pythonknot 0.2.0__cp312-cp312-win_amd64.whl

pythonknot/__init__.py

@@ -0,0 +1,18 @@
+import os
+from pathlib import Path
+
+
+_TABLE_ENV = "PYTHONKNOT_ALEXANDER_TABLE"
+_TABLE_NAME = "table_knot_Alexander_polynomial.txt"
+
+
+def _configure_default_alexander_table() -> None:
+    if os.environ.get(_TABLE_ENV):
+        return
+
+    packaged_table = Path(__file__).resolve().parent / "data" / _TABLE_NAME
+    if packaged_table.exists():
+        os.environ[_TABLE_ENV] = str(packaged_table)
+
+
+_configure_default_alexander_table()

pythonknot/data/__init__.py

@@ -0,0 +1 @@
+# Package data module for bundled runtime resources.

pythonknot/data/table_knot_Alexander_polynomial.txt

@@ -0,0 +1,251 @@
+1       1
+3_1     -1+t-t^2
+4_1     -1+3*t-t^2
+5_1     1-t+t^2-t^3+t^4
+5_2     2-3*t+2*t^2
+6_1     -2+5*t-2*t^2
+6_2     1-3*t+3*t^2-3*t^3+t^4 
+6_3     1-3*t+5*t^2-3*t^3+t^4
+7_1     1-t+t^2-t^3+t^4-t^5+t^6
+7_2     3-5*t+3*t^2
+7_3     2-3*t+3*t^2-3*t^3+2*t^4
+7_4     4-7*t+4*t^2
+7_5     2-4*t+5*t^2-4*t^3+2*t^4
+7_6     1-5*t+7*t^2-5*t^3+t^4
+7_7     1-5*t+9*t^2-5*t^3+t^4
+8_1	3-7*t+3*t^2
+8_2	1-3*t+3*t^2-3*t^3+3*t^4-3*t^5+t^6
+8_3	4-9*t+4*t^2
+8_4	2-5*t+5*t^2-5*t^3+2*t^4
+8_5	1-3*t+4*t^2-5*t^3+4*t^4-3*t^5+t^6
+8_6	2-6*t+7*t^2-6*t^3+2*t^4
+8_7	1-3*t+5*t^2-5*t^3+5*t^4-3*t^5+t^6
+8_8	2-6*t+9*t^2-6*t^3+2*t^4
+8_9	1-3*t+5*t^2-7*t^3+5*t^4-3*t^5+t^6
+8_10	1-3*t+6*t^2-7*t^3+6*t^4-3*t^5+t^6
+8_11	2-7*t+9*t^2-7*t^3+2*t^4
+8_12	1-7*t+13*t^2-7*t^3+t^4
+8_13	2-7*t+11*t^2-7*t^3+2*t^4
+8_14	2-8*t+11*t^2-8*t^3+2*t^4
+8_15	3-8*t+11*t^2-8*t^3+3*t^4
+8_16	1-4*t+8*t^2-9*t^3+8*t^4-4*t^5+t^6
+8_17	1-4*t+8*t^2-11*t^3+8*t^4-4*t^5+t^6
+8_18	1-5*t+10*t^2-13*t^3+10*t^4-5*t^5+t^6
+8_19	1-t+t^3-t^5+t^6
+8_20	1-2*t+3*t^2-2*t^3+t^4
+8_21	1-4*t+5*t^2-4*t^3+t^4
+9_1	1-t+t^2-t^3+t^4-t^5+t^6-t^7+t^8
+9_2	4-7*t+4*t^2
+9_3	2-3*t+3*t^2-3*t^3+3*t^4-3*t^5+2*t^6
+9_4	3-5*t+5*t^2-5*t^3+3*t^4
+9_5	6-11*t+6*t^2
+9_6	2-4*t+5*t^2-5*t^3+5*t^4-4*t^5+2*t^6
+9_7	3-7*t+9*t^2-7*t^3+3*t^4
+9_8	2-8*t+11*t^2-8*t^3+2*t^4
+9_9	2-4*t+6*t^2-7*t^3+6*t^4-4*t^5+2*t^6
+9_10	4-8*t+9*t^2-8*t^3+4*t^4
+9_11	1-5*t+7*t^2-7*t^3+7*t^4-5*t^5+t^6
+9_12	2-9*t+13*t^2-9*t^3+2*t^4
+9_13	4-9*t+11*t^2-9*t^3+4*t^4
+9_14	2-9*t+15*t^2-9*t^3+2*t^4
+9_15	2-10*t+15*t^2-10*t^3+2*t^4
+9_16	2-5*t+8*t^2-9*t^3+8*t^4-5*t^5+2*t^6
+9_17	1-5*t+9*t^2-9*t^3+9*t^4-5*t^5+t^6
+9_18	4-10*t+13*t^2-10*t^3+4*t^4
+9_19	2-10*t+17*t^2-10*t^3+2*t^4
+9_20	1-5*t+9*t^2-11*t^3+9*t^4-5*t^5+t^6
+9_21	2-11*t+17*t^2-11*t^3+2*t^4
+9_22	1-5*t+10*t^2-11*t^3+10*t^4-5*t^5+t^6
+9_23	4-11*t+15*t^2-11*t^3+4*t^4
+9_24	1-5*t+10*t^2-13*t^3+10*t^4-5*t^5+t^6
+9_25	3-12*t+17*t^2-12*t^3+3*t^4
+9_26	1-5*t+11*t^2-13*t^3+11*t^4-5*t^5+t^6
+9_27	1-5*t+11*t^2-15*t^3+11*t^4-5*t^5+t^6
+9_28	1-5*t+12*t^2-15*t^3+12*t^4-5*t^5+t^6
+9_29	1-5*t+12*t^2-15*t^3+12*t^4-5*t^5+t^6
+9_30	1-5*t+12*t^2-17*t^3+12*t^4-5*t^5+t^6
+9_31	1-5*t+13*t^2-17*t^3+13*t^4-5*t^5+t^6
+9_32	1-6*t+14*t^2-17*t^3+14*t^4-6*t^5+t^6
+9_33	1-6*t+14*t^2-19*t^3+14*t^4-6*t^5+t^6
+9_34	1-6*t+16*t^2-23*t^3+16*t^4-6*t^5+t^6
+9_35	7-13*t+7*t^2
+9_36	1-5*t+8*t^2-9*t^3+8*t^4-5*t^5+t^6
+9_37	2-11*t+19*t^2-11*t^3+2*t^4
+9_38	5-14*t+19*t^2-14*t^3+5*t^4
+9_39	3-14*t+21*t^2-14*t^3+3*t^4
+9_40	1-7*t+18*t^2-23*t^3+18*t^4-7*t^5+t^6
+9_41	3-12*t+19*t^2-12*t^3+3*t^4
+9_42	1-2*t+t^2-2*t^3+t^4
+9_43	1-3*t+2*t^2-t^3+2*t^4-3*t^5+t^6
+9_44	1-4*t+7*t^2-4*t^3+t^4
+9_45	1-6*t+9*t^2-6*t^3+t^4
+9_46	2-5*t+2*t^2
+9_47	1-4*t+6*t^2-5*t^3+6*t^4-4*t^5+t^6
+9_48	1-7*t+11*t^2-7*t^3+t^4
+9_49	3-6*t+7*t^2-6*t^3+3*t^4
+10_1	4-9*t+4*t^2
+10_2	1-3*t+3*t^2-3*t^3+3*t^4-3*t^5+3*t^6-3*t^7+t^8
+10_3	6-13*t+6*t^2
+10_4	3-7*t+7*t^2-7*t^3+3*t^4
+10_5	1-3*t+5*t^2-5*t^3+5*t^4-5*t^5+5*t^6-3*t^7+t^8
+10_6	2-6*t+7*t^2-7*t^3+7*t^4-6*t^5+2*t^6
+10_7	3-11*t+15*t^2-11*t^3+3*t^4
+10_8	2-5*t+5*t^2-5*t^3+5*t^4-5*t^5+2*t^6
+10_9	1-3*t+5*t^2-7*t^3+7*t^4-7*t^5+5*t^6-3*t^7+t^8
+10_10	3-11*t+17*t^2-11*t^3+3*t^4
+10_11	4-11*t+13*t^2-11*t^3+4*t^4
+10_12	2-6*t+10*t^2-11*t^3+10*t^4-6*t^5+2*t^6
+10_13	2-13*t+23*t^2-13*t^3+2*t^4
+10_14	2-8*t+12*t^2-13*t^3+12*t^4-8*t^5+2*t^6
+10_15	2-6*t+9*t^2-9*t^3+9*t^4-6*t^5+2*t^6
+10_16	4-12*t+15*t^2-12*t^3+4*t^4
+10_17	1-3*t+5*t^2-7*t^3+9*t^4-7*t^5+5*t^6-3*t^7+t^8
+10_18	4-14*t+19*t^2-14*t^3+4*t^4
+10_19	2-7*t+11*t^2-11*t^3+11*t^4-7*t^5+2*t^6
+10_20	3-9*t+11*t^2-9*t^3+3*t^4
+10_21	2-7*t+9*t^2-9*t^3+9*t^4-7*t^5+2*t^6
+10_22	2-6*t+10*t^2-13*t^3+10*t^4-6*t^5+2*t^6
+10_23	2-7*t+13*t^2-15*t^3+13*t^4-7*t^5+2*t^6
+10_24	4-14*t+19*t^2-14*t^3+4*t^4
+10_25	2-8*t+14*t^2-17*t^3+14*t^4-8*t^5+2*t^6
+10_26	2-7*t+13*t^2-17*t^3+13*t^4-7*t^5+2*t^6
+10_27	2-8*t+16*t^2-19*t^3+16*t^4-8*t^5+2*t^6
+10_28	4-13*t+19*t^2-13*t^3+4*t^4
+10_29	1-7*t+15*t^2-17*t^3+15*t^4-7*t^5+t^6
+10_30	4-17*t+25*t^2-17*t^3+4*t^4
+10_31	4-14*t+21*t^2-14*t^3+4*t^4
+10_32	2-8*t+15*t^2-19*t^3+15*t^4-8*t^5+2*t^6
+10_33	4-16*t+25*t^2-16*t^3+4*t^4
+10_34	3-9*t+13*t^2-9*t^3+3*t^4
+10_35	2-12*t+21*t^2-12*t^3+2*t^4
+10_36	3-13*t+19*t^2-13*t^3+3*t^4
+10_37	4-13*t+19*t^2-13*t^3+4*t^4
+10_38	4-15*t+21*t^2-15*t^3+4*t^4
+10_39	2-8*t+13*t^2-15*t^3+13*t^4-8*t^5+2*t^6
+10_40	2-8*t+17*t^2-21*t^3+17*t^4-8*t^5+2*t^6
+10_41	1-7*t+17*t^2-21*t^3+17*t^4-7*t^5+t^6
+10_42	1-7*t+19*t^2-27*t^3+19*t^4-7*t^5+t^6
+10_43	1-7*t+17*t^2-23*t^3+17*t^4-7*t^5+t^6
+10_44	1-7*t+19*t^2-25*t^3+19*t^4-7*t^5+t^6
+10_45	1-7*t+21*t^2-31*t^3+21*t^4-7*t^5+t^6
+10_46	1-3*t+4*t^2-5*t^3+5*t^4-5*t^5+4*t^6-3*t^7+t^8
+10_47	1-3*t+6*t^2-7*t^3+7*t^4-7*t^5+6*t^6-3*t^7+t^8
+10_48	1-3*t+6*t^2-9*t^3+11*t^4-9*t^5+6*t^6-3*t^7+t^8
+10_49	3-8*t+12*t^2-13*t^3+12*t^4-8*t^5+3*t^6
+10_50	2-7*t+11*t^2-13*t^3+11*t^4-7*t^5+2*t^6
+10_51	2-7*t+15*t^2-19*t^3+15*t^4-7*t^5+2*t^6
+10_52	2-7*t+13*t^2-15*t^3+13*t^4-7*t^5+2*t^6
+10_53	6-18*t+25*t^2-18*t^3+6*t^4
+10_54	2-6*t+10*t^2-11*t^3+10*t^4-6*t^5+2*t^6
+10_55	5-15*t+21*t^2-15*t^3+5*t^4
+10_56	2-8*t+14*t^2-17*t^3+14*t^4-8*t^5+2*t^6
+10_57	2-8*t+18*t^2-23*t^3+18*t^4-8*t^5+2*t^6
+10_58	3-16*t+27*t^2-16*t^3+3*t^4
+10_59	1-7*t+18*t^2-23*t^3+18*t^4-7*t^5+t^6
+10_60	1-7*t+20*t^2-29*t^3+20*t^4-7*t^5+t^6
+10_61	2-5*t+6*t^2-7*t^3+6*t^4-5*t^5+2*t^6
+10_62	1-3*t+6*t^2-8*t^3+9*t^4-8*t^5+6*t^6-3*t^7+t^8
+10_63	5-14*t+19*t^2-14*t^3+5*t^4
+10_64	1-3*t+6*t^2-10*t^3+11*t^4-10*t^5+6*t^6-3*t^7+t^8
+10_65	2-7*t+14*t^2-17*t^3+14*t^4-7*t^5+2*t^6
+10_66	3-9*t+16*t^2-19*t^3+16*t^4-9*t^5+3*t^6
+10_67	4-16*t+23*t^2-16*t^3+4*t^4
+10_68	4-14*t+21*t^2-14*t^3+4*t^4
+10_69	1-7*t+21*t^2-29*t^3+21*t^4-7*t^5+t^6
+10_70	1-7*t+16*t^2-19*t^3+16*t^4-7*t^5+t^6
+10_71	1-7*t+18*t^2-25*t^3+18*t^4-7*t^5+t^6
+10_72	2-9*t+16*t^2-19*t^3+16*t^4-9*t^5+2*t^6
+10_73	1-7*t+20*t^2-27*t^3+20*t^4-7*t^5+t^6
+10_74	4-16*t+23*t^2-16*t^3+4*t^4
+10_75	1-7*t+19*t^2-27*t^3+19*t^4-7*t^5+t^6
+10_76	2-7*t+12*t^2-15*t^3+12*t^4-7*t^5+2*t^6
+10_77	2-7*t+14*t^2-17*t^3+14*t^4-7*t^5+2*t^6
+10_78	1-7*t+16*t^2-21*t^3+16*t^4-7*t^5+t^6
+10_79	1-3*t+7*t^2-12*t^3+15*t^4-12*t^5+7*t^6-3*t^7+t^8
+10_80	3-9*t+15*t^2-17*t^3+15*t^4-9*t^5+3*t^6
+10_81	1-8*t+20*t^2-27*t^3+20*t^4-8*t^5+t^6
+10_82	1-4*t+8*t^2-12*t^3+13*t^4-12*t^5+8*t^6-4*t^7+t^8
+10_83	2-9*t+19*t^2-23*t^3+19*t^4-9*t^5+2*t^6
+10_84	2-9*t+20*t^2-25*t^3+20*t^4-9*t^5+2*t^6
+10_85	1-4*t+8*t^2-10*t^3+11*t^4-10*t^5+8*t^6-4*t^7+t^8
+10_86	2-9*t+19*t^2-25*t^3+19*t^4-9*t^5+2*t^6
+10_87	2-9*t+18*t^2-23*t^3+18*t^4-9*t^5+2*t^6
+10_88	1-8*t+24*t^2-35*t^3+24*t^4-8*t^5+t^6
+10_89	1-8*t+24*t^2-33*t^3+24*t^4-8*t^5+t^6
+10_90	2-8*t+17*t^2-23*t^3+17*t^4-8*t^5+2*t^6
+10_91	1-4*t+9*t^2-14*t^3+17*t^4-14*t^5+9*t^6-4*t^7+t^8
+10_92	2-10*t+20*t^2-25*t^3+20*t^4-10*t^5+2*t^6
+10_93	2-8*t+15*t^2-17*t^3+15*t^4-8*t^5+2*t^6
+10_94	1-4*t+9*t^2-14*t^3+15*t^4-14*t^5+9*t^6-4*t^7+t^8
+10_95	2-9*t+21*t^2-27*t^3+21*t^4-9*t^5+2*t^6
+10_96	1-7*t+22*t^2-33*t^3+22*t^4-7*t^5+t^6
+10_97	5-22*t+33*t^2-22*t^3+5*t^4
+10_98	2-9*t+18*t^2-23*t^3+18*t^4-9*t^5+2*t^6
+10_99	1-4*t+10*t^2-16*t^3+19*t^4-16*t^5+10*t^6-4*t^7+t^8
+10_100	1-4*t+9*t^2-12*t^3+13*t^4-12*t^5+9*t^6-4*t^7+t^8
+10_101	7-21*t+29*t^2-21*t^3+7*t^4
+10_102	2-8*t+16*t^2-21*t^3+16*t^4-8*t^5+2*t^6
+10_103	2-8*t+17*t^2-21*t^3+17*t^4-8*t^5+2*t^6
+10_104	1-4*t+9*t^2-15*t^3+19*t^4-15*t^5+9*t^6-4*t^7+t^8
+10_105	1-8*t+22*t^2-29*t^3+22*t^4-8*t^5+t^6
+10_106	1-4*t+9*t^2-15*t^3+17*t^4-15*t^5+9*t^6-4*t^7+t^8
+10_107	1-8*t+22*t^2-31*t^3+22*t^4-8*t^5+t^6
+10_108	2-8*t+14*t^2-15*t^3+14*t^4-8*t^5+2*t^6
+10_109	1-4*t+10*t^2-17*t^3+21*t^4-17*t^5+10*t^6-4*t^7+t^8
+10_110	1-8*t+20*t^2-25*t^3+20*t^4-8*t^5+t^6
+10_111	2-9*t+17*t^2-21*t^3+17*t^4-9*t^5+2*t^6
+10_112	1-5*t+11*t^2-17*t^3+19*t^4-17*t^5+11*t^6-5*t^7+t^8
+10_113	2-11*t+26*t^2-33*t^3+26*t^4-11*t^5+2*t^6
+10_114	2-10*t+21*t^2-27*t^3+21*t^4-10*t^5+2*t^6
+10_115	1-9*t+26*t^2-37*t^3+26*t^4-9*t^5+t^6
+10_116	1-5*t+12*t^2-19*t^3+21*t^4-19*t^5+12*t^6-5*t^7+t^8
+10_117	2-10*t+24*t^2-31*t^3+24*t^4-10*t^5+2*t^6
+10_118	1-5*t+12*t^2-19*t^3+23*t^4-19*t^5+12*t^6-5*t^7+t^8
+10_119	2-10*t+23*t^2-31*t^3+23*t^4-10*t^5+2*t^6
+10_120	8-26*t+37*t^2-26*t^3+8*t^4
+10_121	2-11*t+27*t^2-35*t^3+27*t^4-11*t^5+2*t^6
+10_122	2-11*t+24*t^2-31*t^3+24*t^4-11*t^5+2*t^6
+10_123	1-6*t+15*t^2-24*t^3+29*t^4-24*t^5+15*t^6-6*t^7+t^8
+10_124	1-t+t^3-t^4+t^5-t^7+t^8
+10_125	1-2*t+2*t^2-t^3+2*t^4-2*t^5+t^6
+10_126	1-2*t+4*t^2-5*t^3+4*t^4-2*t^5+t^6
+10_127	1-4*t+6*t^2-7*t^3+6*t^4-4*t^5+t^6
+10_128	2-3*t+t^2+t^3+t^4-3*t^5+2*t^6
+10_129	2-6*t+9*t^2-6*t^3+2*t^4
+10_130	2-4*t+5*t^2-4*t^3+2*t^4
+10_131	2-8*t+11*t^2-8*t^3+2*t^4
+10_132	1-t+t^2-t^3+t^4
+10_133	1-5*t+7*t^2-5*t^3+t^4
+10_134	2-4*t+4*t^2-3*t^3+4*t^4-4*t^5+2*t^6
+10_135	3-9*t+13*t^2-9*t^3+3*t^4
+10_136	1-4*t+5*t^2-4*t^3+t^4
+10_137	1-6*t+11*t^2-6*t^3+t^4
+10_138	1-5*t+8*t^2-7*t^3+8*t^4-5*t^5+t^6
+10_139	1-t+2*t^3-3*t^4+2*t^5-t^7+t^8
+10_140	1-2*t+3*t^2-2*t^3+t^4
+10_141	1-3*t+4*t^2-5*t^3+4*t^4-3*t^5+t^6
+10_142	2-3*t+2*t^2-t^3+2*t^4-3*t^5+2*t^6
+10_143	1-3*t+6*t^2-7*t^3+6*t^4-3*t^5+t^6
+10_144	3-10*t+13*t^2-10*t^3+3*t^4
+10_145	1+t-3*t^2+t^3+t^4
+10_146	2-8*t+13*t^2-8*t^3+2*t^4
+10_147	2-7*t+9*t^2-7*t^3+2*t^4
+10_148	1-3*t+7*t^2-9*t^3+7*t^4-3*t^5+t^6
+10_149	1-5*t+9*t^2-11*t^3+9*t^4-5*t^5+t^6
+10_150	1-4*t+6*t^2-7*t^3+6*t^4-4*t^5+t^6
+10_151	1-4*t+10*t^2-13*t^3+10*t^4-4*t^5+t^6
+10_152	1-t-t^2+4*t^3-5*t^4+4*t^5-t^6-t^7+t^8
+10_153	1-t-t^2+3*t^3-t^4-t^5+t^6
+10_154	1-4*t^2+7*t^3-4*t^4+t^6
+10_155	1-3*t+5*t^2-7*t^3+5*t^4-3*t^5+t^6
+10_156	1-4*t+8*t^2-9*t^3+8*t^4-4*t^5+t^6
+10_157	1-6*t+11*t^2-13*t^3+11*t^4-6*t^5+t^6
+10_158	1-4*t+10*t^2-15*t^3+10*t^4-4*t^5+t^6
+10_159	1-4*t+9*t^2-11*t^3+9*t^4-4*t^5+t^6
+10_160	1-4*t+4*t^2-3*t^3+4*t^4-4*t^5+t^6
+10_161	1-2*t^2+3*t^3-2*t^4+t^6
+10_162	3-9*t+11*t^2-9*t^3+3*t^4
+10_163	1-5*t+12*t^2-15*t^3+12*t^4-5*t^5+t^6
+10_164	3-11*t+17*t^2-11*t^3+3*t^4
+10_165	2-10*t+15*t^2-10*t^3+2*t^4
+

pythonknot/knot_generator.py

@@ -0,0 +1,22 @@
+import numpy as np
+
+# design for generating knot configurations for diffrent simulation software
+# lammps read_data, gromacs gmx editconf, openmm pdb
+# get the coordinates of the knot, then write to the corresponding file
+class KnotGenerator:
+    def __init__(self, knot):
+        """ knot should be a numpy array with shape (N_atoms, 3)"""
+        self.knot = knot
+
+    def write_lammps_data(self, filename):
+        pass
+
+    def write_gromacs_gro(self, filename):
+        pass
+
+    def write_openmm_pdb(self, filename):
+        pass
+
+    def write_xyz(self, filename):
+        pass
+

pythonknot/polymer.py

@@ -0,0 +1,46 @@
+import numpy as np
+
+def bond_length(xyz:np.ndarray,type = "open"):
+    """计算轨迹的键长分布,输入应该为N_frames, N_atoms, 3的numpy array. type="open"表示开链，type="ring"表示闭链."""
+    #print("original shape:", xyz.shape)
+    temp = xyz.transpose(1,2,0)
+    #print("temp shape:", temp.shape)
+    if(type == "ring"):
+        bond_length = np.linalg.norm(temp[1:] - temp[:-1], axis=1)
+        # 闭链需要计算首尾原子的键长
+        end_to_start_bond = np.linalg.norm(temp[-1] - temp[0], axis=0)
+        #print("end_to_start_bond shape:", end_to_start_bond.shape)
+        # 从(N_frames) 变为 (1, N_frames)
+        end_to_start_bond = end_to_start_bond.reshape(1,-1)
+        bond_length = np.concatenate((bond_length, end_to_start_bond), axis=0)
+    elif(type == "open"):
+        bond_length = np.linalg.norm(temp[1:] - temp[:-1], axis=1)
+    print("bond_length shape:", bond_length.shape)
+    bond_length = bond_length.flatten()
+    return bond_length
+
+def radius_of_gyration(trajectory:np.ndarray):
+    """计算轨迹的质心半径分布,输入应该为N_frames, N_atoms, 3的numpy array."""
+    # 计算每帧的质心
+    centroids = np.mean(trajectory, axis=1)
+    
+    # 广播质心回到trajectory的形状，以便进行逐元素操作
+    # centroids[:, np.newaxis, :] 使得 centroids 从 (N_frames, 3) 扩展为 (N_frames, 1, 3)
+    # 这样可以与 trajectory (N_frames, N_atoms, 3) 对齐
+    displacement = trajectory - centroids[:, np.newaxis, :]
+    
+    # 计算每个原子到质心的距离的平方
+    distances_squared = np.sum(displacement**2, axis=2)
+    
+    # 计算每帧的回转半径
+    gyration_radius = np.sqrt(np.mean(distances_squared, axis=1))
+    
+    return gyration_radius
+
+def end_to_end_distance(trajectory:np.ndarray):
+    """计算轨迹的端到端距离分布,输入应该为N_frames, N_atoms, 3的numpy array."""
+    # 计算每帧的端到端距离
+    end_to_end = trajectory[:,-1] - trajectory[:,0]
+    end_to_end_distance = np.linalg.norm(end_to_end, axis=1)
+    
+    return end_to_end_distance

pythonknot/rmsd.py

@@ -0,0 +1,29 @@
+import rmsd
+import numpy
+
+def rmsd_ref(coords,ref):
+    """
+    Calculate the rmsd of coords to ref, and rotate coords to minimize rmsd.
+    """
+
+    rmsd_all = numpy.zeros(coords.shape[0])
+
+    frames, atoms, _ = coords.shape
+    if(ref.shape != coords[0].shape):
+        raise ValueError("The shape of ref and coords should be the same.")
+    
+    ref = ref - numpy.mean(ref, axis=0)
+    
+    # main loop
+    for i in range(frames):
+        # recenter
+        coords[i] -= numpy.mean(coords[i], axis=0)
+
+        # calculate the rotation matrix
+        R = rmsd.kabsch(coords[i], ref)
+        # rotate the coords
+        coords[i] = numpy.dot(coords[i], R)
+        # calculate the rmsd
+        rmsd_all[i] = rmsd.rmsd(coords[i], ref)
+
+    return rmsd_all

pythonknot/xyz.py

@@ -0,0 +1,31 @@
+import numpy as np
+
+def read_xyz(file):
+    """Read xyz file and get all the conf in same file, so return N_frames*n_atoms*3 np array"""
+    with open(file) as f:
+        lines = f.readlines()
+        N_frames = int(len(lines)/(int(lines[0])+2))
+        N_atoms = int(lines[0])
+        print(N_frames, N_atoms)
+        coords = np.zeros((N_frames, N_atoms, 3))
+        for i in range(N_frames):
+            lines = lines[2:]
+            for j in range(N_atoms):
+                line = lines[j].split()
+                coords[i,j,0] = float(line[1])
+                coords[i,j,1] = float(line[2])
+                coords[i,j,2] = float(line[3])
+            lines = lines[N_atoms:]
+
+    return coords
+
+def write_xyz(file, coords):
+    """Write xyz file with coords, coords is a N_frames*N_atoms*3 np array, all the frames have same number of atoms"""
+    N_atoms = coords.shape[1]
+    N_frames = coords.shape[0]
+    with open(file, 'w') as f:
+        for i in range(N_frames):
+            f.write(str(N_atoms)+'\n')
+            f.write('frame '+str(i)+'\n')
+            for j in range(N_atoms):
+                f.write('1 '+str(coords[i,j,0])+' '+str(coords[i,j,1])+' '+str(coords[i,j,2])+'\n')

pythonknot-0.2.0.dist-info/METADATA

@@ -0,0 +1,17 @@
+Metadata-Version: 2.4
+Name: pythonknot
+Version: 0.2.0
+Summary: pythonknot for knot theory calculation
+Home-page: 
+Author: yjianzhu
+Author-email: yjianzhu@mail.ustc.edu.cn
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: rmsd
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: requires-dist
+Dynamic: summary
+
+Python Knot is a Python package for creating and manipulating knots and links, calculating knot invariants, and more.

pythonknot-0.2.0.dist-info/RECORD

@@ -0,0 +1,12 @@
+pythonknot/__init__.py,sha256=P2DnVoeeIJU1BUBg5bozbyEb1JJTx89obSujymG78Zc,452
+pythonknot/alexander_poly.cp312-win_amd64.pyd,sha256=clemiqe0VMnXPgRb_5wklcJuRj3nSizkfkhXZjhwWnw,887808
+pythonknot/knot_generator.py,sha256=LIz1prX2JD7KfxK9a5wneqVl4sI7m5zaXKMAWRb6zPQ,608
+pythonknot/polymer.py,sha256=w5MJDRuBjDKc190N2zvtVv5KeBmlkxILcoqJybZ7hds,2129
+pythonknot/rmsd.py,sha256=1OxstRvKmn1ic_jNaYZyvb90o1UUSe7ATtXYzbkc9E0,783
+pythonknot/xyz.py,sha256=7DF0clQ1BbqxcPRURUJe74hTtMChmJ9HFk3vqSJ_ns4,1221
+pythonknot/data/__init__.py,sha256=E5qObJsuvfKKENzFgrRaZubpxThaQw49jRPRdrCUfhg,54
+pythonknot/data/table_knot_Alexander_polynomial.txt,sha256=nekErtsQWViKTRWT72cDkD8vXrQnnJYpvtkMl3TqzdA,9786
+pythonknot-0.2.0.dist-info/METADATA,sha256=jpd_6KKmpHUFpGdGYtzDB6hdMYNhl2e00BmhPXDwMSg,468
+pythonknot-0.2.0.dist-info/WHEEL,sha256=rR5QfsWcZl3mra5AmSD7Fd0dzQxZ3lHCpDo70IkfDK4,101
+pythonknot-0.2.0.dist-info/top_level.txt,sha256=qFU8P2xZFLCfmfNZ2QjuyHYn-zeiSUD6znlWAPA9KXw,11
+pythonknot-0.2.0.dist-info/RECORD,,

pythonknot-0.2.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: false
+Tag: cp312-cp312-win_amd64
+

pythonknot-0.2.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+pythonknot