Table of Contents

Module: __init__ _chimera/__init__.py

Declarations of basic Chimera classes (Molecule, Atom, etc.)

Functions   
Camera_hasMode
Camera_modes
Changes
Color_list
Color_lookup
Color_remove
Element_bondLength
Element_bondRadius
GraphSize
LODControl_get
Material_list
Material_lookup
Material_remove
Mol2io_isBlankLine
Mol2io_splitLine
OGLFont_defaultFont
OGLFont_setDefaultFont
OTFPathFinder
OpenModels_get
PDBio_addStandardResidue
PDBio_bondLengthTolerance
PDBio_removeStandardResidue
PDBio_setBondLengthTolerance
PDBio_standardResidue
PixelMap_list
PixelMap_lookup
PixelMap_maxLength
PixelMap_remove
PseudoBondMgr_mgr
PyMol2ioHelper
Residue_getDefaultRibbonStyle
RibbonStyleFixed_narrow
RibbonStyleFixed_wide
RibbonStyleTapered_arrow
RibbonXSection_circle
RibbonXSection_line
RibbonXSection_square
Selectable_count
Spline_makeGeometryVector
Texture_computeComponents
Texture_computeDimension
Texture_computeImageTypeBytes
Texture_computeTarget
Texture_list
Texture_lookup
Texture_remove
TrackChanges_get
Xform_identity
Xform_lookAt
Xform_rotation
Xform_translation
Xform_xRotation
Xform_xform
Xform_yRotation
Xform_zAlign
Xform_zRotation
angle
bondsBetween
clearPickSelectable
cross
dihedral
distance
initializeColors
memoryMap
pathFinder
pdbOrder
pixelFormat
restmplFindResidue
setPickSelectable
sphere
sphere_pts
sphere_tris
sqdistance
  Camera_hasMode 
Camera_hasMode ( self,  mode )

Camera_hasMode(char* mode) -> bool

Camera::hasMode documentation.

  Camera_modes 
Camera_modes ( self )

Camera_modes() -> std::vector<const char*>

Camera::modes documentation.

  Changes 
Changes ( self )

Changes()

Changes constructor documentation.

  Color_list 
Color_list ( self )

Color_list() -> std::pair<Color::NameMap::const_iterator,Color::NameMap::const_iterator>

Color::list documentation.

  Color_lookup 
Color_lookup ( self,  name )

Color_lookup(otf::Symbol name) -> Color*

Color::lookup documentation.

  Color_remove 
Color_remove ( self,  name )

Color_remove(otf::Symbol name)

Color::remove documentation.

  Element_bondLength 
Element_bondLength (
        self,
        e1,
        e2,
        )

Element_bondLength(otf::Element e1, otf::Element e2) -> float

Element::bondLength documentation.

  Element_bondRadius 
Element_bondRadius ( self,  e )

Element_bondRadius(otf::Element e) -> float

Element::bondRadius documentation.

  GraphSize 
GraphSize ( self )

GraphSize()

GraphSize constructor documentation.

  LODControl_get 
LODControl_get ( self )

LODControl_get() -> LODControl*

LODControl::get documentation.

  Material_list 
Material_list ( self )

Material_list() -> std::pair<Material::NameMap::const_iterator,Material::NameMap::const_iterator>

Material::list documentation.

  Material_lookup 
Material_lookup ( self,  name )

Material_lookup(otf::Symbol name) -> Material*

Material::lookup documentation.

  Material_remove 
Material_remove ( self,  name )

Material_remove(otf::Symbol name)

Material::remove documentation.

  Mol2io_isBlankLine 
Mol2io_isBlankLine ( self,  s )

Mol2io_isBlankLine(std::string s) -> bool

Mol2io::isBlankLine documentation.

  Mol2io_splitLine 
Mol2io_splitLine ( self,  s )

Mol2io_splitLine(std::string s) -> std::vector<std::string>

Mol2io::splitLine documentation.

  OGLFont_defaultFont 
OGLFont_defaultFont ( self )

OGLFont_defaultFont() -> OGLFont*

OGLFont::defaultFont documentation.

  OGLFont_setDefaultFont 
OGLFont_setDefaultFont ( self,  f )

OGLFont_setDefaultFont(OGLFont* f)

OGLFont::setDefaultFont documentation.

  OTFPathFinder 
OTFPathFinder ( self )

OTFPathFinder() -> otf::PathFinder*

OTFPathFinder documentation.

  OpenModels_get 
OpenModels_get ( self )

OpenModels_get() -> OpenModels*

OpenModels::get documentation.

  PDBio_addStandardResidue 
PDBio_addStandardResidue ( self,  res )

PDBio_addStandardResidue(std::string res)

PDBio::addStandardResidue documentation.

  PDBio_bondLengthTolerance 
PDBio_bondLengthTolerance ( self )

PDBio_bondLengthTolerance() -> float

PDBio::bondLengthTolerance documentation.

  PDBio_removeStandardResidue 
PDBio_removeStandardResidue ( self,  res )

PDBio_removeStandardResidue(std::string res)

PDBio::removeStandardResidue documentation.

  PDBio_setBondLengthTolerance 
PDBio_setBondLengthTolerance ( self,  t )

PDBio_setBondLengthTolerance(float t)

PDBio::setBondLengthTolerance documentation.

  PDBio_standardResidue 
PDBio_standardResidue ( self,  res )

PDBio_standardResidue(std::string res) -> bool

PDBio::standardResidue documentation.

  PixelMap_list 
PixelMap_list ( self )

PixelMap_list() -> std::pair<PixelMap::NameMap::const_iterator,PixelMap::NameMap::const_iterator>

PixelMap::list documentation.

  PixelMap_lookup 
PixelMap_lookup ( self,  name )

PixelMap_lookup(otf::Symbol name) -> PixelMap*

PixelMap::lookup documentation.

  PixelMap_maxLength 
PixelMap_maxLength ( self )

PixelMap_maxLength() -> int

PixelMap::maxLength documentation.

  PixelMap_remove 
PixelMap_remove ( self,  name )

PixelMap_remove(otf::Symbol name)

PixelMap::remove documentation.

  PseudoBondMgr_mgr 
PseudoBondMgr_mgr ( self )

PseudoBondMgr_mgr() -> PseudoBondMgr*

PseudoBondMgr::mgr documentation.

  PyMol2ioHelper 
PyMol2ioHelper ( self )

PyMol2ioHelper() -> PyMol2ioHelper

PyMol2ioHelper constructor documentation.

  Residue_getDefaultRibbonStyle 
Residue_getDefaultRibbonStyle ( self,  ss )

Residue_getDefaultRibbonStyle(int ss) -> RibbonStyle*

Residue::getDefaultRibbonStyle documentation.

  RibbonStyleFixed_narrow 
RibbonStyleFixed_narrow ( self )

RibbonStyleFixed_narrow() -> RibbonStyleFixed*

RibbonStyleFixed::narrow documentation.

  RibbonStyleFixed_wide 
RibbonStyleFixed_wide ( self )

RibbonStyleFixed_wide() -> RibbonStyleFixed*

RibbonStyleFixed::wide documentation.

  RibbonStyleTapered_arrow 
RibbonStyleTapered_arrow ( self )

RibbonStyleTapered_arrow() -> RibbonStyleTapered*

RibbonStyleTapered::arrow documentation.

  RibbonXSection_circle 
RibbonXSection_circle ( self )

RibbonXSection_circle() -> RibbonXSection*

RibbonXSection::circle documentation.

  RibbonXSection_line 
RibbonXSection_line ( self )

RibbonXSection_line() -> RibbonXSection*

RibbonXSection::line documentation.

  RibbonXSection_square 
RibbonXSection_square ( self )

RibbonXSection_square() -> RibbonXSection*

RibbonXSection::square documentation.

  Selectable_count 
Selectable_count ( self )

Selectable_count() -> int

Selectable::count documentation.

  Spline_makeGeometryVector 
Spline_makeGeometryVector (
        self,
        basisType,
        cp,
        )

Spline_makeGeometryVector(enum Spline::SplineType basisType, GeometryVector cp) -> GeometryVector

Spline::makeGeometryVector documentation.

  Texture_computeComponents 
Texture_computeComponents ( self,  format )

Texture_computeComponents(int format) -> int

Texture::computeComponents documentation.

  Texture_computeDimension 
Texture_computeDimension (
        self,
        w,
        h,
        d,
        )

Texture_computeDimension(int w, int h, int d) -> int

Texture::computeDimension documentation.

  Texture_computeImageTypeBytes 
Texture_computeImageTypeBytes ( self,  type )

Texture_computeImageTypeBytes(int type) -> int

Texture::computeImageTypeBytes documentation.

  Texture_computeTarget 
Texture_computeTarget ( self,  dim )

Texture_computeTarget(int dim) -> int

Texture::computeTarget documentation.

  Texture_list 
Texture_list ( self )

Texture_list() -> std::pair<Texture::NameMap::const_iterator,Texture::NameMap::const_iterator>

Texture::list documentation.

  Texture_lookup 
Texture_lookup ( self,  name )

Texture_lookup(otf::Symbol name) -> Texture*

Texture::lookup documentation.

  Texture_remove 
Texture_remove ( self,  name )

Texture_remove(otf::Symbol name)

Texture::remove documentation.

  TrackChanges_get 
TrackChanges_get ( self )

TrackChanges_get() -> TrackChanges*

TrackChanges::get documentation.

  Xform_identity 
Xform_identity ( self )

Xform_identity() -> otf::Geom3d::Xform

Xform::identity documentation.

  Xform_lookAt 
Xform_lookAt (
        self,
        eye,
        at,
        up,
        )

Xform_lookAt(otf::Geom3d::Point eye, otf::Geom3d::Point at, otf::Geom3d::Point up) -> otf::Geom3d::Xform Xform_lookAt(otf::Geom3d::Point eye, otf::Geom3d::Point at, otf::Geom3d::Vector up) -> otf::Geom3d::Xform

Xform::lookAt documentation.

  Xform_rotation 
Xform_rotation (
        self,
        axis,
        angle,
        )

Xform_rotation(otf::Geom3d::Vector axis, double angle) -> otf::Geom3d::Xform Xform_rotation(double x, double y, double z, double angle) -> otf::Geom3d::Xform

Xform::rotation documentation.

  Xform_translation 
Xform_translation ( self,  v )

Xform_translation(otf::Geom3d::Vector v) -> otf::Geom3d::Xform Xform_translation(double x, double y, double z) -> otf::Geom3d::Xform

Xform::translation documentation.

  Xform_xRotation 
Xform_xRotation ( self,  angle )

Xform_xRotation(double angle) -> otf::Geom3d::Xform

Xform::xRotation documentation.

  Xform_xform 
Xform_xform (
        self,
        r00,
        r01,
        r02,
        t03,
        r10,
        r11,
        r12,
        t13,
        r20,
        r21,
        r22,
        t23,
        orthogonalize,
        )

Xform_xform(double r00, double r01, double r02, double t03, double r10, double r11, double r12, double t13, double r20, double r21, double r22, double t23, bool orthogonalize) -> otf::Geom3d::Xform

Xform::xform documentation.

  Xform_yRotation 
Xform_yRotation ( self,  angle )

Xform_yRotation(double angle) -> otf::Geom3d::Xform

Xform::yRotation documentation.

  Xform_zAlign 
Xform_zAlign (
        self,
        p0,
        p1,
        )

Xform_zAlign(otf::Geom3d::Point p0, otf::Geom3d::Point p1) -> otf::Geom3d::Xform Xform_zAlign(otf::Geom3d::Point p0, otf::Geom3d::Vector v) -> otf::Geom3d::Xform

Xform::zAlign documentation.

  Xform_zRotation 
Xform_zRotation ( self,  angle )

Xform_zRotation(double angle) -> otf::Geom3d::Xform

Xform::zRotation documentation.

  angle 
angle (
        self,
        v0,
        v1,
        )

angle(otf::Geom3d::Vector v0, otf::Geom3d::Vector v1) -> double angle(otf::Geom3d::Point p0, otf::Geom3d::Point p1, otf::Geom3d::Point p2) -> double

angle documentation.

  bondsBetween 
bondsBetween (
        self,
        r0,
        r1,
        onlyOne,
        )

bondsBetween(Residue* r0, Residue* r1, bool onlyOne) -> std::vector<Bond*>

bondsBetween documentation.

  clearPickSelectable 
clearPickSelectable ( self )

clearPickSelectable()

clearPickSelectable documentation.

  cross 
cross (
        self,
        v1,
        v2,
        )

cross(otf::Geom3d::Vector v1, otf::Geom3d::Vector v2) -> otf::Geom3d::Vector

cross documentation.

  dihedral 
dihedral (
        self,
        p0,
        p1,
        p2,
        p3,
        )

dihedral(otf::Geom3d::Point p0, otf::Geom3d::Point p1, otf::Geom3d::Point p2, otf::Geom3d::Point p3) -> double

dihedral documentation.

  distance 
distance (
        self,
        p1,
        p2,
        )

distance(otf::Geom3d::Point p1, otf::Geom3d::Point p2) -> double

distance documentation.

  initializeColors 
initializeColors ( self,  nogui )

initializeColors(bool nogui)

initializeColors documentation.

  memoryMap 
memoryMap (
        self,
        start,
        len,
        type,
        )

memoryMap(void* start, int len, int type) -> struct _object*

memoryMap documentation.

  pathFinder 
pathFinder ( self )

pathFinder() -> otf::PathFinder*

pathFinder documentation.

  pdbOrder 
pdbOrder ( self,  resName )

pdbOrder(otf::Symbol resName) -> std::vector<otf::Symbol>

pdbOrder documentation.

  pixelFormat 
pixelFormat (
        self,
        interpHack,
        tk_window,
        stencil,
        stereo,
        multisample,
        alpha,
        accum,
        )

pixelFormat(struct _object* interpHack, char* tk_window, bool stencil, bool stereo, bool multisample, bool alpha, bool accum) -> long

pixelFormat documentation.

  restmplFindResidue 
restmplFindResidue (
        self,
        name,
        start,
        end,
        )

restmplFindResidue(otf::Symbol name, bool start, bool end) -> TmplResidue*

restmplFindResidue documentation.

  setPickSelectable 
setPickSelectable ( self,  s )

setPickSelectable(Selectable* s)

setPickSelectable documentation.

  sphere 
sphere ( self,  maxlevel )

sphere(int maxlevel)

sphere documentation.

  sphere_pts 
sphere_pts (
        self,
        radius,
        density,
        )

sphere_pts(float radius, float density) -> std::vector<otf::Geom3d::Vector>

sphere_pts documentation.

  sphere_tris 
sphere_tris ( self,  maxlevel )

sphere_tris(int maxlevel) -> std::vector<otf::Geom3d::Vector>

sphere_tris documentation.

  sqdistance 
sqdistance (
        self,
        p1,
        p2,
        )

sqdistance(otf::Geom3d::Point p1, otf::Geom3d::Point p2) -> double

sqdistance documentation.

Classes   

Atom

Atom documentation

BBox

BBox documentation

Bond

Bond documentation

BondRot

BondRot documentation

Camera

Camera documentation

ChangesType

Changes documentation

Color

Color documentation

ColorGroup

ColorGroup documentation

Coord

Coord documentation

CoordSet

CoordSet documentation

Element

Element documentation

GeometryVector

GeometryVector documentation

GraphSizeType

GraphSize documentation

LODControl

LODControl documentation

Lens

Lens documentation

LensViewer

LensViewer documentation

Link

Link documentation

MSMSModel

MSMSModel documentation

Material

Material documentation

MaterialColor

MaterialColor documentation

Model

Model documentation

Mol2io

Mol2io documentation

MolResId

MolResId documentation

Molecule

Molecule documentation

NoGuiViewer

NoGuiViewer documentation

OGLFont

OGLFont documentation

OSLAbbreviation

OSLAbbreviation documentation

OpenModels

OpenModels documentation

OpenState

OpenState documentation

PDBio

PDBio documentation

PathFinderType

PathFinder documentation

PixelMap

PixelMap documentation

Point

Point documentation

PseudoBond

PseudoBond documentation

PseudoBondGroup

PseudoBondGroup documentation

PseudoBondMgr

PseudoBondMgr documentation

PyMol2ioHelperType

PyMol2ioHelper documentation

ReadGaussianFCF

ReadGaussianFCF documentation

Residue

Residue documentation

RibbonData

RibbonData documentation

RibbonStyle

RibbonStyle documentation

RibbonStyleFixed

RibbonStyleFixed documentation

RibbonStyleTapered

RibbonStyleTapered documentation

RibbonXSection

RibbonXSection documentation

Ring

Ring documentation

Root

Root documentation

Selectable

Selectable documentation

SharedState

SharedState documentation

SideViewer

SideViewer documentation

Spline

Spline documentation

Texture

Texture documentation

TextureColor

TextureColor documentation

TmplAtom

TmplAtom documentation

TmplBond

TmplBond documentation

TmplCoord

TmplCoord documentation

TmplResidue

TmplResidue documentation

TrackChanges

TrackChanges documentation

VRMLModel

VRMLModel documentation

Vector

Vector documentation

Viewer

Viewer documentation

Xform

Xform documentation


Table of Contents

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