assign bond by comparison with covalent radii

README.md

@@ -1,12 +1,29 @@
 # xyz2pov
 
-This Python script converts xyz coordinate files into povray scenes.
+This implementation in Python and `numpy` converts xyz coordinate files into
+povray scenes by
+
+``` shell
+python ./xyz2povray.py input.xyz
+```
+
+to yield `input.pov` and `input.ini`.  A subsequent run of `povray ./input.pov`
+writes a single 800x600 px `input.png`.  With `povray ./input.ini` a sequence 
+of 36 frames (640x420 px) yields a full rotation of the structure around
+POVRay's x-axis, which can serve as template for further exploration, and to 
+write an animated .gif e.g. on [ezgif](https://ezgif.com/)
+
+![Example for glucose](glucose.gif)
+
+All atoms starting from 1 (hydrogen, H) up to 96 (curium, Cm) are supported
+by a color scheme close to the one used by Jmol.  If the interatomic
+distance is less or equal the sum of the corresponding covalent radii
+compiled by [Wikipedia](https://en.wikipedia.org/wiki/Covalent_radius), two
+atoms are considered to be bound together; the model depicts them as
+connected by a tube.  An atom "too far out" to bind with an other atom is
+going to be displayed as sphere.
 
-So far, only hydrogen and carbon atoms are supported, but this is extendable for
-other atoms. The style is similar to Avogadro's tube model.
 The camera is automatically directed to the molecule's center of mass and placed
 at an appropriate distance. Two lights are placed relative to the camera
 automatically.
 
-TODO: automatic rotation of the camera to get a horizontal view of the
-molecule.

requirements.txt

@@ -0,0 +1,3 @@
+# Written for Linux Debian 12/bookworm with Python 3.11.2; equally
+# known to work in Linux Xubuntu 22.04.2 Jammy with Python 3.10.6.
+numpy==1.24.3

test_molecules/diethylether.xyz

@@ -0,0 +1,17 @@
+15
+
+C          1.05226       -0.05118       -0.07983
+C          2.56736       -0.00919       -0.07150
+O          3.06571       -1.31944       -0.33155
+C          4.49062       -1.34380       -0.33639
+C          4.95531       -2.75883       -0.61723
+H          0.63467        0.94053        0.11699
+H          0.68037       -0.74731        0.67921
+H          0.68037       -0.40467       -1.04720
+H          2.92318        0.33323        0.90628
+H          2.92318        0.68069       -0.84440
+H          4.86916       -1.01676        0.63832
+H          4.86916       -0.66931       -1.11230
+H          4.57512       -3.44928        0.14301
+H          6.04819       -2.81488       -0.62835
+H          4.57512       -3.10661       -1.58352

test_molecules/ethylpyridine.xyz

@@ -0,0 +1,19 @@
+17
+
+C          1.41296        0.10302        0.00141
+C          0.64113        1.26139        0.02360
+C         -0.73734        1.13219        0.03626
+N         -1.37948       -0.05512        0.03497
+C         -0.60408       -1.16294        0.01072
+C          0.78738       -1.14561       -0.01734
+C          1.58000       -2.42169       -0.05489
+C          1.88600       -2.95600        1.33548
+H          2.49742        0.17960       -0.00851
+H          1.10384        2.24198        0.02822
+H         -1.38148        2.00661        0.04696
+H         -1.15587       -2.09946        0.00969
+H          2.51732       -2.25594       -0.59970
+H          1.02859       -3.17773       -0.62711
+H          2.48501       -2.24360        1.91252
+H          2.44981       -3.89166        1.26320
+H          0.96737       -3.15694        1.89715

test_molecules/glucose.xyz

@@ -0,0 +1,26 @@
+24
+
+O          4.59506        0.44106       -3.18607
+C          4.05938        0.72532       -1.89257
+C          2.98776       -0.30438       -1.50340
+O          1.91330       -0.23175       -2.44604
+C          0.85139       -1.11865       -2.16127
+O         -0.18177       -0.90552       -3.11301
+C          1.33510       -2.58932       -2.18448
+O          0.27087       -3.51063       -1.92486
+C          2.46110       -2.74119       -1.15473
+O          3.00118       -4.06417       -1.13001
+C          3.58139       -1.71941       -1.41795
+O          4.55971       -1.75973       -0.36979
+H          5.16453        1.19425       -3.42069
+H          3.61335        1.72785       -1.93053
+H          4.88306        0.73137       -1.17545
+H          2.60456       -0.01108       -0.51419
+H          0.41460       -0.88077       -1.18320
+H          0.04931       -1.42082       -3.90159
+H          1.71521       -2.84259       -3.18064
+H          0.08274       -3.51136       -0.97050
+H          2.05939       -2.58506       -0.14388
+H          3.30065       -4.28731       -2.03033
+H          4.08740       -1.99062       -2.35084
+H          4.30606       -2.46202        0.25763

test_molecules/iodo.xyz

@@ -0,0 +1,26 @@
+24
+
+C         -3.05938       -3.21987        0.72725
+N         -4.16473       -3.37773        1.50103
+O         -4.09462       -2.71557        2.76828
+P         -2.89848       -3.15224        3.79443
+S         -1.38288       -2.34994        2.64644
+C         -1.80899       -2.78556        1.00485
+C         -0.73339       -2.67949       -0.05568
+C          0.42871       -3.68938        0.06469
+O          1.21780       -3.42398        1.23177
+C          0.03967       -5.17720        0.08063
+C         -0.71431       -5.69635       -1.15397
+I          0.52239       -5.56703       -2.95916
+C         -1.09584       -7.16870       -0.97145
+H         -3.20027       -3.51007       -0.31360
+H         -0.32054       -1.66251       -0.02114
+H         -1.18046       -2.78232       -1.05277
+H          1.10831       -3.50409       -0.77306
+H          0.59060       -3.35347        1.97817
+H         -0.56338       -5.37234        0.97735
+H          0.95274       -5.76943        0.23428
+H         -1.62604       -5.11610       -1.32373
+H         -0.21026       -7.80096       -0.83274
+H         -1.64183       -7.54723       -1.84341
+H         -1.74008       -7.29709       -0.09483

test_molecules/pentylbenzene.xyz

@@ -0,0 +1,29 @@
+27
+
+C         -0.18369        0.78488       -0.95826
+C         -1.06696       -0.27641       -0.75656
+C         -0.90247       -1.12526        0.33602
+C          0.14900       -0.91472        1.22608
+C          1.03081        0.14805        1.02734
+C          0.87632        1.00904       -0.06840
+C          1.81056        2.17724       -0.27248
+C          3.29089        1.79735       -0.39488
+C          3.59115        0.92840       -1.61860
+C          5.08149        0.59670       -1.69771
+C          5.39771       -0.27792       -2.89994
+H         -0.32884        1.43729       -1.81648
+H         -1.88811       -0.43862       -1.45070
+H         -1.59375       -1.94708        0.49639
+H          0.28098       -1.57690        2.07761
+H          1.83998        0.30093        1.73818
+H          1.68607        2.85763        0.57974
+H          1.51423        2.74785       -1.16117
+H          3.62859        1.28375        0.51354
+H          3.87610        2.72310       -0.46124
+H          3.27954        1.45419       -2.52869
+H          3.01784       -0.00437       -1.57039
+H          5.39494        0.07698       -0.78485
+H          5.66594        1.52203       -1.76125
+H          4.85596       -1.22749       -2.84735
+H          6.46886       -0.49940       -2.93416
+H          5.12350        0.22420       -3.83345

test_molecules/thiophene.xyz

@@ -0,0 +1,11 @@
+9
+
+C          1.38296        0.71961        0.00140
+C          0.10409        1.23203       -0.00494
+S         -1.08316       -0.00090       -0.00999
+C          0.11198       -1.22614       -0.00521
+C          1.38752       -0.70558        0.00147
+H          2.27214        1.33793        0.00541
+H         -0.19362        2.27159       -0.00668
+H         -0.17913       -2.26757       -0.00725
+H          2.28065       -1.31820        0.00587