Index

Symbols | _ | A | B | C | D | E | F | G | I | J | M | N | O | P | R | S | T | U | V

Symbols

--charmm
f_extract.py command line option
--cmd
f_timeseries.py command line option
--force
f_extract.py command line option
--frames
f_extract.py command line option
f_timeseries.py command line option
--indexfile
f_timeseries.py command line option
--periodic
f_extract.py command line option
f_timeseries.py command line option
--progress
f_extract.py command line option
--selection_frame
f_extract.py command line option

_

__deepcopy__() (f_core.PDBFile method)
(f_core.PSFFile method)
__init__() (f_core.ExtendedSelectionParser method)
(f_core.GroupSelection method)
(f_core.IdSelection method)
(f_core.PDBFile method)
(f_core.PSFFile method)
(f_tests.RestTestResult method)
_abc_to_hmatrix() (in module f_timeseries)
_add_atom_name() (f_core.PDBFile method)
_add_residue() (f_core.PDBFile method)
_apply() (f_core.GroupSelection method)
(f_core.IdSelection method)
_cartesian_to_scaled_coordinates() (in module f_timeseries)
_check_HETATM() (f_core.PDBFile method)
_check_keywords() (f_core.PDBFile method)
_delete_residues_except() (f_core.PDBFile method)
(f_core.PSFFile method)
_dimension_helper() (in module f_timeseries)
_dump_stack() (in module f_timeseries)
_execute() (in module f_timeseries)
_found_error() (f_core.PDBFile method)
_get_atom_lines() (f_core.PDBFile method)
_index_groups (f_core.UniverseWrapper attribute)
_is_left_justified() (f_core.PDBFile method)
_is_right_justified() (f_core.PDBFile method)
_makeResult() (f_tests.RestFormatter method)
_operator_angle() (in module f_timeseries)
_operator_arraymask() (in module f_timeseries)
_operator_boxdimen() (in module f_timeseries)
_operator_charge() (in module f_timeseries)
_operator_com() (in module f_timeseries)
_operator_diff() (in module f_timeseries)
_operator_dihedral() (in module f_timeseries)
_operator_dist() (in module f_timeseries)
_operator_fitplane() (in module f_timeseries)
_operator_flatten() (in module f_timeseries)
_operator_frac() (in module f_timeseries)
_operator_mask() (in module f_timeseries)
_operator_pile() (in module f_timeseries)
_operator_pos() (in module f_timeseries)
_operator_prod() (in module f_timeseries)
_operator_scaledpos() (in module f_timeseries)
_operator_sum() (in module f_timeseries)
_parse_angles() (f_core.PSFFile method)
_parse_atoms() (f_core.PSFFile method)
_parse_bonds() (f_core.PSFFile method)
_parse_colon_range() (in module f_core)
_parse_dash_range() (in module f_core)
_parse_dihedrals() (f_core.PSFFile method)
_parse_ids() (in module f_core)
_parse_impropers() (f_core.PSFFile method)
_parse_indexfile() (in module f_core)
_require_mda() (in module f_core)
_require_stack_length() (in module f_timeseries)
_scan_section() (f_core.PSFFile method)
_SelectionParser__parse_subexp() (f_core.ExtendedSelectionParser method)
_strip_bom() (f_core.PDBFile method)

A

add_index_groups() (f_core.UniverseWrapper method)
addError() (f_tests.RestTestResult method)
addFailure() (f_tests.RestTestResult method)
addSuccess() (f_tests.RestTestResult method)
angle() (in module f_core)

B

BIN_COUNT_LEQ_Z (f_core.messages attribute)
BINS_2D_SPEC (f_core.messages attribute)
BINS_SORTED (f_core.messages attribute)
BOUNDS_DIMENSION (f_core.messages attribute)
BOUNDS_EQUAL (f_core.messages attribute)
BOUNDS_IGNORED (f_core.messages attribute)
BOUNDS_REVERSED (f_core.messages attribute)

C

CHARMM_SELECTION (f_core.messages attribute)
check_all() (f_core.PDBFile method)
CONVERT_FAILED (f_core.messages attribute)
coordinates
f_extract.py command line option
f_timeseries.py command line option

D

DASH_RANGE_NONNEG (f_core.messages attribute)
DASH_RANGE_SYNTAX (f_core.messages attribute)
delete_atom() (f_core.PSFFile method)
DIM_MISMATCH (f_core.messages attribute)
dot_product() (in module f_core)

E

EMPTY_LINE (f_core.messages attribute)
EMPTY_SELECTION (f_core.messages attribute)
ExtendedSelectionParser (class in f_core)
extract_residue() (f_core.PDBFile method)
(f_core.PSFFile method)

F

f_core (module)
f_extract (module)
f_extract.py command line option
--charmm
--force
--frames
--periodic
--progress
--selection_frame
coordinates
output
topology
f_tests (module)
f_timeseries (module)
f_timeseries.py command line option
--cmd
--frames
--indexfile
--periodic
coordinates
topology
find_atoms() (f_core.PDBFile method)

G

get_all_atom_types() (f_core.PDBFile method)
get_atom() (f_core.PDBFile method)
(f_core.PSFFile method)
get_atom_count() (f_core.PDBFile method)
(f_core.PSFFile method)
get_bond() (f_core.PDBFile method)
get_bond_vector() (f_core.PDBFile method)
get_index() (f_core.PDBFile method)
get_index_groups() (f_core.UniverseWrapper method)
get_pdb_string() (f_core.PDBFile method)
get_psf_string() (f_core.PDBFile method)
(f_core.PSFFile method)
get_residues() (f_core.PDBFile method)
get_total_charge() (f_core.PDBFile method)
(f_core.PSFFile method)
get_total_mass() (f_core.PDBFile method)
(f_core.PSFFile method)
getDescription() (f_tests.RestTestResult method)
GROUP (f_core.ExtendedSelectionParser attribute)
GroupSelection (class in f_core)

I

ID (f_core.ExtendedSelectionParser attribute)
IDENTICAL_GROUPS (f_core.messages attribute)
IdSelection (class in f_core)
IDX_EMPTY_GROUP (f_core.messages attribute)
IDX_GROUP_OVERRIDE (f_core.messages attribute)
IDX_GROUP_SPACE (f_core.messages attribute)
IDX_MINVAL (f_core.messages attribute)
IDX_SYNTAX_ERROR (f_core.messages attribute)
IMPORT_FAILED (f_core.messages attribute)
INT_CONVERSION (f_core.messages attribute)
INVALID_FRAME_SEL (f_core.messages attribute)
INVALID_ORIGIN (f_core.messages attribute)
is_angle() (f_core.PSFFile method)
is_bonded() (f_core.PSFFile method)
is_compatible() (f_core.PSFFile method)
is_dihedral() (f_core.PSFFile method)
is_improper() (f_core.PSFFile method)
iteratoms() (f_core.PSFFile method)

J

join_pdb() (in module f_core)

M

main() (in module f_extract)
(in module f_timeseries)
MANUAL_SEEK (f_core.messages attribute)
MDA_DEP (f_core.messages attribute)
mda_get_framecount() (in module f_core)
mda_goto() (in module f_core)
mda_load_universe() (in module f_core)
mda_patch_parser() (in module f_core)
mda_select() (in module f_core)
mda_select_id() (in module f_core)
mda_set_periodic() (in module f_core)
messages (class in f_core)

N

NEGATIVE_ATOM_NUM (f_core.messages attribute)
NEGATIVE_LENGTH (f_core.messages attribute)
NO_CMD (f_core.messages attribute)
NO_DUPLICATE (f_core.messages attribute)
NO_FRAME (f_core.messages attribute)
NO_NULL_VECTOR (f_core.messages attribute)
NO_SLICE (f_core.messages attribute)
NOT_CONSUMED (f_core.messages attribute)
NOT_EXIST (f_core.messages attribute)

O

ORIGIN_LENGTH (f_core.messages attribute)
OUT_OF_BOUNDS (f_core.messages attribute)
output
f_extract.py command line option
OUTPUT_EXISTS (f_core.messages attribute)
OUTPUT_FAILED (f_core.messages attribute)

P

parse() (f_core.PDBFile method)
(f_core.PSFFile method)
parse_frame_selection() (in module f_core)
parse_indexfiles() (in module f_core)
PDBFile (class in f_core)
PSFFile (class in f_core)
purge_metadata() (f_core.PDBFile method)

R

RANGE_ATOM_NUM (f_core.messages attribute)
read_psf() (f_core.PDBFile method)
remove_index_groups() (f_core.UniverseWrapper method)
RestFormatter (class in f_tests)
RestTestResult (class in f_tests)
REVERSE_BOUNDS (f_core.messages attribute)
rotate() (f_core.PDBFile method)
run() (f_tests.RestFormatter method)

S

SEEK_PAST_FILE (f_core.messages attribute)
SELECT_FAILED (f_core.messages attribute)
set_center_atom() (f_core.PDBFile method)
set_charge() (f_core.PDBFile method)
(f_core.PSFFile method)
setUp() (f_tests.TestRanges method)
SLICE_START_RANGE (f_core.messages attribute)
SLICE_STOP_RANGE (f_core.messages attribute)
STACK_DIMENSION (f_core.messages attribute)
STACK_POP (f_core.messages attribute)
startTest() (f_tests.RestTestResult method)

T

TERNARY_CMD (f_core.messages attribute)
test_comma() (f_tests.TestRanges method)
test_commaspace() (f_tests.TestRanges method)
test_commaspacemix() (f_tests.TestRanges method)
test_exclusion() (f_tests.TestRanges method)
test_mixed_range() (f_tests.TestRanges method)
test_nonnumeric() (f_tests.TestRanges method)
test_precedence() (f_tests.TestRanges method)
test_python_range() (f_tests.TestRanges method)
test_range() (f_tests.TestRanges method)
test_range_stride() (f_tests.TestRanges method)
test_single() (f_tests.TestRanges method)
test_single_exclusion() (f_tests.TestRanges method)
test_sorted() (f_tests.TestRanges method)
test_space() (f_tests.TestRanges method)
test_unique() (f_tests.TestRanges method)
TestRanges (class in f_tests)
to_pdb_file() (f_core.PDBFile method)
to_psf_file() (f_core.PDBFile method)
topology
f_extract.py command line option
f_timeseries.py command line option
translate() (f_core.PDBFile method)
translate_residue() (f_core.PDBFile method)

U

UNDEF_DIHEDRAL (f_core.messages attribute)
UNDEF_PLANE (f_core.messages attribute)
UniverseWrapper (class in f_core)
UNKNOWN_CMD (f_core.messages attribute)
UNKNOWN_LENGTH (f_core.messages attribute)

V

VEL_COORD_MISMATCH (f_core.messages attribute)