Case-file reference

Generated from the nanopnp/case/v0.5 schema by nanopnp.cli.reference; every editable field is listed, and nothing here is written by hand. A path written a.0.b names field b of each element of the list a.

The same schema is published as JSON Schema, generated from the case document's own model, for tools that read or edit case files.

Default is what a document omitting the field is validated with. Validated default is given for each switch of the model: the configuration of the published ePNP-NS model (PHY-21, PHY-22). A run whose switch differs from it lists that switch under the manifest's deviations (FR-25), so the schema default and the validated default are deliberately not the same thing: a document that names no correction solves classical PNP-NS and says so in its manifest.

Top level

Path	Type	Default	Accepts	Validated default
schema	string	required
name	string	required
outputs	list of string	[current]	analyte_force, current, eof_rate, fields, rectification, transport_numbers

inputs

Path	Type	Default	Accepts	Validated default
inputs.mesh.path	path, optional	unset
inputs.mesh.artefact	string, optional	unset
inputs.mesh.format	string, optional	unset
inputs.mesh.groups	mapping of string to string	{}
inputs.charge.path	path, optional	unset
inputs.charge.artefact	string, optional	unset
inputs.charge.format	string, optional	unset
inputs.charge.groups	mapping of string to string	{}
inputs.eps_r.path	path, optional	unset
inputs.eps_r.artefact	string, optional	unset
inputs.eps_r.format	string, optional	unset
inputs.eps_r.groups	mapping of string to string	{}
inputs.profile.path	path, optional	unset
inputs.profile.artefact	string, optional	unset
inputs.profile.format	string, optional	unset
inputs.profile.groups	mapping of string to string	{}
inputs.pqr.path	path, optional	unset
inputs.pqr.artefact	string, optional	unset
inputs.pqr.format	string, optional	unset
inputs.pqr.groups	mapping of string to string	{}

structure

This section drives stage 1, structure ingestion and alignment (FR-01 to FR-03). A case carrying it walks every stage: stages 1 to 4 derive a pore profile, and stages 5 and 6 assemble and mesh it.

Path	Type	Default	Accepts	Validated default
structure.source.path	path	required
structure.source.variant	string, optional	unset
structure.source.chains	string	all
structure.source.selection	string	protein
structure.ensemble.trajectory	path, optional	unset
structure.ensemble.frames.last_ns	number, optional	unset
structure.ensemble.frames.count	integer, optional	unset
structure.symmetry.point_group	string	required
structure.symmetry.axis	choice	auto	auto, z

• structure.source.path: A PDB or mmCIF file, optionally gzipped (.pdb, .ent, .cif, .mmcif). MDAnalysis reads PDB and gemmi reads mmCIF. The file's +z SHALL point from the trans side to the cis side, and every selected atom SHALL carry its element in the file.
• structure.source.variant: A label for the prepared structure (OPN-04). It is recorded in the manifest through the case and keys no stage: relabelling does not re-run anything.
• structure.source.chains: all, or a comma-separated list of chain identifiers. A chain is its chain identifier, or its segment identifier where the chain column is blank. The selected chains SHALL number the point group's n (FR-03).
• structure.source.selection: An MDAnalysis selection applied to the file; alternate locations are refused.
• structure.ensemble.trajectory: A DCD, XTC, TRR or NetCDF trajectory whose frames are the ensemble; without one, the models of the source file are. Every frame is superposed on the C-alpha of the earliest selected frame (FR-01).
• structure.ensemble.frames.last_ns: Keep the frames within this many ns of the last, by the times the file records; refused beyond the recorded span plus one frame interval.
• structure.ensemble.frames.count: Keep this many frames at the uniform stride floor(N/count), ending on the last frame of the window of N.
• structure.symmetry.point_group: C with n >= 1, e.g. C12 for ClyA (FR-03).
• structure.symmetry.axis: auto: the Cn axis by chain-permutation superposition, gated on the chains' spacing, the rotation angle and a 10 degree limit from the file's z (FR-02). z: the file's z axis through its origin, refused where n >= 2 and it strays more than 0.01 nm from the detected axis over the C-alpha extent.

geometry

Of this section, geometry.density drives stages 2 and 3, the density map and its reduction to (r, z) (FR-04 to FR-06), and geometry.contour drives stage 4, the pore wall's contour and its gate (FR-07, FR-08), on a case carrying structure:. The membrane and reservoir keys are read by stage 5, CAD assembly (FR-09); the analyte on a generated mesh is refused naming FR-21. Beside inputs.mesh the section is refused, naming both.

Path	Type	Default	Accepts	Validated default
geometry.density.grid_spacing_nm	number	0.05
geometry.density.kernel	choice	gaussian_vdw	gaussian_vdw
geometry.density.sharpness	number	0.93
geometry.contour.isolevel	number	0.25
geometry.contour.smoothing	choice	taubin	taubin, none
geometry.contour.simplify_tol_nm	number	0.02
geometry.membrane.thickness_nm	number	2.8
geometry.membrane.centre_z_nm	number	0.0
geometry.reservoir.radius_nm	number	250.0
geometry.analyte.shape	choice	required	sphere, prolate_spheroid, oblate_spheroid
geometry.analyte.a_nm	number	required
geometry.analyte.b_nm	number, optional	unset
geometry.analyte.z_nm	number	0.0
geometry.analyte.charge_e	number	0.0
geometry.pore.shape	choice	required	cylinder
geometry.pore.radius_nm	number	required

• geometry.contour.isolevel: The density isolevel whose contour is the pore wall, finite and in (0, 1). The source work used 0.25 without a sensitivity study (section 5.3.1 NOTE on geometry.contour).
• geometry.contour.smoothing: taubin: resample at arc length h/2, then ten Taubin passes of lambda 0.5 and mu -0.53, which keep the enclosed area where Laplacian smoothing shrinks it. none skips both (section 5.2.1).
• geometry.contour.simplify_tol_nm: The Douglas-Peucker tolerance, finite, positive and below the density grid spacing h: a larger one discards resolved geometry and breaks the margin of the closing of radius 2h that the feature-size gate relies on (section 5.2.1 NOTE).

charge

Of this section, ph, forcefield and titration drive the protonation stage, the first half of stage 7 (FR-12, PHY-16 step 3), which runs PDB2PQR and PROPKA on every frame of a structure: case, and which nanopnp stage protonation runs alone. smearing is read by stage 7's deposition, exclusion_offset_nm by stage 5 and dielectric_transition_nm by stage 7. Beside inputs.pqr the three protonation keys are refused set away from their defaults, naming both.

Path	Type	Default	Accepts	Validated default
charge.ph	number	7.5
charge.forcefield	choice	CHARMM	CHARMM, PEOEPB, SWANSON	CHARMM
charge.titration	choice	propka	propka, none	propka
charge.smearing.sharpness	number	0.5		0.5
charge.smearing.grid_spacing_nm	number	0.005
charge.smearing.axis_cutoff_nm	number	0.01
charge.exclusion_offset_nm	number	0.0		0.0
charge.dielectric_transition_nm	number	0.0		0.0

• charge.ph: The pH PROPKA assigns protonation states at, in [0, 14] (PHY-16 step 3). A condition of the experiment, not a deviation; refused away from its default beside titration: none, where it reaches no calculation.
• charge.forcefield: The PDB2PQR force field, passed as both --ff and --ffout. AMBER, PARSE and TYL06 give charged atoms a zero radius and are refused (section 5.3.1 NOTE on the protonation keys).
• charge.titration: propka: PROPKA's states at charge.ph. none: every residue keeps the force field's standard state.
• charge.exclusion_offset_nm: The ion-exclusion shell's width a, in nm: stage 5 offsets the profile by a and meshes the shell as material exclusion, with wall on its outer surface. 0, the validated default, builds none; refused at or below twice the density grid spacing, and beside inputs.mesh (section 5.2.1 NOTE on the ion-exclusion shell).
• charge.dielectric_transition_nm: The width delta, in nm, of the protein's dielectric transition to water: stage 7 derives chi from the profile as a C1 step of width delta. 0, the validated default, keeps PHY-20's sharp split; refused below the density grid spacing, beside inputs.eps_r and beside inputs.mesh (section 4.4 NOTE on the derived solid fraction).

electrolyte

Path	Type	Default	Accepts	Validated default
electrolyte.species.0.name	string	required
electrolyte.species.0.z	integer	required
electrolyte.concentration_M	number	required
electrolyte.temperature_K	number	298.15
electrolyte.parameters	string	willems2020_nacl	willems2020_nacl	willems2020_nacl
electrolyte.driver	choice	average	average, ionic_strength	average
electrolyte.corrections.diffusivity.model	string	none	none, willems2020_nacl	willems2020_nacl
electrolyte.corrections.diffusivity.concentration	boolean	true		true
electrolyte.corrections.diffusivity.wall	boolean	true		true
electrolyte.corrections.mobility.model	string	none	none, willems2020_nacl	willems2020_nacl
electrolyte.corrections.mobility.concentration	boolean	true		true
electrolyte.corrections.mobility.wall	boolean	true		true
electrolyte.corrections.viscosity.model	string	none	none, willems2020_nacl	willems2020_nacl
electrolyte.corrections.viscosity.concentration	boolean	true		true
electrolyte.corrections.viscosity.wall	boolean	true		true
electrolyte.corrections.permittivity.model	string	none	none, willems2020_nacl	willems2020_nacl
electrolyte.corrections.permittivity.concentration	boolean	true		true
electrolyte.corrections.permittivity.wall	boolean	true		true
electrolyte.corrections.density.model	string	none	none, willems2020_nacl	willems2020_nacl
electrolyte.corrections.density.concentration	boolean	true		true
electrolyte.corrections.density.wall	boolean	true		true
electrolyte.corrections.steric.model	choice	none	none, borukhov	borukhov
electrolyte.corrections.steric.a_ion_nm	number, optional	unset
electrolyte.corrections.steric.a_water_nm	number, optional	unset

boundary_conditions

Path	Type	Default	Accepts	Validated default
boundary_conditions.bias_V	number	required
boundary_conditions.ground	choice	cis	cis, trans
boundary_conditions.walls.ion_flux	choice	no_flux	no_flux, prescribed	no_flux
boundary_conditions.walls.slip	choice	no_slip	no_slip, navier, free	no_slip
boundary_conditions.wall_charge_C_m2	number	0.0

• boundary_conditions.wall_charge_C_m2: The uniform surface charge density of an idealised pore's wall, in C/m^2; read only beside geometry.pore..

physics

Path	Type	Default	Accepts	Validated default
physics.model	string	epnp-ns	epnp-ns, pb, pb-linear, pnp, pnp-ns, poisson	epnp-ns
physics.flow	boolean	true		true
physics.variable_density	boolean	true		true
physics.inertia	boolean	true		true
physics.dielectric_gradient_forces	boolean	false		false
physics.solid_permittivities	mapping of string to Annotated[float, FieldInfo(annotation=NoneType, required=True, metadata=[Gt(gt=0.0), _PydanticGeneralMetadata(allow_inf_nan=False)])]	{}

numerics

Path	Type	Default	Accepts	Validated default
numerics.elements.phi	string	P2
numerics.elements.c	string	P2
numerics.elements.u	string	P2
numerics.elements.p	string	P1
numerics.mesh.backend	string	netgen	gmsh, netgen
numerics.mesh.wall_h_nm	number or choice	auto	auto
numerics.mesh.wall_for_concentration_M	number, optional	unset
numerics.mesh.maxh_nm	number, optional	unset
numerics.mesh.size_scale	number	1.0
numerics.mesh.boundary_layer	boolean	false
numerics.nonlinear.strategy	choice	newton	newton, hybrid	newton
numerics.nonlinear.damping	choice	residual	residual, backtracking	residual
numerics.nonlinear.max_iter	integer	100
numerics.nonlinear.rtol	number	1.0e-06
numerics.continuation	choice	default_ladder	default_ladder, none	default_ladder
numerics.stabilisation	string	none	none, reference, supg	none
numerics.wall_distance.sources	string	wall		wall
numerics.wall_distance.max_distance_nm	number	3.0		3.0
numerics.linear.solver	string	umfpack	superlu, umfpack	umfpack

• numerics.mesh.backend: The mesher backend, checked against the mesher registry (section 5.5)..
• numerics.mesh.wall_for_concentration_M: The concentration, in mol/L, at whose Debye length wall_h_nm: auto is sized; none sizes it at the case's own..
• numerics.mesh.maxh_nm: The global element size of an idealised pore, in nm; none takes the global size of the size field. Read only beside geometry.pore..
• numerics.stabilisation: Residual stabilisation mode, checked against the stabilisation registry (section 5.5)..
• numerics.linear.solver: Direct linear solver, checked against the solver registry (section 5.5)..