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Molby: コミット

Molecular Modeling Software

リビジョン	80ee1f456c2ade0868dad345ea6182afeeb15f60 (tree)
日時	2019-08-17 13:11:25
作者	toshinagata1964 <toshinagata1964@a2be...>
コミッター	toshinagata1964

NO2, SO (sulfonyl) and SO3H (sulfonic acid) are now recognized as known fragments.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@622 a2be9bc6-48de-4e38-9406-05402d4bc13c

--- a/Scripts/formula.rb

+++ b/Scripts/formula.rb

		@@ -209,7 +209,7 @@ class Molecule
209	209	sd = self.find_dummy_atoms
210	210	len2 = sd.length
211	211	if len2 < mult
212		- raise "Self has too few dummy atoms (#{len2}) to connect the given molecule (#{mult} bond order)"
	212	+ raise "self has too few dummy atoms (#{len2}) to connect the given molecule (#{mult} bond order)"
213	213	elsif len2 > mult
214	214	sd.shift # Keep the first dummy atom untouched
215	215	sd.slice!(mult..-1)

		@@ -499,9 +499,9 @@ class Molecule
499	499	end
500	500
501	501	# Define atom fragments
502		- elements = %w(C H Li Be B C N O F Na Mg Al Si P S Cl)
503		- valences = [4,1,1,2,3,4,3,2,1,1,2,3,4,3,2,1]
504		- degrees = {"N"=>100, "O"=>110, "P"=>95, "S"=>108}
	502	+ elements = %w(C H Li Be B C N O F Na Mg Al Si P S Cl Zn Ga Ge As Se Br Cd In Sn Sb Te I Hg Tl Pb Bi)
	503	+ valences = [4,1,1, 2, 3,4,3,2,1,1, 2, 3, 4, 3,2,1, 2, 3, 4, 3, 2, 1, 2, 3, 4, 3, 2, 1,2, 3, 4, 3]
	504	+ degrees = {"N"=>100, "O"=>110, "P"=>95, "S"=>108, "As"=>92, "Se"=>91, "Sb"=>92, "Te"=>90, "Bi"=>90}
505	505	elements.each_index { \|i\|
506	506	name = elements[i]
507	507	angle = degrees[name]

--- a/Scripts/mbsf/fragment_def.rb

+++ b/Scripts/mbsf/fragment_def.rb

		@@ -82,20 +82,35 @@ class Molecule
82	82	["MX4 tetrahedral", "coordination/MX4t.mbsf"],
83	83	["MX4 square-planar", "coordination/MX4p.mbsf"],
84	84	["MX5 trigonal bipyramidal", "coordination/MX5.mbsf"],
85		- ["MX6 octahedral", "coordination/MX6.mbsf"]
	85	+ ["MX6 octahedral", "coordination/MX6.mbsf"],
	86	+
	87	+ "...",
	88	+ ["NO2", "fragments/NO2.mbsf", "H1"],
	89	+ ["SO2O", "fragments/SO3H.mbsf", "H1", "H2"],
	90	+ ["SO3", "fragments/SO3H.mbsf", "H1", "H2"],
	91	+ ["SO3H", "fragments/SO3H.mbsf", "H1"],
	92	+ ["SO", "fragments/SO.mbsf", "H1", "H2"]
86	93	]
87	94
88	95	$named_fragments = []
	96	+ subtitle = nil
89	97
90	98	table.each { \|t\|
91	99	if t.is_a?(String)
92		- $named_fragments.push([t, "-"]) # Subtitle
	100	+ if t != "..."
	101	+ subtitle = t
	102	+ $named_fragments.push([t, "-"]) # Subtitle
	103	+ else
	104	+ subtitle = nil
	105	+ end
93	106	next
94	107	end
95	108	fname = t[1]
96	109	if fname =~ /\.mbsf$/
97	110	f = new(MbsfPath + "/" + fname) # Molecule.new
98		- $named_fragments.push([t[0], t[1]]) # Registered fragment
	111	+ if subtitle
	112	+ $named_fragments.push([t[0], t[1]]) # Registered fragment
	113	+ end
99	114	else
100	115	f = known_fragment(fname)
101	116	end

--- /dev/null

+++ b/Scripts/mbsf/fragments/NO2.mbsf

		@@ -0,0 +1,43 @@
	1	+!:atoms
	2	+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
	3	+0 MAIN 1 RES N1 n3 0.00000 14.00670 N 7 1.000000 0.000000 0
	4	+1 MAIN 1 RES O4 o 0.00000 15.99940 O 8 1.000000 0.000000 0
	5	+2 MAIN 1 RES O5 o 0.00000 15.99940 O 8 1.000000 0.000000 0
	6	+3 MAIN 1 RES H1 hn 0.00000 1.00790 H 1 1.000000 0.000000 0
	7	+
	8	+!:positions ; frame 0
	9	+! idx x y z [sx sy sz]
	10	+0 1.28420161 0.24585278 0.20573357
	11	+1 1.79964975 1.10078149 -0.53013352
	12	+2 1.79339434 -0.24814780 1.22295723
	13	+3 -0.10852988 -0.19316457 -0.13714068
	14	+
	15	+!:bonds
	16	+! from1 to1 from2 to2 from3 to3 from4 to4
	17	+0 1 0 2 0 3
	18	+
	19	+!:angles
	20	+! a1 b1 c1 a2 b2 c2 a3 b3 c3
	21	+2 0 1 3 0 1 3 0 2
	22	+
	23	+!:trackball
	24	+! scale; trx try trz; theta_deg x y z
	25	+0.809850
	26	+-0.074035 -0.003156 -0.002550
	27	+20.655737 0.000000 1.000000 0.000000
	28	+
	29	+!:view
	30	+show_unit_cell 0
	31	+show_periodic_box 1
	32	+show_expanded_atoms 1
	33	+show_ellipsoids 0
	34	+show_hydrogens 1
	35	+show_dummy_atoms 1
	36	+show_rotation_center 0
	37	+show_graphite_flag 0
	38	+show_graphite 5
	39	+show_periodic_image_flag 0
	40	+show_periodic_image 0 0 0 0 0 0
	41	+atom_radius 0.200000
	42	+bond_radius 0.100000
	43	+

--- /dev/null

+++ b/Scripts/mbsf/fragments/SO.mbsf

		@@ -0,0 +1,42 @@
	1	+!:atoms
	2	+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
	3	+0 MAIN 1 RES H1 hs 0.00000 1.00790 H 1 1.000000 0.000000 0
	4	+1 MAIN 1 RES S1 s 0.00000 32.06600 S 16 1.000000 0.000000 0
	5	+2 MAIN 1 RES O1 o 0.00000 15.99940 O 8 1.000000 0.000000 0
	6	+3 MAIN 1 RES H2 hs 0.00000 1.00790 H 1 1.000000 0.000000 0
	7	+
	8	+!:positions ; frame 0
	9	+! idx x y z [sx sy sz]
	10	+0 0.04122872 0.00000000 0.15128305
	11	+1 1.53451318 0.00000000 0.00950327
	12	+2 2.46711340 -0.00000000 -1.60580696
	13	+3 2.15837073 0.00000000 1.37361535
	14	+
	15	+!:bonds
	16	+! from1 to1 from2 to2 from3 to3 from4 to4
	17	+1 2 1 0 1 3
	18	+
	19	+!:angles
	20	+! a1 b1 c1 a2 b2 c2 a3 b3 c3
	21	+0 1 2 3 1 2 3 1 0
	22	+
	23	+!:trackball
	24	+! scale; trx try trz; theta_deg x y z
	25	+0.657707
	26	+-0.151090 -0.000000 -0.005041
	27	+68.696009 0.999997 -0.001877 -0.001683
	28	+
	29	+!:view
	30	+show_unit_cell 0
	31	+show_periodic_box 1
	32	+show_expanded_atoms 1
	33	+show_ellipsoids 0
	34	+show_hydrogens 1
	35	+show_dummy_atoms 1
	36	+show_rotation_center 0
	37	+show_graphite_flag 0
	38	+show_graphite 5
	39	+show_periodic_image_flag 0
	40	+show_periodic_image 0 0 0 0 0 0
	41	+atom_radius 0.200000
	42	+bond_radius 0.100000

--- /dev/null

+++ b/Scripts/mbsf/fragments/SO3H.mbsf

		@@ -0,0 +1,54 @@
	1	+!:atoms
	2	+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
	3	+0 MAIN 3 RES H1 hs 0.00000 1.00790 H 1 1.000000 0.000000 0
	4	+1 MAIN 2 RES H2 ho 0.00000 1.00790 H 1 1.000000 0.000000 0
	5	+2 MAIN 1 RES S2 s 0.00000 32.06600 S 16 1.000000 0.000000 0
	6	+3 MAIN 1 RES O5 o 0.00000 15.99940 O 8 1.000000 0.000000 0
	7	+4 MAIN 1 RES O6 o 0.00000 15.99940 O 8 1.000000 0.000000 0
	8	+5 MAIN 2 RES O1 oh 0.00000 15.99940 O 8 1.000000 0.000000 0
	9	+
	10	+!:positions ; frame 0
	11	+! idx x y z [sx sy sz]
	12	+0 0.06138042 -0.12980594 -0.07185998
	13	+1 2.85841283 -1.52612722 -0.92716404
	14	+2 1.55008742 0.03399610 0.01132876
	15	+3 2.04111470 1.25906318 -0.82915005
	16	+4 2.06293505 -0.11310744 1.48226382
	17	+5 1.90468028 -1.36242385 -0.82100022
	18	+
	19	+!:bonds
	20	+! from1 to1 from2 to2 from3 to3 from4 to4
	21	+2 3 2 4 5 1 2 5
	22	+2 0
	23	+
	24	+!:angles
	25	+! a1 b1 c1 a2 b2 c2 a3 b3 c3
	26	+4 2 3 2 5 1 5 2 3
	27	+5 2 4 0 2 3 0 2 4
	28	+0 2 5
	29	+
	30	+!:dihedrals
	31	+! a1 b1 c1 d1 a2 b2 c2 d2
	32	+3 2 5 1 4 2 5 1
	33	+0 2 5 1
	34	+
	35	+!:trackball
	36	+! scale; trx try trz; theta_deg x y z
	37	+0.656495
	38	+-0.149907 0.006742 0.004839
	39	+1.472817 -0.703661 0.068853 -0.706992
	40	+
	41	+!:view
	42	+show_unit_cell 0
	43	+show_periodic_box 1
	44	+show_expanded_atoms 1
	45	+show_ellipsoids 0
	46	+show_hydrogens 1
	47	+show_dummy_atoms 1
	48	+show_rotation_center 0
	49	+show_graphite_flag 0
	50	+show_graphite 5
	51	+show_periodic_image_flag 0
	52	+show_periodic_image 0 0 0 0 0 0
	53	+atom_radius 0.200000
	54	+bond_radius 0.100000