQQ (intermol.forces.abstract_pair_type.AbstractPairType attribute)
(intermol.forces.lj_c_pair_type.LjCPairType attribute)
(intermol.forces.lj_default_pair_type.LjDefaultPairType attribute)
(intermol.forces.lj_sigeps_pair_type.LjSigepsPairType attribute)
(intermol.forces.ljq_c_pair_type.LjqCPairType attribute)
(intermol.forces.ljq_default_pair_type.LjqDefaultPairType attribute)
(intermol.forces.ljq_sigeps_pair_type.LjqSigepsPairType attribute)
set_units() (intermol.lammps.lammps_parser.LammpsParser method)
Settles (class in intermol.forces.settles)
sigma (intermol.atom.Atom attribute)
(intermol.forces.fene_expandable_bond_type.FeneExpandableBondType attribute)
(intermol.forces.lj_sigeps_nonbonded_type.LjSigepsNonbondedType attribute)
(intermol.forces.lj_sigeps_pair_type.LjSigepsPairType attribute)
(intermol.forces.ljq_sigeps_pair_type.LjqSigepsPairType attribute)
specify() (in module intermol.forces.forcefunctions)
summarize_energy_results() (in module intermol.convert)
System (class in intermol.system)

T

theta (intermol.forces.cosine_squared_angle_type.CosineSquaredAngleType attribute)
(intermol.forces.harmonic_angle_type.HarmonicAngleType attribute)
(intermol.forces.quartic_angle_type.QuarticAngleType attribute)
(intermol.forces.three_fad_virtual_type.ThreeFadVirtualType attribute)
(intermol.forces.urey_bradley_angle_type.UreyBradleyAngleType attribute)
ThreeFadVirtual (class in intermol.forces.three_fad_virtual_type)
ThreeFadVirtualType (class in intermol.forces.three_fad_virtual_type)
ThreeFdVirtual (class in intermol.forces.three_fd_virtual_type)
ThreeFdVirtualType (class in intermol.forces.three_fd_virtual_type)
ThreeLinearVirtual (class in intermol.forces.three_linear_virtual_type)
ThreeLinearVirtualType (class in intermol.forces.three_linear_virtual_type)
ThreeOutVirtual (class in intermol.forces.three_out_virtual_type)
ThreeOutVirtualType (class in intermol.forces.three_out_virtual_type)
too_few_fields() (intermol.gromacs.gromacs_parser.GromacsParser method)
TrigDihedral (class in intermol.forces.trig_dihedral_type)
TrigDihedralType (class in intermol.forces.trig_dihedral_type)
TwoVirtual (class in intermol.forces.two_virtual_type)
TwoVirtualType (class in intermol.forces.two_virtual_type)
type (intermol.forces.abstract_nonbonded_type.AbstractNonbondedType attribute)
(intermol.forces.buckingham_nonbonded_type.BuckinghamNonbondedType attribute)
(intermol.forces.lj_c_nonbonded_type.LjCNonbondedType attribute)
(intermol.forces.lj_sigeps_nonbonded_type.LjSigepsNonbondedType attribute)
type_parameters_are_unique() (intermol.gromacs.gromacs_parser.GromacsParser static method)

U

U0 (intermol.forces.quartic_breakable_bond_type.QuarticBreakableBondType attribute)
UnitsException
unitvars (intermol.gromacs.gromacs_parser.GromacsParser attribute)
UreyBradleyAngle (class in intermol.forces.urey_bradley_angle_type)
UreyBradleyAngleType (class in intermol.forces.urey_bradley_angle_type)

V

ValueException
velocity (intermol.atom.Atom attribute)

W

weight (intermol.forces.proper_periodic_dihedral_type.ProperPeriodicDihedralType attribute)
write() (intermol.gromacs.grofile_parser.GromacsGroParser method)
(intermol.gromacs.gromacs_parser.GromacsParser method)
(intermol.lammps.lammps_parser.LammpsParser method)
write_angles() (intermol.gromacs.gromacs_parser.GromacsParser method)
(intermol.lammps.lammps_parser.LammpsParser method)
write_atoms() (intermol.gromacs.gromacs_parser.GromacsParser method)
write_atomtypes() (intermol.gromacs.gromacs_parser.GromacsParser method)
write_bonds() (intermol.gromacs.gromacs_parser.GromacsParser method)
(intermol.lammps.lammps_parser.LammpsParser method)
write_defaults() (intermol.gromacs.gromacs_parser.GromacsParser method)
write_dihedrals() (intermol.gromacs.gromacs_parser.GromacsParser method)
(intermol.lammps.lammps_parser.LammpsParser method)
write_exclusions() (intermol.gromacs.gromacs_parser.GromacsParser method)
write_file() (in module intermol.gromacs.gromacs_driver)
(in module intermol.lammps.lammps_driver)
write_forces() (intermol.lammps.lammps_parser.LammpsParser method)
write_gromacs() (in module intermol.gromacs.gromacs_parser)
write_impropers() (intermol.lammps.lammps_parser.LammpsParser method)
write_lammps() (in module intermol.lammps.lammps_parser)
write_molecules() (intermol.gromacs.gromacs_parser.GromacsParser method)
write_moleculetypes() (intermol.gromacs.gromacs_parser.GromacsParser method)
write_nonbonded_types() (intermol.gromacs.gromacs_parser.GromacsParser method)
write_pairs() (intermol.gromacs.gromacs_parser.GromacsParser method)
write_settles() (intermol.gromacs.gromacs_parser.GromacsParser method)
write_system() (intermol.gromacs.gromacs_parser.GromacsParser method)
write_virtuals() (intermol.lammps.lammps_parser.LammpsParser method)

X

xi (intermol.forces.improper_harmonic_dihedral_type.ImproperHarmonicDihedralType attribute)