List dist: Difference between revisions

Latest revision as of 11:54, 1 February 2012

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-= Overview =
+#REDIRECT [[Get_raw_distances]]
-This script finds atoms involved in polar contacts and lists their information.
-Author:
-:: Takanori Nakane
-Warning:
-:: the atoms are hashed by coordinates; this could cause issues with multi-state MD trajectories -- use caution!
-<source lang="python">
-from pymol import cmd
-def parseDistObj(obj):
-    if (obj[5][0][3][10] != 1): # 'show dashed' flag
-        return ""
-    points = obj[5][2][0][1]
-    ret = []
-    for i in range(len(points) / 6):
-        ret.append([(points[i * 6], points[i * 6 + 1], points[i * 6 + 2]),
-                    (points[i * 6 + 3], points[i * 6 + 4], points[i * 6 + 5])])
-    return ret
-def list_dist():
-    names = cmd.get_session()['names']
-    dist_pairs = []
-    for obj in names:
-        if (obj == None):
-            continue
-        if (obj[1] == 0 and obj[4] == 4):
-            dist_pairs += parseDistObj(obj)
-    namespace = {'dict': {}, 'a': 1}
-    dict = {}
-    cmd.iterate_state(1, 'all', 'dict[x,y,z] = chain+"/"+resn+resi+"/"+name' , space=namespace)
-    dict = namespace['dict']
-    for pair in dist_pairs:
-        print dict.get(pair[0], '?') + " - " + dict.get(pair[1], '?')
-cmd.extend('list_dist', list_dist)
-</source>
-[[Category:Script_Library]]