Home
last modified time | relevance | path

Searched refs:nmol (Results 1 – 25 of 280) sorted by relevance

12345678910>>...12

/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FileParsers/
H A DtestGeneralFileReader.cpp79 ROMol* nmol = sdsup->next(); in testSdf() local
81 if (nmol) { in testSdf()
84 delete nmol; in testSdf()
98 if (nmol) { in testSdf()
101 delete nmol; in testSdf()
113 ROMol* nmol = sdsup2->next(); in testSdf() local
114 if (nmol) { in testSdf()
117 delete nmol; in testSdf()
174 TEST_ASSERT(nmol); in testMae()
246 if (nmol) { in testTdt()
[all …]
H A DtestMolSupplier.cpp47 if (nmol) { in testMolSup()
60 if (nmol) { in testMolSup()
82 if (nmol) { in testMolSup()
97 if (nmol) { in testMolSup()
1700 delete nmol; in testSDErrorHandling()
1710 delete nmol; in testSDErrorHandling()
1720 delete nmol; in testSDErrorHandling()
1730 delete nmol; in testSDErrorHandling()
1988 ROMol *nmol; in testRemoveHs() local
1993 delete nmol; in testRemoveHs()
[all …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/pbam/unittest/
H A DTerminateUnitTest.h30 const int nmol = 3; in TEST_F() local
56 const int nmol = 3; in TEST_F() local
83 const int nmol = 3; in TEST_F() local
110 const int nmol = 3; in TEST_F() local
137 const int nmol = 3; in TEST_F() local
164 const int nmol = 3; in TEST_F() local
191 const int nmol = 3; in TEST_F() local
218 const int nmol = 3; in TEST_F() local
246 const int nmol = 3; in TEST_F() local
278 const int nmol = 3; in TEST_F() local
[all …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/
H A DChemTransformsTests.java48 ROMol nmol=RDKFuncs.fragmentOnBRICSBonds(mol); in test1BRICS() local
50 assertEquals( 10,nmol.getNumAtoms()); in test1BRICS()
51 assertEquals("[16*]c1ccccc1.[3*]OC",nmol.MolToSmiles(true)); in test1BRICS()
57 ROMol nmol=RDKFuncs.fragmentOnBRICSBonds(mol); in test2BRICS() local
59 assertEquals( 7,nmol.getNumAtoms()); in test2BRICS()
60 assertEquals("[7*]=C(C)O.[7*]=CC",nmol.MolToSmiles(true)); in test2BRICS()
66 ROMol nmol=RDKFuncs.fragmentOnBRICSBonds(mol); in test3BRICS() local
68 assertEquals( 20,nmol.getNumAtoms()); in test3BRICS()
69 … assertEquals("[16*]c1ccccc1.[3*]O[3*].[4*]CCC.[4*]CCC([6*])=O",nmol.MolToSmiles(true)); in test3BRICS()
/dports/science/tinker/tinker/source/
H A Dmolecule.f43 nmol = 0
52 nmol = nmol + 1
53 molcule(i) = nmol
62 nmol = nmol - 1
72 nmol = nmol - 1
109 imol(2,nmol) = n
117 do i = 1, nmol
135 do i = 1, nmol
H A Ddiffuse.f175 do i = 1, nmol
182 do i = 1, nmol
190 nmol = k
191 write (iout,120) nmol
216 allocate (xcm(nmol,nframe))
217 allocate (ycm(nmol,nframe))
218 allocate (zcm(nmol,nframe))
243 do i = 1, nmol
295 do k = 1, nmol
317 counts = dble(nmol) * dble(ntime(i))
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemTransforms/
H A DtestChemTransforms.cpp1544 delete nmol; in testFragmentOnBonds()
1564 delete nmol; in testFragmentOnBonds()
1595 delete nmol; in testFragmentOnBonds()
1630 delete nmol; in testFragmentOnBonds()
1668 delete nmol; in testFragmentOnBRICSBonds()
1688 delete nmol; in testFragmentOnBRICSBonds()
1708 delete nmol; in testFragmentOnBRICSBonds()
1723 delete nmol; in testFragmentOnBRICSBonds()
1739 delete nmol; in testFragmentOnBRICSBonds()
1759 delete nmol; in testFragmentOnBRICSBonds()
[all …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/
H A DMolBundle.h55 virtual size_t addMol(boost::shared_ptr<ROMol> nmol) { in addMol() argument
56 PRECONDITION(nmol.get(), "bad mol pointer"); in addMol()
57 d_mols.push_back(nmol); in addMol()
100 size_t addMol(boost::shared_ptr<ROMol> nmol) override { in addMol() argument
101 PRECONDITION(nmol.get(), "bad mol pointer"); in addMol()
103 if (nmol->getNumAtoms() != d_mols[0]->getNumAtoms()) in addMol()
107 if (nmol->getNumBonds() != d_mols[0]->getNumBonds()) in addMol()
111 d_mols.push_back(nmol); in addMol()
/dports/science/openbabel/openbabel-3.1.1/test/
H A Dtestbindings.py711 nmol = ob.OBMol()
715 nmol = ob.OBMol()
733 nmol = ob.OBMol()
739 nmol.SetIsReaction()
877 nmol = ob.OBMol()
889 nmol = ob.OBMol()
896 nmol = ob.OBMol()
907 nmol = ob.OBMol()
1007 nmol = ob.OBMol()
1018 nmol.Clear()
[all …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/scripts/setup/
H A Dmake_starting_xyz.py7 nmol = [ ] variable
17 nmol.append(int(sys.argv[6+typ]))
27 def sample_grid(rad_avg, nmol, nfiles, fname): argument
30 ntypes = len(nmol); mol_tot = sum(nmol)
54 for j in range(nmol[i]):
83 sample_grid(rad_avg, nmol, ntraj)
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/argos/
H A Dargos_diana_center_fold.F14 integer i,j,k,nmol,ncount
28 nmol=0
30 nmol=max(nmol,imol(i))
56 do 5 j=1,nmol
62 nmol=max(nmol,imol(i))
/dports/science/nwchem-data/nwchem-7.0.2-release/src/argos/
H A Dargos_diana_center_fold.F14 integer i,j,k,nmol,ncount
28 nmol=0
30 nmol=max(nmol,imol(i))
56 do 5 j=1,nmol
62 nmol=max(nmol,imol(i))
/dports/science/smoldyn/smoldyn-2.67/source/Smoldyn/
H A Dsmolboxes.c299 bptr->nmol=NULL; in boxalloc()
337 if(bptr->nmol[ll]>maxmol) bptr->nmol[ll]=maxmol; in expandbox()
369 free(bptr->nmol); in boxfree()
674 blist[b]->nmol[ll]=0; in boxesupdateparams()
690 bptr->nmol[ll]++; }}} in boxesupdateparams()
695 mxml=bptr->nmol[ll]; in boxesupdateparams()
696 bptr->nmol[ll]=0; in boxesupdateparams()
894 int m,nmol,m2,ll,b,s; in reassignmolecs() local
914 nmol=sim->mols->nl[ll]; in reassignmolecs()
916 for(m=0;m<nmol;m++) { in reassignmolecs()
[all …]
H A Dsmolport.c419 int ll,nmol,count,m; in portgetmols() local
424 nmol=sim->mols->nl[ll]; in portgetmols()
427 for(m=0;m<nmol;m++) { in portgetmols()
437 int ll,nmol,count,m; in portgetmols2() local
442 nmol=sim->mols->nl[ll]; in portgetmols2()
445 for(m=0;m<nmol;m++) { in portgetmols2()
460 if(!nmol) return 0; in portputmols()
467 for(m=0;m<nmol;m++) { in portputmols()
488 sim->eventcount[ETimport]+=nmol; in portputmols()
494 int i,nmol,er; in porttransport() local
[all …]
/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxana/
H A Dgmx_gyrate.cpp197 static int nmol = 1, nz = 0; in gmx_gyrate() local
200 { "-nmol", FALSE, etINT, { &nmol }, "The number of molecules to analyze" }, in gmx_gyrate()
262 if (bACF && nmol != 1) in gmx_gyrate()
289 if (nmol > gnx || gnx % nmol != 0) in gmx_gyrate()
291 …mx_fatal(FARGS, "The number of atoms in the group (%d) is not a multiple of nmol (%d)", gnx, nmol); in gmx_gyrate()
293 nam = gnx / nmol; in gmx_gyrate()
345 for (mol = 0; mol < nmol; mol++) in gmx_gyrate()
360 if (nmol > 0) in gmx_gyrate()
362 gyro /= nmol; in gmx_gyrate()
363 svmul(1.0 / nmol, gvec, gvec); in gmx_gyrate()
[all …]
H A Dgmx_polystat.cpp186 nmol = 0; in gmx_polystat()
192 molind[nmol++] = i; in gmx_polystat()
199 molind[nmol] = i; in gmx_polystat()
202 for (mol = 0; mol < nmol; mol++) in gmx_polystat()
207 fprintf(stderr, "Group %s consists of %d molecules\n", grpname, nmol); in gmx_polystat()
210 sprintf(title, "Size of %d polymers", nmol); in gmx_polystat()
303 for (mol = 0; mol < nmol; mol++) in gmx_polystat()
380 sum_eed2 /= nmol; in gmx_polystat()
387 gyr_all[d][d2] /= nmol; in gmx_polystat()
401 fprintf(out, " %8.4f", std::sqrt(sum_eig[d] / nmol)); in gmx_polystat()
[all …]
H A Dgmx_spol.cpp119 int nmol, i, j, m; in spol_atom2molindex() local
121 nmol = 0; in spol_atom2molindex()
144 index[nmol++] = m; in spol_atom2molindex()
146 printf("There are %d molecules in the selection\n", nmol); in spol_atom2molindex()
148 *n = nmol; in spol_atom2molindex()
167 double sdip, sdip2, sinp, sdinp, nmol; in gmx_spol() local
374 nmol = 0; in gmx_spol()
377 nmol += hist[i]; in gmx_spol()
378 fprintf(fp, "%g %g\n", i * bw, nmol / nf); in gmx_spol()
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/pbsam/unittest/
H A DEnergyForceUnitTest.h30 int pol(3), nmol(2); in TEST_F()
33 for (int i=0; i<nmol; i++) in TEST_F()
55 for (int i=0; i<nmol; i++) in TEST_F()
95 int pol(3), nmol(3); in TEST_F()
98 for (int i=0; i<nmol; i++) in TEST_F()
122 for (int i=0; i<nmol; i++) in TEST_F()
189 int pol(3), nmol(2); in TEST_F()
192 for (int i=0; i<nmol; i++) in TEST_F()
214 for (int i=0; i<nmol; i++) in TEST_F()
257 TorqueCalcSAM tocal(nmol); in TEST_F()
[all …]
H A DBDUnitTest.h29 int pol(3), nmol(3); in TEST_F()
32 for (int i=0; i<nmol; i++) in TEST_F()
93 int pol(3), nmol(3); in TEST_F()
96 for (int i=0; i<nmol; i++) in TEST_F()
120 for (int i=0; i<nmol; i++) in TEST_F()
153 auto focal = make_shared<ForceCalc> (nmol, sys->get_all_Ik(), in TEST_F()
160 TorqueCalc tocal(nmol); in TEST_F()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/
H A Dmembed.cpp132 int nmol = 0; in get_molblock() local
136 nmol += mblock[i].nmol; in get_molblock()
137 if (mol_id < nmol) in get_molblock()
393 nmol = count = 0; in init_mem_at()
418 nmol++; in init_mem_at()
436 mem_p->nmol = nmol; in init_mem_at()
437 srenew(mol_id, nmol); in init_mem_at()
624 snew(dist, mem_p->nmol); in gen_rm_list()
693 if (i > mem_p->nmol) in gen_rm_list()
866 nmol = mtop->molblock[i].nmol; in rm_bonded()
[all …]
/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/
H A Dqs_loc_molecules.F55 natom, natom_loc, natom_max, nkind, nmol, nstate local
78 nmol = SIZE(local_molecules%list(ikind)%array)
79 DO imol = 1, nmol
114 nmol = SIZE(local_molecules%list(ikind)%array)
115 DO imol = 1, nmol
163 nmol = SIZE(local_molecules%list(ikind)%array)
164 DO imol = 1, nmol
/dports/science/cp2k-data/cp2k-7.1.0/src/
H A Dqs_loc_molecules.F55 natom, natom_loc, natom_max, nkind, nmol, nstate local
78 nmol = SIZE(local_molecules%list(ikind)%array)
79 DO imol = 1, nmol
114 nmol = SIZE(local_molecules%list(ikind)%array)
115 DO imol = 1, nmol
163 nmol = SIZE(local_molecules%list(ikind)%array)
164 DO imol = 1, nmol
/dports/science/gromacs/gromacs-2021.4/src/gromacs/topology/
H A Dmtop_util.cpp80 typecount[tpi] += molb.nmol; in gmx_mtop_count_atomtypes()
90 numMolecules += molb.nmol; in gmx_mtop_num_molecules()
244 *nmol = aloop->mtop->molblock[aloop->mblock].nmol; in gmx_mtop_atomloop_block_next()
289 *nmol = 1; in gmx_mtop_ilistloop_next()
297 *nmol = iloop->mtop->molblock[iloop->mblock].nmol; in gmx_mtop_ilistloop_next()
312 int n, nmol; in gmx_mtop_ftype_count() local
340 int nmol; in gmx_mtop_interaction_count() local
740 natoms += molb.nmol * srcnr; in copyIListsFromMtop()
791 for (int mol = 0; mol < molb.nmol; mol++) in globalExclusionLists()
912 for (int mol = 0; mol < molb.nmol; mol++) in fillMoleculeIndices()
[all …]
/dports/science/py-ase/ase-3.22.0/ase/calculators/
H A Dtip4p.py65 nmol = natoms // 3
76 for a in range(nmol - 1):
85 position_list = np.zeros(((nmol - 1 - a) * 4, 3))
102 self.energy_and_forces(a, xpos, position_list, q_v, nmol, t, dtdd)
114 def energy_and_forces(self, a, xpos, position_list, q_v, nmol, t, dtdd): argument
119 epsil = np.tile([epsilon0], nmol - 1 - a)
120 sigma = np.tile([sigma0], nmol - 1 - a)
141 e_f = e.reshape(nmol - a - 1, 4).sum(1)
/dports/science/gromacs/gromacs-2021.4/src/gromacs/pbcutil/
H A Dpbcmethods.cpp53 int nmol, imol_center; in calc_pbc_cluster() local
70 nmol = top->mols.nr; in calc_pbc_cluster()
72 snew(bMol, nmol); in calc_pbc_cluster()
73 snew(m_com, nmol); in calc_pbc_cluster()
74 snew(m_shift, nmol); in calc_pbc_cluster()
75 snew(cluster, nmol); in calc_pbc_cluster()
76 snew(added, nmol); in calc_pbc_cluster()
86 j1 = nmol - 1; in calc_pbc_cluster()
118 for (i = 0; i < nmol; i++) in calc_pbc_cluster()

12345678910>>...12