Index

A

arr_to_contact_list() (in module BioHelpers_FABER.bio_mod)

arrToList() (in module BioHelpers_FABER.bio_mod) average_coord() (in module BioHelpers_FABER.bio_mod)

B

BioHelpers_FABER.bio_mod module BioHelpers_FABER.cluster module BioHelpers_FABER.cmap module BioHelpers_FABER.contacts module BioHelpers_FABER.gmap module

BioHelpers_FABER.pointList module BioHelpers_FABER.rmsd module BioHelpers_FABER.secstruct module BioHelpers_FABER.visualisation module

C

calc_bary() (in module BioHelpers_FABER.rmsd) calc_contact_matrix() (in module BioHelpers_FABER.bio_mod) calc_dist_matrix() (in module BioHelpers_FABER.bio_mod) calc_residue_dist() (in module BioHelpers_FABER.bio_mod) ceff() (in module BioHelpers_FABER.gmap)

cleanup_chain() (in module BioHelpers_FABER.bio_mod) Cmap (class in BioHelpers_FABER.cmap) comparePDB() (in module BioHelpers_FABER.bio_mod) conMatFromFile() (in module BioHelpers_FABER.bio_mod) contacts (BioHelpers_FABER.cmap.Cmap attribute) create_fig_ax() (BioHelpers_FABER.visualisation.RNA_Arc method)

D

delAtom() (in module BioHelpers_FABER.bio_mod)

deleteNeighbours() (in module BioHelpers_FABER.bio_mod)

F

fillInLargestCluster() (in module BioHelpers_FABER.contacts) findCluster() (in module BioHelpers_FABER.cluster)

findFirstMismatch() (in module BioHelpers_FABER.bio_mod) fixAdditionalOxygen() (in module BioHelpers_FABER.bio_mod)

G

gauss (BioHelpers_FABER.cmap.Cmap attribute) gauss() (in module BioHelpers_FABER.gmap) gaussSum() (in module BioHelpers_FABER.gmap) gaussWeightCon() (in module BioHelpers_FABER.gmap) gaussWeightMap() (in module BioHelpers_FABER.gmap) get_reference_coordinates() (in module BioHelpers_FABER.bio_mod)

get_reference_coordinates_nearest() (in module BioHelpers_FABER.bio_mod) get_reference_coordinates_nitrogen() (in module BioHelpers_FABER.bio_mod) get_rotation_matrix() (in module BioHelpers_FABER.rmsd) get_sequence_position() (in module BioHelpers_FABER.bio_mod) get_translation_vector() (in module BioHelpers_FABER.rmsd) get_unmodelled_regions() (BioHelpers_FABER.cmap.Cmap method) getContactList() (BioHelpers_FABER.secstruct.SecondaryStructure method)

I

is_rnaRes() (in module BioHelpers_FABER.bio_mod)

L

l (BioHelpers_FABER.cmap.Cmap attribute) listToArr() (in module BioHelpers_FABER.bio_mod)

load_contacts_from_restraints() (BioHelpers_FABER.cmap.Cmap method) load_native_pdb() (BioHelpers_FABER.cmap.Cmap method) loadFromFile() (BioHelpers_FABER.secstruct.SecondaryStructure static method)

M

mat_R() (in module BioHelpers_FABER.rmsd) mat_U() (in module BioHelpers_FABER.rmsd) module BioHelpers_FABER.bio_mod BioHelpers_FABER.cluster BioHelpers_FABER.cmap BioHelpers_FABER.contacts BioHelpers_FABER.gmap BioHelpers_FABER.pointList BioHelpers_FABER.rmsd BioHelpers_FABER.secstruct BioHelpers_FABER.visualisation

N

native_contacts (BioHelpers_FABER.cmap.Cmap attribute)

num_to_id() (BioHelpers_FABER.cmap.Cmap method) numberOfResidues() (in module BioHelpers_FABER.bio_mod)

P

pickBestGauss() (in module BioHelpers_FABER.contacts) pickBestGaussFalse() (in module BioHelpers_FABER.contacts) pickInLargestCluster() (in module BioHelpers_FABER.contacts) pickMaxDistance() (in module BioHelpers_FABER.contacts) pickRandom() (in module BioHelpers_FABER.contacts) pickRandomFalse() (in module BioHelpers_FABER.contacts)

Point (class in BioHelpers_FABER.pointList) PointList (class in BioHelpers_FABER.pointList) poisitioning (BioHelpers_FABER.cmap.Cmap attribute) ppv() (in module BioHelpers_FABER.gmap) ppv_mat() (in module BioHelpers_FABER.gmap) ppvs (BioHelpers_FABER.cmap.Cmap attribute)

R

renumber_pdb() (in module BioHelpers_FABER.bio_mod) residue_coord() (in module BioHelpers_FABER.bio_mod) restraintRepr() (BioHelpers_FABER.pointList.Point method) rmsd() (in module BioHelpers_FABER.rmsd)

rmsd_from_rot_tran() (in module BioHelpers_FABER.rmsd) rmsd_pdb() (in module BioHelpers_FABER.rmsd) rmsd_per_residue() (in module BioHelpers_FABER.rmsd) RNA_Arc (class in BioHelpers_FABER.visualisation)

S

SecondaryStructure (class in BioHelpers_FABER.secstruct) sequFromPDB() (in module BioHelpers_FABER.bio_mod)

show_contact_map() (in module BioHelpers_FABER.visualisation) simrna_restraints_to_contacts() (BioHelpers_FABER.cmap.Cmap static method)

T

tp() (in module BioHelpers_FABER.gmap)

tp_mat() (in module BioHelpers_FABER.gmap) triangularMatrix() (in module BioHelpers_FABER.bio_mod)

V

variance (BioHelpers_FABER.cmap.Cmap attribute)

W

weightFunction() (in module BioHelpers_FABER.gmap)