changeset 9:12caa50c0d5f draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
author chemteam
date Tue, 30 Nov 2021 09:59:48 +0000
parents 45dc2555933c
children 608098b3668d
files test-data/cid1.inpcrd test-data/cid1.prmtop
diffstat 2 files changed, 425 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cid1.inpcrd	Tue Nov 30 09:59:48 2021 +0000
@@ -0,0 +1,23 @@
+default_name
+    42
+ 413.7160000 -23.8940000  73.9880000 413.0110000 -23.1360000  73.0600000
+ 410.4130000 -22.8270000  77.7640000 413.0830000 -24.9950000  74.5420000
+ 411.1680000 -24.6150000  73.3300000 412.1350000 -21.4560000  78.2360000
+ 411.7120000 -23.4970000  72.7190000 411.3590000 -22.4680000  78.7560000
+ 410.6390000 -22.0230000  76.6690000 409.9160000 -22.0060000  75.3710000
+ 410.3560000 -20.6120000  70.7060000 411.2760000 -21.2970000  69.7140000
+ 410.9200000 -22.6950000  71.7140000 410.7700000 -21.2020000  72.0480000
+ 411.0860000 -23.8010000  69.4340000 409.7500000 -20.9270000  73.1430000
+ 411.8220000 -25.3760000  74.2360000 411.6890000 -21.1940000  76.9670000
+ 410.3570000 -21.0800000  74.4240000 411.5380000 -22.6710000  70.3070000
+ 408.9730000 -22.7740000  75.2000000 411.4870000 -23.1760000  80.2920000
+ 414.7300000 -23.6320000  74.2690000 413.4810000 -22.2670000  72.6080000
+ 409.6480000 -23.5890000  77.8390000 413.5900000 -25.6180000  75.2710000
+ 410.1590000 -24.9450000  73.1040000 412.9630000 -20.8980000  78.6520000
+ 410.4620000 -19.5230000  70.6760000 409.3110000 -20.8540000  70.4760000
+ 410.8360000 -21.3960000  68.7180000 412.2480000 -20.7980000  69.6480000
+ 409.9150000 -23.1650000  71.6000000 411.7370000 -20.7780000  72.3500000
+ 410.0030000 -23.7210000  69.3180000 411.5930000 -23.7040000  68.4720000
+ 411.3590000 -24.7350000  69.9290000 408.9340000 -21.6350000  73.0500000
+ 409.3820000 -19.9130000  73.0430000 412.0760000 -20.4940000  76.3480000
+ 411.1120000 -20.4360000  74.6780000 412.5590000 -22.7580000  70.4090000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cid1.prmtop	Tue Nov 30 09:59:48 2021 +0000
@@ -0,0 +1,402 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 11/24/21  10:22:01                  
+%FLAG TITLE                                                                     
+%FORMAT(20a4)                                                                   
+default_name                                                                    
+%FLAG POINTERS                                                                  
+%FORMAT(10I8)                                                                   
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+%FLAG ATOM_NAME                                                                 
+%FORMAT(20a4)                                                                   
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+%FLAG CHARGE                                                                    
+%FORMAT(5E16.8)                                                                 
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+%FLAG ATOMIC_NUMBER                                                             
+%FORMAT(10I8)                                                                   
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+%FLAG MASS                                                                      
+%FORMAT(5E16.8)                                                                 
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+%FLAG ATOM_TYPE_INDEX                                                           
+%FORMAT(10I8)                                                                   
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+%FLAG NUMBER_EXCLUDED_ATOMS                                                     
+%FORMAT(10I8)                                                                   
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+%FLAG NONBONDED_PARM_INDEX                                                      
+%FORMAT(10I8)                                                                   
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+%FLAG RESIDUE_LABEL                                                             
+%FORMAT(20a4)                                                                   
+UNL 
+%FLAG RESIDUE_POINTER                                                           
+%FORMAT(10I8)                                                                   
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+%FLAG BOND_FORCE_CONSTANT                                                       
+%FORMAT(5E16.8)                                                                 
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+%FLAG BOND_EQUIL_VALUE                                                          
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+%FLAG ANGLE_FORCE_CONSTANT                                                      
+%FORMAT(5E16.8)                                                                 
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+%FORMAT(5E16.8)                                                                 
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+%FLAG DIHEDRAL_PERIODICITY                                                      
+%FORMAT(5E16.8)                                                                 
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+%FLAG DIHEDRAL_PHASE                                                            
+%FORMAT(5E16.8)                                                                 
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+%FLAG SCEE_SCALE_FACTOR                                                         
+%FORMAT(5E16.8)                                                                 
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+%FLAG SCNB_SCALE_FACTOR                                                         
+%FORMAT(5E16.8)                                                                 
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+%FLAG SOLTY                                                                     
+%FORMAT(5E16.8)                                                                 
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+%FLAG LENNARD_JONES_ACOEF                                                       
+%FORMAT(5E16.8)                                                                 
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+%FLAG LENNARD_JONES_BCOEF                                                       
+%FORMAT(5E16.8)                                                                 
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+%FLAG BONDS_INC_HYDROGEN                                                        
+%FORMAT(10I8)                                                                   
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+%FLAG BONDS_WITHOUT_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
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+%FLAG ANGLES_INC_HYDROGEN                                                       
+%FORMAT(10I8)                                                                   
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+%FLAG ANGLES_WITHOUT_HYDROGEN                                                   
+%FORMAT(10I8)                                                                   
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+%FLAG DIHEDRALS_INC_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
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+      60      27      54     120       7      60      27     -54     120       8
+      57      33      30      84       2      57      33      30      87       2
+      57      36      39      99       2      54      45      39      99       2
+      51      24       6      72       6      66       0       9      48       5
+      45      39      30      84      10      45      39      30      87      10
+      45      39      36      96       2      42      57      33      90       2
+      42      57      33      93       2      42      57      36      96       2
+      39      30      33      90       2      39      30      33      93       2
+      39      36      57     123       2      39      45      54     120       1
+      36      18       3      69       5      36      18      12      78       5
+      36      39      30      84      10      36      39      30      87      10
+      36      39      45     111       2      36      39      45     114       2
+      36      57      33      90       2      36      57      33      93       2
+      36      57      42     102       2      36      57      42     105       2
+      36      57      42     108       2      33      30      39      99      10
+      33      57      36      96       2      33      57      42     102       2
+      33      57      42     105       2      33      57      42     108       2
+      30      33      57     123       2      30      39      36      96       2
+      30      39      45     111       2      30      39      45     114       2
+      27      24       6      72       6      27      24      51     117       4
+      27      54      45     111       1      27      54      45     114       1
+      24      27      54     120       8      24      51      15      81       4
+      21      15      51     117       4      66       0       3      18       5
+      18      36      39      99       2      18      36      57     123       2
+      15      21       6      72       6      12      18       3      69       5
+      12      18      36      96       1      12      48       9      75      18
+       9       0       3      69       5       9      48      12      78      18
+       6      21      15      81       6       6      24      51     117       4
+       3       0       9      75       5       3      18      12      78       5
+       3      18      36      96       1      27      45     -54    -120      19
+      15      24     -51    -117      19      21      81     -15     -51      19
+      18      78     -12     -48      19       0      75      -9     -48      19
+      21      24      -6     -72      19       0      18      -3     -69      19
+      66       0      -9      -3      19
+%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
+%FORMAT(10I8)                                                                   
+      51      15      21      63       6      51      24      27      54       9
+      51      24      27      60       9      45      39      36      57       2
+      45      54      27      60       8      39      30     -33      57       2
+      39      36      57      42       2      36      18      12      48       5
+      36      39      45      54       2      33      30     -39      36      11
+      33      30     -39      36      12      33      30     -39      36      13
+      33      30      39      45      11      33      30     -39      45      12
+      33      30     -39      45      13      33      57     -36      39       2
+      30      33     -57      36       2      30      33      57      42       2
+      30      39     -36      57       2      30      39      45      54       2
+      27      54      45      39      14      27      54     -45      39       1
+      27      54     -45      39      15      27      54     -45      39      16
+      24       6      21      63       6      24      27      54      45       8
+      21       6      24      27       6      21       6     -24      51       6
+      21      15     -51      24       4      18      36      39      30       2
+      18      36      39      45       2      18      36      57      33      17
+      18      36     -57      33       2      18      36      57      42      17
+      18      36     -57      42       2      15      21      -6      24       6
+      15      51      24      27       4      12      18      36      39       1
+      12      18      36      57       1       9       0       3      18       5
+       9      48     -12      18      18       6      21     -15      51       6
+       6      24      27      54       9       6      24      27      60       9
+       6      24     -51      15       4       3       0       9      48       5
+       3      18     -12      48       5       3      18      36      39       1
+       3      18      36      57       1       0       3      18      12       5
+       0       3      18      36       5       0       9     -48      12      18
+      24      54     -27     -60      20      27       6     -24     -51      19
+       6      15     -21     -63      19       3      12     -18     -36      19
+%FLAG EXCLUDED_ATOMS_LIST                                                       
+%FORMAT(10I8)                                                                   
+       2       4       5       7      13      17      23      24      26       4
+       5       7      13      14      17      20      23      24      26      27
+      33       6       8       9      10      18      19      21      22      25
+      28      40       5       7      17      23      24      26      27       7
+      13      14      17      20      24      26      27      33       8       9
+      10      18      22      25      28      40      11      12      13      14
+      15      16      17      20      23      24      27      33      34      42
+       9      10      18      22      25      28      40      10      16      18
+      19      21      22      25      28      40      41      14      16      18
+      19      21      25      38      39      40      41      12      13      14
+      15      16      19      20      29      30      31      32      33      34
+      38      39      42      13      14      15      16      20      29      30
+      31      32      33      34      35      36      37      42      14      15
+      16      17      19      20      24      27      29      30      31      32
+      33      34      35      36      37      38      39      42      15      16
+      19      20      29      30      31      32      33      34      38      39
+      41      42      20      31      32      33      35      36      37      42
+      19      20      21      29      30      33      34      38      39      41
+      23      26      27      19      21      22      25      28      40      21
+      34      38      39      41      29      30      31      32      33      34
+      35      36      37      42      41      25      28      24      26       0
+       0       0       0      40      30      31      32      34      31      32
+      34      32      42      42      34      42      38      39      36      37
+      42      37      42      42      39      41      41       0       0       0
+%FLAG HBOND_ACOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBOND_BCOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBCUT                                                                     
+%FORMAT(5E16.8)                                                                 
+
+%FLAG AMBER_ATOM_TYPE                                                           
+%FORMAT(20a4)                                                                   
+ca  ca  cc  ca  ca  cd  ca  cc  cd  c   c3  c3  c3  c3  c3  c3  nb  na  n   n4  
+o   cl  ha  ha  ha  h4  h4  h4  hc  hc  hx  hx  hx  hc  hx  hx  hx  h1  h1  hn  
+hn  hn  
+%FLAG TREE_CHAIN_CLASSIFICATION                                                 
+%FORMAT(20a4)                                                                   
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA 
+%FLAG JOIN_ARRAY                                                                
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0
+%FLAG IROTAT                                                                    
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0
+%FLAG RADIUS_SET                                                                
+%FORMAT(1a80)                                                                   
+modified Bondi radii (mbondi)                                                   
+%FLAG RADII                                                                     
+%FORMAT(5E16.8)                                                                 
+  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00
+  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00
+  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00
+  1.70000000E+00  1.55000000E+00  1.55000000E+00  1.55000000E+00  1.55000000E+00
+  1.50000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
+  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
+  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
+  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
+  1.30000000E+00  1.30000000E+00
+%FLAG SCREEN                                                                    
+%FORMAT(5E16.8)                                                                 
+  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01
+  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01
+  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01
+  7.20000000E-01  7.90000000E-01  7.90000000E-01  7.90000000E-01  7.90000000E-01
+  8.50000000E-01  8.00000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0