From: <rka...@us...> - 2006-03-17 20:45:10
|
Revision: 4643 Author: rkanters Date: 2006-03-17 12:44:45 -0800 (Fri, 17 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4643&view=rev Log Message: ----------- moving input files from Jmol-datafiles into a subdirectory 'input' at the same level. Added Paths: ----------- trunk/Jmol-datafiles/gaussian/input/ trunk/Jmol-datafiles/gaussian/input/H2O.in trunk/Jmol-datafiles/gaussian/input/H2O_3.in trunk/Jmol-datafiles/gaussian/input/H2O_NoSymm.in trunk/Jmol-datafiles/input/ trunk/Jmol-datafiles/input/HfO2_mol_opt.in trunk/Jmol-datafiles/input/HfO2_on_Si_relax.in trunk/Jmol-datafiles/input/bulk_Si.in trunk/Jmol-datafiles/input/ch2chfme_reagent.inp trunk/Jmol-datafiles/input/pei2h2o.in trunk/Jmol-datafiles/input/t54.in Removed Paths: ------------- trunk/Jmol-datafiles/HfO2_mol_opt.in trunk/Jmol-datafiles/HfO2_on_Si_relax.in trunk/Jmol-datafiles/bulk_Si.in trunk/Jmol-datafiles/ch2chfme_reagent.inp trunk/Jmol-datafiles/gaussian/H2O.in trunk/Jmol-datafiles/gaussian/H2O_3.in trunk/Jmol-datafiles/gaussian/H2O_NoSymm.in trunk/Jmol-datafiles/pei2h2o.in trunk/Jmol-datafiles/t54.in Deleted: trunk/Jmol-datafiles/HfO2_mol_opt.in =================================================================== --- trunk/Jmol-datafiles/HfO2_mol_opt.in 2006-03-17 19:23:46 UTC (rev 4642) +++ trunk/Jmol-datafiles/HfO2_mol_opt.in 2006-03-17 20:44:45 UTC (rev 4643) @@ -1,61 +0,0 @@ -# H2 molecule in a big box -# -# This file will optimize automatically the interatomic distance - -#Define the methodology to find the minimum -ionmov 3 # Use the modified Broyden algorithm -ntime 20 # Maximum number of Broyden "timesteps" -tolmxf 5.0d-4 # Stopping criterion for the geometry optimization : when - # the residual forces are less than tolmxf, the Broyden - # algorithm can stop - -xcart 0.0 0.0 0.0 # Hf - 0.7 -0.7 0.0 # O - 0.7 0.7 0.0 # O - -toldff 5.0d-5 # Will stop the SCF cycle when, twice in a row, - # the difference between two consecutive evaluations of - # forces differ by less than toldff (in Hartree/Bohr) - - -#nband 1 # Only one band is occupied. In order to get the energy, - # forces ..., there is no need to compute more than one band. - -#------------------------------------------------------------------------------- -#The rest of this file is similar to the t11.in file, except -#that xcart has been moved above, and that toldfe has been replaced -#by toldff, see above. - -#Definition of the unit cell -acell 15 15 15 # The keyword "acell" refers to the - # lengths of the primitive vectors (in Bohr) - # The priitive cell is cubic by default - -#Definition of the atom types -ntype 2 # There is only 2 type of atom -zatnum 72 8 # The keyword "zatnum" refers to the atomic number of the - # possible type(s) of atom. The pseudopotential(s) - # mentioned in the "files" file must correspond - # to the type(s) of atom. Here, the only type is Hydrogen. - - -#Definition of the atoms -natom 3 # There are 3 atoms -type 1 2 2 # HfO2 - -#Definition of the planewave basis set -ecut 40.0 # Maximal kinetic energy cut-off, in Hartree - -#Definition of the k-point grid -nkpt 1 # Only one k point is needed for isolated system, - # taken by default to be 0.0 0.0 0.0 - -#Definition of the SCF procedure -nstep 20 # Maximal number of SCF cycles -#toldfe is no more defined, as toldff is used above... -diemac 1.0 # Although this is not mandatory, it is worth to - # precondition the SCF cycle. The model dielectric -diemix 0.5 # function used as the standard preconditioner - # is described in the "dielng" input variable section. - # Here, we follow the prescriptions for molecules - # in a big box Deleted: trunk/Jmol-datafiles/HfO2_on_Si_relax.in =================================================================== --- trunk/Jmol-datafiles/HfO2_on_Si_relax.in 2006-03-17 19:23:46 UTC (rev 4642) +++ trunk/Jmol-datafiles/HfO2_on_Si_relax.in 2006-03-17 20:44:45 UTC (rev 4643) @@ -1,78 +0,0 @@ -# Study of relaxed HfO2 on Silicon [100] non relaxed - -# Dynamic -optcell 0 # This is the default. Don't optimize unit cell -ionmov 3 # Relaxation Broyden-Fletcher -tolmxf 1.0d-6 # Force tolerance -ntime 30 - -# Definition of the k-point grids -kptopt 1 # Option for the automatic generation of k points, - # taking into account the symmetries. - -ngkpt 4 4 1 # unneccessary to sample in the z direction -nshiftk 2 -shiftk 0.5 0.0 0.0 - 0.0 0.5 0.0 - -# Definition of the unit cell - -acell 3*10.216 # Lattice parameters of bulk silicon in Bohr(optimized) -rprim 0.5 -0.5 0.0 # These values will define a tetragonal cell with 4 atoms, - 1.0 1.0 0.0 # NON-primitive, with a different orientation - 0.0 0.0 2.5 # than the primitive cell which is rhombohedral. - -chkprim 0 # This input variable allows to use non-primitive - # unit cells. - -# Definition of the atom types -ntype 3 # There is only one type of atom -zatnum - 14 - 72 - 8 # Atomic number of silicon,Hafnium and Oxygen - - -# Definition of the atoms -natom 20 # There are 20 atoms in the unit cell -type 14*1 2 2 4*3 # They are of type 1, silicon, 2 Hf, 3 O. -xcart # I use xcart (in Bohr) instead of xred because it will - # be easier in the case of a slab of varying - # Silicon and vacuum thickness. - 0.0 0.0 0.0 # atom at the corner - 2.554 2.554 2.554 # 2.554=a_cell/4 - 5.108 0.0 5.108 # 5.108=a_cell/2 - 7.662 2.554 7.662 # 7.662=3*a_cell/4 - 0.0 0.0 10.216 - 2.554 2.554 12.770 # 12.770=a_cell*5/4 - 5.108 0.0 15.324 # 15.324=a_cell*3/2 - 5.108 5.108 0.0 # expanding in x,y direction - 7.662 7.662 2.554 - 10.216 5.108 5.108 - 12.77 7.662 7.662 - 5.108 5.108 10.216 - 7.662 7.662 12.770 - 10.216 5.108 15.324 - 5.108 5.108 15.324 # adding the Hf on top of Si - 10.216 10.216 15.324 # idem in adjacent cell - 2.554 2.554 15.324 # adding oxygens - 7.662 2.554 15.324 - 12.77 5.108 15.324 - 7.662 5.108 15.324 - - -# Definition of the planewave basis set -#ecut 8.0 # Maximal kinetic energy cut-off, in Hartree - # Convergence was not very good -ecut 35.0 - -# Definition of the SCF procedure -nstep 20 # Maximal number of SCF cycles. -toldfe 1.0d-6 # Will stop when, twice in a row, the difference - # between two consecutive evaluations of total - # energy differ by less then toldfe (Ha) -diemac 12.0 # precondition the SCF cycle (12 is good for bulk Si) - - - - Deleted: trunk/Jmol-datafiles/bulk_Si.in =================================================================== --- trunk/Jmol-datafiles/bulk_Si.in 2006-03-17 19:23:46 UTC (rev 4642) +++ trunk/Jmol-datafiles/bulk_Si.in 2006-03-17 20:44:45 UTC (rev 4643) @@ -1,52 +0,0 @@ -# Crystalline silicon : computation of the total energy -# Convergence with respect to the number of k points. - - -#Definition of the k-point grids -kptopt 1 # Option for the automatic generation of k points, taking - # into account the symmetry -nshiftk 4 -shiftk 0.5 0.5 0.5 # These shifts will be the same for all grids - 0.5 0.0 0.0 - 0.0 0.5 0.0 - 0.0 0.0 0.5 - -ngkpt 8 8 8 # Definition of the different grids - - - -#Definition of the unit cell -acell 3*10.18 # This is equivalent to 10.18 10.18 10.18 -rprim 0.0 0.5 0.5 # FCC primitive vectors (to be scaled by acell) - 0.5 0.0 0.5 - 0.5 0.5 0.0 - -#Definition of the atom types -ntype 1 # There is only one type of atom -zatnum 14 # The keyword "zatnum" refers to the atomic number of the - # possible type(s) of atom. The pseudopotential(s) - # mentioned in the "files" file must correspond - # to the type(s) of atom. Here, the only type is Silicon. - - -#Definition of the atoms -natom 2 # There are two atoms -type 1 1 # They both are of type 1, that is, Silicon. -xred # This keyword indicate that the location of the atoms - # will follow, one triplet of number for each atom - 0.0 0.0 0.0 # Triplet giving the REDUCED coordinate of atom 1. - 0.25 0.25 0.25 # Triplet giving the REDUCED coordinate of atom 2. - -#Definition of the planewave basis set -ecut 8.0 # Maximal kinetic energy cut-off, in Hartree - -#Definition of the SCF procedure -nstep 10 # Maximal number of SCF cycles -toldfe 1.0d-6 # Will stop when, twice in a row, the difference - # between two consecutive evaluations of total energy - # differ by less than toldfe (in Hartree) -diemac 12.0 # Although this is not mandatory, it is worth to - # precondition the SCF cycle. The model dielectric - # function used as the standard preconditioner - # is described in the "dielng" input variable section. - # Here, we follow the prescription for bulk silicon. Deleted: trunk/Jmol-datafiles/ch2chfme_reagent.inp =================================================================== --- trunk/Jmol-datafiles/ch2chfme_reagent.inp 2006-03-17 19:23:46 UTC (rev 4642) +++ trunk/Jmol-datafiles/ch2chfme_reagent.inp 2006-03-17 20:44:45 UTC (rev 4643) @@ -1,77 +0,0 @@ -\xFF\xFE# |
From: <mig...@us...> - 2006-03-22 16:52:28
|
Revision: 4682 Author: migueljmol Date: 2006-03-22 08:52:15 -0800 (Wed, 22 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4682&view=rev Log Message: ----------- sample data file and resolver work for MDL v3000 format Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Added Paths: ----------- trunk/Jmol-datafiles/v3000/ trunk/Jmol-datafiles/v3000/WO0119816T.sdf Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2006-03-22 12:29:28 UTC (rev 4681) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2006-03-22 16:52:15 UTC (rev 4682) @@ -103,6 +103,8 @@ LimitedLineReader llr = new LimitedLineReader(bufferedReader, 16384); for (int i = 0; i < lines.length; ++i) lines[i] = llr.readLineWithNewline(); + if (checkV3000(lines)) + return "V3000"; if (checkMol(lines)) return "Mol"; if (checkXyz(lines)) @@ -142,12 +144,20 @@ // file types that need special treatment //////////////////////////////////////////////////////////////// + static boolean checkV3000(String[] lines) { + if (lines[3].length() >= 6) { + String line4trimmed = lines[3].trim(); + if (line4trimmed.endsWith("V3000")) + return true; + } + return false; + } + static boolean checkMol(String[] lines) { if (lines[3].length() >= 6) { String line4trimmed = lines[3].trim(); if (line4trimmed.endsWith("V2000") || - line4trimmed.endsWith("v2000") || - line4trimmed.endsWith("V3000")) + line4trimmed.endsWith("v2000")) return true; try { Integer.parseInt(lines[3].substring(0, 3).trim()); Added: trunk/Jmol-datafiles/v3000/WO0119816T.sdf =================================================================== --- trunk/Jmol-datafiles/v3000/WO0119816T.sdf (rev 0) +++ trunk/Jmol-datafiles/v3000/WO0119816T.sdf 2006-03-22 16:52:15 UTC (rev 4682) @@ -0,0 +1,368 @@ + + 02260622002D 0 0.00000 0.00000 0 +HDR: RoxyName (Build 030), Copyright (c) 2001-2005. All rights reserved. + 0 0 0 0 0 999 V3000 +M V30 BEGIN CTAB +M V30 COUNTS 7 6 0 0 0 +M V30 BEGIN ATOM +M V30 1 S 0.75 2.25 0 0 +M V30 2 C 2.04904 3 0 0 +M V30 3 C 3.34808 2.25 0 0 CFG=2 +M V30 4 N 3.34808 0.75 0 0 +M V30 5 C 4.64711 3 0 0 +M V30 6 O 5.94615 2.25 0 0 +M V30 7 O 4.64711 4.5 0 0 +M V30 END ATOM +M V30 BEGIN BOND +M V30 1 1 1 2 +M V30 2 1 2 3 +M V30 3 1 3 4 CFG=1 +M V30 4 1 3 5 +M V30 5 2 5 6 +M V30 6 1 5 7 +M V30 END BOND +M V30 BEGIN COLLECTION +M V30 MDLV30/STEABS ATOMS=(1 3) +M V30 END COLLECTION +M V30 END CTAB +M END +> <Name> +CYSTEINE + +$$$$ + + 02260622002D 0 0.00000 0.00000 0 +HDR: RoxyName (Build 030), Copyright (c) 2001-2005. All rights reserved. + 0 0 0 0 0 999 V3000 +M V30 BEGIN CTAB +M V30 COUNTS 11 11 0 0 0 +M V30 BEGIN ATOM +M V30 1 N 3.75 0.750001 0 0 +M V30 2 C 3 2.04904 0 0 CFG=2 +M V30 3 C 1.5 2.04904 0 0 +M V30 4 O 0.750001 0.75 0 0 +M V30 5 O 0.75 3.34808 0 0 +M V30 6 C 3.75 3.34808 0 0 +M V30 7 C 5.25 3.34808 0 0 +M V30 8 C 6.13168 4.5616 0 0 +M V30 9 N 7.55826 4.09808 0 0 +M V30 10 C 7.55827 2.59808 0 0 +M V30 11 N 6.13168 2.13455 0 0 +M V30 END ATOM +M V30 BEGIN BOND +M V30 1 1 2 1 CFG=3 +M V30 2 1 2 3 +M V30 3 1 2 6 +M V30 4 2 3 4 +M V30 5 1 3 5 +M V30 6 1 6 7 +M V30 7 2 7 8 +M V30 8 1 7 11 +M V30 9 1 8 9 +M V30 10 1 9 10 +M V30 11 2 10 11 +M V30 END BOND +M V30 BEGIN COLLECTION +M V30 MDLV30/STEABS ATOMS=(1 2) +M V30 END COLLECTION +M V30 END CTAB +M END +> <Name> +histidine + +$$$$ + + + 02260622012D 0 0.00000 0.00000 0 +HDR: RoxyName (Build 030), Copyright (c) 2001-2005. All rights reserved. + 0 0 0 0 0 999 V3000 +M V30 BEGIN CTAB +M V30 COUNTS 12 12 0 0 0 +M V30 BEGIN ATOM +M V30 1 N 4.64711 3.75 0 0 +M V30 2 C 3.34808 3 0 0 CFG=2 +M V30 3 C 2.04904 3.75 0 0 +M V30 4 O 0.75 3 0 0 +M V30 5 O 2.04904 5.25 0 0 +M V30 6 C 3.34808 1.5 0 0 +M V30 7 C 5.94615 3 0 0 CFG=3 +M V30 8 C 7.24519 3.75 0 0 +M V30 9 C 8.54423 3 0 0 +M V30 10 C 8.54423 1.5 0 0 +M V30 11 C 7.2452 0.75 0 0 +M V30 12 C 5.94616 1.5 0 0 +M V30 END ATOM +M V30 BEGIN BOND +M V30 1 1 1 2 +M V30 2 1 1 7 +M V30 3 1 2 3 +M V30 4 1 2 6 CFG=1 +M V30 5 2 3 4 +M V30 6 1 3 5 +M V30 7 1 7 8 +M V30 8 1 7 12 +M V30 9 1 8 9 +M V30 10 1 9 10 +M V30 11 1 10 11 +M V30 12 1 11 12 +M V30 END BOND +M V30 BEGIN COLLECTION +M V30 MDLV30/STEABS ATOMS=(1 2) +M V30 END COLLECTION +M V30 END CTAB +M END +> <Name> +cyclohexyl alanine + +$$$$ + + 02260622032D 0 0.00000 0.00000 0 +HDR: RoxyName (Build 030), Copyright (c) 2001-2005. All rights reserved. + 0 0 0 0 0 999 V3000 +M V30 BEGIN CTAB +M V30 COUNTS 25 27 0 0 0 +M V30 BEGIN ATOM +M V30 1 N 4.17298 3.75483 0 0 CFG=3 +M V30 2 C 4.17298 5.25483 0 0 CFG=1 +M V30 3 C 5.67299 3.75483 0 0 +M V30 4 C 5.67298 5.25483 0 0 CFG=1 +M V30 5 C 2.7464 3.2913 0 0 CFG=2 +M V30 6 S 2.74639 5.71835 0 0 +M V30 7 C 1.86472 4.50483 0 0 CFG=3 +M V30 8 N 6.73364 6.31549 0 0 +M V30 9 C 8.18253 5.92727 0 0 +M V30 10 C 2.28288 1.86472 0 0 +M V30 11 C 9.24319 6.98793 0 0 CFG=1 +M V30 12 O 6.73365 2.69417 0 0 +M V30 13 O 8.57076 4.47838 0 0 +M V30 14 O 3.28657 0.75 0 0 +M V30 15 C 10.6921 6.5997 0 0 +M V30 16 N 8.85496 8.43681 0 0 +M V30 17 O 0.815655 1.55285 0 0 +M V30 18 C 0.75 5.50852 0 0 +M V30 19 C 0.750004 3.50113 0 0 +M V30 20 C 11.7527 7.66036 0 0 +M V30 21 C 11.0803 5.15081 0 0 +M V30 22 C 13.2016 7.27213 0 0 +M V30 23 C 12.5292 4.76258 0 0 +M V30 24 C 13.5899 5.82325 0 0 +M V30 25 H 4.40763 6.73636 0 0 +M V30 END ATOM +M V30 BEGIN BOND +M V30 1 1 1 2 +M V30 2 1 1 3 +M V30 3 1 1 5 +M V30 4 1 2 4 +M V30 5 1 2 6 +M V30 6 1 3 4 +M V30 7 2 3 12 +M V30 8 1 4 8 CFG=3 +M V30 9 1 5 7 +M V30 10 1 5 10 CFG=1 +M V30 11 1 6 7 +M V30 12 1 7 18 +M V30 13 1 7 19 +M V30 14 1 8 9 +M V30 15 1 9 11 +M V30 16 2 9 13 +M V30 17 2 10 14 +M V30 18 1 10 17 +M V30 19 1 11 15 +M V30 20 1 11 16 CFG=3 +M V30 21 2 15 20 +M V30 22 1 15 21 +M V30 23 1 20 22 +M V30 24 2 21 23 +M V30 25 2 22 24 +M V30 26 1 23 24 +M V30 27 1 2 25 CFG=1 +M V30 END BOND +M V30 BEGIN COLLECTION +M V30 MDLV30/STEABS ATOMS=(4 2 4 5 11) +M V30 END COLLECTION +M V30 END CTAB +M END +> <Name> +ampicillin + +$$$$ + + 02260622032D 0 0.00000 0.00000 0 +HDR: RoxyName (Build 030), Copyright (c) 2001-2005. All rights reserved. + 0 0 0 0 0 999 V3000 +M V30 BEGIN CTAB +M V30 COUNTS 34 37 0 0 0 +M V30 BEGIN ATOM +M V30 1 C 5.94616 5.25 0 0 CFG=2 +M V30 2 C 8.54424 5.25001 0 0 +M V30 3 C 3.34808 5.25001 0 0 +M V30 4 C 7.2452 6.00001 0 0 +M V30 5 C 4.64712 6.00001 0 0 +M V30 6 C 5.94616 3.75 0 0 CFG=2 +M V30 7 C 3.34807 3.75001 0 0 +M V30 8 C 9.84328 6.00001 0 0 +M V30 9 C 8.54425 3.75001 0 0 CFG=1 +M V30 10 C 11.1423 5.25001 0 0 +M V30 11 C 9.84328 3.00001 0 0 CFG=1 +M V30 12 C 11.1423 3.75001 0 0 +M V30 13 C 4.64711 3 0 0 CFG=1 +M V30 14 C 7.2452 3 0 0 +M V30 15 C 2.04904 6.00001 0 0 +M V30 16 O 4.64712 7.50001 0 0 +M V30 17 O 9.84328 7.50001 0 0 +M V30 18 N 4.64711 1.5 0 0 CFG=3 +M V30 19 C 12.4414 6.00001 0 0 +M V30 20 O 5.94616 6.75 0 0 +M V30 21 O 0.750001 5.25002 0 0 +M V30 22 O 7.2452 7.50001 0 0 +M V30 23 O 2.04904 3.00001 0 0 +M V30 24 O 8.8791 1.85094 0 0 +M V30 25 N 2.04904 7.50001 0 0 +M V30 26 C 12.4414 3.00001 0 0 +M V30 27 C 10.8075 1.85094 0 0 +M V30 28 O 12.4414 7.50001 0 0 +M V30 29 C 13.7404 3.75001 0 0 +M V30 30 C 13.7404 5.25001 0 0 +M V30 31 C 3.34807 0.750004 0 0 +M V30 32 C 5.94615 0.75 0 0 +M V30 33 H 5.94615 2.25 0 0 +M V30 34 H 8.54425 2.25001 0 0 +M V30 END ATOM +M V30 BEGIN BOND +M V30 1 1 1 4 +M V30 2 1 1 5 +M V30 3 1 1 6 +M V30 4 1 1 20 CFG=3 +M V30 5 2 2 4 +M V30 6 1 2 8 +M V30 7 1 2 9 +M V30 8 1 3 5 +M V30 9 2 3 7 +M V30 10 1 3 15 +M V30 11 1 4 22 +M V30 12 2 5 16 +M V30 13 1 6 13 +M V30 14 1 6 14 +M V30 15 1 7 13 +M V30 16 1 7 23 +M V30 17 1 8 10 +M V30 18 2 8 17 +M V30 19 1 9 11 +M V30 20 1 9 14 +M V30 21 2 10 12 +M V30 22 1 10 19 +M V30 23 1 11 12 +M V30 24 1 11 24 CFG=1 +M V30 25 1 11 27 +M V30 26 1 12 26 +M V30 27 1 13 18 CFG=3 +M V30 28 2 15 21 +M V30 29 1 15 25 +M V30 30 1 18 31 +M V30 31 1 18 32 +M V30 32 1 19 28 +M V30 33 2 19 30 +M V30 34 2 26 29 +M V30 35 1 29 30 +M V30 36 1 6 33 CFG=3 +M V30 37 1 9 34 CFG=3 +M V30 END BOND +M V30 BEGIN COLLECTION +M V30 MDLV30/STEABS ATOMS=(5 1 6 9 11 13) +M V30 END COLLECTION +M V30 END CTAB +M END +> <Name> +tetracycline + +$$$$ + + 02260622032D 1 1.00000 0.00000 0 + + 13 14 0 0 0 999 V2000 + 0.7500 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 + 0.7500 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 + 2.0490 3.7500 0.0000 C 0 0 0 0 0 0 0 0 0 + 2.0490 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 + 3.3481 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 + 3.3481 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 + 4.6471 3.7500 0.0000 C 0 0 0 0 0 0 0 0 0 + 5.9462 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 + 5.9462 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 + 4.6471 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 + 7.2452 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 + 4.6471 5.2500 0.0000 C 0 0 0 0 0 0 0 0 0 + 7.2452 3.7500 0.0000 N 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 + 1 4 1 0 0 0 + 2 3 1 0 0 0 + 3 6 2 0 0 0 + 4 5 2 0 0 0 + 5 6 1 0 0 0 + 5 10 1 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 9 11 2 0 0 0 +M END +> <Name> +amino-4-methylcoumarin + +$$$$ + + 02260622032D 0 0.00000 0.00000 0 +HDR: RoxyName (Build 030), Copyright (c) 2001-2005. All rights reserved. + 0 0 0 0 0 999 V3000 +M V30 BEGIN CTAB +M V30 COUNTS 7 6 0 0 0 +M V30 BEGIN ATOM +M V30 1 N 3.34808 0.75 0 0 +M V30 2 C 3.34808 2.25 0 0 CFG=2 +M V30 3 C 4.64711 3 0 0 +M V30 4 O 5.94615 2.25 0 0 +M V30 5 O 4.64711 4.5 0 0 +M V30 6 C 2.04904 3 0 0 +M V30 7 O 0.75 2.25 0 0 +M V30 END ATOM +M V30 BEGIN BOND +M V30 1 1 2 1 CFG=1 +M V30 2 1 2 3 +M V30 3 1 2 6 +M V30 4 2 3 4 +M V30 5 1 3 5 +M V30 6 1 6 7 +M V30 END BOND +M V30 BEGIN COLLECTION +M V30 MDLV30/STEABS ATOMS=(1 2) +M V30 END COLLECTION +M V30 END CTAB +M END +> <Name> +Serine + +$$$$ + + 02260622032D 0 0.00000 0.00000 0 +HDR: RoxyName (Build 030), Copyright (c) 2001-2005. All rights reserved. + 7 6 0 0 0 999 V2000 + 0.7500 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 + 2.0490 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 + 3.3481 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 + 4.6471 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 + 5.9462 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 + 7.2452 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 + 8.5442 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 1 0 0 0 + 4 5 1 0 0 0 + 5 6 1 0 0 0 + 6 7 1 0 0 0 +M END +> <Name> +[2.2.1] heptane + +$$$$ \ No newline at end of file This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-12-06 17:26:38
|
Revision: 6393 http://svn.sourceforge.net/jmol/?rev=6393&view=rev Author: hansonr Date: 2006-12-06 09:26:35 -0800 (Wed, 06 Dec 2006) Log Message: ----------- new readers Added Paths: ----------- trunk/Jmol-datafiles/c3xml/ trunk/Jmol-datafiles/mol2/ trunk/Jmol-datafiles/sparchive/ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-03-03 12:48:25
|
Revision: 7024 http://svn.sourceforge.net/jmol/?rev=7024&view=rev Author: nicove Date: 2007-03-03 04:48:21 -0800 (Sat, 03 Mar 2007) Log Message: ----------- JUnit tests Added Paths: ----------- trunk/Jmol-datafiles/tests/ trunk/Jmol-datafiles/tests/scripts/ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-11-24 17:35:37
|
Revision: 8662 http://jmol.svn.sourceforge.net/jmol/?rev=8662&view=rev Author: hansonr Date: 2007-11-24 09:35:34 -0800 (Sat, 24 Nov 2007) Log Message: ----------- version=11.3.48_dev spartan06 and generic ZIP file-set reading # new feature: Spartan06 file format reader # new feature: ZIP file reading for multiple models Modified Paths: -------------- trunk/Jmol-datafiles/tests/scripts/check/monster_script.spt trunk/Jmol-datafiles/tests/scripts/check_performance/monster_script.spt Added Paths: ----------- trunk/Jmol-datafiles/molden/ trunk/Jmol-datafiles/molden/br-aug-cc-pvtz-spherical.molden Added: trunk/Jmol-datafiles/molden/br-aug-cc-pvtz-spherical.molden =================================================================== Modified: trunk/Jmol-datafiles/tests/scripts/check/monster_script.spt =================================================================== --- trunk/Jmol-datafiles/tests/scripts/check/monster_script.spt 2007-11-24 17:31:24 UTC (rev 8661) +++ trunk/Jmol-datafiles/tests/scripts/check/monster_script.spt 2007-11-24 17:35:34 UTC (rev 8662) @@ -311,7 +311,7 @@ select within(group,surfacedistance=0);color white ;refresh;# surface residues select not within(group, surfacedistance=0);color red ;refresh;# interior groups load 1crn.pdb -calculate surface +2.0;select surfacedistance=0;color yellow ;refresh;# custom solvent-accessible surface. +calculate surfacedistance WITHIN {*};select surfacedistance=0;color yellow ;refresh;# custom solvent-accessible surface. load caffeine.xyz select nitrogen color halos red Modified: trunk/Jmol-datafiles/tests/scripts/check_performance/monster_script.spt =================================================================== --- trunk/Jmol-datafiles/tests/scripts/check_performance/monster_script.spt 2007-11-24 17:31:24 UTC (rev 8661) +++ trunk/Jmol-datafiles/tests/scripts/check_performance/monster_script.spt 2007-11-24 17:35:34 UTC (rev 8662) @@ -307,7 +307,7 @@ select within(group,surfacedistance=0);color white ;refresh;# surface residues select not within(group, surfacedistance=0);color red ;refresh;# interior groups load 1crn.pdb -calculate surface +2.0;select surfacedistance=0;color yellow ;refresh;# custom solvent-accessible surface. +calculate surfacedistance WITHIN {*};select surfacedistance=0;color yellow ;refresh;# custom solvent-accessible surface. load caffeine.xyz select nitrogen color halos red This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rka...@us...> - 2008-02-07 13:48:23
|
Revision: 8974 http://jmol.svn.sourceforge.net/jmol/?rev=8974&view=rev Author: rkanters Date: 2008-02-07 05:48:18 -0800 (Thu, 07 Feb 2008) Log Message: ----------- Spartan spinput test files Added Paths: ----------- trunk/Jmol-datafiles/spinput/ trunk/Jmol-datafiles/spinput/benzene.spinput trunk/Jmol-datafiles/spinput/benzene_+1.spinput trunk/Jmol-datafiles/spinput/benzene_-1.spinput trunk/Jmol-datafiles/spinput/phenylacetylene_dimer_ion.spinput Added: trunk/Jmol-datafiles/spinput/benzene.spinput =================================================================== --- trunk/Jmol-datafiles/spinput/benzene.spinput (rev 0) +++ trunk/Jmol-datafiles/spinput/benzene.spinput 2008-02-07 13:48:18 UTC (rev 8974) @@ -0,0 +1,48 @@ + OPT PM3 +M001 +0 1 + 1 0.000000000 0.000000000 -2.485812873 + 6 0.000000000 0.000000000 -1.391081765 + 6 0.000000000 0.000000000 1.391081765 + 6 -1.204712187 0.000000000 -0.695540882 + 6 1.204712187 0.000000000 -0.695540882 + 6 1.204712187 0.000000000 0.695540882 + 6 -1.204712187 0.000000000 0.695540882 + 1 -2.152777074 0.000000000 -1.242906437 + 1 2.152777074 0.000000000 -1.242906437 + 1 2.152777074 0.000000000 1.242906437 + 1 -2.152777074 0.000000000 1.242906437 + 1 0.000000000 0.000000000 2.485812873 +ENDCART +ATOMLABELS +"H1" +"C1" +"C4" +"C2" +"C6" +"C5" +"C3" +"H2" +"H6" +"H5" +"H3" +"H4" +ENDATOMLABELS +HESSIAN + 13 3 3 3 3 3 3 13 13 13 13 13 + 1 2 1 + 2 5 5 + 5 6 5 + 3 6 5 + 3 7 5 + 4 7 5 + 2 4 5 + 6 10 1 + 7 11 1 + 3 12 1 + 4 8 1 + 5 9 1 +ENDHESS +BEGINPROPIN + +ENDPROPIN Added: trunk/Jmol-datafiles/spinput/benzene_+1.spinput =================================================================== --- trunk/Jmol-datafiles/spinput/benzene_+1.spinput (rev 0) +++ trunk/Jmol-datafiles/spinput/benzene_+1.spinput 2008-02-07 13:48:18 UTC (rev 8974) @@ -0,0 +1,48 @@ + OPT AM1 +M002 +1 2 + 1 0.000000000 0.000000000 -2.526537330 + 6 0.000000000 0.000000000 -1.416930844 + 6 0.000000000 0.000000000 1.416930844 + 6 -1.227098120 0.000000000 -0.708465448 + 6 1.227098120 0.000000000 -0.708465448 + 6 1.227098120 0.000000000 0.708465448 + 6 -1.227098120 0.000000000 0.708465448 + 1 -2.188045504 0.000000000 -1.263268691 + 1 2.188045504 0.000000000 -1.263268691 + 1 2.188045504 0.000000000 1.263268691 + 1 -2.188045504 0.000000000 1.263268691 + 1 0.000000000 0.000000000 2.526537330 +ENDCART +ATOMLABELS +"H1" +"C1" +"C4" +"C2" +"C6" +"C5" +"C3" +"H2" +"H6" +"H5" +"H3" +"H4" +ENDATOMLABELS +HESSIAN + 13 3 3 3 3 3 3 13 13 13 13 13 + 1 2 1 + 2 5 5 + 5 6 5 + 3 6 5 + 3 7 5 + 4 7 5 + 2 4 5 + 6 10 1 + 7 11 1 + 3 12 1 + 4 8 1 + 5 9 1 +ENDHESS +BEGINPROPIN + +ENDPROPIN Added: trunk/Jmol-datafiles/spinput/benzene_-1.spinput =================================================================== --- trunk/Jmol-datafiles/spinput/benzene_-1.spinput (rev 0) +++ trunk/Jmol-datafiles/spinput/benzene_-1.spinput 2008-02-07 13:48:18 UTC (rev 8974) @@ -0,0 +1,48 @@ + OPT PM3 CONVERGE NOSYMTRY SCFCYCLES=400 +M003 +-1 2 + 1 -0.000127108 0.000000000 -2.498180904 + 6 -0.000049690 0.000000000 -1.409589254 + 6 0.000049690 0.000000000 1.409589254 + 6 -1.215818395 0.000000000 -0.684496641 + 6 1.215706580 0.000000000 -0.684633803 + 6 1.215818395 0.000000000 0.684496641 + 6 -1.215706580 0.000000000 0.684633803 + 1 -2.158034554 0.000000000 -1.239783975 + 1 2.157883262 0.000000000 -1.240010515 + 1 2.158034554 0.000000000 1.239783975 + 1 -2.157883262 0.000000000 1.240010515 + 1 0.000127108 0.000000000 2.498180904 +ENDCART +ATOMLABELS +"H1" +"C1" +"C4" +"C2" +"C6" +"C5" +"C3" +"H2" +"H6" +"H5" +"H3" +"H4" +ENDATOMLABELS +HESSIAN + 13 3 3 3 3 3 3 13 13 13 13 13 + 1 2 1 + 2 5 5 + 5 6 5 + 3 6 5 + 3 7 5 + 4 7 5 + 2 4 5 + 6 10 1 + 7 11 1 + 3 12 1 + 4 8 1 + 5 9 1 +ENDHESS +BEGINPROPIN + +ENDPROPIN Added: trunk/Jmol-datafiles/spinput/phenylacetylene_dimer_ion.spinput =================================================================== --- trunk/Jmol-datafiles/spinput/phenylacetylene_dimer_ion.spinput (rev 0) +++ trunk/Jmol-datafiles/spinput/phenylacetylene_dimer_ion.spinput 2008-02-07 13:48:18 UTC (rev 8974) @@ -0,0 +1,99 @@ + OPT AM1 FREQ GEOMETRYCYCLE=300 SCFCYCLES=300 +M001 +1 2 + 6 -1.411677757 0.000000000 0.913627001 + 6 -1.644757259 0.000000000 -0.290964904 + 6 -2.009195426 0.000000000 -1.598415112 + 6 -1.190839494 0.000000000 -2.728424917 + 1 -1.740149351 0.000000000 -3.697791189 + 6 -1.151019349 0.000000000 2.267939113 + 6 -0.628411764 0.000000000 5.025856334 + 6 0.186769900 0.000000000 2.745796528 + 6 -2.221732965 0.000000000 3.201689975 + 6 -1.951949482 0.000000000 4.565338357 + 6 0.435565165 0.000000000 4.112402586 + 1 1.020141970 0.000000000 2.026899096 + 1 -3.261533914 0.000000000 2.838402132 + 1 -2.783859118 0.000000000 5.288717389 + 1 1.473743392 0.000000000 4.482334669 + 1 -0.422735057 0.000000000 6.108890567 + 6 0.214164335 0.000000000 -2.829448087 + 6 3.015630336 0.000000000 -3.192784508 + 6 1.096544651 0.000000000 -1.714240210 + 6 0.788799597 0.000000000 -4.138552503 + 6 2.164699115 0.000000000 -4.308817689 + 6 2.471459688 0.000000000 -1.899126081 + 1 0.685653580 0.000000000 -0.692295069 + 1 0.124912231 0.000000000 -5.019226434 + 1 2.594970923 0.000000000 -5.324451336 + 1 3.144936535 0.000000000 -1.026455104 + 1 4.109428135 0.000000000 -3.332154172 + 1 -3.109558089 0.000000000 -1.784746483 +ENDCART +ATOMLABELS +"C1" +"C2" +"C3" +"C4" +"H2" +"C5" +"C6" +"C7" +"C8" +"C9" +"C10" +"H1" +"H6" +"H5" +"H7" +"H8" +"C17" +"C18" +"C19" +"C20" +"C21" +"C22" +"H4" +"H13" +"H14" +"H15" +"H16" +"H19" +ENDATOMLABELS +HESSIAN + 4 4 2 2 13 3 3 3 3 3 3 13 + 13 13 13 13 3 3 3 3 3 3 13 13 + 13 13 13 13 + 1 2 3 + 2 3 1 + 4 5 1 + 3 4 2 + 6 9 5 + 9 10 5 + 7 10 5 + 7 11 5 + 8 11 5 + 6 8 5 + 10 14 1 + 11 15 1 + 7 16 1 + 8 12 1 + 9 13 1 + 1 6 1 + 17 20 5 + 20 21 5 + 18 21 5 + 18 22 5 + 19 22 5 + 17 19 5 + 21 25 1 + 22 26 1 + 18 27 1 + 19 23 1 + 20 24 1 + 4 17 1 + 3 28 1 +ENDHESS +BEGINPROPIN + +ENDPROPIN This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |