| /dports/science/tinker/tinker/source/ |
| H A D | chkring.f | 41 if (min(n12(ia),n12(ib)) .le. 1) nset = 0
43 if (min(n12(ia),n12(ic)) .le. 1) nset = 0
45 if (min(n12(ia),n12(id)) .le. 1) nset = 0
51 do j = 1, n12(ia)
74 do j = 1, n12(ia)-1
126 do j = 1, n12(ia)
135 do j = 1, n12(ia)
160 do j = 1, n12(ia)
182 do j = 1, n12(ia)
188 do j = 1, n12(ia)
[all …]
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| H A D | rotlist.f | 46 do k = 1, n12(ia)
49 do k = 1, n12(ib)
61 if (n12(ia).eq.maxval .or. n12(ib).eq.maxval) then
67 n12(ia) = n12(ia) + 1
69 n12(ib) = n12(ib) + 1
77 do i = 1, n12(base)
104 nattach = n12(base)
155 n12(ia) = n12(ia) - 1
156 n12(ib) = n12(ib) - 1
166 do k = 1, n12(ia)
[all …]
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| H A D | connect.f | 32 n12(i) = 0
49 n12(i) = n12(i) + 1
50 n12(k) = n12(k) + 1
51 i12(n12(i),i) = k
52 i12(n12(k),k) = i
61 n12(k) = n12(k) + 1
62 i12(n12(k),k) = iadd(3-j,i)
69 call sort (n12(i),i12(1,i))
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| H A D | prtmol2.f | 175 it = n12(i)
225 do k = 1, n12(i)
302 do m = 1, n12(k)
330 do m = 1, n12(k)
407 do m = 1, n12(i)
443 do m = 1, n12(i)
456 do m = 1, n12(i)
533 do k = 1, n12(ib)
593 do k = 1, n12(i)
641 do m = 1, n12(i)
[all …]
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| H A D | readmol.f | 87 n12(i) = 0
95 n12(ia) = n12(ia) + 1
96 i12(n12(ia),ia) = ib
97 n12(ib) = n12(ib) + 1
98 i12(n12(ib),ib) = ia
107 type(i) = 10*j + n12(i)
117 call sort (n12(i),i12(1,i))
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| H A D | delete.f | 41 n12(i) = n12(i+1)
42 do j = 1, n12(i)
51 do j = 1, n12(i)
54 do k = j, n12(i)-1
59 n12(i) = n12(i) - m
60 do j = 1, n12(i)
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| H A D | ksolv.f | 278 do j = 1, n12(i)
334 do j = 1, n12(i)
574 do j = 1, n12(i)
603 do j = 1, n12(ia)
615 do j = 1, n12(ib)
659 do j = 1, n12(i)
704 do j = 1, n12(i)
775 do j = 1, n12(i)
1590 do j = 1, n12(i)
1810 do j = 1, n12(i)
[all …]
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| H A D | shakeup.f | 148 if (n12(ia).eq.1 .and. n12(ib).eq.1) then
165 if (n12(ia)+n12(ib)+n12(ic) .eq. 4) then
197 do j = 1, n12(i)
202 do j = 1, n12(i)
281 do i = 1, n12(ia)
403 do i = 1, n12(ia)
412 do i = 1, n12(ia)
415 do j = 1, n12(id)
430 do i = 1, n12(ia)
433 do j = 1, n12(ic)
[all …]
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| H A D | readmol2.f | 141 n12(ia) = n12(ia) + 1
142 i12(n12(ia),ia) = ib
143 n12(ib) = n12(ib) + 1
144 i12(n12(ib),ib) = ia
157 type(i) = 10*j + n12(i)
167 call sort (n12(i),i12(1,i))
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| H A D | attach.f | 55 do j = 1, n12(i)
57 do k = 1, n12(jj)
60 do m = 1, n12(i)
83 do k = 1, n12(jj)
86 do m = 1, n12(i)
112 do k = 1, n12(jj)
115 do m = 1, n12(i)
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| H A D | orbital.f | 139 do ii = 1, n12(iorb)
223 do k = 1, n12(iorb)
278 attach = n12(i)
303 do j = 1, n12(i)
331 do j = 1, n12(alpha)
334 & n12(trial).eq.3) then
351 & (n12(alpha).eq.1 .and. atomic(alpha).eq.7))
353 do j = 1, n12(i)
356 & listpi(trial) .and. n12(trial).eq.3) then
361 do j = 1, n12(alpha)
[all …]
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| H A D | insert.f | 41 n12(i) = n12(i-1)
42 do j = 1, n12(i)
54 n12(iatom) = 0
59 do j = 1, n12(i)
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| H A D | readxyz.f | 126 n12(i) = 0
190 n12(i) = j
195 call sort (n12(i),i12(1,i))
203 do j = 1, n12(i)
222 do j = 1, n12(i)
225 call sort (n12(i),i12(1,i))
241 do j = 1, n12(i)
243 do m = 1, n12(k)
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| /dports/science/tinker/tinker/other/ |
| H A D | rotlist.alt | 45 do k = 1, n12(ia)
48 do k = 1, n12(ib)
60 if (n12(ia).eq.maxval .or. n12(ib).eq.maxval) then
66 n12(ia) = n12(ia) + 1
68 n12(ib) = n12(ib) + 1
76 do i = 1, n12(base)
94 nattach = n12(base)
127 n12(ia) = n12(ia) - 1
128 n12(ib) = n12(ib) - 1
138 do k = 1, n12(ia)
[all …]
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| /dports/science/tinker/tinker/utility/ |
| H A D | catrace.f | 65 do j = 1, n12(i)
69 do jj = 1, n12(k)
90 n12(i) = 0
92 n12(i) = n12(i) + 1
93 i12(n12(i),i) = i - 1
96 n12(i) = n12(i) + 1
97 i12(n12(i),i) = i + 1
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/test/ |
| H A D | test_kfunc.c | 41 int n11, int n12, int n21, int n22) in fail() argument
44 n11, n12, n21, n22, test, obs, expected); in fail()
48 void test_fisher(int n11, int n12, int n21, int n22, in test_fisher() argument
52 prob = kt_fisher_exact(n11, n12, n21, n22, &left, &right, &two); in test_fisher()
53 if (differ(left, eleft)) fail("LEFT", left, eleft, n11, n12, n21, n22); in test_fisher()
54 if (differ(right, eright)) fail("RIGHT", right, eright, n11, n12, n21, n22); in test_fisher()
55 if (differ(two, etwo)) fail("TWO-TAIL", two, etwo, n11, n12, n21, n22); in test_fisher()
56 if (differ(prob, eprob)) fail("RESULT", prob, eprob, n11, n12, n21, n22); in test_fisher()
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| /dports/biology/htslib/htslib-1.14/test/ |
| H A D | test_kfunc.c | 41 int n11, int n12, int n21, int n22) in fail() argument
44 n11, n12, n21, n22, test, obs, expected); in fail()
48 void test_fisher(int n11, int n12, int n21, int n22, in test_fisher() argument
52 prob = kt_fisher_exact(n11, n12, n21, n22, &left, &right, &two); in test_fisher()
53 if (differ(left, eleft)) fail("LEFT", left, eleft, n11, n12, n21, n22); in test_fisher()
54 if (differ(right, eright)) fail("RIGHT", right, eright, n11, n12, n21, n22); in test_fisher()
55 if (differ(two, etwo)) fail("TWO-TAIL", two, etwo, n11, n12, n21, n22); in test_fisher()
56 if (differ(prob, eprob)) fail("RESULT", prob, eprob, n11, n12, n21, n22); in test_fisher()
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| /dports/textproc/p5-Text-NSP/Text-NSP-1.31/lib/Text/NSP/Measures/2D/ |
| H A D | Fisher2.pm | 110 $n11 $n12 $n21 $n22 $m11 $m12 $m21 $m22
182 $n12 = $n1p-$n11;
189 $n12 = $n1p - $n11;
198 $n12 = $n1p - $i;
203 $probability{$i} = computeHyperGeometric($i,$n12,$n21,$n22);
212 my $n12 = shift @_;
229 @denominator = sort { $b <=> $a } ($npp, $n22, $n12, $n21, $n11);
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| H A D | Fisher.pm | 95 $n11 $n12 $n21 $n22 $m11 $m12 $m21 $m22
174 $n12 = $n1p-$n11;
181 $n12 = $n1p - $n11;
194 $n12 = $n1p - $i;
199 @denominator = sort { $b <=> $a } ($npp, $n22, $n12, $n21, $i);
252 $subproduct += log $n12;
256 $n12--;
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| /dports/misc/elki/elki-release0.7.1-1166-gfb1fffdf3/elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/birch/ |
| H A D | AverageIntraclusterDistance.java | 57 final int n12 = 1 + cf.n; in squaredDistance() local
58 final double div1 = 1. / n12, div2 = 1. / (n12 - 1); in squaredDistance()
71 final int n12 = cf1.n + cf2.n; in squaredDistance() local
72 final double div1 = 1. / n12, div2 = 1. / (n12 - 1); in squaredDistance()
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| H A D | DiameterCriterion.java | 69 int n12 = f1.n + f2.n; in squaredCriterion() local
70 if(n12 <= 0) { in squaredCriterion()
78 double diameter = (sum1 * n12 - sum2); in squaredCriterion()
79 return diameter > 0 ? diameter * 2. / (n12 * (n12 - 1L)) : 0.; in squaredCriterion()
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| /dports/science/plumed/plumed2-2.7.2/regtest/basic/rt-ghost-1/ |
| H A D | plumed.dat | 7 n12: DISTANCE ATOMS=1,2 COMPONENTS
9 n12nx: MATHEVAL PERIODIC=NO ARG=n12.x,n12.y,n12.z FUNC=x/sqrt(x*x+y*y+z*z)
10 n12ny: MATHEVAL PERIODIC=NO ARG=n12.x,n12.y,n12.z FUNC=y/sqrt(x*x+y*y+z*z)
11 n12nz: MATHEVAL PERIODIC=NO ARG=n12.x,n12.y,n12.z FUNC=z/sqrt(x*x+y*y+z*z)
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| /dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/bcftools/ |
| H A D | fet.c | 61 double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *t… in kt_fisher_exact() argument
68 n1_ = n11 + n12; n_1 = n11 + n21; n = n11 + n12 + n21 + n22; // calculate n1_, n_1 and n in kt_fisher_exact()
105 int n11, n12, n21, n22; in main() local
108 while (scanf("%s%d%d%d%d", id, &n11, &n12, &n21, &n22) == 5) { in main()
109 prob = kt_fisher_exact(n11, n12, n21, n22, &left, &right, &twotail); in main()
110 printf("%s\t%d\t%d\t%d\t%d\t%.6g\t%.6g\t%.6g\t%.6g\n", id, n11, n12, n21, n22, in main()
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| /dports/biology/seqan1/seqan-1.3.1/lib/samtools/bcftools/ |
| H A D | fet.c | 58 double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *t… in kt_fisher_exact() argument
65 n1_ = n11 + n12; n_1 = n11 + n21; n = n11 + n12 + n21 + n22; // calculate n1_, n_1 and n in kt_fisher_exact()
100 int n11, n12, n21, n22; in main() local
103 while (scanf("%s%d%d%d%d", id, &n11, &n12, &n21, &n22) == 5) { in main()
104 prob = kt_fisher_exact(n11, n12, n21, n22, &left, &right, &twotail); in main()
105 printf("%s\t%d\t%d\t%d\t%d\t%.6g\t%.6g\t%.6g\t%.6g\n", id, n11, n12, n21, n22, in main()
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| /dports/biology/bedtools/bedtools2-2.30.0/src/fisher/ |
| H A D | fisher.cpp | 65 long long n12 = (long)max(0L, (long)_queryCounts - (long)_overlapCounts); in giveFinalReport() local
67 long long n22_full = max(n21 + n12 + n11, (long long)(n22_full_bases / bMean)); in giveFinalReport()
68 long long n22 = max(0L, (long)(n22_full - n12 - n21 - n11)); in giveFinalReport()
79 printf("# in -a | %-12lld | %-12lld |\n", n11, n12); in giveFinalReport()
83 kt_fisher_exact(n11, n12, n21, n22, &left, &right, &two); in giveFinalReport()
84 double ratio = ((double)n11 / (double)n12) / ((double)n21 / (double)n22); in giveFinalReport()
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