segmentmodel_from_pdb module#

mrdna.readers.segmentmodel_from_pdb.printv(v)[source]#
mrdna.readers.segmentmodel_from_pdb.read_ter_from_pdb(*args)[source]#
mrdna.readers.segmentmodel_from_pdb.residues_within(cutoff, coords1, coords2, sel1, sel2)[source]#

Returns lists of index of residues within sel1 and sel2 such that sel1.residue[arr_idx1[i]] is within cutoff of sel2.residue[arr_idx2[i]] for all i

Also returns distance_matrix

Ignores residues that are the same in sel1 and sel2

mrdna.readers.segmentmodel_from_pdb.find_base_position_orientation(u, selection_text='nucleic')[source]#
mrdna.readers.segmentmodel_from_pdb.find_basepairs(u, centers, transforms, selection_text='nucleic')[source]#
mrdna.readers.segmentmodel_from_pdb.find_stacks_mdanalysis(u, centers, transforms, selection_text='nucleic')[source]#
mrdna.readers.segmentmodel_from_pdb.basepairs_and_stacks_to_helixmap(basepairs, stacks_above)[source]#
mrdna.readers.segmentmodel_from_pdb.get_crossovers(helixmap, helixrank, stacks_above)[source]#
mrdna.readers.segmentmodel_from_pdb.update_helixmap_with_ssdna(helixmap, helixrank, stacks_above)[source]#
mrdna.readers.segmentmodel_from_pdb.break_into_contiguous_groups(sequence)[source]#
mrdna.readers.segmentmodel_from_pdb.get_lists_from_pdb(*args, **kwargs)[source]#
mrdna.readers.segmentmodel_from_pdb.SegmentModelFromPdb(*args, **kwargs)[source]#