small formatting modifications to example coordinate files

jayponder · jayponder · commit 21b58659696d · 2026-01-17T23:20:49.000-05:00
diff --git a/example/benzbox.xyz b/example/benzbox.xyz
@@ -1,4 +1,4 @@
-  3840  Benzene Liquid  (320 Molecules, 36.204 Ang)
+  3840  Benzene Liquid (320 Molecules, 36.204 Ang)
      1  C     -0.573865  -15.621037   13.013360   220     2     6     7
      2  C     -0.207863  -16.996686   12.972709   220     1     3     8
      3  C      1.090681  -17.339734   13.294344   220     2     4     9
diff --git a/example/bucky.int b/example/bucky.int
@@ -1,4 +1,4 @@
-    60  Buckminsterfullerene  (C60 Bucky Ball)
+    60  Buckminsterfullerene (C60 Bucky Ball)
      1  C       2
      2  C       2     1   1.3930631
      3  C       2     2   1.4508290     1  120.000001
diff --git a/example/bucky.xyz b/example/bucky.xyz
@@ -1,4 +1,4 @@
-    60  Buckminsterfullerene  (C60 Bucky Ball)
+    60  Buckminsterfullerene (C60 Bucky Ball)
      1  C      0.56182991    1.03720708   -3.34153745     2     2     6    16
      2  C     -0.02867841   -0.20922332   -3.53733326     2     1     3    15
      3  C      0.68868170   -1.41687735   -3.17419275     2     2     4     7
diff --git a/example/butane.int b/example/butane.int
@@ -1,4 +1,4 @@
-    14  Butane  (Transoid Conformer)
+    14  Butane (Transoid Conformer)
      1  C       1
      2  C       1     1   1.53407
      3  C       1     2   1.53630     1  112.4088
diff --git a/example/butane.xyz b/example/butane.xyz
@@ -1,4 +1,4 @@
-    14  Butane  (Transoid Conformer)
+    14  Butane (Transoid Conformer)
      1  C      0.000000    0.000000    0.000000     1     2     5     6     7
      2  C      0.000000    0.000000    1.534070     1     1     3     8     9
      3  C      1.420290    0.000000    2.119727     1     2     4    10    11
diff --git a/example/butane2.int b/example/butane2.int
@@ -1,4 +1,4 @@
-    14  Butane  (Gauche Conformer)
+    14  Butane (Gauche Conformer)
      1  C       1
      2  C       1     1   1.53448
      3  C       1     2   1.53775     1  113.6610
diff --git a/example/butane2.xyz b/example/butane2.xyz
@@ -1,4 +1,4 @@
-    14  Butane  (Gauche Conformer)
+    14  Butane (Gauche Conformer)
      1  C      0.028302   -0.016843   -0.015751     1     2     5     6     7
      2  C      0.023683   -0.033543    1.518627     1     1     3     8     9
      3  C      1.430275   -0.031502    2.140062     1     2     4    10    11
diff --git a/example/butanes.dyn b/example/butanes.dyn
@@ -1,5 +1,5 @@
  Number of Atoms and Title :
-   700  Butane  (50 Molecules at Boiling Point of -0.5 C)
+   700  Butane (50 Molecules at Boiling Point of -0.5 C)
  Periodic Box Dimensions :
     0.2001250000000000D+02    0.2001250000000000D+02    0.2001250000000000D+02
     0.9000000000000000D+02    0.9000000000000000D+02    0.9000000000000000D+02
diff --git a/example/butanes.xyz b/example/butanes.xyz
@@ -1,4 +1,4 @@
-   700  Butane  (50 Molecules at Boiling Point of -0.5 C)
+   700  Butane (50 Molecules at Boiling Point of -0.5 C)
      1  C      6.092347  -11.499189   -5.862928     1     2     5     6     7
      2  C      6.192082   -9.976376   -5.980590     1     1     3     8     9
      3  C      5.664569   -9.132650   -4.798978     1     2     4    10    11
diff --git a/example/butopls.int b/example/butopls.int
@@ -1,4 +1,4 @@
-     4  Butane  (Transoid Conformer)
+     4  Butane (Transoid Conformer)
      1  CH3    83
      2  CH2    86     1   1.52625
      3  CH2    86     2   1.52618     1  112.4347
diff --git a/example/butopls.xyz b/example/butopls.xyz
@@ -1,4 +1,4 @@
-     4  Butane  (Transoid Conformer)
+     4  Butane (Transoid Conformer)
      1  CH3    0.000001    0.000000    0.000001    83     2
      2  CH2   -0.000002    0.000000    1.526249    86     1     3
      3  CH2    1.410672    0.000000    2.108690    86     2     4
diff --git a/example/butopls2.int b/example/butopls2.int
@@ -1,4 +1,4 @@
-     4  Butane  (Gauche Conformer)
+     4  Butane (Gauche Conformer)
      1  CH3    83
      2  CH2    86     1   1.52996
      3  CH2    86     2   1.53180     1  114.0598
diff --git a/example/butopls2.xyz b/example/butopls2.xyz
@@ -1,4 +1,4 @@
-     4  Butane  (Gauche Conformer)
+     4  Butane (Gauche Conformer)
      1  CH3   -0.027252   -0.207636   -0.000153    83     2
      2  CH2    0.000938   -0.039679    1.520297    86     1     3
      3  CH2    1.410746    0.003635    2.117779    86     2     4
diff --git a/example/deltorphin.int b/example/deltorphin.int
@@ -1,4 +1,4 @@
-   129  Deltorphin  (Tyr-Met-Phe-His-Leu-Met-Asp-NH2)
+   129  Deltorphin (Tyr-Met-Phe-His-Leu-Met-Asp-NH2)
      1  N3    475
      2  CX    476     1   1.50000
      3  C     477     2   1.51000     1  110.7000
diff --git a/example/deltorphin.make b/example/deltorphin.make
@@ -1,5 +1,5 @@
 deltorphin
-Deltorphin  (Tyr-Met-Phe-His-Leu-Met-Asp-NH2)
+Deltorphin (Tyr-Met-Phe-His-Leu-Met-Asp-NH2)
 tyr
 met
 phe
diff --git a/example/deltorphin.xyz b/example/deltorphin.xyz
@@ -1,4 +1,4 @@
-   129  Deltorphin  (Tyr-Met-Phe-His-Leu-Met-Asp-NH2)
+   129  Deltorphin (Tyr-Met-Phe-His-Leu-Met-Asp-NH2)
      1  N3     0.000000    0.000000    0.000000   475     2     5     6     7
      2  CX     0.000000    0.000000    1.500000   476     1     3     8     9
      3  C      1.412520    0.000000    2.033747   477     2     4    24
diff --git a/example/enkephalin.int b/example/enkephalin.int
@@ -1,4 +1,4 @@
-    75  Met-Enkephalin  (Tyr-Gly-Gly-Phe-Met)
+    75  Met-Enkephalin (Tyr-Gly-Gly-Phe-Met)
      1  N+      9
      2  C       1     1   1.50000
      3  C       2     2   1.51000     1  110.7000
diff --git a/example/enkephalin.make b/example/enkephalin.make
@@ -1,5 +1,5 @@
 enkephalin
-Met-Enkephalin  (Tyr-Gly-Gly-Phe-Met)
+Met-Enkephalin (Tyr-Gly-Gly-Phe-Met)
 tyr   -86  157  180  -165    87
 gly  -165   79  180
 gly    64  -94  180
diff --git a/example/enkephalin.xyz b/example/enkephalin.xyz
@@ -1,4 +1,4 @@
-    75  Met-Enkephalin  (Tyr-Gly-Gly-Phe-Met)
+    75  Met-Enkephalin (Tyr-Gly-Gly-Phe-Met)
      1  N+     0.000000    0.000000    0.000000     9     2     5     6     7
      2  C      0.000000    0.000000    1.500000     1     1     3     8     9
      3  C      1.412520    0.000000    2.033747     2     2     4    24
diff --git a/example/ermer.int b/example/ermer.int
@@ -1,4 +1,4 @@
-    30  Ermer's Hydrocarbon  (H13/H29 Distance is 1.62A in Xtal)
+    30  Ermer's Hydrocarbon (H13/H29 Distance is 1.62A in Xtal)
      1  C       1
      2  C       1     1   1.53627
      3  C       1     2   1.55417     1   99.4072
diff --git a/example/ermer.xyz b/example/ermer.xyz
@@ -1,4 +1,4 @@
-    30  Ermer's Hydrocarbon  (H13/H29 Distance is 1.62A in Xtal)
+    30  Ermer's Hydrocarbon (H13/H29 Distance is 1.62A in Xtal)
      1  C     -0.0255383734    0.0103787317   -0.0228934779     1     2     5    13    14
      2  C     -0.0716849052   -0.0034521548    1.5125267483     1     1     3     7    15
      3  C      1.4527329570   -0.0516715247    1.8117581788     1     2     4    16    17
diff --git a/example/form.xyz b/example/form.xyz
@@ -1,4 +1,4 @@
-    24  Formamide  (Crystal Structure, Unit Cell)
+    24  Formamide (Crystal Structure, Unit Cell)
      1  C     -0.285984   -4.009683   -1.663518   177     2     3     4
      2  N     -0.240301   -3.101967   -2.625594   179     1     5     6
      3  O      0.220615   -5.142521   -1.730911   178     1
diff --git a/example/formbig.xyz b/example/formbig.xyz
@@ -1,4 +1,4 @@
-   864  Formamide  (Crystal Structure, Unit Cell)
+   864  Formamide (Crystal Structure, Unit Cell)
      1  C     -0.285984   -4.009683   -1.663518   177     2     3     4
      2  N     -0.240301   -3.101967   -2.625594   179     1     5     6
      3  O      0.220615   -5.142521   -1.730911   178     1
diff --git a/example/formbox.dyn b/example/formbox.dyn
@@ -1,5 +1,5 @@
  Number of Atoms and Title :
-   600  Formamide  (100 AMOEBA Molecules in 18.778 Ang Box)
+   600  Formamide (100 AMOEBA Molecules in 18.778 Ang Box)
  Periodic Box Dimensions :
     0.1877800000000000D+02    0.1877800000000000D+02    0.1877800000000000D+02
     0.9000000000000000D+02    0.9000000000000000D+02    0.9000000000000000D+02
diff --git a/example/formbox.xyz b/example/formbox.xyz
@@ -1,4 +1,4 @@
-   600  Formamide  (100 AMOEBA Molecules in 18.778 Ang Box)
+   600  Formamide (100 AMOEBA Molecules in 18.778 Ang Box)
      1  C     -4.758803    0.386011   -2.933599   102     2     3     4
      2  H     -3.664878    0.699931   -2.862796   103     1
      3  O     -5.272179   -0.382777   -2.097398   104     1
diff --git a/example/formopls.dyn b/example/formopls.dyn
@@ -1,5 +1,5 @@
  Number of Atoms and Title :
-   600  Formamide  (100 OPLS-AA Molecules in 18.778 Ang Box)
+   600  Formamide (100 OPLS-AA Molecules in 18.778 Ang Box)
  Periodic Box Dimensions :
     0.1877800000000000D+02    0.1877800000000000D+02    0.1877800000000000D+02
     0.9000000000000000D+02    0.9000000000000000D+02    0.9000000000000000D+02
diff --git a/example/formopls.xyz b/example/formopls.xyz
@@ -1,4 +1,4 @@
-   600  Formamide  (100 OPLS-AA Molecules in 18.778 Ang Box)
+   600  Formamide (100 OPLS-AA Molecules in 18.778 Ang Box)
      1  C     -1.437310    6.231635    8.309262   177     2     3     4
      2  HC    -1.844275    6.732456    9.177432   221     1
      3  O     -1.706712    6.643909    7.223036   178     1
diff --git a/example/glucose.xyz b/example/glucose.xyz
@@ -1,4 +1,4 @@
-    24  Glucose  (Test of MM3 Hydrogen Bonding Function)
+    24  Glucose (Test of MM3 Hydrogen Bonding Function)
      1  C      1.066130    4.259240    0.128780     1     2     3     5     8
      2  H     -0.027230    4.490780    0.068990     5     1
      3  O      1.807730    5.435760    0.467630     6     1     4
diff --git a/example/glycerol.dyn b/example/glycerol.dyn
@@ -1,5 +1,5 @@
  Number of Atoms and Title :
-   448  Glycerol  (32 Molecules in 15.87 Ang Cubic Box)
+   448  Glycerol (32 Molecules in 15.87 Ang Cubic Box)
  Periodic Box Dimensions :
     0.1587000000000000D+02    0.1587000000000000D+02    0.1587000000000000D+02
     0.9000000000000000D+02    0.9000000000000000D+02    0.9000000000000000D+02
diff --git a/example/glycerol.xyz b/example/glycerol.xyz
@@ -1,4 +1,4 @@
-   448  Glycerol  (32 Molecules in 15.87 Ang Cubic Box)
+   448  Glycerol (32 Molecules in 15.87 Ang Cubic Box)
      1  C      6.877358    6.203314   -3.312750     1     2     4     5     6
      2  C      7.241377    4.955868   -2.594534     1     1     3     8     9
      3  C      8.729920    4.760488   -2.358259     1     2    11    12    13
diff --git a/example/glyphosate.key b/example/glyphosate.key
@@ -0,0 +1 @@
+parameters        ../params/basic
diff --git a/example/glyphosate.xyz b/example/glyphosate.xyz
@@ -0,0 +1,17 @@
+    16  Glyphosate (Roundup herbicide, possible carcinogen)
+     1  P     -2.355586    0.011892   -0.281987   154     2     3     4     8
+     2  O     -2.225285   -0.334641   -1.715676    81     1
+     3  O     -3.392165    1.023946    0.021259    81     1
+     4  O     -2.318818   -1.138970    0.648975    81     1
+     5  O      3.323208   -0.036359   -1.187805    81    10
+     6  O      3.244349   -0.714620    0.806487    81    10
+     7  N+     0.371308    0.084791   -0.149328    74     8     9    13    14
+     8  C     -0.835701    0.900174    0.080278    64     1     7    11    12
+     9  C      1.588181    0.845952    0.157707    64     7    10    15    16
+    10  C      2.800970   -0.007825   -0.084707    63     5     6     9
+    11  H     -0.862058    1.225357    1.142608    11     8
+    12  H     -0.794595    1.805487   -0.562919    11     8
+    13  H      0.316499   -0.760940    0.456804    11     7
+    14  H      0.379939   -0.215391   -1.147065    11     7
+    15  H      1.570744    1.169790    1.221179    11     9
+    16  H      1.638308    1.750657   -0.486610    11     9
diff --git a/example/graphite.xyz b/example/graphite.xyz
@@ -1,4 +1,4 @@
-  2304  Graphite  (Hexagonal Form)
+  2304  Graphite (Hexagonal Form)
      1  C    -12.012266  -14.077301   11.754211    50     3   130   157
      2  C     -9.183921  -14.077301   11.754211    50     4    17   160
      3  C    -11.305197  -12.852525   11.754211    50     1     4     5
diff --git a/example/meohbox.xyz b/example/meohbox.xyz
@@ -1,4 +1,4 @@
-  2400  Methanol  (400 AMOEBA Molecules in 30.000 Ang Box)
+  2400  Methanol (400 AMOEBA Molecules in 30.000 Ang Box)
      1  C      0.899696  -11.723867  -10.565595    43     2     3     4     5
      2  H      0.477564  -12.095229  -11.479761    44     1
      3  H      0.458185  -12.364028   -9.700866    44     1
diff --git a/example/nmabox.xyz b/example/nmabox.xyz
@@ -1,4 +1,4 @@
-  1500  N-MethylAcetamide  (125 NMA in 25.725 Ang Cubic Box)
+  1500  N-MethylAcetamide (125 NMA in 25.725 Ang Cubic Box)
      1  C     -9.829753  -13.925080   -4.285918   340     2     6     7     8
      2  C    -10.850357  -12.980494   -3.701737   342     1     3     5
      3  N    -12.016237  -12.898054   -4.276517   346     2     4     9
diff --git a/example/polyala.xyz b/example/polyala.xyz
@@ -1,4 +1,4 @@
-    40  Alanine 20-mer  (Hoch-Stern Force Field)
+    40  Alanine 20-mer (Hoch-Stern Force Field)
      1  CA     0.000000    0.000000    1.500000     1     2     3
      2  CB    -0.697507   -1.273116    2.014063     2     1
      3  CA     3.627787   -0.968206    1.721317     1     1     4     5
diff --git a/example/skunk.xyz b/example/skunk.xyz
@@ -1,4 +1,4 @@
-    16  3-Methylbut-2-ene-1-thiol  (Skunky Beer Odor)
+    16  3-Methylbut-2-ene-1-thiol (Skunky Beer Odor)
      1  C      1.060548    0.843431    0.090435     1     3     7     8     9
      2  C      0.003894   -0.829265    1.693450     1     3    10    11    12
      3  C      0.931831    0.365093    1.527529     2     1     2     4
diff --git a/example/ubiquitin.xyz b/example/ubiquitin.xyz
@@ -1,4 +1,4 @@
-  9737  Ubiquitin  (Amber ff99 Protein + 2835 TIP3P Waters)
+  9737  Ubiquitin (Amber ff99 Protein + 2835 TIP3P Waters)
      1  N3    10.075238    7.433904    1.585139   472     2     5     6     7
      2  CT     9.484599    7.435956    0.252846   473     1     3     8     9
      3  C      8.042581    7.911998    0.456706   474     2     4    20
diff --git a/example/ubiquitin2.xyz b/example/ubiquitin2.xyz
@@ -1,4 +1,4 @@
-  9737  UBIQUITIN  (AMOEBA PROTEIN + 2835 WATERS)
+  9737  Ubiquitin (AMOEBA Protein + 2835 Waters)
      1  N      9.963103    5.604761    0.008413   234     2     5     6     7
      2  CA     9.595854    5.616857   -1.387669     8     1     3     8     9
      3  C      8.190092    6.079015   -1.537478     9     2     4    20
diff --git a/example/white.int b/example/white.int
@@ -1,4 +1,4 @@
-    25  5-Methyl-1-azabicyclo[3.3.1]nonan-2-one  (White's Amide)
+    25  5-Methyl-1-azabicyclo[3.3.1]nonan-2-one (White's Amide)
      1  N       9
      2  C       3     1   1.34500
      3  C       1     2   1.54000     1  115.0000
diff --git a/example/white.xyz b/example/white.xyz
@@ -1,4 +1,4 @@
-    25  5-Methyl-1-azabicyclo[3.3.1]nonan-2-one  (White's Amide)
+    25  5-Methyl-1-azabicyclo[3.3.1]nonan-2-one (White's Amide)
      1  N      0.000000    0.000000    0.000000     9     2     8     9
      2  C      0.000000    0.000000    1.345000     3     1     3    11
      3  C      1.395714    0.000000    1.995832     1     2     4    13    14

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`- 3840 Benzene Liquid (320 Molecules, 36.204 Ang)`
	`1`	`+ 3840 Benzene Liquid (320 Molecules, 36.204 Ang)`
`2`	`2`	`1 C -0.573865 -15.621037 13.013360 220 2 6 7`
`3`	`3`	`2 C -0.207863 -16.996686 12.972709 220 1 3 8`
`4`	`4`	`3 C 1.090681 -17.339734 13.294344 220 2 4 9`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`- 60 Buckminsterfullerene (C60 Bucky Ball)`
	`1`	`+ 60 Buckminsterfullerene (C60 Bucky Ball)`
`2`	`2`	`1 C 2`
`3`	`3`	`2 C 2 1 1.3930631`
`4`	`4`	`3 C 2 2 1.4508290 1 120.000001`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`- 14 Butane (Transoid Conformer)`
	`1`	`+ 14 Butane (Transoid Conformer)`
`2`	`2`	`1 C 1`
`3`	`3`	`2 C 1 1 1.53407`
`4`	`4`	`3 C 1 2 1.53630 1 112.4088`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`- 14 Butane (Gauche Conformer)`
	`1`	`+ 14 Butane (Gauche Conformer)`
`2`	`2`	`1 C 1`
`3`	`3`	`2 C 1 1 1.53448`
`4`	`4`	`3 C 1 2 1.53775 1 113.6610`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`- 700 Butane (50 Molecules at Boiling Point of -0.5 C)`
	`1`	`+ 700 Butane (50 Molecules at Boiling Point of -0.5 C)`
`2`	`2`	`1 C 6.092347 -11.499189 -5.862928 1 2 5 6 7`
`3`	`3`	`2 C 6.192082 -9.976376 -5.980590 1 1 3 8 9`
`4`	`4`	`3 C 5.664569 -9.132650 -4.798978 1 2 4 10 11`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`- 4 Butane (Transoid Conformer)`
	`1`	`+ 4 Butane (Transoid Conformer)`
`2`	`2`	`1 CH3 83`
`3`	`3`	`2 CH2 86 1 1.52625`
`4`	`4`	`3 CH2 86 2 1.52618 1 112.4347`