Index

Symbols

--altloc pycurves command line option pycurves-md-batch command line option --axis-convention pycurves command line option pycurves-md-batch command line option --axis-weighting pycurves command line option pycurves-md-batch command line option --batch-size pycurves-md-batch command line option --block pycurves-md-plot command line option --comb pycurves command line option pycurves-md-batch command line option --continuous-strands pycurves command line option pycurves-md-batch command line option --curvesplus-axis-steps pycurves-md-batch command line option --diagnose-outliers pycurves-md-plot command line option --drop-terminal pycurves-md-plot command line option --dssr-json pycurves command line option --dssr-unit pycurves command line option --duplex-contains pycurves-md-plot command line option --duplex-only pycurves command line option pycurves-md-batch command line option --ends pycurves command line option pycurves-md-batch command line option --export-csv pycurves-md-plot command line option --fit pycurves command line option pycurves-md-batch command line option --fit-quality pycurves-md-batch command line option --format pycurves command line option pycurves-md command line option --frame-convention pycurves command line option pycurves-md-batch command line option --frames pycurves-md command line option --generate-inp-only pycurves command line option --grooves pycurves command line option pycurves-md-batch command line option --inp pycurves-md command line option --inp-only pycurves command line option --levels pycurves-md-plot command line option --mini pycurves command line option --mode pycurves-md command line option --no-axis-continuity pycurves-md command line option --no-axis-weighting pycurves command line option pycurves-md-batch command line option

--no-comb pycurves command line option pycurves-md-batch command line option --no-ends pycurves command line option pycurves-md-batch command line option --no-fit pycurves command line option pycurves-md-batch command line option --no-grooves pycurves command line option pycurves-md-batch command line option --no-mini pycurves command line option --no-output pycurves command line option --no-plots pycurves-md-plot command line option --no-warm-start pycurves-md command line option --outdir pycurves-md-plot command line option --outlier-abs pycurves-md-plot command line option --outlier-z pycurves-md-plot command line option --output pycurves-pymol command line option pycurves-viewer command line option --output-dir pycurves command line option pycurves-md command line option --output-file pycurves command line option pycurves-md command line option --parameter pycurves-md-plot command line option --pdb pycurves command line option --scene-prefix pycurves-pymol command line option --start pycurves-md command line option --stat pycurves-md-plot command line option --step pycurves-md command line option --stop pycurves-md command line option --strands pycurves-md-plot command line option --structure pycurves-viewer command line option --time-label pycurves-md-plot command line option --time-scale pycurves-md-plot command line option --topology-mode pycurves-md command line option --verbose pycurves-md command line option --verbose-opt pycurves command line option --visualization pycurves command line option --visualize pycurves command line option --workers pycurves-md-batch command line option -o pycurves-pymol command line option pycurves-viewer command line option

A

add_time_axis() (in module pycurves_md_plot) analyze() (pycurves_lib.curves_wrapper.CurvesWrapper method)

analyze_molecule() (pycurves_lib.curves_wrapper.CurvesWrapper method) analyze_trajectory() (in module pycurves_md) analyze_trajectory_batch() (in module pycurves_md_batch)

C

CurvesOutputFormatter (class in pycurves_lib.io.curves_output)

CurvesWrapper (class in pycurves_lib.curves_wrapper)

E

extract_block() (in module pycurves_md_plot) extract_summary_block() (in module pycurves_md_plot)

extract_summary_table() (in module pycurves_md_plot) extract_table() (in module pycurves_md_plot)

F

filter_rows() (in module pycurves_md_plot)

from_file() (pycurves_lib.curves_wrapper.CurvesWrapper class method)

G

generate_inp() (pycurves_lib.curves_wrapper.CurvesWrapper method)

get_dataframes() (pycurves_lib.io.curves_output.CurvesOutputFormatter method) getFeatures() (pycurves_lib.curves_wrapper.CurvesWrapper method)

I

iter_pycurves_frames() (in module pycurves_md_plot)

L

list_dssr_units() (pycurves_lib.curves_wrapper.CurvesWrapper method)

load_trajectory_payload() (in module pycurves_md_plot)

M

MDTrajectoryAnalyzer (class in pycurves_md)

N

normalize_conventions() (pycurves_lib.curves_wrapper.CurvesWrapper class method)

O

outlier_rows() (in module pycurves_md_plot)

output() (pycurves_lib.curves_wrapper.CurvesWrapper method)

P

parameter_timeseries() (in module pycurves_md_plot) pivot_parameter_matrix() (in module pycurves_md_plot) pycurves command line option --altloc --axis-convention --axis-weighting --comb --continuous-strands --dssr-json --dssr-unit --duplex-only --ends --fit --format --frame-convention --generate-inp-only --grooves --inp-only --mini --no-axis-weighting --no-comb --no-ends --no-fit --no-grooves --no-mini --no-output --output-dir --output-file --pdb --verbose-opt --visualization --visualize pycurves-md command line option --format --frames --inp --mode --no-axis-continuity --no-warm-start --output-dir --output-file --start --step --stop --topology-mode --verbose

pycurves-md-batch command line option --altloc --axis-convention --axis-weighting --batch-size --comb --continuous-strands --curvesplus-axis-steps --duplex-only --ends --fit --fit-quality --frame-convention --grooves --no-axis-weighting --no-comb --no-ends --no-fit --no-grooves --workers pycurves-md-plot command line option --block --diagnose-outliers --drop-terminal --duplex-contains --export-csv --levels --no-plots --outdir --outlier-abs --outlier-z --parameter --stat --strands --time-label --time-scale pycurves-pymol command line option --output --scene-prefix -o pycurves-viewer command line option --output --structure -o

R

render() (pycurves_lib.io.curves_output.CurvesOutputFormatter method) render_csv() (pycurves_lib.io.curves_output.CurvesOutputFormatter method) render_curves_text() (pycurves_lib.io.curves_output.CurvesOutputFormatter method) render_json() (pycurves_lib.io.curves_output.CurvesOutputFormatter method)

render_pymol_script() (in module pycurves_pymol) render_viewer_html() (in module pycurves_viewer) run() (pycurves_lib.curves_wrapper.CurvesWrapper method) (pycurves_md.MDTrajectoryAnalyzer method)

W

wrap_degrees() (in module pycurves_md_plot) write_csv() (pycurves_md.MDTrajectoryAnalyzer method)

write_output() (pycurves_lib.curves_wrapper.CurvesWrapper method) write_pymol_scene() (in module pycurves_pymol) write_viewer() (in module pycurves_viewer)