Index

_

__repr__() (porems.atom.Atom method) (porems.molecule.Molecule method) __str__() (porems.molecule.Molecule method) _back() (porems.dice.Dice method) _block() (porems.pattern.AlphaCristobalit method) (porems.pattern.BetaCristobalit method) (porems.pattern.Pattern method) _bot() (porems.dice.Dice method) _box_size() (porems.molecule.Molecule method) _concat() (porems.molecule.Molecule method) _fill() (porems.dice.Dice method) _front() (porems.dice.Dice method) _hexagonal() (porems.pattern.BetaCristobalit method)

_left() (porems.dice.Dice method) _normal_ex() (porems.system.PoreKit method) _orientation() (porems.pattern.AlphaCristobalit method) (porems.pattern.BetaCristobalit method) (porems.pattern.Pattern method) _pos_to_index() (porems.dice.Dice method) _read() (porems.molecule.Molecule method) _right() (porems.dice.Dice method) _siloxane() (porems.system.PoreKit method) _split() (porems.dice.Dice method) _step() (porems.dice.Dice method) _temp() (porems.molecule.Molecule method) _top() (porems.dice.Dice method) _vector() (porems.molecule.Molecule method)

A

add() (porems.matrix.Matrix method) (porems.molecule.Molecule method) add_shape() (porems.system.PoreKit method) alcohol() (in module porems.generic) alkane() (in module porems.generic) allocation() (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method) AlphaCristobalit (class in porems.pattern) amorph() (porems.pore.Pore method) angle() (in module porems.geometry)

angle_azi() (in module porems.geometry) angle_polar() (in module porems.geometry) append() (porems.molecule.Molecule method) Atom (class in porems.atom) attach() (porems.pore.Pore method) (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method) attach_special() (porems.system.PoreAmorphCylinder method) (porems.system.PoreCylinder method) (porems.system.PoreSlit method)

B

BetaCristobalit (class in porems.pattern) bond() (porems.molecule.Molecule method) bound() (porems.matrix.Matrix method) box() (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method)

build() (porems.system.PoreKit method)

C

centroid() (porems.molecule.Molecule method) (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method) column() (in module porems.utils) column_pos() (porems.molecule.Molecule method) com() (porems.molecule.Molecule method)

Cone (class in porems.shape) convert() (porems.shape.Cone method) (porems.shape.Cuboid method) (porems.shape.Cylinder method) (porems.shape.Shape method) (porems.shape.Sphere method) copy() (in module porems.utils) cross_product() (in module porems.geometry) Cuboid (class in porems.shape) Cylinder (class in porems.shape)

D

d_Phi_phi() (porems.shape.Cone method) (porems.shape.Cylinder method) (porems.shape.Sphere method) d_Phi_theta() (porems.shape.Sphere method) d_Phi_z() (porems.shape.Cone method) (porems.shape.Cylinder method) delete() (porems.molecule.Molecule method)

diameter() (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method) Dice (class in porems.dice) dot_product() (in module porems.geometry)

E

exterior() (porems.pore.Pore method) (porems.system.PoreKit method)

F

fill_sites() (porems.pore.Pore method) finalize() (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method)

find_bond() (porems.dice.Dice method) find_parallel() (porems.dice.Dice method)

G

generate() (porems.pattern.AlphaCristobalit method) (porems.pattern.BetaCristobalit method) (porems.pattern.Pattern method) get_atom_list() (porems.molecule.Molecule method) get_atom_type() (porems.atom.Atom method) (porems.molecule.Molecule method) get_block() (porems.pattern.AlphaCristobalit method) (porems.pattern.BetaCristobalit method) (porems.pattern.Pattern method) (porems.pore.Pore method) get_box() (porems.molecule.Molecule method) (porems.pore.Pore method) get_charge() (porems.molecule.Molecule method) get_count() (porems.dice.Dice method) get_gap() (porems.pattern.AlphaCristobalit method) (porems.pattern.BetaCristobalit method) (porems.pattern.Pattern method) get_inp() (porems.shape.Cone method) (porems.shape.Cuboid method) (porems.shape.Cylinder method) (porems.shape.Shape method) (porems.shape.Sphere method) get_mass() (in module porems.database) (porems.molecule.Molecule method) get_masses() (porems.molecule.Molecule method) get_matrix() (porems.matrix.Matrix method)

get_mol() (porems.dice.Dice method) get_mol_dict() (porems.pore.Pore method) get_name() (porems.atom.Atom method) (porems.molecule.Molecule method) (porems.pore.Pore method) get_num() (porems.molecule.Molecule method) get_num_in_ex() (porems.pore.Pore method) get_orient() (porems.pattern.AlphaCristobalit method) (porems.pattern.BetaCristobalit method) (porems.pattern.Pattern method) get_origin() (porems.dice.Dice method) get_pointer() (porems.dice.Dice method) get_pos() (porems.atom.Atom method) get_repeat() (porems.pattern.AlphaCristobalit method) (porems.pattern.BetaCristobalit method) (porems.pattern.Pattern method) get_residue() (porems.atom.Atom method) get_short() (porems.molecule.Molecule method) get_site_dict() (porems.pore.Pore method) get_sites() (porems.pore.Pore method) get_size() (porems.dice.Dice method) (porems.pattern.AlphaCristobalit method) (porems.pattern.BetaCristobalit method) (porems.pattern.Pattern method) grid() (porems.store.Store method) gro() (porems.store.Store method)

I

is_in() (porems.shape.Cone method) (porems.shape.Cuboid method) (porems.shape.Cylinder method) (porems.shape.Sphere method)

J

job() (porems.store.Store method)

K

ketone() (in module porems.generic)

L

length() (in module porems.geometry)

lmp() (porems.store.Store method) load() (in module porems.utils)

M

main_axis() (in module porems.geometry) Matrix (class in porems.matrix) mkdirp() (in module porems.utils) mmol_g_to_mumol_m2() (in module porems.utils) mmol_l_to_mols() (in module porems.utils) module porems.database porems.generic porems.geometry porems.utils

Molecule (class in porems.molecule) mols_to_mmol_l() (in module porems.utils) mols_to_mumol_m2() (in module porems.utils) move() (porems.molecule.Molecule method) mumol_m2_to_mols() (in module porems.utils)

N

neighbor() (porems.dice.Dice method) normal() (porems.shape.Cone method) (porems.shape.Cuboid method) (porems.shape.Cylinder method) (porems.shape.Sphere method)

O

obj() (porems.store.Store method)

objectify() (porems.pore.Pore method) overlap() (porems.molecule.Molecule method)

P

part_angle() (porems.molecule.Molecule method) part_move() (porems.molecule.Molecule method) part_rotate() (porems.molecule.Molecule method) Pattern (class in porems.pattern) pattern() (porems.pattern.AlphaCristobalit method) (porems.pattern.BetaCristobalit method) pdb() (porems.store.Store method) Phi() (porems.shape.Cone method) (porems.shape.Cuboid method) (porems.shape.Cylinder method) (porems.shape.Sphere method) plot() (porems.shape.Cone method) (porems.shape.Cuboid method) (porems.shape.Cylinder method) (porems.shape.Shape method) (porems.shape.Sphere method) Pore (class in porems.pore)

PoreAmorphCylinder (class in porems.system) PoreCapsule (class in porems.system) PoreCylinder (class in porems.system) PoreKit (class in porems.system) porems.database module porems.generic module porems.geometry module porems.utils module PoreSlit (class in porems.system) pos() (porems.molecule.Molecule method) prepare() (porems.pore.Pore method) (porems.system.PoreKit method) put() (porems.molecule.Molecule method)

R

replace() (in module porems.utils) reservoir() (porems.pore.Pore method) (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method) rim() (porems.shape.Cone method) (porems.shape.Cuboid method) (porems.shape.Cylinder method) (porems.shape.Sphere method)

rotate() (in module porems.geometry) (porems.molecule.Molecule method) roughness() (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method)

S

save() (in module porems.utils) set_atom_name() (porems.molecule.Molecule method) set_atom_residue() (porems.molecule.Molecule method) set_atom_type() (porems.atom.Atom method) (porems.molecule.Molecule method) set_box() (porems.molecule.Molecule method) (porems.pore.Pore method) set_charge() (porems.molecule.Molecule method) set_mass() (porems.molecule.Molecule method) set_masses() (porems.molecule.Molecule method) set_name() (porems.atom.Atom method) (porems.molecule.Molecule method) (porems.pore.Pore method) set_pbc() (porems.dice.Dice method) set_pos() (porems.atom.Atom method) set_residue() (porems.atom.Atom method) set_short() (porems.molecule.Molecule method) Shape (class in porems.shape) shape() (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method) shape_cone() (porems.system.PoreKit method) shape_cylinder() (porems.system.PoreKit method) shape_slit() (porems.system.PoreKit method) shape_sphere() (porems.system.PoreKit method)

silanol() (in module porems.generic) siloxane() (porems.pore.Pore method) sites() (porems.pore.Pore method) Sphere (class in porems.shape) split() (porems.matrix.Matrix method) Store (class in porems.store) store() (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method) strip() (porems.matrix.Matrix method) structure() (porems.system.PoreKit method) surf() (porems.shape.Cone method) (porems.shape.Cuboid method) (porems.shape.Cylinder method) (porems.shape.Sphere method) surface() (porems.shape.Cone method) (porems.shape.Cuboid method) (porems.shape.Cylinder method) (porems.shape.Sphere method) (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method) switch_atom_order() (porems.molecule.Molecule method)

T

table() (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method)

tic() (in module porems.utils) tms() (in module porems.generic) toc() (in module porems.utils) top() (porems.store.Store method) translate() (porems.molecule.Molecule method)

U

unit() (in module porems.geometry)

V

vector() (in module porems.geometry) volume() (porems.shape.Cone method) (porems.shape.Cuboid method) (porems.shape.Cylinder method) (porems.shape.Sphere method) (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method)

X

xyz() (porems.store.Store method)

Y

yml() (porems.system.PoreAmorphCylinder method) (porems.system.PoreCapsule method) (porems.system.PoreCylinder method) (porems.system.PoreKit method) (porems.system.PoreSlit method)

Z

zero() (porems.molecule.Molecule method)