Index

A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | V | W | Z

A

accel_plateau() (in module pydna.gel)
accession (pydna.dseqrecord.Dseqrecord attribute)
(pydna.seqrecord.SeqRecord attribute)
add_feature() (pydna.dseqrecord.Dseqrecord method)
Amplicon (class in pydna.amplicon)
Anneal (class in pydna.amplify)
ape() (in module pydna.editor)
append_primer_list() (in module pydna.myprimers)
Assembly (class in pydna.assembly)
assembly_fragments() (in module pydna.design)
assign_quantitiesB() (in module pydna.gel)

B

bandbroadening() (in module pydna.gel)
basictm() (in module pydna.tm)

C

ChenFoxLyndon() (in module pydna.utils)
ChenFoxLyndonBreakpoints() (in module pydna.utils)
circular (pydna.dseq.Dseq attribute)
(pydna.dseqrecord.Dseqrecord attribute)
common_sub_strings() (in module pydna.common_sub_strings)
concat_dict() (in module pydna.genbankfixer)
Contig (class in pydna.contig)
contour_length() (in module pydna.gel)
copy_features() (in module pydna.utils)
cseguid() (in module pydna.utils)
(pydna.dseqrecord.Dseqrecord method)
cut() (pydna.dseq.Dseq method)
(pydna.dseqrecord.Dseqrecord method)

D

dbd_program() (pydna.amplicon.Amplicon method)
Dblob() (in module pydna.gel)
definition (pydna.dseqrecord.Dseqrecord attribute)
(pydna.seqrecord.SeqRecord attribute)
detailed_fig() (pydna.contig.Contig method)
detailed_figure() (pydna.contig.Contig method)
diff_Zimm_Rouse() (in module pydna.gel)
diffusion_coefficient() (in module pydna.gel)
dim_or_units() (in module pydna.gel)
DKuhn() (in module pydna.gel)
Dseq (class in pydna.dseq)
Dseqrecord (class in pydna.dseqrecord)
dsrecs (pydna.assembly.Assembly attribute)

E

Editor (class in pydna.editor)
eq() (in module pydna.utils)
equil_accel() (in module pydna.gel)
extract_feature() (pydna.dseqrecord.Dseqrecord method)

F

Fakeseq (class in pydna.gel)
ferguson_to_mu0() (in module pydna.gel)
fig() (pydna.dseq.Dseq method)
figure() (pydna.amplicon.Amplicon method)
(pydna.contig.Contig method)
fill_in() (pydna.dseq.Dseq method)
find() (pydna.dseq.Dseq method)
(pydna.dseqrecord.Dseqrecord method)
find_aa() (pydna.dseqrecord.Dseqrecord method)
find_aminoacids() (pydna.dseqrecord.Dseqrecord method)
find_module() (pydna.ipynb_importer.NotebookFinder method)
five_prime_end() (pydna.dseq.Dseq method)
flankdn() (pydna.amplicon.Amplicon method)
flankup() (pydna.amplicon.Amplicon method)
flatten() (in module pydna.gel)
footprint (pydna.primer.Primer attribute)
format() (pydna.dseqrecord.Dseqrecord method)
free_solution() (in module pydna.gel)

G

Gauss_dev() (in module pydna.gel)
Gauss_FWHM() (in module pydna.gel)
Gauss_hgt() (in module pydna.gel)
Gaussian() (in module pydna.gel)
gbtext_clean() (in module pydna.genbankfixer)
gc() (pydna.dseqrecord.Dseqrecord method)
(pydna.seqrecord.SeqRecord method)
Gel (class in pydna.gel)
gelplot_imshow() (in module pydna.gel)
gen_sample() (in module pydna.gel)
Genbank (class in pydna.genbank)
genbank() (in module pydna.genbank)
GenbankFile (class in pydna.genbankfile)
GenbankRecord (class in pydna.genbankrecord)
get_env() (in module pydna)

H

H2Oviscosity() (in module pydna.gel)

I

isorf() (pydna.dseqrecord.Dseqrecord method)
(pydna.seqrecord.SeqRecord method)

L

limit (pydna.assembly.Assembly attribute)
lin_div_Qty() (in module pydna.gel)
linear (pydna.dseq.Dseq attribute)
(pydna.dseqrecord.Dseqrecord attribute)
linearize() (pydna.dseqrecord.Dseqrecord method)
list_features() (pydna.dseqrecord.Dseqrecord method)
(pydna.seqrecord.SeqRecord method)
load_module() (pydna.ipynb_importer.NotebookLoader method)
locstr() (in module pydna.genbankfixer)
locus (pydna.dseqrecord.Dseqrecord attribute)
(pydna.seqrecord.SeqRecord attribute)
logspace_int() (in module pydna.gel)
looped() (pydna.dseq.Dseq method)
(pydna.dseqrecord.Dseqrecord method)
lseguid() (pydna.dseqrecord.Dseqrecord method)

M

m() (pydna.dseqrecord.Dseqrecord method)
map_trace_files() (pydna.dseqrecord.Dseqrecord method)
max_nodes (pydna.assembly.Assembly attribute)
memorize() (in module pydna.utils)
mung() (pydna.dseq.Dseq method)
mw() (pydna.dseq.Dseq method)

N

N_to_Nbp() (in module pydna.gel)
N_to_NKuhn() (in module pydna.gel)
Nbp_to_N() (in module pydna.gel)
Nbp_to_NKuhn() (in module pydna.gel)
NKuhn_to_N() (in module pydna.gel)
NKuhn_to_Nbp() (in module pydna.gel)
nopcr() (in module pydna.amplify)
NotebookFinder (class in pydna.ipynb_importer)
NotebookLoader (class in pydna.ipynb_importer)
nucleotide() (pydna.genbank.Genbank method)
number_of_cuts() (pydna.dseqrecord.Dseqrecord method)

O

Ogston_Rouse() (in module pydna.gel)
Ogston_Zimm() (in module pydna.gel)
olaps() (pydna.dseqrecord.Dseqrecord method)
only_terminal_overlaps (pydna.assembly.Assembly attribute)
open() (pydna.editor.Editor method)
open_cache_folder() (in module pydna)
open_config_folder() (in module pydna)
open_current_folder() (in module pydna)
open_log_folder() (in module pydna)
originstr() (in module pydna.genbankfixer)
ovhg (pydna.dseq.Dseq attribute)

P

pairwise() (in module pydna.utils)
parse() (in module pydna.parsers)
parse2() (in module pydna.parsers)
parse_primers() (in module pydna.parsers)
parseGBLoc() (in module pydna.genbankfixer)
pcr() (in module pydna.amplify)
pfu_sso7d_program() (pydna.amplicon.Amplicon method)
pore_size() (in module pydna.gel)
pore_size_fit() (in module pydna.gel)
Primer (class in pydna.primer)
primer_design() (in module pydna.design)
products (pydna.amplify.Anneal attribute)
program() (pydna.amplicon.Amplicon method)
pydna (module)
pydna.amplicon (module)
pydna.amplify (module)
pydna.assembly (module)
pydna.common_sub_strings (module)
pydna.contig (module)
pydna.design (module)
pydna.download (module)
pydna.dseq (module)
pydna.dseqrecord (module)
pydna.editor (module)
pydna.gel (module)
pydna.genbank (module)
pydna.genbankfile (module)
pydna.genbankfixer (module)
pydna.genbankrecord (module)
pydna.ipynb_importer (module)
pydna.myprimers (module)
pydna.parsers (module)
pydna.primer (module)
pydna.readers (module)
pydna.seqrecord (module)
pydna.tm (module)
pydna.utils (module)

Q

Q5() (in module pydna.tm)

R

radius_gyration() (in module pydna.gel)
random_Dseqs() (in module pydna.gel)
rc() (in module pydna.utils)
(pydna.dseq.Dseq method)
(pydna.dseqrecord.Dseqrecord method)
read() (in module pydna.readers)
read_primer() (in module pydna.readers)
reduced_field() (in module pydna.gel)
reduced_field_Kuhn() (in module pydna.gel)
report() (pydna.amplify.Anneal method)
reptation_accelerated() (in module pydna.gel)
reptation_equilibrium() (in module pydna.gel)
reptation_plateau() (in module pydna.gel)
reverse_complement() (pydna.dseq.Dseq method)
(pydna.dseqrecord.Dseqrecord method)
run() (pydna.gel.Gel method)
rundistance() (in module pydna.gel)
runtime() (in module pydna.gel)

S

seguid() (in module pydna.utils)
(pydna.dseq.Dseq method)
(pydna.dseqrecord.Dseqrecord method)
SeqRecord (class in pydna.seqrecord)
set_DNAspace_for_mu0() (pydna.gel.Gel method)
set_DNAspace_for_vWBRfit() (pydna.gel.Gel method)
set_field() (pydna.gel.Gel method)
set_gelength() (pydna.gel.Gel method)
set_percentgel() (pydna.gel.Gel method)
set_temperature() (pydna.gel.Gel method)
set_Tvals_for_mu0() (pydna.gel.Gel method)
set_wellsep() (pydna.gel.Gel method)
set_wellx() (pydna.gel.Gel method)
set_welly() (pydna.gel.Gel method)
shift_origin() (in module pydna.utils)
shifted() (pydna.dseqrecord.Dseqrecord method)
size_to_mobility() (in module pydna.gel)
small_fig() (pydna.contig.Contig method)
small_figure() (pydna.contig.Contig method)
SmallestRotation() (in module pydna.utils)
spread_ape_colors() (pydna.dseqrecord.Dseqrecord method)
(pydna.seqrecord.SeqRecord method)
stamp() (pydna.dseqrecord.Dseqrecord method)
strip_indent() (in module pydna.genbankfixer)
strip_multiline() (in module pydna.genbankfixer)
synced() (pydna.dseqrecord.Dseqrecord method)

T

T4() (pydna.dseq.Dseq method)
t4() (pydna.dseq.Dseq method)
tail (pydna.primer.Primer attribute)
taq_program() (pydna.amplicon.Amplicon method)
terminal_overlap() (in module pydna.common_sub_strings)
three_prime_end() (pydna.dseq.Dseq method)
tm() (pydna.primer.Primer method)
tmbreslauer86() (in module pydna.tm)
tmbresluc() (in module pydna.tm)
tmstaluc98() (in module pydna.tm)
to_units() (in module pydna.gel)
toGB() (in module pydna.genbankfixer)
toInt() (in module pydna.genbankfixer)
toJSON() (in module pydna.genbankfixer)
tolinear() (pydna.dseq.Dseq method)
(pydna.dseqrecord.Dseqrecord method)

V

verify_stamp() (pydna.dseqrecord.Dseqrecord method)
vWBR() (in module pydna.gel)
vWBRfit() (in module pydna.gel)

W

weight_standard_sample() (in module pydna.gel)
wrapstring() (in module pydna.genbankfixer)
write() (pydna.dseqrecord.Dseqrecord method)

Z

Zimm_g() (in module pydna.gel)
Zimm_Rouse() (in module pydna.gel)