/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FileParsers/ |
H A D | testGeneralFileReader.cpp | 79 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 …]
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H A D | testMolSupplier.cpp | 47 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 …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/pbam/unittest/ |
H A D | TerminateUnitTest.h | 30 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 …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/ |
H A D | ChemTransformsTests.java | 48 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()
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/dports/science/tinker/tinker/source/ |
H A D | molecule.f | 43 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
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H A D | diffuse.f | 175 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))
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemTransforms/ |
H A D | testChemTransforms.cpp | 1544 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 …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
H A D | MolBundle.h | 55 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()
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/dports/science/openbabel/openbabel-3.1.1/test/ |
H A D | testbindings.py | 711 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 …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/scripts/setup/ |
H A D | make_starting_xyz.py | 7 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)
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/argos/ |
H A D | argos_diana_center_fold.F | 14 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))
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/argos/ |
H A D | argos_diana_center_fold.F | 14 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))
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/dports/science/smoldyn/smoldyn-2.67/source/Smoldyn/ |
H A D | smolboxes.c | 299 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 …]
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H A D | smolport.c | 419 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 …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxana/ |
H A D | gmx_gyrate.cpp | 197 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 …]
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H A D | gmx_polystat.cpp | 186 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 …]
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H A D | gmx_spol.cpp | 119 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()
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/pbsam/unittest/ |
H A D | EnergyForceUnitTest.h | 30 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 …]
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H A D | BDUnitTest.h | 29 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()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/ |
H A D | membed.cpp | 132 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 …]
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/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/ |
H A D | qs_loc_molecules.F | 55 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
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/dports/science/cp2k-data/cp2k-7.1.0/src/ |
H A D | qs_loc_molecules.F | 55 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
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/topology/ |
H A D | mtop_util.cpp | 80 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 …]
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/dports/science/py-ase/ase-3.22.0/ase/calculators/ |
H A D | tip4p.py | 65 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)
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/pbcutil/ |
H A D | pbcmethods.cpp | 53 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()
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