Index

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__init__() (bcc_build.BicontinuousCubicBuild method) (correlation_function.Correlation method) (genmdp.SimulationMdp method) (gentop.SystemTopology method) (hbonds.System method) (hexagonal_build.BuildHexagonal method) (physical.region method) (rdf.System method) (solvation_equilibration.System method) (stats.Cdf method) (topology.LC method) (topology.ReadItp method) (topology.Residue method) (xlink.System method) (xlink.Topology method) (xlink_schemes.Dibrpyr14 method) (xlink_schemes.DieneScheme method) (xlink_schemes.XlinkReaction method)

A

add_pull_groups() (genmdp.SimulationMdp method) add_residue() (gentop.SystemTopology method)

atoms() (topology.ReadItp method) avg_pore_loc() (in module p2p) (in module physical)

B

BicontinuousCubicBuild (class in bcc_build) bootstrap() (rdf.System method) build_column() (hexagonal_build.BuildHexagonal method)

build_com() (rdf.System method) build_spline() (rdf.System method) BuildHexagonal (class in hexagonal_build)

C

calculate_pore_water() (solvation_equilibration.System method) Cdf (class in stats) cdf() (stats.Cdf method) center_of_mass() (in module physical)

compdensity() (in module physical) conc() (in module physical) confidence_interval() (in module stats) Correlation (class in correlation_function)

D

determine_monomer_placement() (bcc_build.BicontinuousCubicBuild method) determine_reaction_type() (xlink_schemes.DieneScheme method)

Dibrpyr14 (class in xlink_schemes) DieneScheme (class in xlink_schemes) distance_from_pore_center() (in module physical)

E

equilibrate() (solvation_equilibration.System method)

F

file_rw (module)

fix_names() (in module topology) full_equilibration() (solvation_equilibration.System method)

G

gen_grid() (bcc_build.BicontinuousCubicBuild method) get_bonds() (topology.ReadItp method) get_improper_dihedrals() (topology.ReadItp method)

get_vsites() (topology.ReadItp method) gromacs (module) grps() (in module rdf)

H

head2tail() (xlink_schemes.DieneScheme method)

hexagonal_build (module)

I

identify_hbonds() (hbonds.System method)

insert_molecules() (in module gromacs)

L

LC (class in topology)

limits() (in module physical)

M

make_slice() (correlation_function.Correlation method) map_atoms() (in module topology)

minimum_image_distance() (in module physical) monoclinic_to_cubic() (in module transform)

O

organize_bonds() (topology.ReadItp method)

outliers() (in module stats)

P

p2p (module) p2p() (in module p2p) (in module physical) p2p_stats() (in module p2p) partition() (in module physical) physical (module)

place_monomers() (bcc_build.BicontinuousCubicBuild method) place_water_tails() (solvation_equilibration.System method) plot() (rdf.System method) plot_hbonds() (hbonds.System method) plot_slice() (correlation_function.Correlation method) put_in_box() (in module physical)

Q

query_database() (solvation_equilibration.System method)

R

radial_distance_spline() (in module physical) radial_distribution_function() (rdf.System method) radical_c2() (xlink_schemes.DieneScheme method) random_orientation() (in module transform) random_sample() (stats.Cdf method) rdf (module) ReadItp (class in topology) region (class in physical) remove_residue() (gentop.SystemTopology method) reorder() (bcc_build.BicontinuousCubicBuild method) (hexagonal_build.BuildHexagonal method) rescale() (in module transform)

Residue (class in topology) residue_center_of_mass() (in module physical) restrict_atoms() (in module p2p) rotate_coords() (in module transform) rotate_coords_x() (in module transform) rotate_coords_z() (in module transform) rotate_vector() (in module transform) rotate_x() (in module transform) rotate_z() (in module transform) rotateplane() (in module transform) rotateplane_coords() (in module transform) Rvect2vect() (in module transform)

S

set_eligible() (hbonds.System method) simulate() (in module gromacs) SimulationMdp (class in genmdp) stats (module)

System (class in hbonds) (class in rdf) (class in solvation_equilibration) (class in xlink) SystemTopology (class in gentop)

T

terminate() (xlink_schemes.DieneScheme method) thickness() (in module physical) Topology (class in xlink)

topology (module) trace_pores() (in module physical) transform (module) translate() (in module transform)

U

update_cdf() (stats.Cdf method)

W

wrap_box() (in module physical) write_assembly() (in module file_rw) write_em_mdp() (genmdp.SimulationMdp method) (in module file_rw) write_final_pore_configuration() (solvation_equilibration.System method) write_gro() (hexagonal_build.BuildHexagonal method) (in module file_rw)

write_gro_pos() (in module file_rw) write_npt_mdp() (genmdp.SimulationMdp method) write_nve_mdp() (genmdp.SimulationMdp method) write_nvt_mdp() (genmdp.SimulationMdp method) write_top() (gentop.SystemTopology method) write_water_ndx() (in module file_rw)

X

XlinkReaction (class in xlink_schemes)

xyregion() (physical.region method)

Z

z_correlation() (in module hexagonal_build)