-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathXmlCreate.py~
224 lines (173 loc) · 10.1 KB
/
XmlCreate.py~
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
#! /usr/bin/env python
#coding=utf-8
import datetime
from xml.dom.minidom import Document
class write_xml():
def __init__(self):
self.doc=Document()
def set_tag(self,inputFilePath,OutputPath):
self.tagDragon = self.doc.createElement("DRAGON")
self.doc.appendChild(self.tagDragon)
self.tagDragon.setAttribute("generation_date",str(datetime.datetime.now()))
self.tagDragon.setAttribute("script_version","1")
self.tagDragon.setAttribute("version","6.0.22")
#############OPTIONS的参数
self.OPTIONS = self.doc.createElement("OPTIONS")
self.Decimal_Separator=self.doc.createElement("Decimal_Separator")
self.Decimal_Separator.setAttribute("value",".")
self.OPTIONS.appendChild(self.Decimal_Separator)
self.Missing_String=self.doc.createElement("Missing_String")
self.Missing_String.setAttribute("value","NaN")
self.OPTIONS.appendChild(self.Missing_String)
self.Add2DHydrogens=self.doc.createElement("Add2DHydrogens ")
self.Add2DHydrogens.setAttribute("value","false")
self.OPTIONS.appendChild(self.Add2DHydrogens )
self.LogPathWalk=self.doc.createElement("LogPathWalk ")
self.LogPathWalk.setAttribute("value","true")
self.OPTIONS.appendChild(self.LogPathWalk )
self.LogEdge=self.doc.createElement("LogEdge ")
self.LogEdge.setAttribute("value","true")
self.OPTIONS.appendChild(self.LogEdge )
self.Weights = self.doc.createElement("Weights")
self.weight=self.doc.createElement("weight")
self.weight.setAttribute("name","Mass")
self.Weights.appendChild(self.weight)
self.weight=self.doc.createElement("weight")
self.weight.setAttribute("name","VdWVolume")
self.Weights.appendChild(self.weight )
self.weight=self.doc.createElement("weight")
self.weight.setAttribute("name","Electronegativity")
self.Weights.appendChild(self.weight )
self.weight=self.doc.createElement("weight")
self.weight.setAttribute("name","Polarizability")
self.Weights.appendChild(self.weight )
self.weight=self.doc.createElement("weight")
self.weight.setAttribute("name","Ionization")
self.Weights.appendChild(self.weight )
self.weight=self.doc.createElement("weight")
self.weight.setAttribute("name","I-State")
self.Weights.appendChild(self.weight )
self.Weights.appendChild(self.weight)
self.OPTIONS.appendChild(self.Weights )
self.LogPathWalk=self.doc.createElement("LogPathWalk ")
self.LogPathWalk.setAttribute("value","true")
self.OPTIONS.appendChild(self.LogPathWalk )
self.SaveOnlyData=self.doc.createElement("SaveOnlyData ")
self.SaveOnlyData.setAttribute("value","false")
self.OPTIONS.appendChild(self.SaveOnlyData )
self.SaveLabelsOnSeparateFile= self.doc.createElement("SaveLabelsOnSeparateFile ")
self.SaveLabelsOnSeparateFile.setAttribute("value","false")
self.OPTIONS.appendChild(self.SaveLabelsOnSeparateFile )
self.SaveFormatBlock= self.doc.createElement("SaveFormatBlock ")
self.SaveFormatBlock.setAttribute("value","%b - %n.txt")
self.OPTIONS.appendChild(self.SaveFormatBlock )
self.SaveFormatSubBlock= self.doc.createElement("SaveFormatSubBlock ")
self.SaveFormatSubBlock.setAttribute("value","%b-%s - %n - %m.txt")
self.OPTIONS.appendChild(self.SaveFormatSubBlock )
self.SaveExcludeMisVal = self.doc.createElement("SaveExcludeMisVal ")
self.SaveExcludeMisVal .setAttribute("value","false")
self.OPTIONS.appendChild(self.SaveExcludeMisVal )
self.SaveExcludeAllMisVal= self.doc.createElement("SaveExcludeAllMisVal ")
self.SaveExcludeAllMisVal.setAttribute("value","false")
self.OPTIONS.appendChild(self.SaveExcludeAllMisVal )
self.SaveExcludeConst = self.doc.createElement("SaveExcludeConst ")
self.SaveExcludeConst.setAttribute("value","false")
self.OPTIONS.appendChild(self.SaveExcludeConst )
self.SaveExcludeNearConst= self.doc.createElement("SaveExcludeNearConst ")
self.SaveExcludeNearConst.setAttribute("value","false")
self.OPTIONS.appendChild(self.SaveExcludeNearConst )
self.SaveExcludeStdDev = self.doc.createElement("SaveExcludeStdDev ")
self.SaveExcludeStdDev.setAttribute("value","false")
self.OPTIONS.appendChild(self.SaveExcludeStdDev )
self.SaveStdDevThreshold = self.doc.createElement("SaveStdDevThreshold ")
self.SaveStdDevThreshold.setAttribute("value","0.0001")
self.OPTIONS.appendChild(self.SaveStdDevThreshold)
self.SaveExcludeCorrelated = self.doc.createElement("SaveExcludeCorrelated ")
self.SaveExcludeCorrelated.setAttribute("value","false")
self.OPTIONS.appendChild(self.SaveExcludeCorrelated )
self.SaveCorrThreshold = self.doc.createElement("SaveCorrThreshold ")
self.SaveCorrThreshold.setAttribute("value","0.98")
self.OPTIONS.appendChild(self.SaveExcludeConst )
self.SaveExclusionOptionsToVariables = self.doc.createElement("SaveExclusionOptionsToVariables ")
self.SaveExclusionOptionsToVariables .setAttribute("value","false")
self.OPTIONS.appendChild(self.SaveExclusionOptionsToVariables )
#怎样设定？
self.SaveExcludeMisMolecules = self.doc.createElement("SaveExcludeMisMolecules ")
self.SaveExcludeMisMolecules .setAttribute("value","false")
self.OPTIONS.appendChild(self.SaveExcludeMisMolecules)
self.SaveExcludeRejectedMolecules = self.doc.createElement("SaveExcludeRejectedMolecules ")
self.SaveExcludeRejectedMolecules .setAttribute("value","false")
self.OPTIONS.appendChild(self.SaveExcludeRejectedMolecules )
#self.OPTIONS.appendChild(self.hello)
self.tagDragon.appendChild(self.OPTIONS)
#####################
######################descriptors的参数 参数设定完毕~~
self.DESCRIPTORS = self.doc.createElement("DESCRIPTORS")
for numbers in range(1,29):
self.block = self.doc.createElement("block")
self.block.setAttribute("id",str(numbers))
self.block.setAttribute("SelectAll","true")
self.DESCRIPTORS.appendChild(self.block)
self.tagDragon.appendChild(self.DESCRIPTORS)
######################MOLIFILES的参数 参数设定完毕~~
self.MOLFILES = self.doc.createElement("MOLFILES")
self.molInput= self.doc.createElement("molInput")
self.molInput.setAttribute("value","file")
self.MOLFILES.appendChild(self.molInput )
self.molFile= self.doc.createElement("molFile ")
self.molFile.setAttribute("value",inputFilePath)
self.MOLFILES.appendChild(self.molFile )
self.tagDragon.appendChild(self.MOLFILES)
####################################
#######################################################OUTPUT的参数
self.OUTPUT = self.doc.createElement("OUTPUT")
self.SaveStdOut = self.doc.createElement("SaveStdOut")
self.SaveStdOut .setAttribute("value","false")
self.OUTPUT.appendChild(self.SaveStdOut)
self.SaveProject= self.doc.createElement("SaveProject")
self.SaveProject.setAttribute("value","false")
self.OUTPUT.appendChild(self.SaveProject )
self.SaveProjectFile = self.doc.createElement("SaveProjectFile")
self.SaveProjectFile.setAttribute("value","[file]")
self.OUTPUT.appendChild(self.SaveProjectFile )
self.SaveFile = self.doc.createElement("SaveFile ")
self.SaveFile .setAttribute("value","true")
self.OUTPUT.appendChild(self.SaveFile)
self.SaveType = self.doc.createElement("SaveType ")
self.SaveType .setAttribute("value","singlefile")
self.OUTPUT.appendChild(self.SaveType )
#生成结果的保存路径
self.SaveFilePath = self.doc.createElement("SaveFilePath")
self.SaveFilePath .setAttribute("value",OutputPath)
self.OUTPUT.appendChild(self.SaveFilePath )
self.logMode= self.doc.createElement("logMode ")
self.logMode.setAttribute("value","none")
self.OUTPUT.appendChild(self.logMode )
self.logFile= self.doc.createElement("logFile ")
self.logFile .setAttribute("value","[file]")
self.OUTPUT.appendChild(self.logFile )
self.tagDragon.appendChild(self.OUTPUT)
###################################################################
################################################EXTERNAL参数
self.EXTERNAL = self.doc.createElement("EXTERNAL")
self.fileName = self.doc.createElement("fileName ")
self.fileName.setAttribute("value","[VALUE]")
self.EXTERNAL.appendChild(self.fileName )
self.delimiter= self.doc.createElement("delimiter ")
self.delimiter.setAttribute("value","[VALUE]")
self.EXTERNAL.appendChild(self.delimiter )
self.consecutiveDelimiter = self.doc.createElement("consecutiveDelimiter ")
self.consecutiveDelimiter .setAttribute("value","true")
self.EXTERNAL.appendChild(self.consecutiveDelimiter )
self.MissingValue = self.doc.createElement("MissingValue ")
self.MissingValue .setAttribute("value","[VALUE]")
self.EXTERNAL.appendChild(self.MissingValue )
self.tagDragon.appendChild(self.EXTERNAL)
############################################################3
f = open(OutputPath, "w")
self.doc.writexml(f, "\t", "\t", "\n", "utf-8")
def display(self):
print self.doc.toprettyxml(indent=" ")
wx = write_xml()
wx.set_tag("/home/est863/Desktop/toluene.mol","/home/est863/Desktop/toluene.drs")
wx.display()