Hello Developers,
In the recent chimera release candidates and the imminent 1.2180 production
release, there several API changes that may trip up existing code. Many of
these changes are due to our improved method of moving data between Python
and the underlying C++ layer (roughly 2X faster). Most of the changes are
detailed below.
Greg Couch
gregc(a)cgl.ucsf.edu
------
The new code works much better with the Python help function. In the IDLE
window, try help(chimera.Atom) and you'll see all of Atom's methods and
their argument types and return values.
For the changes below assume:
m is a Molecule
r is a Residue
a is an Atom
b is a Bond
x is a Xform
Atoms have a simpified interface to their bonds:
a.bonds() returns a list of bonds
a.neighbors() returns a list of adjacent atoms (via bonds)
a.bondsMap() is both of the above combined as a dictionary
and is what a.bonds() used to return
If a structure has alternate locations, you can get just the
highest occupancy bonds/atoms with a.primaryBonds() and
a.primaryNeighbors(). Molecules have a corresponding
m.primaryAtoms() function.
Residues have a simpified interface to their atoms:
r.atoms() returns a list of atoms
r.atomNames() returns a list of atom names
r.atomsMap() is both of the above combined as a dictionary
with atom name as the key and a list of atoms with
that name as the value
Residue ids (of type MolResId) no longer have an exposed str method:
r.id.str() is now 'str(r.id)' or 'print r.id'
MolResId, Point, Vector, and Xform now have copy constructors. You can
make copies in the C++ style, 'xprime = Xform(x)', or in the Python style
with the copy module or the __copy__ method.
The following chimera module functions are now static methods:
Atom_getIdatmInfoMap -> Atom.getIdatmInfoMap
Camera_hasMode -> Camera.hasMode
Camera_modes -> Camera.modes
Color_list -> Color.list
Color_lookup -> Color.lookup
Color_remove**
Element_bondLength -> Element.bondLength
Element_bondRadius -> Element.bondRadius
LODControl_get -> LODControl.get
Material_list -> Material.list
Material_lookup -> Material.lookup
Material_remove**
Mol2io_isBlankLine -> Mol2io.isBlankLine
Mol2io_splitLine -> Mol2io.splitLine
OGLFont_defaultFont -> OGLFont.defaultFont
OGLFont_setDefaultFont -> OGLFont.setDefaultFont
OpenModels_get -> OpenModels.get
PDBio_addStandardResidue -> PDBio.addStandardResidue
PDBio_bondLengthTolerance -> PDBio.bondLengthTolerance
PDBio_removeStandardResidue -> PDBio.removeStandardResidue
PDBio_setBondLengthTolerance -> PDBio.setBondLengthTolerance
PDBio_standardResidue -> PDBio.standardResidue
PixelMap_list -> PixelMap.list
PixelMap_lookup -> PixelMap.lookup
PixelMap_maxLength -> PixelMap.maxLength
PixelMap_remove**
PseudoBondMgr_mgr -> PseudoBondMgr.mgr
Residue_getDefaultRibbonStyle -> Residue.getDefaultRibbonStyle
RibbonResidueClass_classes -> RibbonResidueClass.classes
RibbonResidueClass_deregisterClass -> RibbonResidueClass.deregisterClass
RibbonResidueClass_registerClass -> RibbonResidueClass.registerClass
RibbonXSection_circle -> RibbonXSection.circle
RibbonXSection_line -> RibbonXSection.line
RibbonXSection_square -> RibbonXSection.square
Selectable_count -> Selectable.count
Shader_list -> Shader.list
Shader_lookup -> Shader.lookup
Shader_remove**
Spline_makeGeometryVector -> Spline.makeGeometryVector
Texture_computeComponents -> Texture.computeComponents
Texture_computeDimension -> Texture.computeDimension
Texture_computeImageTypeBytes -> Texture.computeImageTypeBytes
Texture_computeTarget -> Texture.computeTarget
Texture_list -> Texture.list
Texture_lookup -> Texture.lookup
Texture_remove**
TrackChanges_get -> TrackChanges.get
Xform_coordFrame -> Xform.coordFrame
Xform_identity -> Xform.identity
Xform_lookAt -> Xform.lookAt
Xform_rotation -> Xform.rotation
Xform_translation -> Xform.translation
Xform_xRotation -> Xform.xRotation
Xform_xform -> Xform.xform
Xform_yRotation -> Xform.yRotation
Xform_zAlign -> Xform.zAlign
Xform_zRotation -> Xform.zRotation
** Color_remove, Material_remove, PixelMap_remove, Shader_remove, and Texture_remove
Unlike C++, Python can not have a method and a static method with
the same name. So the static method versions have been excised
from the Python layer.
