pymolで周期境界の箱を描く方法：分子動力学で使用する計算系の描写
（１）本ページ下のコードをコピぺしてdrawBoudingBox.pyというファイルを作成
（２）pymol上のコマンドラインで
run drawBoundingBox.py
を実行
（３）再度コマンドライン上で
drawBoundingBox
と入力
これでpymol周期境界の箱を描くことができる。
*サンプル
以下コード
# -*- coding: utf-8 -*- from pymol.cgo import * from pymol import cmd from random import randint ############################################################################# # # drawBoundingBox.py -- Draws a box surrounding a selection # # # AUTHOR: Jason Vertrees # DATE : 2/20/2009 # NOTES : See comments below. # ############################################################################# def drawBoundingBox(selection="(all)", padding=0.0, linewidth=2.0, r=0.0, g=0.0, b=0.0): """ DESCRIPTION Given selection, draw the bounding box around it. USAGE: drawBoundingBox [selection, [padding, [linewidth, [r, [g, b]]]]] PARAMETERS: selection, the selection to enboxen. :-) defaults to (all) padding, defaults to 0 linewidth, width of box lines defaults to 2.0 r, red color component, valid range is [0.0, 1.0] defaults to 1.0 g, green color component, valid range is [0.0, 1.0] defaults to 1.0 b, blue color component, valid range is [0.0, 1.0] defaults to 1.0 RETURNS string, the name of the CGO box NOTES * This function creates a randomly named CGO box that minimally spans the protein. The user can specify the width of the lines, the padding and also the color. """ ([minX, minY, minZ],[maxX, maxY, maxZ]) = cmd.get_extent(selection) print "Box dimensions (%.2f, %.2f, %.2f)" % (maxX-minX, maxY-minY, maxZ-minZ) minX = minX - float(padding) minY = minY - float(padding) minZ = minZ - float(padding) maxX = maxX + float(padding) maxY = maxY + float(padding) maxZ = maxZ + float(padding) if padding != 0: print "Box dimensions + padding (%.2f, %.2f, %.2f)" % (maxX-minX, maxY-minY, maxZ-minZ) boundingBox = [ LINEWIDTH, float(linewidth), BEGIN, LINES, COLOR, float(r), float(g), float(b), VERTEX, minX, minY, minZ, #1 VERTEX, minX, minY, maxZ, #2 VERTEX, minX, maxY, minZ, #3 VERTEX, minX, maxY, maxZ, #4 VERTEX, maxX, minY, minZ, #5 VERTEX, maxX, minY, maxZ, #6 VERTEX, maxX, maxY, minZ, #7 VERTEX, maxX, maxY, maxZ, #8 VERTEX, minX, minY, minZ, #1 VERTEX, maxX, minY, minZ, #5 VERTEX, minX, maxY, minZ, #3 VERTEX, maxX, maxY, minZ, #7 VERTEX, minX, maxY, maxZ, #4 VERTEX, maxX, maxY, maxZ, #8 VERTEX, minX, minY, maxZ, #2 VERTEX, maxX, minY, maxZ, #6 VERTEX, minX, minY, minZ, #1 VERTEX, minX, maxY, minZ, #3 VERTEX, maxX, minY, minZ, #5 VERTEX, maxX, maxY, minZ, #7 VERTEX, minX, minY, maxZ, #2 VERTEX, minX, maxY, maxZ, #4 VERTEX, maxX, minY, maxZ, #6 VERTEX, maxX, maxY, maxZ, #8 END ] boxName = "box_" + str(randint(0,10000)) while boxName in cmd.get_names(): boxName = "box_" + str(randint(0,10000)) cmd.load_cgo(boundingBox,boxName) return boxName cmd.extend ("drawBoundingBox", drawBoundingBox)
