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jaredsampsonjaredsampson
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Merge branch 'master' into generalize-cbf
* master: (21 commits) Fix combo box not showing all options. New virtual screening interface based on AutoDock Vina ecosystem. Update vina.py added initial docstring, revised import section, and added .py to name Create cgoCircle Update tmalign.py List plugins documentation (Pymol-Scripts#146) Fix support for multiple objects selection Add support for multiple object haystack in findseq.py Independent color and as_putty options for color_by_conservation.py (Pymol-Scripts#145) Add output message for findseq + don't create empty selection when seq was not found (Pymol-Scripts#141) Update tmalign.py Outline plugin version 0.2 minor fix An attempt to improve plugin the plugin documentations. Delete documentation.md Rename documentation.html to documentation.md Create documentation.html Port dynoplot to Qt Add tab-completion to findseq ...
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‎PluginsDocs.md‎

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‎README.md‎

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## PyMOL Script Repository
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This repository hosts most of the scripts and (single file) plugins from the [PyMOL Wiki](http://www.pymolwiki.org/). If you have a new script or plugin consider place it here. There is a [Git intro](http://www.pymolwiki.org/index.php/Git_intro) page for new contributors.
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This repository hosts most of the scripts and (single file) plugins from the [PyMOL Wiki](http://www.pymolwiki.org/). If you have a new script
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or plugin consider place it here. There is a [Git intro](http://www.pymolwiki.org/index.php/Git_intro) page for new contributors.
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The [PluginsDocs](PluginsDocs.md) file contains documentation for many of the plugins hosted here. They are summarized
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by [_summarize.py](_summarize.py) command line script (not a PyMOL one).

‎_summarize.py‎

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import ast
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import tempfile
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import webbrowser
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from collections import defaultdict
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from glob import glob
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from textwrap import indent
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from jinja2 import Template
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FOUND = defaultdict(dict)
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NeedRefactor = object()
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class Visitor1pass(ast.NodeVisitor):
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def __init__(self, module):
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self.module = module
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def visit_Call(self, call):
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if hasattr(call.func, 'attr') and call.func.attr == "extend":
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if len(call.args) == 2:
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if call.func.attr == "extend" and call.func.value.id == "cmd":
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funcname = call.args[0].value
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FOUND[self.module][funcname] = None
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class Visitor2Pass(ast.NodeVisitor):
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def __init__(self, module):
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self.module = module
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def visit_FunctionDef(self, functionDef):
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if functionDef.col_offset == 0 and functionDef.name == "__init__":
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FOUND[self.module] = NeedRefactor
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class Visitor3pass(ast.NodeVisitor):
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def __init__(self, module):
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self.module = module
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def visit_FunctionDef(self, functiondef):
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if functiondef.name in FOUND[self.module]:
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try:
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if isinstance(functiondef.body[0].value.value, str):
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docstring = functiondef.body[0].value.value
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docstring = indent(docstring, " " * 4)
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FOUND[self.module][functiondef.name] = docstring
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except Exception as exc:
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pass
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for module in [*glob("*.py"), *glob("plugins/*.py")]:
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if module.startswith('_'):
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continue
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with open(module) as module_file:
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src = ''.join(module_file.readlines())
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tree = ast.parse(src, filename=module)
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v = Visitor1pass(module)
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v.visit(tree)
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v = Visitor2Pass(module)
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v.visit(tree)
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if FOUND[module] is not NeedRefactor:
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v = Visitor3pass(module)
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v.visit(tree)
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else:
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del FOUND[module]
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print("%s:: NeedRefactor" % module)
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tmpl = Template("""
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# PyMOL Script Repo: Plugin List
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{% for module in commands %}
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* ## {{ module }}
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{% for command in commands[module] %}
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* # {{ command }}
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```{{ commands[module][command] }}```
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{% endfor %}
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{% endfor %}
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""")
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_, path = tempfile.mkstemp(suffix=".md")
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with open(path, "w") as fd:
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fd.write(tmpl.render(commands=FOUND))
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print("DOCUMENTATION: %s" % path)

‎cgoCircle.py‎

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"""
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This script was initially copied from https://pymolwiki.org/index.php/CgoCircle on Sept. 23, 2024.
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The PyMOL Wiki page containing the code that was copied is licensed under GNU Free Documentation License 1.2.
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Probable Author: Jason Vertrees.
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"""
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import math
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import pymol
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from pymol.cgo import *
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from pymol import cmd
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def cgoCircle(x, y, z, r=8.0, cr=1.0, cg=0.4, cb=0.8, w=2.0):
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"""
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Create a CGO circle
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PARAMS
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x, y, z
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X, Y and Z coordinates of the origin
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r
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Radius of the circle
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cr, cg, cb
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Color triplet, [r,g,b] where r,g,b are all [0.0,1.0].
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w
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Line width of the circle
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RETURNS
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the CGO object (it also loads it into PyMOL, too).
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"""
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x = float(x)
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y = float(y)
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z = float(z)
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r = abs(float(r))
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cr = abs(float(cr))
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cg = abs(float(cg))
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cb = abs(float(cb))
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w = float(w)
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obj = [ BEGIN, LINES, COLOR, cr, cg, cb ]
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for i in range(180):
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obj.append( VERTEX )
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obj.append(r*math.cos(i) + x )
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obj.append(r*math.sin(i) + y )
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obj.append(z)
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obj.append( VERTEX )
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obj.append(r*math.cos(i+0.1) + x )
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obj.append(r*math.sin(i+0.1) + y )
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obj.append(z)
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obj.append(END)
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cName = cmd.get_unused_name("circle_")
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cmd.load_cgo( obj, cName )
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cmd.set("cgo_line_width", w, cName )
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return obj
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def circleSelection( selName, r=None, cr=1.0, cg=0.4, cb=0.8, w=2.0 ):
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"""
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circleSelection -- draws a cgo circle around a given selection or object
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PARAMS
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selName
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Name of the thing to encircle.
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r
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Radius of circle.
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DEFAULT: This cript automatically defines the radius for you. If
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you select one atom and the resultant circle is too small, then
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you can override the script's calculation of r and specify your own.
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cr, cg, cb
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red, green and blue coloring, each a value in the range [0.0, 1.0]
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RETURNS
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The circle object.
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"""
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((minX, minY, minZ), (maxX, maxY, maxZ)) = cmd.get_extent(selName)
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if r==None:
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r = max( [maxX-minX, maxY-minY, maxZ-minZ] )
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stored.coords = []
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cmd.iterate_state(1, selName, "stored.coords.append([x,y,z])")
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l = len(stored.coords)
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centerX = sum(map(lambda x: x[0], stored.coords)) / l
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centerY = sum(map(lambda x: x[1], stored.coords)) / l
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centerZ = sum(map(lambda x: x[2], stored.coords)) / l
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return cgoCircle( centerX, centerY, centerZ, r, cr, cg, cb, w )
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cmd.extend( "cgoCircle", cgoCircle )
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cmd.extend( "circleSelection", circleSelection )

‎color_by_conservation.py‎

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'''
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See more here: http://www.pymolwiki.org/index.php/color_by_conservation
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from pymol import cmd, CmdException
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PARAMETERS
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aln
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(string) the alignment object name
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names
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(list) a list of object names that are in the alignment;
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if (), then PyMOL will attempt to glean the names
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from the alignment object
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color
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(string) valid PyMOL spectrum name
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as_putty
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(0 or 1) if 0 display is not changed, else participating objects are shown
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as cartoon putty, colored by the 'color' field
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'''
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@cmd.extend
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def color_by_conservation(aln, names=(), color=None, as_putty=0, _self=cmd):
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'''
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See more here: http://www.pymolwiki.org/index.php/color_by_conservation
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from __future__ import print_function
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from pymol import cmd
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PARAMETERS
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aln
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(string) the alignment object name
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names
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(list) a list of object names that are in the alignment;
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if (), then PyMOL will attempt to glean the names
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from the alignment object
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color
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(string) valid PyMOL spectrum name
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as_putty
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(0 or 1) if 0 display is not changed, else participating objects are shown
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as cartoon putty, colored by the 'color' field
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'''
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def color_by_conservation(aln, names=(), color="rainbow", as_putty=0, _self=cmd):
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# PyMOL doesn't yet know about object:alignment
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# but we need to check that this exists or we might crash
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if _self.get_type(aln) not in ("object:", "object:alignment"):
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print("Error: Bad or incorrectly specified alignment object.")
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return None
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if _self.get_type(aln) != "object:alignment":
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raise CmdException("Error: Bad or incorrectly specified alignment object.")
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r = cmd.get_raw_alignment(aln)
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r = _self.get_raw_alignment(aln)
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if names == ():
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known_objs = []
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for y in af:
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_self.alter("%s and index %s" % (y[0], y[1]), "b=c", space={'c': c})
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if as_putty != 0:
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if int(as_putty) != 0:
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for obj in known_objs:
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_self.show_as("cartoon", "%s" % obj)
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_self.cartoon("putty", "%s" % obj)
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if color is not None:
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for obj in known_objs:
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_self.spectrum('b', color, obj)
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_self.sort()
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_self.rebuild()
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return None
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cmd.extend("color_by_conservation", color_by_conservation)
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_self.sort()
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_self.rebuild()

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