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Difference between revisions of "Get Coordinates I"
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There are several ways to extract or load atomic coordinates in PyMOL using the python API. | There are several ways to extract or load atomic coordinates in PyMOL using the python API. | ||
| + | |||
| + | == Extract coordinates using [[get_coords]] == | ||
| + | |||
| + | ''New in PyMOL 1.7.4''. This is the fastest method to extract coordinates from a selection. It considers the object rotation matrix. | ||
| + | |||
| + | <source lang="python"> | ||
| + | xyz = cmd.get_coords('sele', 1) | ||
| + | </source> | ||
| + | |||
| + | == Extract coordinates using [[get_coordset]] == | ||
| + | |||
| + | ''New in PyMOL 1.7.4''. Operates on the object-state level, not on selections. Does '''not''' consider the object rotation matrix. Retrieves coordinates in original order (e.g. PDB file atom order), not in sorted atom order. Faster than [[get_coords]]. | ||
| + | |||
| + | <source lang="python"> | ||
| + | xyz = cmd.get_coordset(objectname, 1) | ||
| + | </source> | ||
== Extract coordinates using [[Get_Model|get_model]] == | == Extract coordinates using [[Get_Model|get_model]] == | ||
| − | + | Before 1.7.4, this was the fastest method to extract coordinates. It considers the object rotation matrix. | |
<source lang="python"> | <source lang="python"> | ||
| Line 42: | Line 58: | ||
</source> | </source> | ||
| − | == Load coordinates using load_coords == | + | == Load coordinates using [[load_coords]] == |
| + | |||
| + | ''Changed in PyMOL 1.7.3''. Update selection coordinates from a Nx3 float array. | ||
| + | |||
| + | <source lang="python"> | ||
| + | cmd.load_coords(xyz, selection) | ||
| + | </source> | ||
| + | |||
| + | == Load coordinates using [[load_coordset]] == | ||
| + | |||
| + | ''New in PyMOL 1.7.4''. Update object state coordinates from a Nx3 float array. Can also append a state. Order of coordinates equivalent to [[get_coordset]]. | ||
| + | |||
| + | <source lang="python"> | ||
| + | cmd.load_coordset(xyz, objectname, 1) | ||
| + | </source> | ||
| + | |||
| + | == Load coordinates using [[get_coordset]] == | ||
| − | + | ''New in PyMOL 1.7.4''. The [[get_coordset]] function can also return a memory view instead of a copy. This allows modifying the coordinates in place. | |
<source lang="python"> | <source lang="python"> | ||
| − | + | xyz = cmd.get_coordset(objectname, 1, copy=0) | |
| − | + | xyz[:] = newxyz | |
| − | |||
</source> | </source> | ||
[[Category:Script_Library|Get Coordinates I]] | [[Category:Script_Library|Get Coordinates I]] | ||
[[Category:ObjSel_Scripts]] | [[Category:ObjSel_Scripts]] | ||
Revision as of 01:40, 29 December 2015
There are several ways to extract or load atomic coordinates in PyMOL using the python API.
Extract coordinates using get_coords
New in PyMOL 1.7.4. This is the fastest method to extract coordinates from a selection. It considers the object rotation matrix.
xyz = cmd.get_coords('sele', 1)
Extract coordinates using get_coordset
New in PyMOL 1.7.4. Operates on the object-state level, not on selections. Does not consider the object rotation matrix. Retrieves coordinates in original order (e.g. PDB file atom order), not in sorted atom order. Faster than get_coords.
xyz = cmd.get_coordset(objectname, 1)
Extract coordinates using get_model
Before 1.7.4, this was the fastest method to extract coordinates. It considers the object rotation matrix.
xyz = cmd.get_model('sele', 1).get_coord_list()
Extract coordinates using iterate_state
This is much slower than the first method. It does not consider the object rotation matrix.
xyz = []
cmd.iterate_state(1, 'sele', 'xyz.append([x,y,z])', space=locals(), atomic=0)
Load coordinates using alter_state
This is the most convenient way to load coordinates and works equivalent to iterate_state.
xyz = [...] # some Nx3 list with coordinates
xyz_iter = iter(xyz)
cmd.alter_state(1, 'sele', '(x,y,z) = xyz_iter.next()', space=locals())
Load coordinates using update
This example gets a copy of the coordinates in Python, rotates the object about the Z axis, and then updates the coordinates in the original object.
model = cmd.get_model('pept')
for a in model.atom:
a.coord = [ -a.coord[1], a.coord[0], a.coord[2]]
cmd.load_model(model, "_tmp")
cmd.update("pept", "_tmp")
cmd.delete("_tmp")
Load coordinates using load_coords
Changed in PyMOL 1.7.3. Update selection coordinates from a Nx3 float array.
cmd.load_coords(xyz, selection)
Load coordinates using load_coordset
New in PyMOL 1.7.4. Update object state coordinates from a Nx3 float array. Can also append a state. Order of coordinates equivalent to get_coordset.
cmd.load_coordset(xyz, objectname, 1)
Load coordinates using get_coordset
New in PyMOL 1.7.4. The get_coordset function can also return a memory view instead of a copy. This allows modifying the coordinates in place.
xyz = cmd.get_coordset(objectname, 1, copy=0)
xyz[:] = newxyz