mmLib Documentation
__add__
__builtin__.list
object
__builtin__
__bases__
__builtin__.type
__basicsize__
__call__
mmLib.SpaceGroups.SymOp
type
__cmp__
__builtin__.dict
__contains__
mmLib.Structure.Atom
mmLib.Structure.Fragment
mmLib.Structure.Model
mmLib.Structure.Segment
mmLib.Structure.Structure
mmLib.mmCIF.mmCIFRow
__deepcopy__
mmLib.Structure.Altloc
mmLib.Structure.AminoAcidResidue
mmLib.Structure.Bond
mmLib.Structure.Chain
mmLib.Structure.NucleicAcidResidue
mmLib.mmCIF.mmCIFData
mmLib.mmCIF.mmCIFFile
mmLib.mmCIF.mmCIFTable
__delattr__
__builtin__.object
__delitem__
__delslice__
__dictoffset__
__eq__
mmLib.mmTypes.FragmentID
__flags__
__ge__
__getattribute__
__getitem__
exceptions.Exception
__getslice__
__gt__
__hash__
__iadd__
__imul__
__init__
mmLib.GLViewer.GLAtom
mmLib.GLViewer.GLAtomList
mmLib.GLViewer.GLAxes
mmLib.GLViewer.GLChain
mmLib.GLViewer.GLDrawList
mmLib.GLViewer.GLFragment
mmLib.GLViewer.GLObject
mmLib.GLViewer.GLPropertyDict
mmLib.GLViewer.GLStructure
mmLib.GLViewer.GLUnitCell
mmLib.GLViewer.GLViewer
mmLib.Library.Element
mmLib.Library.ElementInterface
mmLib.Library.Library
mmLib.Library.Monomer
mmLib.Library.MonomerInterface
mmLib.PDB.PDBValueError
mmLib.PDB.RecordProcessor
mmLib.SpaceGroups.SpaceGroup
mmLib.Structure.AlphaHelix
mmLib.Structure.AtomOverwrite
mmLib.Structure.BetaSheet
mmLib.Structure.Site
mmLib.Structure.Strand
mmLib.StructureBuilder.StructureBuilder
mmLib.StructureBuilder.StructureBuilderError
mmLib.UnitCell.UnitCell
mmLib.mmCIF.mmCIFSyntaxError
__itemsize__
__iter__
__le__
__len__
__lt__
__mro__
__mul__
__name__
__ne__
__new__
__reduce__
__reduce_ex__
__repr__
__rmul__
__setattr__
mmLib.PDB.PDBFile
__setitem__
__setslice__
__slots__
mmLib.PDB.ANISOU
mmLib.PDB.ATOM
mmLib.PDB.AUTHOR
mmLib.PDB.CAVEAT
mmLib.PDB.CISPEP
mmLib.PDB.COMPND
mmLib.PDB.CONECT
mmLib.PDB.CRYST1
mmLib.PDB.CRYST2
mmLib.PDB.CRYST3
mmLib.PDB.CRYSTn
mmLib.PDB.DBREF
mmLib.PDB.END
mmLib.PDB.ENDMDL
mmLib.PDB.EXPDTA
mmLib.PDB.FORMUL
mmLib.PDB.HEADER
mmLib.PDB.HELIX
mmLib.PDB.HET
mmLib.PDB.HETATM
mmLib.PDB.HETNAM
mmLib.PDB.HETSYN
mmLib.PDB.HYDBND
mmLib.PDB.JRNL
mmLib.PDB.KEYWDS
mmLib.PDB.LINK
mmLib.PDB.MASTER
mmLib.PDB.MODEL
mmLib.PDB.MODRES
mmLib.PDB.MTRIX1
mmLib.PDB.MTRIX2
mmLib.PDB.MTRIX3
mmLib.PDB.MTRIXn
mmLib.PDB.OBSLTE
mmLib.PDB.ORIGX1
mmLib.PDB.ORIGX2
mmLib.PDB.ORIGX3
mmLib.PDB.ORIGXn
mmLib.PDB.REMARK
mmLib.PDB.REVDAT
mmLib.PDB.SCALE1
mmLib.PDB.SCALE2
mmLib.PDB.SCALE3
mmLib.PDB.SCALEn
mmLib.PDB.SEQADV
mmLib.PDB.SEQRES
mmLib.PDB.SHEET
mmLib.PDB.SIGUIJ
mmLib.PDB.SITE
mmLib.PDB.SLTBRG
mmLib.PDB.SOURCE
mmLib.PDB.SPRSDE
mmLib.PDB.SSBOND
mmLib.PDB.TER
mmLib.PDB.TITLE
mmLib.PDB.TURN
mmLib.PDB.TVECT
__str__
mmLib.PDB.PDBRecord
mmLib.Structure.FinishMe
mmLib.Structure.Residue
mmLib.mmCIFDB.mmCIFDB
__subclasses__
__weakrefoffset__
add_alpha_helix
add_atom
add_beta_sheet
add_bonds_from_covalent_distance
add_bonds_from_library
add_chain
add_fragment
add_model
add_segment
add_site
add_strand
add_table
add_tables
addquaternion
mmLib.AtomMath
AlphaHelix
mmLib.Structure
alt_loc_list
Altloc
AminoAcidResidue
ANISOU
mmLib.PDB
append
ATOM
Atom
ATOM_get_name
AtomList
AtomMath
mmLib
AtomOverwrite
AUTHOR
autoset_columns
B2U
mmLib.mmTypes
b2u
BetaSheet
Bond
calc_adv_anisotropy
mmLib.Structure.AtomList
calc_adv_anisotropy3
calc_adv_temp_factor
calc_adv_U
calc_alpha_deg
calc_angle
calc_anisotropy
calc_anisotropy3
calc_beta_deg
calc_CCuij
calc_cell
calc_centroid
calc_distance
calc_DP2uij
calc_frac_to_orth
calc_fractionalization_matrix
calc_gamma_deg
calc_length
calc_mainchain_bond_angle
calc_mainchain_bond_length
calc_next_alt_loc_id
calc_orth_symop
calc_orth_symop2
calc_orth_to_frac
calc_orthogonalization_matrix
calc_pucker_torsion
calc_reciprocal_unit_cell
calc_sequence
calc_Suij
calc_torsion
calc_torsion_angle
calc_torsion_chi
calc_torsion_chi1
calc_torsion_chi2
calc_torsion_chi3
calc_torsion_chi4
calc_torsion_omega
calc_torsion_phi
calc_torsion_psi
calc_Uiso
calc_v
calc_volume
call_processor
CAVEAT
cell_search_iter
Chain
ChainOverwrite
check_group_name
CISPEP
clear
columns
COMPND
CONECT
confirm_table
construct_fragments
construct_segment
construct_segments
construct_sequence_list
construct_sub_segment
copy
count
count_all_atoms
count_amino_acids
count_atoms
count_bonds
count_chains
count_fragments
count_models
count_non_standard_residues
count_nucleic_acids
count_standard_residues
count_waters
create_bond
create_bonds
cross
CRYST1
CRYST2
CRYST3
CRYSTn
data
data_type
mmLib.mmCIF.mmCIFFileWriter
DBREF
debug
decode_format
mmLib.FileLoader
DEG2RAD
deg2rad
DEG2RAD2
deg2rad2
dict
dmatrix
dmatrixu
draw_axes
draw_ball_stick
draw_cell
draw_cpk
draw_cross
draw_labels
draw_lines
draw_symmetry_debug
draw_trace
draw_Uaxes
draw_Uellipse
draw_unit_cell
draw_Urms
Element
mmLib.Library
ElementInterface
END
ENDMDL
Exception
exceptions
EXPDTA
extend
file
FileLoader
FinishMe
form_mstring
FORMUL
Fragment
fragment_id_eq
fragment_id_ge
fragment_id_gt
fragment_id_le
fragment_id_lt
fragment_id_split
FragmentID
FragmentOverwrite
fromkeys
gen_token_iter
mmLib.mmCIF.mmCIFFileParser
get
get_alt_loc
get_atom
get_atom1
get_atom2
get_beta_sheet
get_bond
get_chain
get_chain1
get_chain2
get_data
get_default_alt_loc
get_default_model
get_deposition_date
get_element
mmLib.Library.LibraryInterface
get_entry_id
get_fragment
get_fragment1
get_fragment2
get_fragment_sequence_index
get_model
get_model1
get_model2
get_monomer
get_offset_fragment
get_offset_residue
get_partner
get_polymer_bond_list
get_row
get_segment
get_single
get_struct_keywords
get_structure
get_structure1
get_structure2
get_table
get_tag
get_U
GetSpaceGroup
mmLib.SpaceGroups
glal_calc_color
glal_calc_color_label
glal_calc_color_range
glal_calc_color_trace
glal_calc_color_Uaxes
glal_calc_color_Uellipse
glal_calc_color_Urms
glal_calc_position
glal_calc_U
glal_iter_atoms
glal_iter_atoms_filtered
glal_iter_chains
glal_iter_fragments
glal_iter_models
glal_iter_visible_atoms
glal_rebuild_atom_dicts
glal_res_type_color_dict
glal_update_color_value
glal_update_properties
GLAtom
mmLib.GLViewer
GLAtomList
GLAxes
GLChain
gldl_color_list
gldl_delete_list
gldl_draw
gldl_draw_method_check_visible
gldl_draw_method_get
gldl_draw_method_gl_draw_list_compile
gldl_draw_method_gl_draw_list_delete
gldl_draw_method_install
gldl_draw_method_recompile
gldl_draw_method_recompile_all
gldl_draw_method_remove
gldl_draw_method_set_transparent
gldl_draw_transparent
gldl_get_glviewer
gldl_install_draw_methods
gldl_iter_multidraw_all
gldl_iter_multidraw_self
gldl_pop_matrix
gldl_property_color_rgbf
gldl_push_matrix
gldl_redraw
gldl_render
gldl_render_draw_methods
gldl_update_cb
GLDrawList
GLFragment
glo_add_child
glo_add_property
glo_add_update_callback
glo_append_child
glo_count_descendants
glo_get_child
glo_get_degree
glo_get_depth
glo_get_glstructure
glo_get_index_path
glo_get_lowest_common_ancestor
glo_get_parent
glo_get_parent_list
glo_get_path
glo_get_properties_id
glo_get_property_desc
glo_get_root
glo_init_properties
glo_install_properties
glo_is_descendant_of
glo_iter_children
glo_iter_preorder_traversal
glo_iter_property_desc
glo_link_child_property
glo_name
glo_prepend_child
glo_remove
glo_remove_child
glo_remove_update_callback
glo_set_name
glo_set_properties_id
glo_update_properties
GLObject
GLPropertyDefault
GLPropertyDict
glr_axis
mmLib.GLViewer.OpenGLRenderMethods
glr_cross
glr_mult_matrix
glr_set_material_rgb
glr_sphere
glr_text
glr_translate
glr_tube
glr_Uaxes
glr_Uellipse
glr_Urms
gls_add_chain
GLStructure
GLUnitCell
glv_add_draw_list
glv_add_struct
glv_clip
glv_init
glv_pre_render
glv_redraw
glv_remove_draw_list
glv_render
glv_resize
glv_straif
glv_trackball
glv_update_cb
glv_zoom
GLViewer
has_amino_acids
has_key
has_non_standard_residues
has_nucleic_acids
has_standard_residues
has_waters
HEADER
HELIX
HET
HETATM
HETNAM
HETSYN
HYDBND
index
insert
is_amino_acid
is_cis
is_identity
is_multi_record
is_nucleic_acid
is_single
is_standard_residue
is_sucsessive_record
is_water
items
iter_all_amino_acids
iter_all_atoms
iter_all_chains
iter_all_fragments
iter_all_nucleic_acids
iter_alpha_helicies
iter_alt_loc
iter_amino_acids
iter_atoms
iter_atoms_by_distance
iter_beta_sheets
iter_bonded_atoms
iter_bonds
iter_chains
iter_equivalent_positions
iter_fragments
iter_models
iter_non_standard_residues
iter_nucleic_acids
iter_orth_symops
iter_rows
iter_sequence
iter_sites
iter_standard_residues
iter_strands
iter_struct_orth_symops
iter_symops
iter_waters
iteritems
iterkeys
itervalues
join_tag
JRNL
keys
KEYWDS
length
Library
LibraryInterface
LINK
list
load_alpha_helicies
load_atom
load_beta_sheets
load_bonds
load_file
load_sequence
load_sites
load_unit_cell
LoadStructure
main
mmLib.UnitCell
MASTER
MAX_LINE
mmLib.mmCIF
mget
mmCIF
mmCIFData
mmCIFDB
mmLib.mmCIFDB
mmCIFDictionary
mmCIFError
mmCIFFile
mmCIFFileParser
mmCIFFileWriter
mmCIFRow
mmCIFSave
mmCIFSyntaxError
mmCIFTable
mmTypes
MODEL
Model
ModelOverwrite
MODRES
Monomer
MonomerInterface
mro
MTRIX1
MTRIX2
MTRIX3
MTRIXn
name
name_service
normalize
NucleicAcidResidue
OBSLTE
OpenFile
OpenGLRenderMethods
ORIGX1
ORIGX2
ORIGX3
ORIGXn
parse
parse_file
PDB
PDBError
PDBFile
PDBRecord
PDBRecordMap
PDBRecordOrder
PDBValueError
pop
popitem
process
PROP_LINE_RANGE
PROP_OPACITY_RANGE
PROP_PROBABILTY_RANGE
PropertyDefault
RAD2DEG
rad2deg
RAD2DEG2
rad2deg2
read
read_atoms
read_atoms_finalize
read_end
read_end_finalize
read_metadata
read_metadata_finalize
read_start
read_start_finalize
reccat
reccat_dictlist
reccat_list
reccat_multi
reccat_tuplelist
record_processor
RecordProcessor
REMARK
remove
remove_alpha_helix
remove_alt_loc
remove_atom
remove_beta_sheet
remove_chain
remove_fragment
remove_model
remove_sequence
remove_site
Residue
REVDAT
reverse
rmatrix
rmatrixquaternion
rmatrixu
rmatrixz
Rot_mX_mXY_mZ
Rot_mX_mXY_Z
Rot_mX_mY_mZ
Rot_mX_mY_Z
Rot_mX_mZ_mY
Rot_mX_mZ_Y
Rot_mX_Y_mZ
Rot_mX_Y_Z
Rot_mX_Z_mY
Rot_mX_Z_Y
Rot_mXY_mX_mZ
Rot_mXY_mX_Z
Rot_mXY_Y_mZ
Rot_mXY_Y_Z
Rot_mY_mX_mZ
Rot_mY_mX_Z
Rot_mY_mZ_mX
Rot_mY_mZ_X
Rot_mY_X_mZ
Rot_mY_X_Z
Rot_mY_XmY_mZ
Rot_mY_XmY_Z
Rot_mY_Z_mX
Rot_mY_Z_X
Rot_mZ_mX_mY
Rot_mZ_mX_Y
Rot_mZ_mY_mX
Rot_mZ_mY_X
Rot_mZ_X_mY
Rot_mZ_X_Y
Rot_mZ_Y_mX
Rot_mZ_Y_X
Rot_X_mY_mZ
Rot_X_mY_Z
Rot_X_mZ_mY
Rot_X_mZ_Y
Rot_X_XmY_mZ
Rot_X_XmY_Z
Rot_X_Y_mZ
Rot_X_Y_Z
Rot_X_Z_mY
Rot_X_Z_Y
Rot_XmY_mY_mZ
Rot_XmY_mY_Z
Rot_XmY_X_mZ
Rot_XmY_X_Z
Rot_Y_mX_mZ
Rot_Y_mX_Z
Rot_Y_mXY_mZ
Rot_Y_mXY_Z
Rot_Y_mZ_mX
Rot_Y_mZ_X
Rot_Y_X_mZ
Rot_Y_X_Z
Rot_Y_Z_mX
Rot_Y_Z_X
Rot_Z_mX_mY
Rot_Z_mX_Y
Rot_Z_mY_mX
Rot_Z_mY_X
Rot_Z_X_mY
Rot_Z_X_Y
Rot_Z_Y_mX
Rot_Z_Y_X
row_index_dict
rquaternionu
save_file
SaveStructure
SCALE1
SCALE2
SCALE3
SCALEn
Segment
SEQADV
SEQRES
sequence_one_letter_code
set_chain_id
set_default_alt_loc
set_default_model
set_deposition_date
set_entry_id
set_fragment_id
set_model
set_sequence
set_sig_U
set_single
set_struct_keywords
set_tag
set_U
setdefault
setmap
setmapf
setmapfd
setmapi
setmapid
setmaps
setmapsd
sg1
sg10
sg100
sg1003
sg1004
sg1005
sg1006
sg1007
sg1008
sg1009
sg101
sg1010
sg1011
sg1012
sg1013
sg1014
sg1015
sg1017
sg1018
sg102
sg1020
sg1021
sg1022
sg1023
sg103
sg104
sg105
sg1059
sg106
sg107
sg108
sg109
sg1094
sg11
sg110
sg111
sg112
sg113
sg114
sg1146
sg1148
sg115
sg1155
sg116
sg1160
sg1161
sg1166
sg1167
sg117
sg118
sg119
sg1197
sg12
sg120
sg121
sg122
sg123
sg124
sg125
sg126
sg127
sg128
sg129
sg13
sg130
sg131
sg132
sg133
sg134
sg135
sg136
sg137
sg138
sg139
sg14
sg140
sg141
sg142
sg143
sg144
sg145
sg146
sg147
sg148
sg149
sg15
sg150
sg151
sg152
sg153
sg154
sg155
sg156
sg157
sg158
sg159
sg16
sg160
sg161
sg162
sg163
sg164
sg165
sg166
sg167
sg168
sg169
sg17
sg170
sg171
sg172
sg173
sg174
sg175
sg176
sg177
sg178
sg179
sg18
sg180
sg181
sg182
sg183
sg184
sg185
sg186
sg187
sg188
sg189
sg19
sg190
sg191
sg192
sg193
sg194
sg195
sg196
sg197
sg198
sg199
sg2
sg20
sg200
sg2005
sg201
sg2017
sg2018
sg202
sg203
sg204
sg205
sg206
sg207
sg208
sg209
sg21
sg210
sg211
sg212
sg213
sg214
sg215
sg216
sg217
sg218
sg219
sg22
sg220
sg221
sg222
sg223
sg224
sg225
sg226
sg227
sg228
sg229
sg23
sg230
sg24
sg25
sg26
sg27
sg28
sg29
sg3
sg30
sg3004
sg3005
sg3018
sg31
sg32
sg33
sg34
sg35
sg36
sg37
sg38
sg39
sg4
sg40
sg41
sg42
sg43
sg44
sg45
sg46
sg47
sg48
sg49
sg5
sg50
sg51
sg52
sg53
sg54
sg55
sg56
sg57
sg58
sg59
sg6
sg60
sg61
sg62
sg63
sg64
sg65
sg66
sg67
sg68
sg69
sg7
sg70
sg71
sg72
sg73
sg74
sg75
sg76
sg77
sg78
sg79
sg8
sg80
sg81
sg82
sg83
sg84
sg85
sg86
sg87
sg88
sg89
sg9
sg90
sg91
sg92
sg93
sg94
sg95
sg96
sg97
sg98
sg99
SHEET
SIGATM
SIGUIJ
SITE
Site
SLTBRG
sort
SOURCE
SpaceGroup
SpaceGroupList
SpaceGroups
split_tag
split_token
SPRSDE
SSBOND
Strand
strRT
Structure
StructureBuilder
mmLib.StructureBuilder
StructureBuilderError
StructureError
SymOp
syntax_error
table
TER
TITLE
Tr_0_0_0
Tr_0_0_12
Tr_0_0_13
Tr_0_0_14
Tr_0_0_16
Tr_0_0_23
Tr_0_0_34
Tr_0_0_56
Tr_0_12_0
Tr_0_12_12
Tr_0_12_14
Tr_0_12_34
Tr_12_0_0
Tr_12_0_12
Tr_12_0_14
Tr_12_0_34
Tr_12_12_0
Tr_12_12_12
Tr_12_12_14
Tr_12_12_34
Tr_13_23_16
Tr_13_23_23
Tr_14_14_14
Tr_14_14_34
Tr_14_34_14
Tr_14_34_34
Tr_23_13_13
Tr_23_13_56
Tr_34_14_14
Tr_34_14_34
Tr_34_34_14
Tr_34_34_34
TURN
TVECT
U2B
u2b
UnitCell
update
values
warning
write
write_cif_data
write_file
write_mstring
write_multi_row_table
write_one_row_table
writeln