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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/chemenv/coordination_environments/
H A Dvoronoi.py52 voronoi_list[isite] = []
62 voronoi_list[isite].append(dd)
151 for jj, isite in enumerate(indices):
153 site = self.structure[isite]
154 neighbors1 = [(site, 0.0, isite)]
210 for isite in indices:
284 … self.neighbors_distances[isite][-1]["next"] = dfact * self.neighbors_distances[isite][0]["min"]
350 … self.neighbors_angles[isite][-1]["next"] = afact * self.neighbors_angles[isite][0]["max"]
481 isite=isite, plot_type=plot_type, max_dist=max_dist
553 isite, argument
[all …]
H A Dstructure_environments.py69 self.isite = isite
556 isite=isite,
561 self.add_neighbors_set(isite=isite, nb_set=nb_set)
698 fig = self.get_csm_and_maps(isite=isite, max_csm=max_csm)
850 isite, argument
1049 isite, argument
1073 isite=isite,
1086 isite, argument
1108 isite=isite,
1453 self.isite = isite
[all …]
H A Dchemenv_strategies.py398 isite=isite,
618 isite=isite,
755 isite=isite,
801 isite=isite,
999 isite=isite,
1027 isite=isite,
1722 isite = nb_set.isite
1779 isite=isite,
1786 isite=isite,
1793 isite=isite,
[all …]
H A Dcoordination_geometry_finder.py635 sites_indices = [isite for isite in indices if self.valences[isite] >= 0]
642 isite
650 isite
656 sites_indices = [isite for isite in indices if isite in only_indices]
743 isite=isite,
759 isite=isite,
788 isite=isite,
823 se.add_neighbors_set(isite=isite, nb_set=missing_nb_set_to_add["new_nb_set"])
847 … se.update_site_info(isite=isite, info_dict={"time": t2 - t1, "nb_sets_info": nb_sets_info})
870 ce = se.get_coordination_environments(isite=isite, cn=cn, nb_set=nb_set)
[all …]
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/chemenv/connectivity/
H A Dstructure_connectivity.py147 isite,
149 start=isite,
187 isite,
196 isite,
210 isite,
218 isite1 = node1.isite
221 isite2 = node2.isite
257 start=node1.isite,
258 end=node2.isite,
335 n2.isite,
[all …]
H A Denvironment_nodes.py41 def isite(self): member in AbstractEnvironmentNode
54 return self.__class__ == other.__class__ and self.isite == other.isite
60 return self.isite < other.isite
95 … return "Node #{:d} {} ({})".format(self.isite, self.atom_symbol, self.coordination_environment)
H A Dconnectivity_finder.py50 for isite, site in enumerate(light_structure_environments.structure):
51 site_neighbors_sets = light_structure_environments.neighbors_sets[isite]
57 … "Local environment of site {:d} is a mix and " "nothing is asked about it".format(isite)
61 … [ee["ce_fraction"] for ee in light_structure_environments.coordination_environments[isite]]
69 structure_connectivity.add_bonds(isite, site_neighbors_set)
H A Dconnected_components.py143 inodes = [isite for isite, data in nodes]
144 indices_nodes = {isite: inodes.index(isite) for isite in inodes}
346 visited = {(source_node.isite, *current_delta)}
362 if (nb.isite, *new_delta) not in visited:
364 visited.add((nb.isite, *new_delta))
365 if nb.isite == current_node_end.isite: # Handle self loops
450 if path_indices == [test_node.isite, test_node_neighbor.isite]:
452 path_indices.append(test_node.isite)
763 if edata["start"] == node.isite and edata["end"] != node.isite:
765 elif edata["end"] == node.isite:
[all …]
/dports/science/tinker/tinker/source/
H A Dpmestuf.f661 do isite = 1, nion
784 do isite = 1, npole
816 term0 = fmp(1,isite)*u0*v0 + fmp(3,isite)*u1*v0
817 & + fmp(4,isite)*u0*v1 + fmp(6,isite)*u2*v0
818 & + fmp(7,isite)*u0*v2 + fmp(10,isite)*u1*v1
819 term1 = fmp(2,isite)*u0*v0 + fmp(8,isite)*u1*v0
920 do isite = 1, npole
1164 integer isite,iatm
1189 do isite = 1, npole
1332 integer isite,iatm
[all …]
H A Drotpole.f285 subroutine rotsite (isite,a) argument
290 integer isite local
298 rpole(1,isite) = pole(1,isite)
303 rpole(i,isite) = 0.0d0
305 rpole(i,isite) = rpole(i,isite) + pole(j,isite)*a(i-1,j-1)
314 mp(i,j) = pole(k,isite)
335 rpole(k,isite) = rp(i,j)
/dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.pde.ui/ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/site/
H A DSiteModelFactory.java18 import org.eclipse.pde.internal.core.isite.IRepositoryReference;
19 import org.eclipse.pde.internal.core.isite.ISite;
20 import org.eclipse.pde.internal.core.isite.ISiteArchive;
21 import org.eclipse.pde.internal.core.isite.ISiteBundle;
22 import org.eclipse.pde.internal.core.isite.ISiteCategory;
24 import org.eclipse.pde.internal.core.isite.ISiteDescription;
25 import org.eclipse.pde.internal.core.isite.ISiteFeature;
26 import org.eclipse.pde.internal.core.isite.ISiteModel;
27 import org.eclipse.pde.internal.core.isite.ISiteModelFactory;
28 import org.eclipse.pde.internal.core.isite.ISiteObject;
[all …]
H A DSite.java24 import org.eclipse.pde.internal.core.isite.IRepositoryReference;
25 import org.eclipse.pde.internal.core.isite.ISite;
26 import org.eclipse.pde.internal.core.isite.ISiteArchive;
27 import org.eclipse.pde.internal.core.isite.ISiteBundle;
28 import org.eclipse.pde.internal.core.isite.ISiteCategoryDefinition;
29 import org.eclipse.pde.internal.core.isite.ISiteDescription;
30 import org.eclipse.pde.internal.core.isite.ISiteFeature;
31 import org.eclipse.pde.internal.core.isite.ISiteObject;
32 import org.eclipse.pde.internal.core.isite.IStatsInfo;
H A DSiteCategory.java19 import org.eclipse.pde.internal.core.isite.ISite;
20 import org.eclipse.pde.internal.core.isite.ISiteCategory;
21 import org.eclipse.pde.internal.core.isite.ISiteCategoryDefinition;
H A DStatsInfo.java22 import org.eclipse.pde.internal.core.isite.ISiteBundle;
23 import org.eclipse.pde.internal.core.isite.ISiteFeature;
24 import org.eclipse.pde.internal.core.isite.ISiteObject;
25 import org.eclipse.pde.internal.core.isite.IStatsInfo;
H A DAbstractSiteModel.java26 import org.eclipse.pde.internal.core.isite.ISite;
27 import org.eclipse.pde.internal.core.isite.ISiteModel;
28 import org.eclipse.pde.internal.core.isite.ISiteModelFactory;
H A DSiteCategoryDefinition.java22 import org.eclipse.pde.internal.core.isite.ISiteCategory;
23 import org.eclipse.pde.internal.core.isite.ISiteCategoryDefinition;
24 import org.eclipse.pde.internal.core.isite.ISiteDescription;
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/lobster/
H A Dlobsterenv.py272 if isite in only_indices:
689 … isite for isite, site in enumerate(self.structure) if neighbor.is_periodic_image(site)
720 isite=isite,
830 if atomnr1 == isite:
835 elif atomnr2 == isite:
844 if atomnr1 == isite:
859 if atomnr1 == isite:
891 if atomnr1 == isite:
906 if atomnr1 == isite:
950 site=isite,
[all …]
/dports/biology/emboss/EMBOSS-6.6.0/emboss/
H A Dsigcleave.c96 ajint isite; in main() local
260 isite=ajUintGet(hp,ajUintGet(hi,i)); in main()
261 if(isite != maxsite) in main()
263 if(isite+pval<0) /*pval = -isite*/ continue; in main()
268 "%d\n\n", xweight,isite+begin); in main()
272 isite+pval,isite-1); in main()
276 if(isite+49<len) se=isite+49; in main()
279 isite+pval+begin, isite+begin-1, in main()
282 ajStrAssignSubC(&stmp,ajStrGetPtr(sstr),isite,se); in main()
294 isite+pval+begin, in main()
[all …]
/dports/biology/bio-mocha/bcftools-1.14/
H A Dvcfcnv.c629 float baf = smpl->baf[isite]; in set_observed_prob()
679 static void set_emission_prob(args_t *args, int isite) in set_emission_prob() argument
681 double *eprob = &args->eprob[args->nstates*isite]; in set_emission_prob()
687 static void set_emission_prob2(args_t *args, int isite) in set_emission_prob2() argument
689 double *eprob = &args->eprob[args->nstates*isite]; in set_emission_prob2()
1036 for (isite=0; isite<args->nsites; isite++) in cnv_flush_viterbi()
1038 int state = vpath[args->nstates*isite]; in cnv_flush_viterbi()
1039 double *pval = fwd + isite*args->nstates; in cnv_flush_viterbi()
1097 istart_pos = isite; in cnv_flush_viterbi()
1098 start_pos = args->sites[isite]; in cnv_flush_viterbi()
[all …]
/dports/biology/bcftools/bcftools-1.14/
H A Dvcfcnv.c629 float baf = smpl->baf[isite]; in set_observed_prob()
679 static void set_emission_prob(args_t *args, int isite) in set_emission_prob() argument
681 double *eprob = &args->eprob[args->nstates*isite]; in set_emission_prob()
687 static void set_emission_prob2(args_t *args, int isite) in set_emission_prob2() argument
689 double *eprob = &args->eprob[args->nstates*isite]; in set_emission_prob2()
1036 for (isite=0; isite<args->nsites; isite++) in cnv_flush_viterbi()
1038 int state = vpath[args->nstates*isite]; in cnv_flush_viterbi()
1039 double *pval = fwd + isite*args->nstates; in cnv_flush_viterbi()
1097 istart_pos = isite; in cnv_flush_viterbi()
1098 start_pos = args->sites[isite]; in cnv_flush_viterbi()
[all …]
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dvcfcnv.c629 float baf = smpl->baf[isite]; in set_observed_prob()
679 static void set_emission_prob(args_t *args, int isite) in set_emission_prob() argument
681 double *eprob = &args->eprob[args->nstates*isite]; in set_emission_prob()
687 static void set_emission_prob2(args_t *args, int isite) in set_emission_prob2() argument
689 double *eprob = &args->eprob[args->nstates*isite]; in set_emission_prob2()
1036 for (isite=0; isite<args->nsites; isite++) in cnv_flush_viterbi()
1038 int state = vpath[args->nstates*isite]; in cnv_flush_viterbi()
1039 double *pval = fwd + isite*args->nstates; in cnv_flush_viterbi()
1097 istart_pos = isite; in cnv_flush_viterbi()
1098 start_pos = args->sites[isite]; in cnv_flush_viterbi()
[all …]
H A Dvcfcnv.c.pysam.c631 float baf = smpl->baf[isite]; in set_observed_prob()
681 static void set_emission_prob(args_t *args, int isite) in set_emission_prob() argument
683 double *eprob = &args->eprob[args->nstates*isite]; in set_emission_prob()
689 static void set_emission_prob2(args_t *args, int isite) in set_emission_prob2() argument
691 double *eprob = &args->eprob[args->nstates*isite]; in set_emission_prob2()
1038 for (isite=0; isite<args->nsites; isite++) in cnv_flush_viterbi()
1040 int state = vpath[args->nstates*isite]; in cnv_flush_viterbi()
1041 double *pval = fwd + isite*args->nstates; in cnv_flush_viterbi()
1099 istart_pos = isite; in cnv_flush_viterbi()
1100 start_pos = args->sites[isite]; in cnv_flush_viterbi()
[all …]
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/chemenv/utils/
H A Dscripts_utils.py301 isite = se.structure.index(site)
321 str(isite),
329 str(isite),
342 … mingeoms = se.ce_list[isite][thecg.coordination_number][0].minimum_geometries()
356 for isite in indices:
357 if isite < 0:
359 se.plot_environments(isite)
395 for isite, site in enumerate(se.structure):
/dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.pde.ui/ui/org.eclipse.pde.ui/src/org/eclipse/pde/internal/ui/editor/site/
H A DSynchronizePropertiesWizard.java18 import org.eclipse.pde.internal.core.isite.ISiteFeature;
19 import org.eclipse.pde.internal.core.isite.ISiteModel;
H A DSynchronizePropertiesAction.java19 import org.eclipse.pde.internal.core.isite.ISiteFeature;
20 import org.eclipse.pde.internal.core.isite.ISiteModel;

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