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88 lines
3.0 KiB
Python
88 lines
3.0 KiB
Python
#!/usr/bin/env python
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import tkFileDialog
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import tkSimpleDialog
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from pymol import cmd
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import math
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DEFAULT_CUTOFF = 10
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DEFAULT_FLOOR = 0.6
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DEFAULT_MAX_CONTACTS = -1
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def __init__(self):
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self.menuBar.addmenuitem('Plugin', 'command', 'MSA Scores', label='MSA Scores', command=lambda s=self: load_scores_dialog(s))
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def load_scores_dialog(app):
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scores_file = tkFileDialog.askopenfile(initialdir=".", title="Load scores")
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if scores_file is None:
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return
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cutoff = tkSimpleDialog.askinteger("Cutoff", "Backbone cutoff", initialvalue=DEFAULT_CUTOFF, minvalue=1)
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if cutoff is None:
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return
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floor = tkSimpleDialog.askfloat("Minimal Score", "Minimal Score", initialvalue=DEFAULT_FLOOR)
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if floor is None:
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return
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max_contacts = tkSimpleDialog.askfloat("Limit contacts", "Maximal contacts to show", initialvalue=DEFAULT_MAX_CONTACTS)
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if max_contacts is None:
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return
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show_scores(scores=scores_file, cutoff=cutoff, floor=floor, max_contacts=max_contacts)
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def show_scores(selection='all', scores="scores.csv", floor=DEFAULT_FLOOR, cutoff=DEFAULT_CUTOFF, max_contacts=None):
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""" Visualize score csv
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selection: Selection for visualization
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floor: minimal score for visualization
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cutoff: minimal distance between amino acids
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scores: scores file for visualization
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"""
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cutoff = int(cutoff)
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floor = float(floor)
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scores = read_scores(scores)
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max_contacts = int(max_contacts)
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if max_contacts is None or max_contacts == -1:
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max_contacts = len(scores)
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# filter for cutoff
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scores = list(filter(lambda x: x[1] - x[0] >= cutoff, scores))
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# filter for score floor
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scores = list(filter(lambda x: x[2] >= floor, scores))
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# show distances
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counter = 0
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for score in scores:
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if counter > max_contacts:
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print("max contacts reached! (%s contacts not shown)" % (len(scores)-int(max_contacts)))
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break
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print("new msa contact between %s and %s" % (score[0], score[1]))
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name = "msa{}-{}_{:.3f}".format(score[0], score[1], score[2])
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seleA = "resid %s and n. CA and %s" % (score[0], selection)
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seleB = "resid %s and n. CA and %s" % (score[1], selection)
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if cmd.select("seleA", seleA) == "0" or cmd.select("seleB", seleB) == "0":
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continue
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cmd.distance(name, seleA, seleB)
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counter += 1
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cmd.delete('seleA')
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cmd.delete('seleB')
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def read_scores(scores_file):
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scores = []
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if not isinstance(scores_file, file):
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scores_file = open(scores_file, 'r')
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for line in scores_file.readlines():
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split = line.split(",")
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resA = int(split[0])
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resB = int(split[1])
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score = float(split[2])
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dist = abs(resB - resA)
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scores.append([resA, resB, score, dist])
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scores_file.close()
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return scores
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def remove_scores():
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cmd.delete("msa*")
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cmd.extend("remove_scores", remove_scores)
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cmd.extend("show_scores", show_scores)
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