Skip to content
Snippets Groups Projects
Commit 35bdf7fe authored by sandipde's avatar sandipde
Browse files

Ensured that weights and periodicities are output when landmarks are output

parent 8df714e8
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 486 additions and 467 deletions
regtest/analysis/rt-reselect-land/data.reference
+ 3
− 3
View file @ 35bdf7fe
#! FIELDS dist
1.2626
1.3934
#! FIELDS dist weight
1.2626 2.0000
1.3934 3.0000
regtest/analysis/rt-store-print/analysis.0.output-half.pdb.reference
+ 7
− 7
View file @ 35bdf7fe
#! FIELDS d1
0.000000
1.000000
2.000000
3.000000
4.000000
5.000000
#! FIELDS d1 weight
0.000000 1.000000
1.000000 1.000000
2.000000 1.000000
3.000000 1.000000
4.000000 1.000000
5.000000 1.000000
regtest/analysis/rt-store-print/analysis.0.output-stride2.pdb.reference
+ 4
− 4
View file @ 35bdf7fe
#! FIELDS d1
0.000000
2.000000
4.000000
#! FIELDS d1 weight
0.000000 1.000000
2.000000 1.000000
4.000000 1.000000
regtest/analysis/rt-store-print/output-all.pdb.reference
+ 14
− 14
View file @ 35bdf7fe
#! FIELDS d1
0.000000
0.000000
1.000000
2.000000
3.000000
4.000000
5.000000
6.000000
7.000000
8.000000
9.000000
10.000000
11.000000
#! FIELDS d1 weight
0.000000 1.000000
0.000000 1.000000
1.000000 1.000000
2.000000 1.000000
3.000000 1.000000
4.000000 1.000000
5.000000 1.000000
6.000000 1.000000
7.000000 1.000000
8.000000 1.000000
9.000000 1.000000
10.000000 1.000000
11.000000 1.000000
regtest/analysis/rt-store-print/output-half.pdb.reference
+ 7
− 7
View file @ 35bdf7fe
#! FIELDS d1
6.000000
7.000000
8.000000
9.000000
10.000000
11.000000
#! FIELDS d1 weight
6.000000 1.000000
7.000000 1.000000
8.000000 1.000000
9.000000 1.000000
10.000000 1.000000
11.000000 1.000000
regtest/analysis/rt-store-print/output-reuse.pdb.reference
+ 14
− 14
View file @ 35bdf7fe
#! FIELDS d1
0.000000
0.000000
1.000000
2.000000
3.000000
4.000000
5.000000
6.000000
7.000000
8.000000
9.000000
10.000000
11.000000
#! FIELDS d1 weight
0.000000 1.000000
0.000000 1.000000
1.000000 1.000000
2.000000 1.000000
3.000000 1.000000
4.000000 1.000000
5.000000 1.000000
6.000000 1.000000
7.000000 1.000000
8.000000 1.000000
9.000000 1.000000
10.000000 1.000000
11.000000 1.000000
regtest/analysis/rt-store-print/output-stride.pdb.reference
+ 6
− 6
View file @ 35bdf7fe
#! FIELDS d1
0.000000
1.000000
3.000000
5.000000
7.000000
#! FIELDS d1 weight
0.000000 1.000000
1.000000 1.000000
3.000000 1.000000
5.000000 1.000000
7.000000 1.000000
regtest/analysis/rt-store-print/output-stride2.pdb.reference
+ 4
− 4
View file @ 35bdf7fe
#! FIELDS d1
6.000000
8.000000
10.000000
#! FIELDS d1 weight
6.000000 1.000000
8.000000 1.000000
10.000000 1.000000
regtest/dimred/rt-mds/analysis.0.list_embed.reference
+ 101
− 101
View file @ 35bdf7fe
#! FIELDS mds.1 mds.2
0.0873 0.0013
0.0535 0.0044
0.0150 0.0044
-0.0136 0.0019
-0.0308 -0.0012
-0.0355 -0.0018
-0.0090 -0.0015
0.0145 0.0004
0.0191 0.0022
0.0278 0.0015
0.0091 -0.0004
-0.0359 -0.0012
-0.0540 0.0004
-0.0322 -0.0034
-0.0205 -0.0150
-0.0282 -0.0289
-0.0530 -0.0358
-0.0769 -0.0312
-0.0893 -0.0259
-0.0697 -0.0246
-0.0302 -0.0196
0.0093 -0.0072
0.0274 0.0009
0.0301 0.0016
0.0265 -0.0033
0.0433 -0.0053
0.0514 -0.0019
0.0222 0.0031
-0.0129 0.0061
-0.0322 0.0084
-0.0355 0.0080
-0.0337 0.0067
-0.0308 0.0047
-0.0253 0.0016
-0.0132 -0.0021
0.0040 -0.0031
0.0107 0.0011
0.0299 0.0060
0.0540 0.0070
0.0650 0.0039
0.0415 0.0025
0.0074 0.0033
-0.0185 0.0059
-0.0413 0.0073
-0.0548 0.0074
-0.0385 0.0041
-0.0383 -0.0006
-0.0584 -0.0008
-0.0584 0.0023
-0.0553 0.0090
-0.0772 0.0146
-0.0757 0.0157
-0.0644 0.0144
-0.0816 0.0141
-0.1045 0.0148
-0.0867 0.0111
-0.0365 0.0014
0.0113 -0.0067
0.0272 -0.0074
0.0381 -0.0012
0.0548 0.0021
0.0470 0.0012
0.0227 -0.0019
0.0132 -0.0022
0.0040 0.0004
-0.0045 0.0008
-0.0145 0.0006
-0.0116 0.0025
-0.0031 0.0044
-0.0148 0.0086
-0.0318 0.0109
-0.0166 0.0078
0.0154 0.0036
0.0451 0.0018
0.0364 0.0021
0.0125 0.0036
0.0330 0.0045
0.0605 0.0048
0.0417 0.0041
0.0115 0.0011
0.0257 -0.0018
0.0451 -0.0029
0.0387 -0.0032
0.0254 -0.0017
0.0311 -0.0001
0.0448 0.0006
0.0499 0.0020
0.0543 0.0037
0.0486 0.0054
0.0459 0.0051
0.0715 -0.0001
0.0764 -0.0063
0.0603 -0.0119
0.0378 -0.0153
0.0214 -0.0124
0.0063 -0.0091
-0.0095 -0.0016
-0.0259 0.0036
-0.0234 0.0061
0.0012 0.0060
#! FIELDS mds.1 mds.2 weight
0.0873 0.0013 1.0000
0.0535 0.0044 1.0000
0.0150 0.0044 1.0000
-0.0136 0.0019 1.0000
-0.0308 -0.0012 1.0000
-0.0355 -0.0018 1.0000
-0.0090 -0.0015 1.0000
0.0145 0.0004 1.0000
0.0191 0.0022 1.0000
0.0278 0.0015 1.0000
0.0091 -0.0004 1.0000
-0.0359 -0.0012 1.0000
-0.0540 0.0004 1.0000
-0.0322 -0.0034 1.0000
-0.0205 -0.0150 1.0000
-0.0282 -0.0289 1.0000
-0.0530 -0.0358 1.0000
-0.0769 -0.0312 1.0000
-0.0893 -0.0259 1.0000
-0.0697 -0.0246 1.0000
-0.0302 -0.0196 1.0000
0.0093 -0.0072 1.0000
0.0274 0.0009 1.0000
0.0301 0.0016 1.0000
0.0265 -0.0033 1.0000
0.0433 -0.0053 1.0000
0.0514 -0.0019 1.0000
0.0222 0.0031 1.0000
-0.0129 0.0061 1.0000
-0.0322 0.0084 1.0000
-0.0355 0.0080 1.0000
-0.0337 0.0067 1.0000
-0.0308 0.0047 1.0000
-0.0253 0.0016 1.0000
-0.0132 -0.0021 1.0000
0.0040 -0.0031 1.0000
0.0107 0.0011 1.0000
0.0299 0.0060 1.0000
0.0540 0.0070 1.0000
0.0650 0.0039 1.0000
0.0415 0.0025 1.0000
0.0074 0.0033 1.0000
-0.0185 0.0059 1.0000
-0.0413 0.0073 1.0000
-0.0548 0.0074 1.0000
-0.0385 0.0041 1.0000
-0.0383 -0.0006 1.0000
-0.0584 -0.0008 1.0000
-0.0584 0.0023 1.0000
-0.0553 0.0090 1.0000
-0.0772 0.0146 1.0000
-0.0757 0.0157 1.0000
-0.0644 0.0144 1.0000
-0.0816 0.0141 1.0000
-0.1045 0.0148 1.0000
-0.0867 0.0111 1.0000
-0.0365 0.0014 1.0000
0.0113 -0.0067 1.0000
0.0272 -0.0074 1.0000
0.0381 -0.0012 1.0000
0.0548 0.0021 1.0000
0.0470 0.0012 1.0000
0.0227 -0.0019 1.0000
0.0132 -0.0022 1.0000
0.0040 0.0004 1.0000
-0.0045 0.0008 1.0000
-0.0145 0.0006 1.0000
-0.0116 0.0025 1.0000
-0.0031 0.0044 1.0000
-0.0148 0.0086 1.0000
-0.0318 0.0109 1.0000
-0.0166 0.0078 1.0000
0.0154 0.0036 1.0000
0.0451 0.0018 1.0000
0.0364 0.0021 1.0000
0.0125 0.0036 1.0000
0.0330 0.0045 1.0000
0.0605 0.0048 1.0000
0.0417 0.0041 1.0000
0.0115 0.0011 1.0000
0.0257 -0.0018 1.0000
0.0451 -0.0029 1.0000
0.0387 -0.0032 1.0000
0.0254 -0.0017 1.0000
0.0311 -0.0001 1.0000
0.0448 0.0006 1.0000
0.0499 0.0020 1.0000
0.0543 0.0037 1.0000
0.0486 0.0054 1.0000
0.0459 0.0051 1.0000
0.0715 -0.0001 1.0000
0.0764 -0.0063 1.0000
0.0603 -0.0119 1.0000
0.0378 -0.0153 1.0000
0.0214 -0.0124 1.0000
0.0063 -0.0091 1.0000
-0.0095 -0.0016 1.0000
-0.0259 0.0036 1.0000
-0.0234 0.0061 1.0000
0.0012 0.0060 1.0000
regtest/dimred/rt-mds/list_embed.reference
+ 101
− 101
View file @ 35bdf7fe
#! FIELDS mds.1 mds.2
0.0594 0.0053
0.0683 0.0034
0.0705 0.0006
0.0729 -0.0019
0.0874 -0.0069
0.0961 -0.0095
0.0867 -0.0062
0.0719 -0.0008
0.0575 0.0031
0.0552 0.0034
0.0682 -0.0002
0.0781 -0.0024
0.0785 -0.0025
0.0763 -0.0027
0.0755 -0.0041
0.0792 -0.0069
0.0778 -0.0062
0.0727 -0.0025
0.0726 0.0014
0.0756 0.0030
0.0821 0.0017
0.0816 0.0001
0.0774 0.0008
0.0766 0.0008
0.0838 -0.0005
0.0931 -0.0016
0.0936 -0.0010
0.0923 -0.0009
0.0906 -0.0008
0.0706 0.0025
0.0664 0.0050
0.0901 0.0019
0.1059 -0.0015
0.0917 0.0006
0.0876 0.0021
0.1008 -0.0001
0.0955 -0.0014
0.0858 -0.0018
0.0894 -0.0005
0.0922 0.0014
0.0917 0.0010
0.0925 -0.0043
0.0967 -0.0102
0.1073 -0.0096
0.1065 -0.0047
0.0935 -0.0003
0.0668 0.0049
0.0410 0.0086
0.0264 0.0110
0.0254 0.0125
0.0503 0.0085
0.0855 0.0007
0.0975 -0.0028
0.0983 -0.0035
0.0997 -0.0044
0.0877 -0.0021
0.0501 0.0053
0.0104 0.0140
-0.0199 0.0221
-0.0416 0.0277
-0.0688 0.0338
-0.0858 0.0354
-0.0897 0.0313
-0.0920 0.0254
-0.1168 0.0227
-0.1447 0.0227
-0.1636 0.0221
-0.1461 0.0182
-0.1212 0.0139
-0.0775 0.0056
-0.0008 -0.0041
0.0469 -0.0038
0.0771 -0.0004
0.0917 0.0005
0.0656 0.0042
-0.0034 0.0115
-0.0901 0.0141
-0.1784 0.0069
-0.2253 -0.0077
-0.2372 -0.0248
-0.2415 -0.0448
-0.2562 -0.0539
-0.2901 -0.0433
-0.3173 -0.0215
-0.3117 0.0096
-0.2787 0.0317
-0.2319 0.0372
-0.1897 0.0305
-0.1592 0.0142
-0.1212 -0.0049
-0.0960 -0.0150
-0.0842 -0.0162
-0.0813 -0.0187
-0.0823 -0.0193
-0.0773 -0.0179
-0.0621 -0.0202
-0.0449 -0.0215
-0.0269 -0.0307
-0.0075 -0.0368
0.0266 -0.0342
#! FIELDS mds.1 mds.2 weight
0.0594 0.0053 1.0000
0.0683 0.0034 1.0000
0.0705 0.0006 1.0000
0.0729 -0.0019 1.0000
0.0874 -0.0069 1.0000
0.0961 -0.0095 1.0000
0.0867 -0.0062 1.0000
0.0719 -0.0008 1.0000
0.0575 0.0031 1.0000
0.0552 0.0034 1.0000
0.0682 -0.0002 1.0000
0.0781 -0.0024 1.0000
0.0785 -0.0025 1.0000
0.0763 -0.0027 1.0000
0.0755 -0.0041 1.0000
0.0792 -0.0069 1.0000
0.0778 -0.0062 1.0000
0.0727 -0.0025 1.0000
0.0726 0.0014 1.0000
0.0756 0.0030 1.0000
0.0821 0.0017 1.0000
0.0816 0.0001 1.0000
0.0774 0.0008 1.0000
0.0766 0.0008 1.0000
0.0838 -0.0005 1.0000
0.0931 -0.0016 1.0000
0.0936 -0.0010 1.0000
0.0923 -0.0009 1.0000
0.0906 -0.0008 1.0000
0.0706 0.0025 1.0000
0.0664 0.0050 1.0000
0.0901 0.0019 1.0000
0.1059 -0.0015 1.0000
0.0917 0.0006 1.0000
0.0876 0.0021 1.0000
0.1008 -0.0001 1.0000
0.0955 -0.0014 1.0000
0.0858 -0.0018 1.0000
0.0894 -0.0005 1.0000
0.0922 0.0014 1.0000
0.0917 0.0010 1.0000
0.0925 -0.0043 1.0000
0.0967 -0.0102 1.0000
0.1073 -0.0096 1.0000
0.1065 -0.0047 1.0000
0.0935 -0.0003 1.0000
0.0668 0.0049 1.0000
0.0410 0.0086 1.0000
0.0264 0.0110 1.0000
0.0254 0.0125 1.0000
0.0503 0.0085 1.0000
0.0855 0.0007 1.0000
0.0975 -0.0028 1.0000
0.0983 -0.0035 1.0000
0.0997 -0.0044 1.0000
0.0877 -0.0021 1.0000
0.0501 0.0053 1.0000
0.0104 0.0140 1.0000
-0.0199 0.0221 1.0000
-0.0416 0.0277 1.0000
-0.0688 0.0338 1.0000
-0.0858 0.0354 1.0000
-0.0897 0.0313 1.0000
-0.0920 0.0254 1.0000
-0.1168 0.0227 1.0000
-0.1447 0.0227 1.0000
-0.1636 0.0221 1.0000
-0.1461 0.0182 1.0000
-0.1212 0.0139 1.0000
-0.0775 0.0056 1.0000
-0.0008 -0.0041 1.0000
0.0469 -0.0038 1.0000
0.0771 -0.0004 1.0000
0.0917 0.0005 1.0000
0.0656 0.0042 1.0000
-0.0034 0.0115 1.0000
-0.0901 0.0141 1.0000
-0.1784 0.0069 1.0000
-0.2253 -0.0077 1.0000
-0.2372 -0.0248 1.0000
-0.2415 -0.0448 1.0000
-0.2562 -0.0539 1.0000
-0.2901 -0.0433 1.0000
-0.3173 -0.0215 1.0000
-0.3117 0.0096 1.0000
-0.2787 0.0317 1.0000
-0.2319 0.0372 1.0000
-0.1897 0.0305 1.0000
-0.1592 0.0142 1.0000
-0.1212 -0.0049 1.0000
-0.0960 -0.0150 1.0000
-0.0842 -0.0162 1.0000
-0.0813 -0.0187 1.0000
-0.0823 -0.0193 1.0000
-0.0773 -0.0179 1.0000
-0.0621 -0.0202 1.0000
-0.0449 -0.0215 1.0000
-0.0269 -0.0307 1.0000
-0.0075 -0.0368 1.0000
0.0266 -0.0342 1.0000
regtest/dimred/rt-mds2/analysis.0.list_embed.reference
+ 101
− 101
View file @ 35bdf7fe
#! FIELDS mds.1 mds.2
0.0873 0.0013
0.0535 0.0044
0.0150 0.0044
-0.0136 0.0019
-0.0308 -0.0012
-0.0355 -0.0018
-0.0090 -0.0015
0.0145 0.0004
0.0191 0.0022
0.0278 0.0015
0.0091 -0.0004
-0.0359 -0.0012
-0.0540 0.0004
-0.0322 -0.0034
-0.0205 -0.0150
-0.0282 -0.0289
-0.0530 -0.0358
-0.0769 -0.0312
-0.0893 -0.0259
-0.0697 -0.0246
-0.0302 -0.0196
0.0093 -0.0072
0.0274 0.0009
0.0301 0.0016
0.0265 -0.0033
0.0433 -0.0053
0.0514 -0.0019
0.0222 0.0031
-0.0129 0.0061
-0.0322 0.0084
-0.0355 0.0080
-0.0337 0.0067
-0.0308 0.0047
-0.0253 0.0016
-0.0132 -0.0021
0.0040 -0.0031
0.0107 0.0011
0.0299 0.0060
0.0540 0.0070
0.0650 0.0039
0.0415 0.0025
0.0074 0.0033
-0.0185 0.0059
-0.0413 0.0073
-0.0548 0.0074
-0.0385 0.0041
-0.0383 -0.0006
-0.0584 -0.0008
-0.0584 0.0023
-0.0553 0.0090
-0.0772 0.0146
-0.0757 0.0157
-0.0644 0.0144
-0.0816 0.0141
-0.1045 0.0148
-0.0867 0.0111
-0.0365 0.0014
0.0113 -0.0067
0.0272 -0.0074
0.0381 -0.0012
0.0548 0.0021
0.0470 0.0012
0.0227 -0.0019
0.0132 -0.0022
0.0040 0.0004
-0.0045 0.0008
-0.0145 0.0006
-0.0116 0.0025
-0.0031 0.0044
-0.0148 0.0086
-0.0318 0.0109
-0.0166 0.0078
0.0154 0.0036
0.0451 0.0018
0.0364 0.0021
0.0125 0.0036
0.0330 0.0045
0.0605 0.0048
0.0417 0.0041
0.0115 0.0011
0.0257 -0.0018
0.0451 -0.0029
0.0387 -0.0032
0.0254 -0.0017
0.0311 -0.0001
0.0448 0.0006
0.0499 0.0020
0.0543 0.0037
0.0486 0.0054
0.0459 0.0051
0.0715 -0.0001
0.0764 -0.0063
0.0603 -0.0119
0.0378 -0.0153
0.0214 -0.0124
0.0063 -0.0091
-0.0095 -0.0016
-0.0259 0.0036
-0.0234 0.0061
0.0012 0.0060
#! FIELDS mds.1 mds.2 weight
0.0873 0.0013 1.0000
0.0535 0.0044 1.0000
0.0150 0.0044 1.0000
-0.0136 0.0019 1.0000
-0.0308 -0.0012 1.0000
-0.0355 -0.0018 1.0000
-0.0090 -0.0015 1.0000
0.0145 0.0004 1.0000
0.0191 0.0022 1.0000
0.0278 0.0015 1.0000
0.0091 -0.0004 1.0000
-0.0359 -0.0012 1.0000
-0.0540 0.0004 1.0000
-0.0322 -0.0034 1.0000
-0.0205 -0.0150 1.0000
-0.0282 -0.0289 1.0000
-0.0530 -0.0358 1.0000
-0.0769 -0.0312 1.0000
-0.0893 -0.0259 1.0000
-0.0697 -0.0246 1.0000
-0.0302 -0.0196 1.0000
0.0093 -0.0072 1.0000
0.0274 0.0009 1.0000
0.0301 0.0016 1.0000
0.0265 -0.0033 1.0000
0.0433 -0.0053 1.0000
0.0514 -0.0019 1.0000
0.0222 0.0031 1.0000
-0.0129 0.0061 1.0000
-0.0322 0.0084 1.0000
-0.0355 0.0080 1.0000
-0.0337 0.0067 1.0000
-0.0308 0.0047 1.0000
-0.0253 0.0016 1.0000
-0.0132 -0.0021 1.0000
0.0040 -0.0031 1.0000
0.0107 0.0011 1.0000
0.0299 0.0060 1.0000
0.0540 0.0070 1.0000
0.0650 0.0039 1.0000
0.0415 0.0025 1.0000
0.0074 0.0033 1.0000
-0.0185 0.0059 1.0000
-0.0413 0.0073 1.0000
-0.0548 0.0074 1.0000
-0.0385 0.0041 1.0000
-0.0383 -0.0006 1.0000
-0.0584 -0.0008 1.0000
-0.0584 0.0023 1.0000
-0.0553 0.0090 1.0000
-0.0772 0.0146 1.0000
-0.0757 0.0157 1.0000
-0.0644 0.0144 1.0000
-0.0816 0.0141 1.0000
-0.1045 0.0148 1.0000
-0.0867 0.0111 1.0000
-0.0365 0.0014 1.0000
0.0113 -0.0067 1.0000
0.0272 -0.0074 1.0000
0.0381 -0.0012 1.0000
0.0548 0.0021 1.0000
0.0470 0.0012 1.0000
0.0227 -0.0019 1.0000
0.0132 -0.0022 1.0000
0.0040 0.0004 1.0000
-0.0045 0.0008 1.0000
-0.0145 0.0006 1.0000
-0.0116 0.0025 1.0000
-0.0031 0.0044 1.0000
-0.0148 0.0086 1.0000
-0.0318 0.0109 1.0000
-0.0166 0.0078 1.0000
0.0154 0.0036 1.0000
0.0451 0.0018 1.0000
0.0364 0.0021 1.0000
0.0125 0.0036 1.0000
0.0330 0.0045 1.0000
0.0605 0.0048 1.0000
0.0417 0.0041 1.0000
0.0115 0.0011 1.0000
0.0257 -0.0018 1.0000
0.0451 -0.0029 1.0000
0.0387 -0.0032 1.0000
0.0254 -0.0017 1.0000
0.0311 -0.0001 1.0000
0.0448 0.0006 1.0000
0.0499 0.0020 1.0000
0.0543 0.0037 1.0000
0.0486 0.0054 1.0000
0.0459 0.0051 1.0000
0.0715 -0.0001 1.0000
0.0764 -0.0063 1.0000
0.0603 -0.0119 1.0000
0.0378 -0.0153 1.0000
0.0214 -0.0124 1.0000
0.0063 -0.0091 1.0000
-0.0095 -0.0016 1.0000
-0.0259 0.0036 1.0000
-0.0234 0.0061 1.0000
0.0012 0.0060 1.0000
regtest/dimred/rt-mds2/list_embed.reference
+ 101
− 101
View file @ 35bdf7fe
#! FIELDS mds.1 mds.2
0.0594 0.0053
0.0683 0.0034
0.0705 0.0006
0.0729 -0.0019
0.0874 -0.0069
0.0961 -0.0095
0.0867 -0.0062
0.0719 -0.0008
0.0575 0.0031
0.0552 0.0034
0.0682 -0.0002
0.0781 -0.0024
0.0785 -0.0025
0.0763 -0.0027
0.0755 -0.0041
0.0792 -0.0069
0.0778 -0.0062
0.0727 -0.0025
0.0726 0.0014
0.0756 0.0030
0.0821 0.0017
0.0816 0.0001
0.0774 0.0008
0.0766 0.0008
0.0838 -0.0005
0.0931 -0.0016
0.0936 -0.0010
0.0923 -0.0009
0.0906 -0.0008
0.0706 0.0025
0.0664 0.0050
0.0901 0.0019
0.1059 -0.0015
0.0917 0.0006
0.0876 0.0021
0.1008 -0.0001
0.0955 -0.0014
0.0858 -0.0018
0.0894 -0.0005
0.0922 0.0014
0.0917 0.0010
0.0925 -0.0043
0.0967 -0.0102
0.1073 -0.0096
0.1065 -0.0047
0.0935 -0.0003
0.0668 0.0049
0.0410 0.0086
0.0264 0.0110
0.0254 0.0125
0.0503 0.0085
0.0855 0.0007
0.0975 -0.0028
0.0983 -0.0035
0.0997 -0.0044
0.0877 -0.0021
0.0501 0.0053
0.0104 0.0140
-0.0199 0.0221
-0.0416 0.0277
-0.0688 0.0338
-0.0858 0.0354
-0.0897 0.0313
-0.0920 0.0254
-0.1168 0.0227
-0.1447 0.0227
-0.1636 0.0221
-0.1461 0.0182
-0.1212 0.0139
-0.0775 0.0056
-0.0008 -0.0041
0.0469 -0.0038
0.0771 -0.0004
0.0917 0.0005
0.0656 0.0042
-0.0034 0.0115
-0.0901 0.0141
-0.1784 0.0069
-0.2253 -0.0077
-0.2372 -0.0248
-0.2415 -0.0448
-0.2562 -0.0539
-0.2901 -0.0433
-0.3173 -0.0215
-0.3117 0.0096
-0.2787 0.0317
-0.2319 0.0372
-0.1897 0.0305
-0.1592 0.0142
-0.1212 -0.0049
-0.0960 -0.0150
-0.0842 -0.0162
-0.0813 -0.0187
-0.0823 -0.0193
-0.0773 -0.0179
-0.0621 -0.0202
-0.0449 -0.0215
-0.0269 -0.0307
-0.0075 -0.0368
0.0266 -0.0342
#! FIELDS mds.1 mds.2 weight
0.0594 0.0053 1.0000
0.0683 0.0034 1.0000
0.0705 0.0006 1.0000
0.0729 -0.0019 1.0000
0.0874 -0.0069 1.0000
0.0961 -0.0095 1.0000
0.0867 -0.0062 1.0000
0.0719 -0.0008 1.0000
0.0575 0.0031 1.0000
0.0552 0.0034 1.0000
0.0682 -0.0002 1.0000
0.0781 -0.0024 1.0000
0.0785 -0.0025 1.0000
0.0763 -0.0027 1.0000
0.0755 -0.0041 1.0000
0.0792 -0.0069 1.0000
0.0778 -0.0062 1.0000
0.0727 -0.0025 1.0000
0.0726 0.0014 1.0000
0.0756 0.0030 1.0000
0.0821 0.0017 1.0000
0.0816 0.0001 1.0000
0.0774 0.0008 1.0000
0.0766 0.0008 1.0000
0.0838 -0.0005 1.0000
0.0931 -0.0016 1.0000
0.0936 -0.0010 1.0000
0.0923 -0.0009 1.0000
0.0906 -0.0008 1.0000
0.0706 0.0025 1.0000
0.0664 0.0050 1.0000
0.0901 0.0019 1.0000
0.1059 -0.0015 1.0000
0.0917 0.0006 1.0000
0.0876 0.0021 1.0000
0.1008 -0.0001 1.0000
0.0955 -0.0014 1.0000
0.0858 -0.0018 1.0000
0.0894 -0.0005 1.0000
0.0922 0.0014 1.0000
0.0917 0.0010 1.0000
0.0925 -0.0043 1.0000
0.0967 -0.0102 1.0000
0.1073 -0.0096 1.0000
0.1065 -0.0047 1.0000
0.0935 -0.0003 1.0000
0.0668 0.0049 1.0000
0.0410 0.0086 1.0000
0.0264 0.0110 1.0000
0.0254 0.0125 1.0000
0.0503 0.0085 1.0000
0.0855 0.0007 1.0000
0.0975 -0.0028 1.0000
0.0983 -0.0035 1.0000
0.0997 -0.0044 1.0000
0.0877 -0.0021 1.0000
0.0501 0.0053 1.0000
0.0104 0.0140 1.0000
-0.0199 0.0221 1.0000
-0.0416 0.0277 1.0000
-0.0688 0.0338 1.0000
-0.0858 0.0354 1.0000
-0.0897 0.0313 1.0000
-0.0920 0.0254 1.0000
-0.1168 0.0227 1.0000
-0.1447 0.0227 1.0000
-0.1636 0.0221 1.0000
-0.1461 0.0182 1.0000
-0.1212 0.0139 1.0000
-0.0775 0.0056 1.0000
-0.0008 -0.0041 1.0000
0.0469 -0.0038 1.0000
0.0771 -0.0004 1.0000
0.0917 0.0005 1.0000
0.0656 0.0042 1.0000
-0.0034 0.0115 1.0000
-0.0901 0.0141 1.0000
-0.1784 0.0069 1.0000
-0.2253 -0.0077 1.0000
-0.2372 -0.0248 1.0000
-0.2415 -0.0448 1.0000
-0.2562 -0.0539 1.0000
-0.2901 -0.0433 1.0000
-0.3173 -0.0215 1.0000
-0.3117 0.0096 1.0000
-0.2787 0.0317 1.0000
-0.2319 0.0372 1.0000
-0.1897 0.0305 1.0000
-0.1592 0.0142 1.0000
-0.1212 -0.0049 1.0000
-0.0960 -0.0150 1.0000
-0.0842 -0.0162 1.0000
-0.0813 -0.0187 1.0000
-0.0823 -0.0193 1.0000
-0.0773 -0.0179 1.0000
-0.0621 -0.0202 1.0000
-0.0449 -0.0215 1.0000
-0.0269 -0.0307 1.0000
-0.0075 -0.0368 1.0000
0.0266 -0.0342 1.0000
src/analysis/AnalysisBase.h
+ 7
− 0
View file @ 35bdf7fe
......@@ -81,6 +81,8 @@ public:
virtual double getDissimilarity( const unsigned& i, const unsigned& j );
/// This returns the label of the object that contains the base data
virtual std::string getBaseDataLabel() const ;
/// Overwrite getArguments so we get arguments from underlying class
virtual const std::vector<Value*> & getArguments() const ;
/// Get the ith data point
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (in dimensionality reduction this returns the projection)
......@@ -153,6 +155,11 @@ double AnalysisBase::getDissimilarity( const unsigned& i, const unsigned& j ){
return mydata->getDissimilarity( i, j );
}
inline
const std::vector<Value*> & AnalysisBase::getArguments() const {
return mydata->getArguments();
}
inline
std::string AnalysisBase::getBaseDataLabel() const {
return mydata->getBaseDataLabel();
......
src/analysis/AnalysisWithDataCollection.h
+ 8
− 0
View file @ 35bdf7fe
......@@ -100,6 +100,8 @@ public:
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (in dimensionality reduction this returns the projection)
virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat, const bool& calcdist );
/// Now we can get the arguments from the right place
const std::vector<Value*> & getArguments() const ;
/// This ensures that the energy is stored if we are reweighting
void prepare();
/// This stores the data and calls the analysis to be performed
......@@ -158,6 +160,12 @@ inline
unsigned AnalysisWithDataCollection::getNumberOfArguments() const {
unsigned nargs=ActionWithArguments::getNumberOfArguments();
return nargs - biases.size();
}
inline
const std::vector<Value*> & AnalysisWithDataCollection::getArguments() const {
if( !mydata ) return ActionWithArguments::getArguments();
return AnalysisBase::getArguments();
}
}
......
src/analysis/LandmarkSelectionBase.cpp
+ 1
− 1
View file @ 35bdf7fe
......@@ -60,7 +60,7 @@ void LandmarkSelectionBase::performAnalysis(){
std::vector<unsigned> tmpass( mydata->getNumberOfDataPoints() );
voronoiAnalysis( landmark_indices, lweights, tmpass );
} else {
for(unsigned i=0;i<nlandmarks;++i) lweights[i]=getWeight( landmark_indices[i] );
for(unsigned i=0;i<nlandmarks;++i) lweights[i]=mydata->getWeight( landmark_indices[i] );
}
}
......
src/analysis/OutputColvarFile.cpp
+ 6
− 2
View file @ 35bdf7fe
......@@ -89,7 +89,10 @@ void OutputColvarFile::performAnalysis(){
gfile.open( filename.c_str() );
ReferenceConfiguration* myp = getReferenceConfiguration(0,false);
if( myp->getNumberOfProperties()==0 ) plumed_assert( !dynamic_cast<ReferenceAtoms*>( myp ) );
if( myp->getNumberOfProperties()==0 ){
plumed_assert( !dynamic_cast<ReferenceAtoms*>( myp ) );
for(unsigned j=0;j<myp->getReferenceArguments().size();++j) gfile.setupPrintValue( getArguments()[j] );
}
// Print embedding coordinates
for(unsigned i=0;i<getNumberOfDataPoints();++i){
......@@ -101,9 +104,10 @@ void OutputColvarFile::performAnalysis(){
ReferenceArguments* myref=dynamic_cast<ReferenceArguments*>( mypoint );
plumed_assert( myref );
for(unsigned j=0;j<myref->getReferenceArguments().size();++j){
gfile.printField( myref->getArgumentNames()[j], myref->getReferenceArgument(j) );
gfile.printField( getArguments()[j], myref->getReferenceArgument(j) );
}
}
gfile.printField( "weight", getWeight(i) );
gfile.printField();
}
gfile.close();
......
src/core/ActionWithArguments.h
+ 1
− 1
View file @ 35bdf7fe
......@@ -78,7 +78,7 @@ public:
void lockRequests();
void unlockRequests();
/// Returns an array of pointers to the arguments
const std::vector<Value*> & getArguments() const ;
virtual const std::vector<Value*> & getArguments() const ;
/// Convert a list of argument names into a list of pointers to the values
void interpretArgumentList(const std::vector<std::string>& c, std::vector<Value*>&arg);
};
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment