igf1

1b68_critical_residues.tsv

@@ -0,0 +1,146 @@
+# ATOMICA Critical Residue Analysis: 1b68_all
+# Structure ID: 1b68
+# Total residues analyzed: 137
+# Mean ATOMICA_SCORE: 0.999961
+# Std Dev: 0.000047
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	A	32	ARG	0.999685	0.0315	9
+2	A	121	GLU	0.999728	0.0272	96
+3	A	128	GLN	0.999756	0.0244	103
+4	A	114	ARG	0.999828	0.0172	89
+5	A	106	ALA	0.999853	0.0147	81
+6	A	24	GLN	0.999855	0.0145	1
+7	A	43	LEU	0.999881	0.0119	20
+8	A	57	THR	0.999882	0.0118	34
+9	A	52	LEU	0.999889	0.0111	29
+10	A	44	SER	0.999899	0.0101	21
+11	A	34	TRP	0.999908	0.0092	11
+12	A	65	ASP	0.999912	0.0088	42
+13	A	54	SER	0.999913	0.0087	31
+14	A	141	LEU	0.999915	0.0085	116
+15	A	159	LEU	0.999918	0.0082	134
+16	A	123	GLN	0.999919	0.0081	98
+17	A	53	SER	0.999932	0.0068	30
+18	A	58	GLN	0.999935	0.0065	35
+19	A	90	ARG	0.999938	0.0062	65
+20	A	61	ARG	0.999938	0.0062	38
+21	A	27	GLU	0.999939	0.0061	4
+22	A	41	GLN	0.999944	0.0056	18
+23	A	80	GLU	0.999944	0.0056	57
+24	A	116	VAL	0.999946	0.0054	91
+25	A	138	ALA	0.999946	0.0054	113
+26	A	35	ASP	0.999949	0.0051	12
+27	A	119	ARG	0.999949	0.0051	94
+28	A	104	LEU	0.999950	0.0050	79
+29	A	154	ASP	0.999950	0.0050	129
+30	A	134	ARG	0.999951	0.0049	109
+31	A	38	ARG	0.999952	0.0048	15
+32	A	42	THR	0.999954	0.0046	19
+33	A	87	GLU	0.999955	0.0045	62
+34	A	71	LEU	0.999956	0.0044	48
+35	A	129	SER	0.999956	0.0044	104
+36	A	75	LYS	0.999957	0.0043	52
+37	A	133	LEU	0.999957	0.0043	108
+38	A	139	SER	0.999958	0.0042	114
+39	A	152	ALA	0.999958	0.0042	127
+40	A	118	TYR	0.999959	0.0041	93
+41	A	151	ASP	0.999960	0.0040	126
+42	A	142	ARG	0.999961	0.0039	117
+43	A	95	LYS	0.999963	0.0037	70
+44	A	127	GLY	0.999964	0.0036	102
+45	A	156	GLN	0.999965	0.0035	131
+46	A	33	PHE	0.999965	0.0035	10
+47	A	115	LEU	0.999966	0.0034	90
+48	A	45	GLU	0.999966	0.0034	22
+49	A	158	ARG	0.999967	0.0033	133
+50	A	147	ARG	0.999967	0.0033	122
+51	A	136	ARG	0.999968	0.0032	111
+52	A	157	LYS	0.999968	0.0032	132
+53	A	162	TYR	0.999968	0.0032	137
+54	A	130	THR	0.999969	0.0031	105
+55	A	99	ALA	0.999970	0.0030	74
+56	A	37	LEU	0.999970	0.0030	14
+57	A	137	LEU	0.999971	0.0029	112
+58	A	48	GLN	0.999971	0.0029	25
+59	A	31	GLY	0.999971	0.0029	8
+60	A	117	GLN	0.999971	0.0029	92
+61	A	102	ALA	0.999971	0.0029	77
+62	A	125	MET	0.999971	0.0029	100
+63	A	135	VAL	0.999972	0.0028	110
+64	A	51	LEU	0.999972	0.0028	28
+65	A	140	HIS	0.999973	0.0027	115
+66	A	46	GLN	0.999973	0.0027	23
+67	A	149	LEU	0.999974	0.0026	124
+68	A	25	ARG	0.999974	0.0026	2
+69	A	67	THR	0.999975	0.0025	44
+70	A	83	THR	0.999975	0.0025	60
+71	A	105	GLY	0.999976	0.0024	80
+72	A	64	MET	0.999976	0.0024	41
+73	A	131	GLU	0.999976	0.0024	106
+74	A	101	GLN	0.999976	0.0024	76
+75	A	112	ARG	0.999977	0.0023	87
+76	A	49	GLU	0.999977	0.0023	26
+77	A	76	SER	0.999977	0.0023	53
+78	A	86	ALA	0.999977	0.0023	61
+79	A	89	THR	0.999978	0.0022	64
+80	A	55	GLN	0.999978	0.0022	32
+81	A	73	ALA	0.999978	0.0022	50
+82	A	150	ARG	0.999978	0.0022	125
+83	A	144	LEU	0.999979	0.0021	119
+84	A	82	LEU	0.999979	0.0021	59
+85	A	78	LEU	0.999980	0.0020	55
+86	A	36	TYR	0.999981	0.0019	13
+87	A	145	ARG	0.999981	0.0019	120
+88	A	59	GLU	0.999982	0.0018	36
+89	A	56	VAL	0.999982	0.0018	33
+90	A	28	LEU	0.999982	0.0018	5
+91	A	72	LYS	0.999982	0.0018	49
+92	A	47	VAL	0.999982	0.0018	24
+93	A	120	GLY	0.999983	0.0017	95
+94	A	40	VAL	0.999984	0.0016	17
+95	A	93	LEU	0.999984	0.0016	68
+96	A	88	GLU	0.999984	0.0016	63
+97	A	50	GLU	0.999985	0.0015	27
+98	A	26	TRP	0.999985	0.0015	3
+99	A	107	ASP	0.999985	0.0015	82
+100	A	98	GLN	0.999985	0.0015	73
+101	A	69	LYS	0.999986	0.0014	46
+102	A	81	GLN	0.999986	0.0014	58
+103	A	146	LYS	0.999986	0.0014	121
+104	A	94	SER	0.999987	0.0013	69
+105	A	60	LEU	0.999987	0.0013	37
+106	A	62	ALA	0.999988	0.0012	39
+107	A	132	GLU	0.999988	0.0012	107
+108	A	110	ASP	0.999988	0.0012	85
+109	A	155	LEU	0.999988	0.0012	130
+110	A	66	GLU	0.999988	0.0012	43
+111	A	113	GLY	0.999989	0.0011	88
+112	A	91	ALA	0.999989	0.0011	66
+113	A	97	LEU	0.999989	0.0011	72
+114	A	92	ARG	0.999989	0.0011	67
+115	A	68	MET	0.999989	0.0011	45
+116	A	39	TRP	0.999990	0.0010	16
+117	A	109	GLU	0.999990	0.0010	84
+118	A	96	GLU	0.999990	0.0010	71
+119	A	77	GLU	0.999990	0.0010	54
+120	A	122	VAL	0.999990	0.0010	97
+121	A	70	GLU	0.999991	0.0009	47
+122	A	124	ALA	0.999991	0.0009	99
+123	A	100	ALA	0.999991	0.0009	75
+124	A	74	TYR	0.999992	0.0008	51
+125	A	143	LYS	0.999992	0.0008	118
+126	A	63	LEU	0.999992	0.0008	40
+127	A	29	ALA	0.999993	0.0007	6
+128	A	160	ALA	0.999994	0.0006	135
+129	A	111	VAL	0.999995	0.0005	86
+130	A	79	GLU	0.999995	0.0005	56
+131	A	126	LEU	0.999995	0.0005	101
+132	A	161	VAL	0.999996	0.0004	136
+133	A	108	MET	0.999997	0.0003	83
+134	A	148	LEU	0.999998	0.0002	123
+135	A	103	ARG	0.999998	0.0002	78
+136	A	153	ASP	0.999998	0.0002	128
+137	A	30	LEU	0.999999	0.0001	7

1b68_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1b68_all", "cos_distances": [0.999855101108551, 0.9999744892120361, 0.9999851584434509, 0.9999393820762634, 0.9999819993972778, 0.9999929666519165, 0.9999987483024597, 0.9999710321426392, 0.9996850490570068, 0.9999651312828064, 0.9999079704284668, 0.9999486804008484, 0.9999805688858032, 0.9999704360961914, 0.9999518394470215, 0.9999897480010986, 0.9999836683273315, 0.9999439716339111, 0.9999538660049438, 0.9998806715011597, 0.9998990297317505, 0.9999662041664124, 0.9999730587005615, 0.999982476234436, 0.9999707937240601, 0.9999769926071167, 0.999984622001648, 0.9999721050262451, 0.9998889565467834, 0.9999316930770874, 0.9999127984046936, 0.9999775886535645, 0.9999819397926331, 0.9998824000358582, 0.9999347925186157, 0.9999818801879883, 0.9999874830245972, 0.9999380707740784, 0.9999876022338867, 0.9999920725822449, 0.999975860118866, 0.9999123811721802, 0.9999883770942688, 0.999975323677063, 0.9999894499778748, 0.9999856948852539, 0.999990701675415, 0.9999561309814453, 0.9999821186065674, 0.9999777674674988, 0.9999915361404419, 0.9999569654464722, 0.9999769926071167, 0.9999901056289673, 0.999980092048645, 0.9999949932098389, 0.9999444484710693, 0.9999856948852539, 0.9999791979789734, 0.999975323677063, 0.9999770522117615, 0.9999551177024841, 0.9999844431877136, 0.9999775290489197, 0.9999376535415649, 0.9999890923500061, 0.99998939037323, 0.9999841451644897, 0.9999868869781494, 0.9999634027481079, 0.9999898672103882, 0.9999892115592957, 0.9999852776527405, 0.9999696612358093, 0.9999914169311523, 0.9999761581420898, 0.9999712705612183, 0.9999984502792358, 0.9999495148658752, 0.9999756217002869, 0.9998531341552734, 0.9999852180480957, 0.9999973177909851, 0.9999897480010986, 0.9999878406524658, 0.9999949336051941, 0.9999769330024719, 0.9999889135360718, 0.9998278617858887, 0.9999659657478333, 0.9999457001686096, 0.9999711513519287, 0.9999591708183289, 0.9999489188194275, 0.9999834299087524, 0.9997280836105347, 0.9999904632568359, 0.9999186396598816, 0.999990701675415, 0.9999712705612183, 0.9999954104423523, 0.9999640583992004, 0.9997560977935791, 0.999956488609314, 0.999968945980072, 0.999975860118866, 0.999987781047821, 0.9999569654464722, 0.9999513626098633, 0.9999720454216003, 0.9999676942825317, 0.999970555305481, 0.999945878982544, 0.9999577403068542, 0.9999729990959167, 0.9999147653579712, 0.9999606609344482, 0.9999915957450867, 0.9999788999557495, 0.9999806880950928, 0.9999856948852539, 0.999967098236084, 0.9999980926513672, 0.9999736547470093, 0.999978244304657, 0.9999601244926453, 0.9999583959579468, 0.9999984502792358, 0.9999502897262573, 0.9999879598617554, 0.9999650716781616, 0.9999682903289795, 0.9999666810035706, 0.9999178647994995, 0.9999939203262329, 0.9999963641166687, 0.999968409538269, 0.9999372959136963], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138], "time_seconds": 22.0014, "peak_memory_mb": 1035.62}

1b68_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1b68",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1b68_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1b68
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1b68.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 32+121+128+114+106+24+43+57+52+44 and chain A
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 32 and chain A
+color red, critical_rank1
+select critical_rank2, resi 121 and chain A
+color tv_red, critical_rank2
+select critical_rank3, resi 128 and chain A
+color salmon, critical_rank3
+select critical_rank4, resi 114 and chain A
+color lightsalmon, critical_rank4
+select critical_rank5, resi 106 and chain A
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1b68_critical.pse
+# To save image: png 1b68_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1b68_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 22.0,
+  "total_time_minutes": 0.37,
+  "time_per_structure": {
+    "mean": 22.0014,
+    "std": 0.0,
+    "min": 22.0014,
+    "max": 22.0014
+  },
+  "output_file": "output/1b68_interact_scores.json",
+  "input_file": "downloads/pdbs/1b68.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 1035.62,
+    "max": 1035.62
+  }
+}

1le2_critical_residues.tsv

@@ -0,0 +1,152 @@
+# ATOMICA Critical Residue Analysis: 1le2_all
+# Structure ID: 1le2
+# Total residues analyzed: 143
+# Mean ATOMICA_SCORE: 0.999959
+# Std Dev: 0.000047
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	A	166	ALA	0.999772	0.0228	143
+2	A	32	ARG	0.999782	0.0218	9
+3	A	114	ARG	0.999792	0.0208	91
+4	A	85	VAL	0.999797	0.0203	62
+5	A	128	GLN	0.999819	0.0181	105
+6	A	24	GLN	0.999831	0.0169	1
+7	A	106	ALA	0.999843	0.0157	83
+8	A	58	GLN	0.999858	0.0142	35
+9	A	113	GLY	0.999868	0.0132	90
+10	A	121	GLU	0.999871	0.0129	98
+11	A	119	ARG	0.999878	0.0122	96
+12	A	75	LYS	0.999881	0.0119	52
+13	A	152	ALA	0.999882	0.0118	129
+14	A	159	LEU	0.999883	0.0117	136
+15	A	109	GLU	0.999886	0.0114	86
+16	A	41	GLN	0.999887	0.0113	18
+17	A	104	LEU	0.999890	0.0110	81
+18	A	163	GLN	0.999905	0.0095	140
+19	A	65	ASP	0.999906	0.0094	42
+20	A	112	CYS	0.999919	0.0081	89
+21	A	61	ARG	0.999920	0.0080	38
+22	A	48	GLN	0.999930	0.0070	25
+23	A	160	ALA	0.999932	0.0068	137
+24	A	158	CYS	0.999940	0.0060	135
+25	A	44	SER	0.999941	0.0059	21
+26	A	34	TRP	0.999942	0.0058	11
+27	A	38	ARG	0.999943	0.0057	15
+28	A	141	LEU	0.999943	0.0057	118
+29	A	27	GLU	0.999946	0.0054	4
+30	A	97	LEU	0.999946	0.0054	74
+31	A	131	GLU	0.999947	0.0053	108
+32	A	64	MET	0.999948	0.0052	41
+33	A	54	SER	0.999950	0.0050	31
+34	A	99	ALA	0.999951	0.0049	76
+35	A	125	MET	0.999957	0.0043	102
+36	A	165	GLY	0.999957	0.0043	142
+37	A	133	LEU	0.999957	0.0043	110
+38	A	43	LEU	0.999958	0.0042	20
+39	A	105	GLY	0.999959	0.0041	82
+40	A	127	GLY	0.999959	0.0041	104
+41	A	139	SER	0.999960	0.0040	116
+42	A	110	ASP	0.999960	0.0040	87
+43	A	123	GLN	0.999962	0.0038	100
+44	A	59	GLU	0.999964	0.0036	36
+45	A	120	GLY	0.999964	0.0036	97
+46	A	108	MET	0.999964	0.0036	85
+47	A	164	ALA	0.999964	0.0036	141
+48	A	118	TYR	0.999965	0.0035	95
+49	A	138	ALA	0.999965	0.0035	115
+50	A	95	LYS	0.999966	0.0034	72
+51	A	86	ALA	0.999967	0.0033	63
+52	A	45	GLU	0.999967	0.0033	22
+53	A	35	ASP	0.999967	0.0033	12
+54	A	129	SER	0.999968	0.0032	106
+55	A	57	THR	0.999969	0.0031	34
+56	A	124	ALA	0.999970	0.0030	101
+57	A	151	ASP	0.999972	0.0028	128
+58	A	67	THR	0.999972	0.0028	44
+59	A	94	SER	0.999972	0.0028	71
+60	A	156	GLN	0.999973	0.0027	133
+61	A	130	THR	0.999973	0.0027	107
+62	A	88	GLU	0.999974	0.0026	65
+63	A	100	ALA	0.999974	0.0026	77
+64	A	98	GLN	0.999974	0.0026	75
+65	A	102	ALA	0.999975	0.0025	79
+66	A	55	GLN	0.999975	0.0025	32
+67	A	56	VAL	0.999975	0.0025	33
+68	A	50	GLU	0.999976	0.0024	27
+69	A	71	LEU	0.999976	0.0024	48
+70	A	92	ARG	0.999976	0.0024	69
+71	A	126	LEU	0.999977	0.0023	103
+72	A	84	PRO	0.999977	0.0023	61
+73	A	53	SER	0.999978	0.0022	30
+74	A	134	ARG	0.999978	0.0022	111
+75	A	47	VAL	0.999979	0.0021	24
+76	A	68	MET	0.999979	0.0021	45
+77	A	91	ALA	0.999980	0.0020	68
+78	A	33	PHE	0.999980	0.0020	10
+79	A	28	LEU	0.999980	0.0020	5
+80	A	37	LEU	0.999980	0.0020	14
+81	A	40	VAL	0.999980	0.0020	17
+82	A	162	TYR	0.999980	0.0020	139
+83	A	157	LYS	0.999980	0.0020	134
+84	A	136	ARG	0.999981	0.0019	113
+85	A	89	THR	0.999982	0.0018	66
+86	A	60	LEU	0.999982	0.0018	37
+87	A	42	THR	0.999982	0.0018	19
+88	A	76	SER	0.999982	0.0018	53
+89	A	132	GLU	0.999982	0.0018	109
+90	A	140	HIS	0.999983	0.0017	117
+91	A	116	VAL	0.999983	0.0017	93
+92	A	145	ARG	0.999983	0.0017	122
+93	A	96	GLU	0.999983	0.0017	73
+94	A	79	GLU	0.999983	0.0017	56
+95	A	107	ASP	0.999984	0.0016	84
+96	A	72	LYS	0.999984	0.0016	49
+97	A	74	TYR	0.999984	0.0016	51
+98	A	39	TRP	0.999985	0.0015	16
+99	A	101	GLN	0.999985	0.0015	78
+100	A	90	ARG	0.999985	0.0015	67
+101	A	78	LEU	0.999985	0.0015	55
+102	A	103	ARG	0.999986	0.0014	80
+103	A	63	LEU	0.999986	0.0014	40
+104	A	137	LEU	0.999986	0.0014	114
+105	A	83	THR	0.999986	0.0014	60
+106	A	77	GLU	0.999986	0.0014	54
+107	A	117	GLN	0.999986	0.0014	94
+108	A	144	LEU	0.999986	0.0014	121
+109	A	66	GLU	0.999987	0.0013	43
+110	A	69	LYS	0.999987	0.0013	46
+111	A	146	LYS	0.999987	0.0013	123
+112	A	154	ASP	0.999987	0.0013	131
+113	A	87	GLU	0.999987	0.0013	64
+114	A	81	GLN	0.999988	0.0012	58
+115	A	80	GLU	0.999988	0.0012	57
+116	A	52	LEU	0.999990	0.0010	29
+117	A	46	GLN	0.999991	0.0009	23
+118	A	36	TYR	0.999991	0.0009	13
+119	A	148	LEU	0.999991	0.0009	125
+120	A	150	ARG	0.999991	0.0009	127
+121	A	143	LYS	0.999992	0.0008	120
+122	A	135	VAL	0.999992	0.0008	112
+123	A	25	ARG	0.999992	0.0008	2
+124	A	142	ARG	0.999992	0.0008	119
+125	A	70	GLU	0.999993	0.0007	47
+126	A	161	VAL	0.999993	0.0007	138
+127	A	82	LEU	0.999993	0.0007	59
+128	A	147	ARG	0.999994	0.0006	124
+129	A	51	LEU	0.999994	0.0006	28
+130	A	153	ASP	0.999994	0.0006	130
+131	A	62	ALA	0.999994	0.0006	39
+132	A	149	LEU	0.999994	0.0006	126
+133	A	73	ALA	0.999994	0.0006	50
+134	A	93	LEU	0.999994	0.0006	70
+135	A	31	GLY	0.999994	0.0006	8
+136	A	155	LEU	0.999995	0.0005	132
+137	A	26	TRP	0.999995	0.0005	3
+138	A	115	LEU	0.999995	0.0005	92
+139	A	29	ALA	0.999995	0.0005	6
+140	A	49	GLU	0.999996	0.0004	26
+141	A	30	LEU	0.999997	0.0003	7
+142	A	122	VAL	0.999997	0.0003	99
+143	A	111	VAL	0.999998	0.0002	88

1le2_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1le2_all", "cos_distances": [0.9998307228088379, 0.9999924898147583, 0.9999949932098389, 0.9999459981918335, 0.9999796748161316, 0.999995231628418, 0.9999969005584717, 0.9999944567680359, 0.999781608581543, 0.9999796152114868, 0.9999420046806335, 0.9999673366546631, 0.9999908208847046, 0.9999797344207764, 0.9999427199363708, 0.999984860420227, 0.9999797344207764, 0.9998874664306641, 0.9999822378158569, 0.9999582767486572, 0.9999406337738037, 0.9999672770500183, 0.999990701675415, 0.9999785423278809, 0.9999295473098755, 0.9999958276748657, 0.9999756217002869, 0.9999937415122986, 0.9999899864196777, 0.9999775290489197, 0.9999500513076782, 0.9999754428863525, 0.9999754428863525, 0.9999688863754272, 0.9998582601547241, 0.9999638199806213, 0.9999819397926331, 0.9999202489852905, 0.9999938011169434, 0.999985933303833, 0.9999477863311768, 0.9999060034751892, 0.9999865293502808, 0.9999717473983765, 0.9999791383743286, 0.9999865293502808, 0.9999927282333374, 0.9999761581420898, 0.9999840259552002, 0.999994158744812, 0.9999841451644897, 0.9998810291290283, 0.9999822378158569, 0.9999862313270569, 0.9999854564666748, 0.9999834299087524, 0.999988317489624, 0.9999880790710449, 0.9999934434890747, 0.9999861717224121, 0.9999767541885376, 0.9997968673706055, 0.9999668598175049, 0.9999874830245972, 0.9999740123748779, 0.9999818801879883, 0.9999852180480957, 0.999979555606842, 0.9999761581420898, 0.9999942779541016, 0.9999723434448242, 0.9999656677246094, 0.9999830722808838, 0.9999463558197021, 0.9999744892120361, 0.9999510645866394, 0.999974250793457, 0.999984860420227, 0.9999752640724182, 0.9999858736991882, 0.9998903274536133, 0.9999587535858154, 0.9998430013656616, 0.9999839663505554, 0.9999643564224243, 0.9998857975006104, 0.9999603629112244, 0.9999975562095642, 0.9999186396598816, 0.9998675584793091, 0.9997924566268921, 0.9999951124191284, 0.9999828338623047, 0.9999862909317017, 0.9999648332595825, 0.9998779296875, 0.9999639391899109, 0.999871015548706, 0.9999972581863403, 0.9999617338180542, 0.9999703764915466, 0.9999568462371826, 0.9999765157699585, 0.999958872795105, 0.9998190402984619, 0.9999678730964661, 0.9999732971191406, 0.9999473094940186, 0.9999824166297913, 0.9999569058418274, 0.999977707862854, 0.9999919533729553, 0.9999808073043823, 0.9999860525131226, 0.9999653100967407, 0.9999598264694214, 0.9999827742576599, 0.9999433159828186, 0.9999924898147583, 0.9999915957450867, 0.9999864101409912, 0.9999829530715942, 0.9999869465827942, 0.9999936819076538, 0.9999909400939941, 0.9999940991401672, 0.9999909996986389, 0.9999715089797974, 0.9998820424079895, 0.9999937415122986, 0.9999872446060181, 0.9999946355819702, 0.9999727606773376, 0.9999803900718689, 0.9999399185180664, 0.9998832941055298, 0.999931812286377, 0.9999929070472717, 0.9999797940254211, 0.9999046325683594, 0.9999644756317139, 0.9999568462371826, 0.9997718334197998, 0.9999099373817444], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144], "time_seconds": 22.984, "peak_memory_mb": 1060.61}

1le2_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1le2",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1le2_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1le2
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1le2.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 166+32+114+85+128+24+106+58+113+121 and chain A
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 166 and chain A
+color red, critical_rank1
+select critical_rank2, resi 32 and chain A
+color tv_red, critical_rank2
+select critical_rank3, resi 114 and chain A
+color salmon, critical_rank3
+select critical_rank4, resi 85 and chain A
+color lightsalmon, critical_rank4
+select critical_rank5, resi 128 and chain A
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1le2_critical.pse
+# To save image: png 1le2_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1le2_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 22.99,
+  "total_time_minutes": 0.38,
+  "time_per_structure": {
+    "mean": 22.984,
+    "std": 0.0,
+    "min": 22.984,
+    "max": 22.984
+  },
+  "output_file": "output/1le2_interact_scores.json",
+  "input_file": "downloads/pdbs/1le2.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 1060.61,
+    "max": 1060.61
+  }
+}

1le4_critical_residues.tsv

@@ -0,0 +1,147 @@
+# ATOMICA Critical Residue Analysis: 1le4_all
+# Structure ID: 1le4
+# Total residues analyzed: 138
+# Mean ATOMICA_SCORE: 0.999962
+# Std Dev: 0.000048
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	A	121	GLU	0.999693	0.0307	97
+2	A	32	ARG	0.999738	0.0262	8
+3	A	128	GLN	0.999741	0.0259	104
+4	A	106	ALA	0.999784	0.0216	82
+5	A	114	ARG	0.999835	0.0165	90
+6	A	58	GLN	0.999866	0.0134	34
+7	A	41	GLN	0.999867	0.0133	17
+8	A	67	THR	0.999887	0.0113	43
+9	A	109	GLU	0.999890	0.0110	85
+10	A	104	LEU	0.999896	0.0104	80
+11	A	52	LEU	0.999904	0.0096	28
+12	A	43	LEU	0.999918	0.0082	19
+13	A	34	TRP	0.999922	0.0078	10
+14	A	139	SER	0.999924	0.0076	115
+15	A	65	ASP	0.999924	0.0076	41
+16	A	27	GLU	0.999927	0.0073	3
+17	A	53	SER	0.999928	0.0072	29
+18	A	91	ALA	0.999929	0.0071	67
+19	A	54	SER	0.999935	0.0065	30
+20	A	133	LEU	0.999940	0.0060	109
+21	A	44	SER	0.999947	0.0053	20
+22	A	90	ARG	0.999948	0.0052	66
+23	A	152	ALA	0.999948	0.0052	128
+24	A	116	VAL	0.999949	0.0051	92
+25	A	141	LEU	0.999949	0.0051	117
+26	A	140	HIS	0.999951	0.0049	116
+27	A	123	GLN	0.999953	0.0047	99
+28	A	105	GLY	0.999955	0.0045	81
+29	A	94	SER	0.999956	0.0044	70
+30	A	147	ARG	0.999956	0.0044	123
+31	A	37	LEU	0.999957	0.0043	13
+32	A	119	ARG	0.999957	0.0043	95
+33	A	73	ALA	0.999959	0.0041	49
+34	A	42	THR	0.999959	0.0041	18
+35	A	113	GLY	0.999959	0.0041	89
+36	A	129	SER	0.999961	0.0039	105
+37	A	144	LEU	0.999961	0.0039	120
+38	A	77	GLU	0.999963	0.0037	53
+39	A	131	GLU	0.999963	0.0037	107
+40	A	78	LEU	0.999963	0.0037	54
+41	A	150	ARG	0.999964	0.0036	126
+42	A	57	THR	0.999964	0.0036	33
+43	A	99	ALA	0.999964	0.0036	75
+44	A	75	LYS	0.999965	0.0035	51
+45	A	51	LEU	0.999965	0.0035	27
+46	A	89	THR	0.999967	0.0033	65
+47	A	60	LEU	0.999967	0.0033	36
+48	A	25	ARG	0.999967	0.0033	1
+49	A	107	ASP	0.999967	0.0033	83
+50	A	100	ALA	0.999967	0.0033	76
+51	A	28	LEU	0.999967	0.0033	4
+52	A	71	LEU	0.999968	0.0032	47
+53	A	137	LEU	0.999968	0.0032	113
+54	A	157	LYS	0.999968	0.0032	133
+55	A	151	ASP	0.999969	0.0031	127
+56	A	61	ARG	0.999970	0.0030	37
+57	A	66	GLU	0.999971	0.0029	42
+58	A	35	ASP	0.999971	0.0029	11
+59	A	149	LEU	0.999971	0.0029	125
+60	A	50	GLU	0.999972	0.0028	26
+61	A	126	LEU	0.999972	0.0028	102
+62	A	98	GLN	0.999973	0.0027	74
+63	A	69	LYS	0.999973	0.0027	45
+64	A	138	ALA	0.999973	0.0027	114
+65	A	142	ARG	0.999973	0.0027	118
+66	A	76	SER	0.999973	0.0027	52
+67	A	83	THR	0.999973	0.0027	59
+68	A	64	MET	0.999974	0.0026	40
+69	A	159	LEU	0.999975	0.0025	135
+70	A	130	THR	0.999975	0.0025	106
+71	A	108	MET	0.999976	0.0024	84
+72	A	96	GLU	0.999976	0.0024	72
+73	A	145	ARG	0.999977	0.0023	121
+74	A	56	VAL	0.999977	0.0023	32
+75	A	112	ARG	0.999977	0.0023	88
+76	A	117	GLN	0.999977	0.0023	93
+77	A	47	VAL	0.999977	0.0023	23
+78	A	84	PRO	0.999977	0.0023	60
+79	A	46	GLN	0.999977	0.0023	22
+80	A	38	ARG	0.999978	0.0022	14
+81	A	85	VAL	0.999978	0.0022	61
+82	A	86	ALA	0.999979	0.0021	62
+83	A	33	PHE	0.999979	0.0021	9
+84	A	95	LYS	0.999979	0.0021	71
+85	A	120	GLY	0.999979	0.0021	96
+86	A	81	GLN	0.999980	0.0020	57
+87	A	132	GLU	0.999981	0.0019	108
+88	A	97	LEU	0.999981	0.0019	73
+89	A	26	TRP	0.999981	0.0019	2
+90	A	155	LEU	0.999982	0.0018	131
+91	A	127	GLY	0.999982	0.0018	103
+92	A	134	ARG	0.999982	0.0018	110
+93	A	146	LYS	0.999982	0.0018	122
+94	A	82	LEU	0.999983	0.0017	58
+95	A	118	TYR	0.999983	0.0017	94
+96	A	135	VAL	0.999984	0.0016	111
+97	A	102	ALA	0.999984	0.0016	78
+98	A	48	GLN	0.999985	0.0015	24
+99	A	55	GLN	0.999985	0.0015	31
+100	A	148	LEU	0.999985	0.0015	124
+101	A	29	ALA	0.999985	0.0015	5
+102	A	40	VAL	0.999985	0.0015	16
+103	A	49	GLU	0.999986	0.0014	25
+104	A	45	GLU	0.999987	0.0013	21
+105	A	59	GLU	0.999987	0.0013	35
+106	A	154	ASP	0.999987	0.0013	130
+107	A	79	GLU	0.999987	0.0013	55
+108	A	124	ALA	0.999988	0.0012	100
+109	A	143	LYS	0.999988	0.0012	119
+110	A	92	ARG	0.999990	0.0010	68
+111	A	80	GLU	0.999990	0.0010	56
+112	A	36	TYR	0.999990	0.0010	12
+113	A	31	GLY	0.999991	0.0009	7
+114	A	158	ARG	0.999991	0.0009	134
+115	A	62	ALA	0.999991	0.0009	38
+116	A	115	LEU	0.999992	0.0008	91
+117	A	125	MET	0.999992	0.0008	101
+118	A	93	LEU	0.999992	0.0008	69
+119	A	160	ALA	0.999992	0.0008	136
+120	A	30	LEU	0.999992	0.0008	6
+121	A	161	VAL	0.999993	0.0007	137
+122	A	68	MET	0.999993	0.0007	44
+123	A	63	LEU	0.999993	0.0007	39
+124	A	88	GLU	0.999993	0.0007	64
+125	A	87	GLU	0.999993	0.0007	63
+126	A	162	TYR	0.999993	0.0007	138
+127	A	101	GLN	0.999994	0.0006	77
+128	A	70	GLU	0.999994	0.0006	46
+129	A	74	TYR	0.999995	0.0005	50
+130	A	39	TRP	0.999995	0.0005	15
+131	A	136	ARG	0.999995	0.0005	112
+132	A	122	VAL	0.999997	0.0003	98
+133	A	72	LYS	0.999997	0.0003	48
+134	A	110	ASP	0.999998	0.0002	86
+135	A	111	VAL	0.999998	0.0002	87
+136	A	103	ARG	0.999998	0.0002	79
+137	A	153	ASP	0.999998	0.0002	129
+138	A	156	GLN	0.999999	0.0001	132

1le4_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1le4_all", "cos_distances": [0.999967098236084, 0.9999813437461853, 0.9999271631240845, 0.9999673962593079, 0.9999852180480957, 0.9999921321868896, 0.999990701675415, 0.9997376203536987, 0.9999791979789734, 0.9999224543571472, 0.9999709725379944, 0.9999902248382568, 0.9999566674232483, 0.9999778270721436, 0.9999951124191284, 0.99998539686203, 0.9998669624328613, 0.9999586343765259, 0.9999175071716309, 0.9999467134475708, 0.9999865293502808, 0.9999772906303406, 0.9999772310256958, 0.9999849200248718, 0.9999861717224121, 0.9999716281890869, 0.9999653697013855, 0.9999042749404907, 0.9999277591705322, 0.99993497133255, 0.9999849796295166, 0.9999767541885376, 0.9999637603759766, 0.9998661279678345, 0.9999868869781494, 0.9999669790267944, 0.9999698996543884, 0.9999909400939941, 0.9999930262565613, 0.9999738931655884, 0.999923825263977, 0.9999706149101257, 0.9998865127563477, 0.999992847442627, 0.9999731183052063, 0.999994158744812, 0.9999675750732422, 0.9999974966049194, 0.9999585151672363, 0.9999946355819702, 0.9999645948410034, 0.999973475933075, 0.9999626278877258, 0.9999630451202393, 0.9999873042106628, 0.9999898672103882, 0.9999797940254211, 0.9999827146530151, 0.999973475933075, 0.9999772310256958, 0.9999783635139465, 0.9999786019325256, 0.9999932050704956, 0.999993085861206, 0.9999668598175049, 0.9999476671218872, 0.9999287128448486, 0.9999895095825195, 0.9999917149543762, 0.9999560117721558, 0.9999792575836182, 0.9999760389328003, 0.9999812841415405, 0.9999725818634033, 0.9999644756317139, 0.9999673366546631, 0.9999938011169434, 0.9999841451644897, 0.9999982118606567, 0.9998958706855774, 0.9999547004699707, 0.9997841119766235, 0.999967098236084, 0.9999759197235107, 0.999890148639679, 0.9999975562095642, 0.999998152256012, 0.9999767541885376, 0.9999591708183289, 0.9998345375061035, 0.9999915361404419, 0.9999492764472961, 0.9999771118164062, 0.9999828338623047, 0.9999574422836304, 0.9999793767929077, 0.9996930360794067, 0.9999966621398926, 0.9999525547027588, 0.9999884366989136, 0.9999915361404419, 0.9999722242355347, 0.9999821186065674, 0.9997407793998718, 0.9999607801437378, 0.9999754428863525, 0.9999629259109497, 0.9999805688858032, 0.9999397993087769, 0.9999821186065674, 0.9999837279319763, 0.9999953508377075, 0.9999679923057556, 0.9999731779098511, 0.999923586845398, 0.9999511241912842, 0.9999492764472961, 0.9999734163284302, 0.9999884963035583, 0.9999614953994751, 0.999976634979248, 0.9999823570251465, 0.9999560117721558, 0.9999849796295166, 0.9999710917472839, 0.999963641166687, 0.9999686479568481, 0.9999477863311768, 0.9999982118606567, 0.9999871253967285, 0.9999816417694092, 0.9999991655349731, 0.9999679923057556, 0.999990701675415, 0.9999750256538391, 0.999991774559021, 0.9999926686286926, 0.9999933242797852, 0.9999579191207886], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139], "time_seconds": 22.1792, "peak_memory_mb": 1045.54}

1le4_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1le4",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1le4_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1le4
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1le4.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 121+32+128+106+114+58+41+67+109+104 and chain A
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 121 and chain A
+color red, critical_rank1
+select critical_rank2, resi 32 and chain A
+color tv_red, critical_rank2
+select critical_rank3, resi 128 and chain A
+color salmon, critical_rank3
+select critical_rank4, resi 106 and chain A
+color lightsalmon, critical_rank4
+select critical_rank5, resi 114 and chain A
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1le4_critical.pse
+# To save image: png 1le4_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1le4_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 22.18,
+  "total_time_minutes": 0.37,
+  "time_per_structure": {
+    "mean": 22.1792,
+    "std": 0.0,
+    "min": 22.1792,
+    "max": 22.1792
+  },
+  "output_file": "output/1le4_interact_scores.json",
+  "input_file": "downloads/pdbs/1le4.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 1045.54,
+    "max": 1045.54
+  }
+}

1lpe_critical_residues.tsv

@@ -0,0 +1,152 @@
+# ATOMICA Critical Residue Analysis: 1lpe_all
+# Structure ID: 1lpe
+# Total residues analyzed: 143
+# Mean ATOMICA_SCORE: 0.999959
+# Std Dev: 0.000051
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	A	166	ALA	0.999725	0.0275	143
+2	A	121	GLU	0.999726	0.0274	98
+3	A	128	GLN	0.999744	0.0256	105
+4	A	32	ARG	0.999774	0.0226	9
+5	A	114	ARG	0.999791	0.0209	91
+6	A	106	ALA	0.999810	0.0190	83
+7	A	24	GLN	0.999822	0.0178	1
+8	A	85	VAL	0.999851	0.0149	62
+9	A	163	GLN	0.999862	0.0138	140
+10	A	41	GLN	0.999879	0.0121	18
+11	A	58	GLN	0.999879	0.0121	35
+12	A	57	THR	0.999886	0.0114	34
+13	A	34	TRP	0.999896	0.0104	11
+14	A	162	TYR	0.999901	0.0099	139
+15	A	141	LEU	0.999909	0.0091	118
+16	A	54	SER	0.999915	0.0085	31
+17	A	119	ARG	0.999918	0.0082	96
+18	A	38	ARG	0.999929	0.0071	15
+19	A	44	SER	0.999941	0.0059	21
+20	A	61	ARG	0.999941	0.0059	38
+21	A	43	LEU	0.999946	0.0054	20
+22	A	164	ALA	0.999947	0.0053	141
+23	A	104	LEU	0.999951	0.0049	81
+24	A	159	LEU	0.999951	0.0049	136
+25	A	140	HIS	0.999951	0.0049	117
+26	A	75	LYS	0.999952	0.0048	52
+27	A	113	GLY	0.999953	0.0047	90
+28	A	37	LEU	0.999953	0.0047	14
+29	A	152	ALA	0.999954	0.0046	129
+30	A	45	GLU	0.999956	0.0044	22
+31	A	25	ARG	0.999956	0.0044	2
+32	A	42	THR	0.999957	0.0043	19
+33	A	46	GLN	0.999957	0.0043	23
+34	A	147	ARG	0.999957	0.0043	124
+35	A	138	ALA	0.999958	0.0042	115
+36	A	158	ARG	0.999958	0.0042	135
+37	A	64	MET	0.999959	0.0041	41
+38	A	55	GLN	0.999959	0.0041	32
+39	A	53	SER	0.999960	0.0040	30
+40	A	52	LEU	0.999961	0.0039	29
+41	A	77	GLU	0.999961	0.0039	54
+42	A	144	LEU	0.999961	0.0039	121
+43	A	56	VAL	0.999962	0.0038	33
+44	A	99	ALA	0.999963	0.0037	76
+45	A	90	ARG	0.999963	0.0037	67
+46	A	112	CYS	0.999964	0.0036	89
+47	A	71	LEU	0.999964	0.0036	48
+48	A	149	LEU	0.999964	0.0036	126
+49	A	105	GLY	0.999964	0.0036	82
+50	A	74	TYR	0.999964	0.0036	51
+51	A	150	ARG	0.999965	0.0035	127
+52	A	135	VAL	0.999966	0.0034	112
+53	A	131	GLU	0.999966	0.0034	108
+54	A	129	SER	0.999967	0.0033	106
+55	A	130	THR	0.999967	0.0033	107
+56	A	48	GLN	0.999967	0.0033	25
+57	A	84	PRO	0.999968	0.0032	61
+58	A	95	LYS	0.999968	0.0032	72
+59	A	50	GLU	0.999969	0.0031	27
+60	A	67	THR	0.999969	0.0031	44
+61	A	117	GLN	0.999969	0.0031	94
+62	A	137	LEU	0.999969	0.0031	114
+63	A	139	SER	0.999970	0.0030	116
+64	A	76	SER	0.999970	0.0030	53
+65	A	102	ALA	0.999971	0.0029	79
+66	A	118	TYR	0.999971	0.0029	95
+67	A	33	PHE	0.999971	0.0029	10
+68	A	98	GLN	0.999971	0.0029	75
+69	A	59	GLU	0.999972	0.0028	36
+70	A	109	GLU	0.999972	0.0028	86
+71	A	108	MET	0.999972	0.0028	85
+72	A	65	ASP	0.999973	0.0027	42
+73	A	156	GLN	0.999973	0.0027	133
+74	A	134	ARG	0.999973	0.0027	111
+75	A	88	GLU	0.999974	0.0026	65
+76	A	29	ALA	0.999974	0.0026	6
+77	A	40	VAL	0.999975	0.0025	17
+78	A	136	ARG	0.999975	0.0025	113
+79	A	27	GLU	0.999976	0.0024	4
+80	A	161	VAL	0.999976	0.0024	138
+81	A	165	GLY	0.999976	0.0024	142
+82	A	127	GLY	0.999976	0.0024	104
+83	A	80	GLU	0.999977	0.0023	57
+84	A	126	LEU	0.999977	0.0023	103
+85	A	142	ARG	0.999981	0.0019	119
+86	A	78	LEU	0.999981	0.0019	55
+87	A	89	THR	0.999981	0.0019	66
+88	A	116	VAL	0.999981	0.0019	93
+89	A	39	TRP	0.999982	0.0018	16
+90	A	47	VAL	0.999982	0.0018	24
+91	A	145	ARG	0.999982	0.0018	122
+92	A	66	GLU	0.999982	0.0018	43
+93	A	35	ASP	0.999982	0.0018	12
+94	A	68	MET	0.999982	0.0018	45
+95	A	124	ALA	0.999983	0.0017	101
+96	A	26	TRP	0.999983	0.0017	3
+97	A	94	SER	0.999983	0.0017	71
+98	A	36	TYR	0.999984	0.0016	13
+99	A	101	GLN	0.999984	0.0016	78
+100	A	111	VAL	0.999984	0.0016	88
+101	A	72	LYS	0.999985	0.0015	49
+102	A	157	LYS	0.999986	0.0014	134
+103	A	160	ALA	0.999986	0.0014	137
+104	A	96	GLU	0.999986	0.0014	73
+105	A	28	LEU	0.999986	0.0014	5
+106	A	107	ASP	0.999986	0.0014	84
+107	A	120	GLY	0.999986	0.0014	97
+108	A	146	LYS	0.999986	0.0014	123
+109	A	73	ALA	0.999986	0.0014	50
+110	A	155	LEU	0.999987	0.0013	132
+111	A	110	ASP	0.999987	0.0013	87
+112	A	91	ALA	0.999987	0.0013	68
+113	A	125	MET	0.999987	0.0013	102
+114	A	100	ALA	0.999987	0.0013	77
+115	A	49	GLU	0.999987	0.0013	26
+116	A	148	LEU	0.999987	0.0013	125
+117	A	81	GLN	0.999988	0.0012	58
+118	A	151	ASP	0.999988	0.0012	128
+119	A	31	GLY	0.999989	0.0011	8
+120	A	123	GLN	0.999989	0.0011	100
+121	A	143	LYS	0.999989	0.0011	120
+122	A	132	GLU	0.999990	0.0010	109
+123	A	97	LEU	0.999990	0.0010	74
+124	A	83	THR	0.999990	0.0010	60
+125	A	51	LEU	0.999990	0.0010	28
+126	A	79	GLU	0.999990	0.0010	56
+127	A	60	LEU	0.999991	0.0009	37
+128	A	153	ASP	0.999991	0.0009	130
+129	A	82	LEU	0.999992	0.0008	59
+130	A	103	ARG	0.999992	0.0008	80
+131	A	30	LEU	0.999992	0.0008	7
+132	A	133	LEU	0.999993	0.0007	110
+133	A	69	LYS	0.999993	0.0007	46
+134	A	87	GLU	0.999994	0.0006	64
+135	A	93	LEU	0.999994	0.0006	70
+136	A	122	VAL	0.999994	0.0006	99
+137	A	86	ALA	0.999994	0.0006	63
+138	A	70	GLU	0.999995	0.0005	47
+139	A	154	ASP	0.999995	0.0005	131
+140	A	92	ARG	0.999996	0.0004	69
+141	A	115	LEU	0.999996	0.0004	92
+142	A	63	LEU	0.999997	0.0003	40
+143	A	62	ALA	0.999998	0.0002	39

1lpe_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1lpe_all", "cos_distances": [0.9998215436935425, 0.9999563694000244, 0.9999833106994629, 0.9999758005142212, 0.9999859929084778, 0.9999744296073914, 0.9999921917915344, 0.9999889135360718, 0.9997735023498535, 0.9999713897705078, 0.9998962879180908, 0.999982476234436, 0.9999838471412659, 0.9999530911445618, 0.9999292492866516, 0.9999817609786987, 0.9999750852584839, 0.9998788833618164, 0.9999566078186035, 0.999945878982544, 0.9999406337738037, 0.9999556541442871, 0.9999568462371826, 0.9999819993972778, 0.9999672770500183, 0.9999873638153076, 0.9999685287475586, 0.9999902248382568, 0.999960720539093, 0.99996018409729, 0.9999147057533264, 0.9999591112136841, 0.999962329864502, 0.9998857975006104, 0.9998794794082642, 0.9999715089797974, 0.9999905228614807, 0.9999408721923828, 0.9999977946281433, 0.9999968409538269, 0.9999586939811707, 0.9999726414680481, 0.9999821782112122, 0.9999688863754272, 0.999982476234436, 0.9999932050704956, 0.9999949336051941, 0.9999637007713318, 0.9999853372573853, 0.999986469745636, 0.9999640583992004, 0.9999523162841797, 0.999970018863678, 0.9999610781669617, 0.9999810457229614, 0.9999902248382568, 0.9999769330024719, 0.9999884366989136, 0.9999915957450867, 0.9999901652336121, 0.9999677538871765, 0.9998506307601929, 0.9999943971633911, 0.9999942183494568, 0.999973714351654, 0.9999810457229614, 0.9999634623527527, 0.9999868869781494, 0.9999956488609314, 0.9999942183494568, 0.9999833106994629, 0.9999681711196899, 0.9999857544898987, 0.9999899864196777, 0.9999713897705078, 0.999962568283081, 0.9999871253967285, 0.9999841451644897, 0.9999709129333496, 0.999991774559021, 0.9999505877494812, 0.9999638795852661, 0.9998095631599426, 0.9999860525131226, 0.999971866607666, 0.9999716281890869, 0.9999868273735046, 0.9999843835830688, 0.999963641166687, 0.9999529123306274, 0.9997912645339966, 0.9999962449073792, 0.9999812841415405, 0.9999691247940063, 0.9999712705612183, 0.9999176263809204, 0.9999861717224121, 0.9997258186340332, 0.9999943375587463, 0.9999890327453613, 0.9999827146530151, 0.9999868869781494, 0.9999771118164062, 0.999976396560669, 0.9997442960739136, 0.9999666810035706, 0.999967098236084, 0.9999661445617676, 0.9999898672103882, 0.999992847442627, 0.9999734163284302, 0.9999656081199646, 0.9999750852584839, 0.999969482421875, 0.9999575614929199, 0.9999699592590332, 0.9999510049819946, 0.9999091029167175, 0.9999806880950928, 0.9999892711639404, 0.9999613761901855, 0.9999819993972778, 0.9999861717224121, 0.9999570846557617, 0.9999874234199524, 0.9999637603759766, 0.9999645352363586, 0.9999884366989136, 0.9999544620513916, 0.9999911189079285, 0.9999953508377075, 0.9999866485595703, 0.9999730587005615, 0.9999856948852539, 0.9999584555625916, 0.9999508857727051, 0.9999856948852539, 0.9999760389328003, 0.999901294708252, 0.9998615384101868, 0.999947190284729, 0.9999760389328003, 0.9997249841690063, 0.9999381303787231], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144], "time_seconds": 23.1079, "peak_memory_mb": 1063.86}

1lpe_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1lpe",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1lpe_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1lpe
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1lpe.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 166+121+128+32+114+106+24+85+163+41 and chain A
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 166 and chain A
+color red, critical_rank1
+select critical_rank2, resi 121 and chain A
+color tv_red, critical_rank2
+select critical_rank3, resi 128 and chain A
+color salmon, critical_rank3
+select critical_rank4, resi 32 and chain A
+color lightsalmon, critical_rank4
+select critical_rank5, resi 114 and chain A
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1lpe_critical.pse
+# To save image: png 1lpe_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1lpe_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 23.11,
+  "total_time_minutes": 0.39,
+  "time_per_structure": {
+    "mean": 23.1079,
+    "std": 0.0,
+    "min": 23.1079,
+    "max": 23.1079
+  },
+  "output_file": "output/1lpe_interact_scores.json",
+  "input_file": "downloads/pdbs/1lpe.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 1063.86,
+    "max": 1063.86
+  }
+}

1nfn_critical_residues.tsv

@@ -0,0 +1,140 @@
+# ATOMICA Critical Residue Analysis: 1nfn_all
+# Structure ID: 1nfn
+# Total residues analyzed: 131
+# Mean ATOMICA_SCORE: 0.999961
+# Std Dev: 0.000049
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	A	32	ARG	0.999701	0.0299	9
+2	A	128	GLN	0.999742	0.0258	95
+3	A	121	GLU	0.999762	0.0238	88
+4	A	24	GLN	0.999779	0.0221	1
+5	A	114	ARG	0.999794	0.0206	81
+6	A	106	ALA	0.999800	0.0200	73
+7	A	41	GLN	0.999878	0.0122	18
+8	A	43	LEU	0.999879	0.0121	20
+9	A	93	LEU	0.999883	0.0117	60
+10	A	54	SER	0.999896	0.0104	31
+11	A	80	GLU	0.999904	0.0096	57
+12	A	141	LEU	0.999906	0.0094	108
+13	A	137	LEU	0.999923	0.0077	104
+14	A	34	TRP	0.999929	0.0071	11
+15	A	44	SER	0.999930	0.0070	21
+16	A	118	TYR	0.999944	0.0056	85
+17	A	102	ALA	0.999949	0.0051	69
+18	A	119	ARG	0.999951	0.0049	86
+19	A	27	GLU	0.999952	0.0048	4
+20	A	58	GLN	0.999953	0.0047	35
+21	A	76	SER	0.999953	0.0047	53
+22	A	42	THR	0.999955	0.0045	19
+23	A	35	ASP	0.999956	0.0044	12
+24	A	46	GLN	0.999957	0.0043	23
+25	A	138	ALA	0.999957	0.0043	105
+26	A	73	ALA	0.999958	0.0042	50
+27	A	163	GLN	0.999959	0.0041	130
+28	A	96	GLU	0.999959	0.0041	63
+29	A	71	LEU	0.999960	0.0040	48
+30	A	105	GLY	0.999961	0.0039	72
+31	A	56	VAL	0.999961	0.0039	33
+32	A	25	ARG	0.999963	0.0037	2
+33	A	129	SER	0.999963	0.0037	96
+34	A	162	TYR	0.999963	0.0037	129
+35	A	52	LEU	0.999963	0.0037	29
+36	A	37	LEU	0.999964	0.0036	14
+37	A	74	TYR	0.999964	0.0036	51
+38	A	139	SER	0.999965	0.0035	106
+39	A	123	GLN	0.999966	0.0034	90
+40	A	57	THR	0.999967	0.0033	34
+41	A	132	GLU	0.999968	0.0032	99
+42	A	134	ARG	0.999968	0.0032	101
+43	A	157	LYS	0.999968	0.0032	124
+44	A	65	ASP	0.999969	0.0031	42
+45	A	47	VAL	0.999969	0.0031	24
+46	A	94	SER	0.999969	0.0031	61
+47	A	117	GLN	0.999969	0.0031	84
+48	A	159	LEU	0.999970	0.0030	126
+49	A	51	LEU	0.999970	0.0030	28
+50	A	112	CYS	0.999970	0.0030	79
+51	A	133	LEU	0.999970	0.0030	100
+52	A	28	LEU	0.999971	0.0029	5
+53	A	116	VAL	0.999971	0.0029	83
+54	A	158	ARG	0.999971	0.0029	125
+55	A	124	ALA	0.999971	0.0029	91
+56	A	145	ARG	0.999971	0.0029	112
+57	A	33	PHE	0.999971	0.0029	10
+58	A	95	LYS	0.999973	0.0027	62
+59	A	152	ALA	0.999973	0.0027	119
+60	A	101	GLN	0.999973	0.0027	68
+61	A	131	GLU	0.999974	0.0026	98
+62	A	92	ARG	0.999974	0.0026	59
+63	A	155	LEU	0.999974	0.0026	122
+64	A	97	LEU	0.999974	0.0026	64
+65	A	153	ASP	0.999974	0.0026	120
+66	A	149	LEU	0.999974	0.0026	116
+67	A	108	MET	0.999975	0.0025	75
+68	A	59	GLU	0.999975	0.0025	36
+69	A	75	LYS	0.999975	0.0025	52
+70	A	140	HIS	0.999976	0.0024	107
+71	A	142	ARG	0.999976	0.0024	109
+72	A	53	SER	0.999977	0.0023	30
+73	A	48	GLN	0.999977	0.0023	25
+74	A	156	GLN	0.999977	0.0023	123
+75	A	36	TYR	0.999978	0.0022	13
+76	A	31	GLY	0.999978	0.0022	8
+77	A	77	GLU	0.999978	0.0022	54
+78	A	61	ARG	0.999978	0.0022	38
+79	A	150	ARG	0.999978	0.0022	117
+80	A	98	GLN	0.999979	0.0021	65
+81	A	109	GLU	0.999979	0.0021	76
+82	A	72	LYS	0.999979	0.0021	49
+83	A	38	ARG	0.999979	0.0021	15
+84	A	113	GLY	0.999979	0.0021	80
+85	A	127	GLY	0.999979	0.0021	94
+86	A	99	ALA	0.999981	0.0019	66
+87	A	107	ASP	0.999981	0.0019	74
+88	A	45	GLU	0.999981	0.0019	22
+89	A	151	ASP	0.999981	0.0019	118
+90	A	78	LEU	0.999981	0.0019	55
+91	A	104	LEU	0.999981	0.0019	71
+92	A	60	LEU	0.999981	0.0019	37
+93	A	29	ALA	0.999982	0.0018	6
+94	A	69	LYS	0.999982	0.0018	46
+95	A	55	GLN	0.999982	0.0018	32
+96	A	81	GLN	0.999983	0.0017	58
+97	A	49	GLU	0.999983	0.0017	26
+98	A	164	ALA	0.999983	0.0017	131
+99	A	160	ALA	0.999984	0.0016	127
+100	A	146	LYS	0.999985	0.0015	113
+101	A	100	ALA	0.999985	0.0015	67
+102	A	110	ASP	0.999985	0.0015	77
+103	A	62	ALA	0.999985	0.0015	39
+104	A	50	GLU	0.999985	0.0015	27
+105	A	130	THR	0.999985	0.0015	97
+106	A	66	GLU	0.999985	0.0015	43
+107	A	122	VAL	0.999986	0.0014	89
+108	A	126	LEU	0.999986	0.0014	93
+109	A	67	THR	0.999987	0.0013	44
+110	A	103	ARG	0.999987	0.0013	70
+111	A	125	MET	0.999987	0.0013	92
+112	A	154	ASP	0.999987	0.0013	121
+113	A	144	LEU	0.999988	0.0012	111
+114	A	148	LEU	0.999988	0.0012	115
+115	A	161	VAL	0.999989	0.0011	128
+116	A	70	GLU	0.999990	0.0010	47
+117	A	79	GLU	0.999990	0.0010	56
+118	A	120	GLY	0.999990	0.0010	87
+119	A	64	MET	0.999990	0.0010	41
+120	A	40	VAL	0.999991	0.0009	17
+121	A	135	VAL	0.999991	0.0009	102
+122	A	147	ARG	0.999991	0.0009	114
+123	A	68	MET	0.999991	0.0009	45
+124	A	26	TRP	0.999991	0.0009	3
+125	A	136	ARG	0.999993	0.0007	103
+126	A	143	LYS	0.999994	0.0006	110
+127	A	30	LEU	0.999995	0.0005	7
+128	A	39	TRP	0.999996	0.0004	16
+129	A	115	LEU	0.999997	0.0003	82
+130	A	63	LEU	0.999998	0.0002	40
+131	A	111	VAL	0.999998	0.0002	78

1nfn_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1nfn_all", "cos_distances": [0.999779462814331, 0.9999625086784363, 0.9999914169311523, 0.9999524354934692, 0.9999706745147705, 0.9999818801879883, 0.9999954700469971, 0.9999778866767883, 0.9997014403343201, 0.9999712109565735, 0.9999289512634277, 0.9999555945396423, 0.9999775886535645, 0.9999637603759766, 0.9999791383743286, 0.9999958276748657, 0.999990701675415, 0.9998783469200134, 0.9999549388885498, 0.9998787045478821, 0.9999299645423889, 0.9999809265136719, 0.9999570846557617, 0.9999687671661377, 0.9999767541885376, 0.9999830722808838, 0.9999849796295166, 0.9999698400497437, 0.9999634027481079, 0.9999765157699585, 0.9998964071273804, 0.9999821186065674, 0.9999610185623169, 0.9999666213989258, 0.9999525547027588, 0.9999749064445496, 0.9999811053276062, 0.9999780654907227, 0.999984860420227, 0.999997615814209, 0.9999904632568359, 0.9999685287475586, 0.99998539686203, 0.9999870657920837, 0.9999911189079285, 0.9999819993972778, 0.9999895095825195, 0.9999595880508423, 0.9999788999557495, 0.9999582767486572, 0.9999644756317139, 0.9999749660491943, 0.9999526143074036, 0.9999780058860779, 0.9999810457229614, 0.9999895691871643, 0.999903678894043, 0.9999827742576599, 0.9999736547470093, 0.9998828768730164, 0.999969482421875, 0.9999725222587585, 0.9999593496322632, 0.9999740123748779, 0.99997878074646, 0.9999805092811584, 0.9999847412109375, 0.999973475933075, 0.9999492168426514, 0.9999872446060181, 0.9999810457229614, 0.9999607801437378, 0.9997998476028442, 0.9999805688858032, 0.9999746084213257, 0.9999788403511047, 0.9999847412109375, 0.9999977350234985, 0.999970018863678, 0.9999793171882629, 0.9997944831848145, 0.9999973773956299, 0.9999708533287048, 0.999969482421875, 0.9999441504478455, 0.9999505281448364, 0.9999899864196777, 0.9997618794441223, 0.9999855160713196, 0.9999659061431885, 0.9999709725379944, 0.9999873638153076, 0.9999864101409912, 0.9999793767929077, 0.9997416734695435, 0.9999630451202393, 0.9999852776527405, 0.9999735355377197, 0.999967634677887, 0.9999700784683228, 0.9999677538871765, 0.9999910593032837, 0.999993085861206, 0.9999234080314636, 0.9999573230743408, 0.9999651908874512, 0.9999758005142212, 0.9999057650566101, 0.9999761581420898, 0.9999944567680359, 0.9999876618385315, 0.9999711513519287, 0.9999845027923584, 0.9999910593032837, 0.999988317489624, 0.9999741315841675, 0.999978244304657, 0.9999809265136719, 0.9999729990959167, 0.9999740123748779, 0.9999874830245972, 0.9999737739562988, 0.9999768733978271, 0.9999680519104004, 0.9999708533287048, 0.9999695420265198, 0.9999842643737793, 0.9999886155128479, 0.9999632835388184, 0.9999588131904602, 0.9999833106994629, 0.9999610185623169], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132], "time_seconds": 21.0377, "peak_memory_mb": 990.49}

1nfn_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1nfn",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1nfn_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1nfn
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1nfn.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 32+128+121+24+114+106+41+43+93+54 and chain A
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 32 and chain A
+color red, critical_rank1
+select critical_rank2, resi 128 and chain A
+color tv_red, critical_rank2
+select critical_rank3, resi 121 and chain A
+color salmon, critical_rank3
+select critical_rank4, resi 24 and chain A
+color lightsalmon, critical_rank4
+select critical_rank5, resi 114 and chain A
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1nfn_critical.pse
+# To save image: png 1nfn_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1nfn_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 21.04,
+  "total_time_minutes": 0.35,
+  "time_per_structure": {
+    "mean": 21.0377,
+    "std": 0.0,
+    "min": 21.0377,
+    "max": 21.0377
+  },
+  "output_file": "output/1nfn_interact_scores.json",
+  "input_file": "downloads/pdbs/1nfn.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 990.49,
+    "max": 990.49
+  }
+}

1o4x_critical_residues.tsv

@@ -0,0 +1,214 @@
+# ATOMICA Critical Residue Analysis: 1o4x_all
+# Structure ID: 1o4x
+# Total residues analyzed: 205
+# Mean ATOMICA_SCORE: 0.999970
+# Std Dev: 0.000033
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	B	270	LYS	0.999772	0.0228	193
+2	B	210	ARG	0.999822	0.0178	133
+3	B	282	LYS	0.999856	0.0144	205
+4	A	138	ALA	0.999865	0.0135	103
+5	B	260	GLU	0.999867	0.0133	183
+6	B	257	PHE	0.999878	0.0122	180
+7	A	74	TRP	0.999887	0.0113	69
+8	A	67	LEU	0.999888	0.0112	62
+9	B	256	PRO	0.999889	0.0111	179
+10	A	112	GLU	0.999897	0.0103	77
+11	A	78	ALA	0.999904	0.0096	73
+12	A	140	GLN	0.999907	0.0093	105
+13	A	58	ASN	0.999915	0.0085	53
+14	B	273	PRO	0.999918	0.0082	196
+15	B	229	GLU	0.999919	0.0081	152
+16	B	232	LYS	0.999920	0.0080	155
+17	B	227	ALA	0.999921	0.0079	150
+18	A	153	CYS	0.999921	0.0079	118
+19	A	9	ASP	0.999923	0.0077	4
+20	A	71	LEU	0.999923	0.0077	66
+21	A	69	PRO	0.999926	0.0074	64
+22	B	233	MET	0.999929	0.0071	156
+23	A	48	GLN	0.999931	0.0069	43
+24	B	211	PRO	0.999933	0.0067	134
+25	A	49	THR	0.999935	0.0065	44
+26	B	231	PRO	0.999936	0.0064	154
+27	B	226	MET	0.999939	0.0061	149
+28	B	281	ARG	0.999943	0.0057	204
+29	A	121	LYS	0.999949	0.0051	86
+30	A	136	MET	0.999952	0.0048	101
+31	A	72	GLU	0.999954	0.0046	67
+32	A	17	ALA	0.999955	0.0045	12
+33	B	246	TRP	0.999956	0.0044	169
+34	A	110	SER	0.999956	0.0044	75
+35	A	143	MET	0.999957	0.0043	108
+36	A	77	ASP	0.999959	0.0041	72
+37	A	154	ASN	0.999961	0.0039	119
+38	B	252	THR	0.999962	0.0038	175
+39	A	51	ILE	0.999962	0.0038	46
+40	A	8	SER	0.999963	0.0037	3
+41	B	254	LYS	0.999963	0.0037	177
+42	A	36	LEU	0.999963	0.0037	31
+43	A	52	SER	0.999964	0.0036	47
+44	B	235	ASN	0.999964	0.0036	158
+45	A	111	ILE	0.999964	0.0036	76
+46	A	118	ALA	0.999964	0.0036	83
+47	B	207	ARG	0.999965	0.0035	130
+48	A	119	LEU	0.999966	0.0034	84
+49	A	151	TRP	0.999966	0.0034	116
+50	A	133	GLU	0.999966	0.0034	98
+51	A	60	SER	0.999966	0.0034	55
+52	A	156	ARG	0.999966	0.0034	121
+53	A	144	GLU	0.999968	0.0032	109
+54	B	240	LYS	0.999968	0.0032	163
+55	A	137	ILE	0.999968	0.0032	102
+56	B	217	VAL	0.999969	0.0031	140
+57	A	145	LYS	0.999970	0.0030	110
+58	A	66	LYS	0.999970	0.0030	61
+59	A	123	PHE	0.999970	0.0030	88
+60	A	19	THR	0.999971	0.0029	14
+61	A	11	GLU	0.999971	0.0029	6
+62	A	113	THR	0.999971	0.0029	78
+63	B	275	TYR	0.999971	0.0029	198
+64	A	15	GLN	0.999971	0.0029	10
+65	A	142	ASN	0.999971	0.0029	107
+66	B	247	LYS	0.999972	0.0028	170
+67	A	18	LYS	0.999973	0.0027	13
+68	B	250	SER	0.999973	0.0027	173
+69	B	258	ILE	0.999974	0.0026	181
+70	A	157	GLN	0.999974	0.0026	122
+71	B	228	GLN	0.999974	0.0026	151
+72	A	148	ILE	0.999974	0.0026	113
+73	B	259	ASP	0.999975	0.0025	182
+74	A	79	GLU	0.999975	0.0025	74
+75	A	73	LYS	0.999975	0.0025	68
+76	A	33	ASP	0.999976	0.0024	28
+77	A	31	GLN	0.999976	0.0024	26
+78	A	76	ASN	0.999976	0.0024	71
+79	A	10	LEU	0.999976	0.0024	5
+80	A	135	THR	0.999976	0.0024	100
+81	A	163	ASN	0.999976	0.0024	128
+82	A	130	THR	0.999977	0.0023	95
+83	B	274	ASP	0.999977	0.0023	197
+84	A	35	GLY	0.999977	0.0023	30
+85	A	14	GLU	0.999978	0.0022	9
+86	A	128	LYS	0.999978	0.0022	93
+87	A	117	VAL	0.999978	0.0022	82
+88	A	55	GLU	0.999978	0.0022	50
+89	A	65	ALA	0.999978	0.0022	60
+90	B	251	GLU	0.999979	0.0021	174
+91	B	277	TYR	0.999979	0.0021	200
+92	A	64	MET	0.999979	0.0021	59
+93	B	271	GLU	0.999979	0.0021	194
+94	B	262	LYS	0.999980	0.0020	185
+95	A	162	ILE	0.999980	0.0020	127
+96	A	131	SER	0.999980	0.0020	96
+97	B	279	PRO	0.999981	0.0019	202
+98	B	248	LEU	0.999981	0.0019	171
+99	B	234	HIS	0.999981	0.0019	157
+100	A	57	LEU	0.999981	0.0019	52
+101	B	269	MET	0.999981	0.0019	192
+102	B	264	LEU	0.999982	0.0018	187
+103	A	139	ASP	0.999982	0.0018	104
+104	A	6	GLU	0.999982	0.0018	1
+105	B	221	GLY	0.999982	0.0018	144
+106	B	268	HIS	0.999982	0.0018	191
+107	A	13	LEU	0.999982	0.0018	8
+108	A	12	GLU	0.999982	0.0018	7
+109	A	39	GLY	0.999983	0.0017	34
+110	A	62	LYS	0.999983	0.0017	57
+111	A	125	GLU	0.999983	0.0017	90
+112	A	134	ILE	0.999983	0.0017	99
+113	B	280	ARG	0.999983	0.0017	203
+114	A	38	MET	0.999983	0.0017	33
+115	A	24	ARG	0.999984	0.0016	19
+116	B	209	LYS	0.999984	0.0016	132
+117	A	25	ILE	0.999984	0.0016	20
+118	B	238	ILE	0.999984	0.0016	161
+119	A	28	GLY	0.999985	0.0015	23
+120	A	161	ARG	0.999985	0.0015	126
+121	A	20	PHE	0.999985	0.0015	15
+122	B	241	ARG	0.999985	0.0015	164
+123	B	265	ARG	0.999985	0.0015	188
+124	B	263	ARG	0.999985	0.0015	186
+125	B	272	HIS	0.999986	0.0014	195
+126	B	255	ARG	0.999986	0.0014	178
+127	B	261	ALA	0.999986	0.0014	184
+128	A	50	THR	0.999986	0.0014	45
+129	B	215	PHE	0.999986	0.0014	138
+130	A	43	GLY	0.999986	0.0014	38
+131	A	129	PRO	0.999986	0.0014	94
+132	B	206	ASP	0.999986	0.0014	129
+133	A	63	ASN	0.999987	0.0013	58
+134	A	126	ASN	0.999987	0.0013	91
+135	A	160	LYS	0.999987	0.0013	125
+136	A	53	ARG	0.999987	0.0013	48
+137	B	245	GLU	0.999988	0.0012	168
+138	A	47	SER	0.999988	0.0012	42
+139	A	70	LEU	0.999988	0.0012	65
+140	B	224	ARG	0.999988	0.0012	147
+141	A	7	PRO	0.999988	0.0012	2
+142	A	30	THR	0.999988	0.0012	25
+143	A	122	SER	0.999988	0.0012	87
+144	A	141	LEU	0.999989	0.0011	106
+145	B	218	TRP	0.999989	0.0011	141
+146	B	225	LYS	0.999989	0.0011	148
+147	B	249	LEU	0.999989	0.0011	172
+148	B	236	SER	0.999989	0.0011	159
+149	B	244	ALA	0.999989	0.0011	167
+150	B	242	LEU	0.999990	0.0010	165
+151	A	22	GLN	0.999990	0.0010	17
+152	B	208	VAL	0.999990	0.0010	131
+153	B	276	LYS	0.999990	0.0010	199
+154	A	27	LEU	0.999990	0.0010	22
+155	A	34	VAL	0.999990	0.0010	29
+156	B	222	GLN	0.999990	0.0010	145
+157	A	26	LYS	0.999990	0.0010	21
+158	B	237	GLU	0.999991	0.0009	160
+159	A	23	ARG	0.999991	0.0009	18
+160	A	132	GLU	0.999991	0.0009	97
+161	A	155	ARG	0.999991	0.0009	120
+162	A	127	GLN	0.999991	0.0009	92
+163	B	219	SER	0.999991	0.0009	142
+164	B	230	ASN	0.999991	0.0009	153
+165	A	59	LEU	0.999991	0.0009	54
+166	A	159	GLU	0.999992	0.0008	124
+167	A	46	PHE	0.999992	0.0008	41
+168	A	116	ARG	0.999992	0.0008	81
+169	A	146	GLU	0.999992	0.0008	111
+170	B	278	ARG	0.999992	0.0008	201
+171	A	40	LYS	0.999992	0.0008	35
+172	A	158	LYS	0.999992	0.0008	123
+173	A	16	PHE	0.999992	0.0008	11
+174	A	42	TYR	0.999992	0.0008	37
+175	A	44	ASN	0.999993	0.0007	39
+176	B	243	GLY	0.999993	0.0007	166
+177	A	152	PHE	0.999993	0.0007	117
+178	B	267	LEU	0.999993	0.0007	190
+179	B	216	MET	0.999993	0.0007	139
+180	A	115	ILE	0.999993	0.0007	80
+181	A	120	GLU	0.999993	0.0007	85
+182	A	150	VAL	0.999993	0.0007	115
+183	B	214	ALA	0.999993	0.0007	137
+184	A	37	ALA	0.999993	0.0007	32
+185	A	45	ASP	0.999993	0.0007	40
+186	B	239	SER	0.999993	0.0007	162
+187	A	147	VAL	0.999994	0.0006	112
+188	A	149	ARG	0.999994	0.0006	114
+189	B	266	ALA	0.999995	0.0005	189
+190	A	56	ALA	0.999995	0.0005	51
+191	B	212	MET	0.999995	0.0005	135
+192	B	213	ASN	0.999995	0.0005	136
+193	A	29	PHE	0.999995	0.0005	24
+194	B	223	ARG	0.999995	0.0005	146
+195	B	220	ARG	0.999996	0.0004	143
+196	A	75	LEU	0.999996	0.0004	70
+197	A	21	LYS	0.999997	0.0003	16
+198	B	253	GLU	0.999998	0.0002	176
+199	A	32	GLY	0.999998	0.0002	27
+200	A	41	LEU	0.999998	0.0002	36
+201	A	68	LYS	0.999998	0.0002	63
+202	A	54	PHE	0.999998	0.0002	49
+203	A	124	LEU	0.999998	0.0002	89
+204	A	61	PHE	0.999999	0.0001	56
+205	A	114	ASN	0.999999	0.0001	79

1o4x_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1o4x_all", "cos_distances": [0.9999818801879883, 0.9999880790710449, 0.9999625086784363, 0.9999232292175293, 0.9999760389328003, 0.9999708533287048, 0.9999823570251465, 0.9999822378158569, 0.9999779462814331, 0.9999712705612183, 0.9999924898147583, 0.9999548196792603, 0.9999730587005615, 0.9999707937240601, 0.9999852180480957, 0.9999970197677612, 0.9999896287918091, 0.9999905824661255, 0.9999839663505554, 0.9999842643737793, 0.9999904632568359, 0.9999898076057434, 0.9999847412109375, 0.9999954104423523, 0.9999881386756897, 0.9999755620956421, 0.9999979734420776, 0.9999755024909973, 0.9999898672103882, 0.9999772906303406, 0.9999628663063049, 0.9999933242797852, 0.9999833106994629, 0.9999828338623047, 0.9999922513961792, 0.9999980926513672, 0.9999924898147583, 0.9999861717224121, 0.9999926090240479, 0.9999933838844299, 0.999991774559021, 0.9999877214431763, 0.9999313354492188, 0.9999346137046814, 0.9999861121177673, 0.999962329864502, 0.9999637007713318, 0.9999874234199524, 0.999998152256012, 0.9999784231185913, 0.9999946355819702, 0.9999812245368958, 0.9999151229858398, 0.9999911785125732, 0.9999663233757019, 0.9999989867210388, 0.9999829530715942, 0.999987006187439, 0.9999793171882629, 0.9999784231185913, 0.9999698996543884, 0.9998881816864014, 0.9999980926513672, 0.9999256134033203, 0.9999878406524658, 0.9999233484268188, 0.9999544620513916, 0.9999752640724182, 0.9998871088027954, 0.9999958872795105, 0.9999758005142212, 0.9999589920043945, 0.999904453754425, 0.9999752044677734, 0.9999560117721558, 0.9999641180038452, 0.9998968839645386, 0.9999710321426392, 0.9999994039535522, 0.9999932050704956, 0.9999919533729553, 0.9999783039093018, 0.9999644160270691, 0.9999657273292542, 0.9999932050704956, 0.9999493956565857, 0.9999884366989136, 0.9999703764915466, 0.9999984502792358, 0.9999830722808838, 0.999987006187439, 0.9999907612800598, 0.9999780058860779, 0.999986469745636, 0.9999768137931824, 0.999980092048645, 0.9999905824661255, 0.9999661445617676, 0.9999831318855286, 0.9999760389328003, 0.999951958656311, 0.999968409538269, 0.9998645782470703, 0.9999815821647644, 0.9999065399169922, 0.9999885559082031, 0.9999712705612183, 0.999957263469696, 0.9999679327011108, 0.9999697804450989, 0.9999920129776001, 0.9999935030937195, 0.9999743700027466, 0.9999943375587463, 0.9999932050704956, 0.9999657273292542, 0.9999927282333374, 0.9999213218688965, 0.9999610781669617, 0.9999905824661255, 0.9999664425849915, 0.9999741315841675, 0.9999924302101135, 0.9999916553497314, 0.999987006187439, 0.9999850988388062, 0.9999800324440002, 0.9999762773513794, 0.999986469745636, 0.9999654293060303, 0.9999896287918091, 0.9999841451644897, 0.9998222589492798, 0.9999325275421143, 0.9999947547912598, 0.9999949336051941, 0.9999932646751404, 0.9999861121177673, 0.9999931454658508, 0.9999688863754272, 0.9999890327453613, 0.9999908208847046, 0.999995768070221, 0.9999820590019226, 0.9999898672103882, 0.9999954104423523, 0.9999879598617554, 0.9999890327453613, 0.99993896484375, 0.999920666217804, 0.9999741315841675, 0.9999191164970398, 0.9999908804893494, 0.9999363422393799, 0.9999195337295532, 0.9999290704727173, 0.999981164932251, 0.9999638199806213, 0.9999892115592957, 0.9999905228614807, 0.9999843835830688, 0.9999933838844299, 0.9999682903289795, 0.9999852180480957, 0.9999895691871643, 0.9999926090240479, 0.99998939037323, 0.9999876618385315, 0.9999558925628662, 0.9999722242355347, 0.9999810457229614, 0.9999890923500061, 0.9999731779098511, 0.9999790191650391, 0.9999617338180542, 0.999997615814209, 0.9999626874923706, 0.9999856948852539, 0.9998894929885864, 0.9998781681060791, 0.9999738335609436, 0.9999751448631287, 0.9998669028282166, 0.9999858140945435, 0.9999799132347107, 0.9999854564666748, 0.9999815225601196, 0.9999853372573853, 0.9999945759773254, 0.999992847442627, 0.9999821186065674, 0.9999814033508301, 0.9997720122337341, 0.9999793171882629, 0.9999855160713196, 0.9999175071716309, 0.9999769330024719, 0.9999710321426392, 0.9999896883964539, 0.9999790191650391, 0.9999921917915344, 0.9999805688858032, 0.9999832510948181, 0.9999432563781738, 0.9998564720153809, 0.9999905824661255, 0.9999908804893494, 0.9999570250511169, 0.9999515414237976, 0.9999815225601196, 0.9999805688858032, 0.9999872446060181, 0.9999892711639404, 0.9999879598617554, 0.9999916553497314, 0.9999809265136719, 0.9999878406524658, 0.9998100996017456, 0.9999704360961914, 0.9999758005142212, 0.9999914765357971, 0.9999918341636658, 0.9999913573265076, 0.9999557137489319, 0.9999807476997375, 0.999964714050293, 0.9999915361404419, 0.9999932050704956, 0.9999833106994629, 0.9999060034751892, 0.9999816417694092, 0.9999858736991882, 0.9999920129776001, 0.9999441504478455, 0.9998670220375061, 0.9999934434890747, 0.9999740719795227, 0.9999692440032959, 0.9999639391899109, 0.9999746084213257, 0.9999523162841797, 0.9999515414237976, 0.9999747276306152, 0.9998961687088013], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244], "time_seconds": 52.1905, "peak_memory_mb": 2209.01}

1o4x_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1o4x",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1o4x_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1o4x
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1o4x.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 270+210+282+138+260+257+74+67+256+112 and chain B
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 270 and chain B
+color red, critical_rank1
+select critical_rank2, resi 210 and chain B
+color tv_red, critical_rank2
+select critical_rank3, resi 282 and chain B
+color salmon, critical_rank3
+select critical_rank4, resi 138 and chain A
+color lightsalmon, critical_rank4
+select critical_rank5, resi 260 and chain B
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1o4x_critical.pse
+# To save image: png 1o4x_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1o4x_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 52.19,
+  "total_time_minutes": 0.87,
+  "time_per_structure": {
+    "mean": 52.1905,
+    "std": 0.0,
+    "min": 52.1905,
+    "max": 52.1905
+  },
+  "output_file": "output/1o4x_interact_scores.json",
+  "input_file": "downloads/pdbs/1o4x.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 2209.01,
+    "max": 2209.01
+  }
+}

1oef_critical_residues.tsv

@@ -0,0 +1,32 @@
+# ATOMICA Critical Residue Analysis: 1oef_all
+# Structure ID: 1oef
+# Total residues analyzed: 23
+# Mean ATOMICA_SCORE: 0.999018
+# Std Dev: 0.001075
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	A	279	LEU	0.997222	0.2778	16
+2	A	268	LEU	0.997646	0.2354	5
+3	A	270	GLU	0.997975	0.2025	7
+4	A	280	VAL	0.998317	0.1683	17
+5	A	275	GLN	0.998459	0.1541	12
+6	A	269	VAL	0.998580	0.1420	6
+7	A	281	GLU	0.998991	0.1009	18
+8	A	264	TRP	0.999145	0.0855	1
+9	A	286	ALA	0.999295	0.0705	23
+10	A	267	PRO	0.999416	0.0584	4
+11	A	276	TRP	0.999568	0.0432	13
+12	A	266	GLU	0.999575	0.0425	3
+13	A	284	GLN	0.999580	0.0420	21
+14	A	283	VAL	0.999590	0.0410	20
+15	A	274	ARG	0.999591	0.0409	11
+16	A	272	MET	0.999618	0.0382	9
+17	A	271	ASP	0.999619	0.0381	8
+18	A	273	GLN	0.999712	0.0288	10
+19	A	285	ALA	0.999754	0.0246	22
+20	A	265	PHE	0.999822	0.0178	2
+21	A	277	ALA	0.999855	0.0145	14
+22	A	282	LYS	0.999882	0.0118	19
+23	A	278	GLY	0.999952	0.0048	15

1oef_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1oef_all", "cos_distances": [0.9991451501846313, 0.9998222589492798, 0.9995747804641724, 0.9994158148765564, 0.9976457357406616, 0.9985799789428711, 0.9979747533798218, 0.9996190071105957, 0.9996178150177002, 0.9997122287750244, 0.9995914697647095, 0.9984586238861084, 0.9995677471160889, 0.9998552203178406, 0.9999517798423767, 0.9972220063209534, 0.998316764831543, 0.9989914894104004, 0.9998823404312134, 0.9995895028114319, 0.999579906463623, 0.9997535943984985, 0.9992954134941101, 0.9952763319015503], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24], "time_seconds": 8.6861, "peak_memory_mb": 210.14}

1oef_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1oef",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1oef_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1oef
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1oef.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 279+268+270+280+275+269+281+264+286+267 and chain A
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 279 and chain A
+color red, critical_rank1
+select critical_rank2, resi 268 and chain A
+color tv_red, critical_rank2
+select critical_rank3, resi 270 and chain A
+color salmon, critical_rank3
+select critical_rank4, resi 280 and chain A
+color lightsalmon, critical_rank4
+select critical_rank5, resi 275 and chain A
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1oef_critical.pse
+# To save image: png 1oef_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1oef_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 8.69,
+  "total_time_minutes": 0.14,
+  "time_per_structure": {
+    "mean": 8.6861,
+    "std": 0.0,
+    "min": 8.6861,
+    "max": 8.6861
+  },
+  "output_file": "output/1oef_interact_scores.json",
+  "input_file": "downloads/pdbs/1oef.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 210.14,
+    "max": 210.14
+  }
+}

1u6d_critical_residues.tsv

@@ -0,0 +1,296 @@
+# ATOMICA Critical Residue Analysis: 1u6d_all
+# Structure ID: 1u6d
+# Total residues analyzed: 287
+# Mean ATOMICA_SCORE: 0.999964
+# Std Dev: 0.000035
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	X	399	MET	0.999782	0.0218	77
+2	X	576	THR	0.999792	0.0208	254
+3	X	575	HIS	0.999801	0.0199	253
+4	X	574	GLY	0.999836	0.0164	252
+5	X	348	SER	0.999843	0.0157	26
+6	X	406	CYS	0.999860	0.0140	84
+7	X	324	VAL	0.999860	0.0140	2
+8	X	368	CYS	0.999860	0.0140	46
+9	X	333	GLY	0.999873	0.0127	11
+10	X	478	PHE	0.999875	0.0125	156
+11	X	424	HIS	0.999882	0.0118	102
+12	X	519	ILE	0.999884	0.0116	197
+13	X	452	LEU	0.999886	0.0114	130
+14	X	446	GLU	0.999892	0.0108	124
+15	X	565	ARG	0.999895	0.0105	243
+16	X	525	TYR	0.999899	0.0101	203
+17	X	571	GLY	0.999901	0.0099	249
+18	X	601	ARG	0.999901	0.0099	279
+19	X	420	VAL	0.999902	0.0098	98
+20	X	334	TYR	0.999903	0.0097	12
+21	X	528	GLN	0.999906	0.0094	206
+22	X	524	GLY	0.999907	0.0093	202
+23	X	563	GLN	0.999908	0.0092	241
+24	X	326	ARG	0.999914	0.0086	4
+25	X	323	LYS	0.999917	0.0083	1
+26	X	477	GLY	0.999918	0.0082	155
+27	X	379	GLY	0.999920	0.0080	57
+28	X	373	LEU	0.999921	0.0079	51
+29	X	604	VAL	0.999922	0.0078	282
+30	X	559	ILE	0.999922	0.0078	237
+31	X	430	GLY	0.999924	0.0076	108
+32	X	437	HIS	0.999925	0.0075	115
+33	X	510	ALA	0.999926	0.0074	188
+34	X	365	LEU	0.999926	0.0074	43
+35	X	587	ASP	0.999927	0.0073	265
+36	X	527	GLY	0.999928	0.0072	205
+37	X	463	VAL	0.999929	0.0071	141
+38	X	512	VAL	0.999930	0.0070	190
+39	X	465	VAL	0.999930	0.0070	143
+40	X	418	VAL	0.999931	0.0069	96
+41	X	431	SER	0.999932	0.0068	109
+42	X	466	ALA	0.999935	0.0065	144
+43	X	380	ARG	0.999936	0.0064	58
+44	X	572	TYR	0.999938	0.0062	250
+45	X	387	ASN	0.999938	0.0062	65
+46	X	372	GLY	0.999938	0.0062	50
+47	X	550	MET	0.999938	0.0062	228
+48	X	351	THR	0.999939	0.0061	29
+49	X	606	VAL	0.999941	0.0059	284
+50	X	513	CYS	0.999942	0.0058	191
+51	X	591	TRP	0.999942	0.0058	269
+52	X	607	ALA	0.999943	0.0057	285
+53	X	515	LEU	0.999943	0.0057	193
+54	X	434	CYS	0.999943	0.0057	112
+55	X	425	ILE	0.999943	0.0057	103
+56	X	503	MET	0.999944	0.0056	181
+57	X	573	ASP	0.999946	0.0054	251
+58	X	498	ARG	0.999947	0.0053	176
+59	X	433	GLY	0.999948	0.0052	111
+60	X	456	MET	0.999948	0.0052	134
+61	X	405	PRO	0.999949	0.0051	83
+62	X	435	ILE	0.999949	0.0051	113
+63	X	481	THR	0.999949	0.0051	159
+64	X	409	MET	0.999952	0.0048	87
+65	X	569	LEU	0.999952	0.0048	247
+66	X	393	LEU	0.999952	0.0048	71
+67	X	493	GLU	0.999953	0.0047	171
+68	X	413	ARG	0.999953	0.0047	91
+69	X	517	ASN	0.999953	0.0047	195
+70	X	529	ASP	0.999954	0.0046	207
+71	X	360	VAL	0.999955	0.0045	38
+72	X	496	GLU	0.999955	0.0045	174
+73	X	570	GLY	0.999955	0.0045	248
+74	X	432	HIS	0.999956	0.0044	110
+75	X	480	GLY	0.999956	0.0044	158
+76	X	391	SER	0.999957	0.0043	69
+77	X	352	TRP	0.999957	0.0043	30
+78	X	609	THR	0.999957	0.0043	287
+79	X	546	PHE	0.999957	0.0043	224
+80	X	350	GLY	0.999957	0.0043	28
+81	X	542	GLU	0.999958	0.0042	220
+82	X	328	ILE	0.999958	0.0042	6
+83	X	419	GLY	0.999958	0.0042	97
+84	X	472	LEU	0.999959	0.0041	150
+85	X	589	ASP	0.999960	0.0040	267
+86	X	367	GLY	0.999961	0.0039	45
+87	X	441	GLU	0.999961	0.0039	119
+88	X	397	ASN	0.999961	0.0039	75
+89	X	339	LEU	0.999961	0.0039	17
+90	X	448	ASP	0.999961	0.0039	126
+91	X	384	PRO	0.999962	0.0038	62
+92	X	444	GLU	0.999962	0.0038	122
+93	X	422	ASP	0.999962	0.0038	100
+94	X	357	ASP	0.999964	0.0036	35
+95	X	579	ASP	0.999964	0.0036	257
+96	X	599	SER	0.999964	0.0036	277
+97	X	401	ASN	0.999964	0.0036	79
+98	X	595	THR	0.999964	0.0036	273
+99	X	486	SER	0.999964	0.0036	164
+100	X	487	ALA	0.999965	0.0035	165
+101	X	530	GLN	0.999965	0.0035	208
+102	X	327	LEU	0.999965	0.0035	5
+103	X	501	THR	0.999965	0.0035	179
+104	X	429	GLY	0.999965	0.0035	107
+105	X	378	GLY	0.999966	0.0034	56
+106	X	592	SER	0.999966	0.0034	270
+107	X	582	GLU	0.999967	0.0033	260
+108	X	447	ARG	0.999967	0.0033	125
+109	X	421	ILE	0.999967	0.0033	99
+110	X	468	LEU	0.999968	0.0032	146
+111	X	562	HIS	0.999968	0.0032	240
+112	X	581	VAL	0.999968	0.0032	259
+113	X	593	GLU	0.999968	0.0032	271
+114	X	540	GLU	0.999968	0.0032	218
+115	X	491	TYR	0.999969	0.0031	169
+116	X	594	VAL	0.999969	0.0031	272
+117	X	375	TYR	0.999969	0.0031	53
+118	X	412	PRO	0.999969	0.0031	90
+119	X	497	TRP	0.999969	0.0031	175
+120	X	584	TYR	0.999970	0.0030	262
+121	X	374	LEU	0.999970	0.0030	52
+122	X	580	SER	0.999971	0.0029	258
+123	X	464	GLY	0.999971	0.0029	142
+124	X	523	GLY	0.999971	0.0029	201
+125	X	590	THR	0.999971	0.0029	268
+126	X	359	GLN	0.999972	0.0028	37
+127	X	560	THR	0.999972	0.0028	238
+128	X	585	ASP	0.999972	0.0028	263
+129	X	346	ASN	0.999972	0.0028	24
+130	X	438	ASN	0.999972	0.0028	116
+131	X	392	ALA	0.999972	0.0028	70
+132	X	600	GLY	0.999972	0.0028	278
+133	X	586	PRO	0.999972	0.0028	264
+134	X	458	THR	0.999972	0.0028	136
+135	X	511	GLY	0.999973	0.0027	189
+136	X	453	VAL	0.999973	0.0027	131
+137	X	353	LEU	0.999973	0.0027	31
+138	X	538	ASP	0.999973	0.0027	216
+139	X	507	ARG	0.999973	0.0027	185
+140	X	544	TRP	0.999974	0.0026	222
+141	X	436	HIS	0.999974	0.0026	114
+142	X	385	ASP	0.999974	0.0026	63
+143	X	520	TYR	0.999974	0.0026	198
+144	X	547	VAL	0.999974	0.0026	225
+145	X	414	ASN	0.999974	0.0026	92
+146	X	354	ARG	0.999975	0.0025	32
+147	X	382	ASN	0.999975	0.0025	60
+148	X	407	ALA	0.999975	0.0025	85
+149	X	577	PHE	0.999975	0.0025	255
+150	X	345	TYR	0.999975	0.0025	23
+151	X	532	ASN	0.999975	0.0025	210
+152	X	459	ARG	0.999976	0.0024	137
+153	X	482	ASN	0.999976	0.0024	160
+154	X	535	GLU	0.999976	0.0024	213
+155	X	370	VAL	0.999976	0.0024	48
+156	X	474	ALA	0.999976	0.0024	152
+157	X	483	ARG	0.999976	0.0024	161
+158	X	439	SER	0.999977	0.0023	117
+159	X	543	THR	0.999977	0.0023	221
+160	X	451	HIS	0.999977	0.0023	129
+161	X	506	ILE	0.999977	0.0023	184
+162	X	473	TYR	0.999977	0.0023	151
+163	X	508	SER	0.999977	0.0023	186
+164	X	402	GLN	0.999978	0.0022	80
+165	X	505	THR	0.999978	0.0022	183
+166	X	548	ALA	0.999978	0.0022	226
+167	X	450	TRP	0.999978	0.0022	128
+168	X	340	SER	0.999979	0.0021	18
+169	X	329	TYR	0.999979	0.0021	7
+170	X	552	HIS	0.999979	0.0021	230
+171	X	514	VAL	0.999979	0.0021	192
+172	X	371	GLY	0.999979	0.0021	49
+173	X	404	SER	0.999979	0.0021	82
+174	X	578	LEU	0.999979	0.0021	256
+175	X	376	ALA	0.999980	0.0020	54
+176	X	485	ASN	0.999980	0.0020	163
+177	X	341	TYR	0.999980	0.0020	19
+178	X	361	PRO	0.999981	0.0019	39
+179	X	539	VAL	0.999981	0.0019	217
+180	X	428	VAL	0.999981	0.0019	106
+181	X	388	THR	0.999981	0.0019	66
+182	X	335	PHE	0.999981	0.0019	13
+183	X	553	ARG	0.999981	0.0019	231
+184	X	396	TYR	0.999981	0.0019	74
+185	X	440	VAL	0.999981	0.0019	118
+186	X	534	VAL	0.999981	0.0019	212
+187	X	596	ARG	0.999982	0.0018	274
+188	X	462	GLY	0.999982	0.0018	140
+189	X	516	HIS	0.999982	0.0018	194
+190	X	561	VAL	0.999982	0.0018	239
+191	X	394	ASP	0.999983	0.0017	72
+192	X	423	GLY	0.999983	0.0017	101
+193	X	568	VAL	0.999983	0.0017	246
+194	X	400	THR	0.999983	0.0017	78
+195	X	502	ALA	0.999983	0.0017	180
+196	X	557	LEU	0.999984	0.0016	235
+197	X	470	ARG	0.999984	0.0016	148
+198	X	490	TYR	0.999984	0.0016	168
+199	X	518	CYS	0.999984	0.0016	196
+200	X	605	GLY	0.999984	0.0016	283
+201	X	555	SER	0.999984	0.0016	233
+202	X	526	ASP	0.999984	0.0016	204
+203	X	551	LYS	0.999985	0.0015	229
+204	X	386	GLY	0.999985	0.0015	64
+205	X	479	ASP	0.999985	0.0015	157
+206	X	347	PRO	0.999985	0.0015	25
+207	X	449	GLU	0.999986	0.0014	127
+208	X	533	SER	0.999986	0.0014	211
+209	X	522	ALA	0.999986	0.0014	200
+210	X	597	MET	0.999986	0.0014	275
+211	X	398	PRO	0.999986	0.0014	76
+212	X	603	GLY	0.999986	0.0014	281
+213	X	330	THR	0.999987	0.0013	8
+214	X	476	GLY	0.999987	0.0013	154
+215	X	495	ASN	0.999987	0.0013	173
+216	X	332	GLY	0.999987	0.0013	10
+217	X	383	SER	0.999987	0.0013	61
+218	X	504	ASN	0.999987	0.0013	182
+219	X	426	TYR	0.999987	0.0013	104
+220	X	541	THR	0.999987	0.0013	219
+221	X	608	VAL	0.999987	0.0013	286
+222	X	494	ARG	0.999988	0.0012	172
+223	X	363	SER	0.999988	0.0012	41
+224	X	342	LEU	0.999988	0.0012	20
+225	X	500	ILE	0.999988	0.0012	178
+226	X	415	ARG	0.999988	0.0012	93
+227	X	364	GLY	0.999988	0.0012	42
+228	X	509	GLY	0.999989	0.0011	187
+229	X	567	TYR	0.999989	0.0011	245
+230	X	389	ASP	0.999989	0.0011	67
+231	X	343	GLU	0.999989	0.0011	21
+232	X	475	VAL	0.999989	0.0011	153
+233	X	602	SER	0.999990	0.0010	280
+234	X	536	ARG	0.999990	0.0010	214
+235	X	325	GLY	0.999990	0.0010	3
+236	X	381	ASN	0.999990	0.0010	59
+237	X	484	LEU	0.999990	0.0010	162
+238	X	356	ALA	0.999990	0.0010	34
+239	X	457	LEU	0.999990	0.0010	135
+240	X	598	THR	0.999990	0.0010	276
+241	X	349	ASP	0.999991	0.0009	27
+242	X	337	GLN	0.999991	0.0009	15
+243	X	411	VAL	0.999991	0.0009	89
+244	X	336	ARG	0.999991	0.0009	14
+245	X	454	ALA	0.999991	0.0009	132
+246	X	588	THR	0.999991	0.0009	266
+247	X	445	PRO	0.999991	0.0009	123
+248	X	566	ILE	0.999991	0.0009	244
+249	X	455	PRO	0.999991	0.0009	133
+250	X	554	ARG	0.999991	0.0009	232
+251	X	531	LEU	0.999991	0.0009	209
+252	X	545	THR	0.999992	0.0008	223
+253	X	549	PRO	0.999992	0.0008	227
+254	X	395	CYS	0.999992	0.0008	73
+255	X	461	ILE	0.999992	0.0008	139
+256	X	331	ALA	0.999992	0.0008	9
+257	X	338	SER	0.999992	0.0008	16
+258	X	417	GLY	0.999992	0.0008	95
+259	X	408	PRO	0.999992	0.0008	86
+260	X	369	VAL	0.999993	0.0007	47
+261	X	492	PRO	0.999993	0.0007	170
+262	X	362	ARG	0.999993	0.0007	40
+263	X	427	ALA	0.999994	0.0006	105
+264	X	556	ALA	0.999994	0.0006	234
+265	X	467	VAL	0.999994	0.0006	145
+266	X	377	VAL	0.999994	0.0006	55
+267	X	488	GLU	0.999994	0.0006	166
+268	X	521	ALA	0.999994	0.0006	199
+269	X	564	GLY	0.999994	0.0006	242
+270	X	471	LEU	0.999994	0.0006	149
+271	X	489	CYS	0.999994	0.0006	167
+272	X	537	TYR	0.999995	0.0005	215
+273	X	366	ALA	0.999995	0.0005	44
+274	X	460	ARG	0.999995	0.0005	138
+275	X	358	LEU	0.999996	0.0004	36
+276	X	442	ARG	0.999996	0.0004	120
+277	X	355	LEU	0.999996	0.0004	33
+278	X	403	TRP	0.999997	0.0003	81
+279	X	410	SER	0.999997	0.0003	88
+280	X	499	MET	0.999997	0.0003	177
+281	X	390	SER	0.999997	0.0003	68
+282	X	469	ASN	0.999998	0.0002	147
+283	X	583	CYS	0.999998	0.0002	261
+284	X	443	TYR	0.999999	0.0001	121
+285	X	416	ILE	0.999999	0.0001	94
+286	X	558	GLY	0.999999	0.0001	236
+287	X	344	ALA	1.000000	0.0000	22

1u6d_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1u6d_all", "cos_distances": [0.9999166131019592, 0.9998597502708435, 0.9999898672103882, 0.9999141693115234, 0.9999650120735168, 0.9999582767486572, 0.9999788999557495, 0.9999865889549255, 0.9999920129776001, 0.999987006187439, 0.9998733997344971, 0.9999034404754639, 0.9999808073043823, 0.9999909400939941, 0.9999907612800598, 0.9999920129776001, 0.9999613165855408, 0.99997878074646, 0.999980092048645, 0.9999878406524658, 0.9999890923500061, 0.9999995231628418, 0.9999750852584839, 0.9999717473983765, 0.9999854564666748, 0.9998431205749512, 0.9999906420707703, 0.9999572038650513, 0.9999386072158813, 0.9999569058418274, 0.9999727010726929, 0.9999746084213257, 0.9999961853027344, 0.9999902248382568, 0.999963641166687, 0.9999957084655762, 0.9999716281890869, 0.9999546408653259, 0.9999805092811584, 0.9999933242797852, 0.9999877214431763, 0.9999881982803345, 0.9999262690544128, 0.9999951124191284, 0.9999605417251587, 0.9998598098754883, 0.9999925494194031, 0.999975860118866, 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50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288], "time_seconds": 59.6424, "peak_memory_mb": 1950.96}

1u6d_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1u6d",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1u6d_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1u6d
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1u6d.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 399+576+575+574+348+406+324+368+333+478 and chain X
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 399 and chain X
+color red, critical_rank1
+select critical_rank2, resi 576 and chain X
+color tv_red, critical_rank2
+select critical_rank3, resi 575 and chain X
+color salmon, critical_rank3
+select critical_rank4, resi 574 and chain X
+color lightsalmon, critical_rank4
+select critical_rank5, resi 348 and chain X
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1u6d_critical.pse
+# To save image: png 1u6d_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1u6d_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 59.64,
+  "total_time_minutes": 0.99,
+  "time_per_structure": {
+    "mean": 59.6424,
+    "std": 0.0,
+    "min": 59.6424,
+    "max": 59.6424
+  },
+  "output_file": "output/1u6d_interact_scores.json",
+  "input_file": "downloads/pdbs/1u6d.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 1950.96,
+    "max": 1950.96
+  }
+}

1ya9_critical_residues.tsv

@@ -0,0 +1,176 @@
+# ATOMICA Critical Residue Analysis: 1ya9_all
+# Structure ID: 1ya9
+# Total residues analyzed: 167
+# Mean ATOMICA_SCORE: 0.999957
+# Std Dev: 0.000057
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	A	165	GLY	0.999671	0.0329	155
+2	A	77	VAL	0.999671	0.0329	73
+3	A	33	GLN	0.999708	0.0292	29
+4	A	109	GLN	0.999759	0.0241	105
+5	A	157	GLY	0.999772	0.0228	153
+6	A	76	PRO	0.999808	0.0192	72
+7	A	98	ALA	0.999827	0.0173	94
+8	A	120	GLN	0.999827	0.0173	116
+9	A	175	PRO	0.999838	0.0162	165
+10	A	158	ALA	0.999858	0.0142	154
+11	A	18	TRP	0.999866	0.0134	14
+12	A	166	VAL	0.999866	0.0134	156
+13	A	19	GLU	0.999869	0.0131	15
+14	A	176	LEU	0.999872	0.0128	166
+15	A	104	ARG	0.999876	0.0124	100
+16	A	116	THR	0.999886	0.0114	112
+17	A	171	GLU	0.999892	0.0108	161
+18	A	87	LYS	0.999895	0.0105	83
+19	A	40	GLN	0.999904	0.0096	36
+20	A	54	ALA	0.999910	0.0090	50
+21	A	49	THR	0.999911	0.0089	45
+22	A	26	TRP	0.999911	0.0089	22
+23	A	122	THR	0.999915	0.0085	118
+24	A	85	LEU	0.999920	0.0080	81
+25	A	133	LEU	0.999920	0.0080	129
+26	A	108	GLY	0.999920	0.0080	104
+27	A	44	GLN	0.999926	0.0074	40
+28	A	35	LEU	0.999928	0.0072	31
+29	A	36	SER	0.999930	0.0070	32
+30	A	67	LYS	0.999932	0.0068	63
+31	A	123	GLU	0.999932	0.0068	119
+32	A	90	GLN	0.999934	0.0066	86
+33	A	21	ALA	0.999935	0.0065	17
+34	A	115	HIS	0.999935	0.0065	111
+35	A	10	LEU	0.999937	0.0063	6
+36	A	61	THR	0.999940	0.0060	57
+37	A	62	GLU	0.999943	0.0057	58
+38	A	134	ARG	0.999948	0.0052	130
+39	A	30	ARG	0.999949	0.0051	26
+40	A	143	ASP	0.999949	0.0051	139
+41	A	60	MET	0.999952	0.0048	56
+42	A	65	ALA	0.999952	0.0048	61
+43	A	14	SER	0.999953	0.0047	10
+44	A	174	GLY	0.999955	0.0045	164
+45	A	155	LYS	0.999956	0.0044	151
+46	A	151	LEU	0.999957	0.0043	147
+47	A	29	LEU	0.999958	0.0042	25
+48	A	131	THR	0.999958	0.0042	127
+49	A	132	HIS	0.999958	0.0042	128
+50	A	148	GLN	0.999959	0.0041	144
+51	A	172	ARG	0.999960	0.0040	162
+52	A	24	ARG	0.999960	0.0040	20
+53	A	111	ARG	0.999961	0.0039	107
+54	A	7	THR	0.999961	0.0039	3
+55	A	117	MET	0.999962	0.0038	113
+56	A	146	ASP	0.999963	0.0037	142
+57	A	119	GLY	0.999963	0.0037	115
+58	A	46	SER	0.999964	0.0036	42
+59	A	103	LEU	0.999964	0.0036	99
+60	A	128	ARG	0.999965	0.0035	124
+61	A	37	ASP	0.999965	0.0035	33
+62	A	177	VAL	0.999966	0.0034	167
+63	A	142	ARG	0.999967	0.0033	138
+64	A	63	VAL	0.999967	0.0033	59
+65	A	45	SER	0.999968	0.0032	41
+66	A	144	ALA	0.999969	0.0031	140
+67	A	156	ALA	0.999969	0.0031	152
+68	A	88	GLU	0.999970	0.0030	84
+69	A	50	GLN	0.999970	0.0030	46
+70	A	91	ALA	0.999971	0.0029	87
+71	A	53	THR	0.999973	0.0027	49
+72	A	15	ASN	0.999973	0.0027	11
+73	A	83	ALA	0.999974	0.0026	79
+74	A	8	ASP	0.999974	0.0026	4
+75	A	94	ALA	0.999974	0.0026	90
+76	A	145	GLU	0.999974	0.0026	141
+77	A	71	GLU	0.999975	0.0025	67
+78	A	58	ASP	0.999976	0.0024	54
+79	A	130	SER	0.999976	0.0024	126
+80	A	149	LYS	0.999977	0.0023	145
+81	A	80	GLU	0.999978	0.0022	76
+82	A	66	TYR	0.999979	0.0021	62
+83	A	124	GLU	0.999979	0.0021	120
+84	A	51	GLU	0.999979	0.0021	47
+85	A	112	ASN	0.999979	0.0021	108
+86	A	11	GLU	0.999980	0.0020	7
+87	A	110	TYR	0.999980	0.0020	106
+88	A	154	TYR	0.999980	0.0020	150
+89	A	17	PRO	0.999981	0.0019	13
+90	A	72	GLU	0.999981	0.0019	68
+91	A	75	GLY	0.999982	0.0018	71
+92	A	38	GLN	0.999982	0.0018	34
+93	A	39	VAL	0.999982	0.0018	35
+94	A	97	GLY	0.999982	0.0018	93
+95	A	121	SER	0.999983	0.0017	117
+96	A	114	VAL	0.999983	0.0017	110
+97	A	48	VAL	0.999984	0.0016	44
+98	A	57	GLU	0.999984	0.0016	53
+99	A	82	ARG	0.999984	0.0016	78
+100	A	78	ALA	0.999984	0.0016	74
+101	A	169	ILE	0.999985	0.0015	159
+102	A	102	ASP	0.999985	0.0015	98
+103	A	64	LYS	0.999986	0.0014	60
+104	A	70	LEU	0.999986	0.0014	66
+105	A	22	LEU	0.999986	0.0014	18
+106	A	32	VAL	0.999986	0.0014	28
+107	A	47	GLN	0.999986	0.0014	43
+108	A	118	LEU	0.999986	0.0014	114
+109	A	79	GLU	0.999987	0.0013	75
+110	A	34	THR	0.999987	0.0013	30
+111	A	140	LEU	0.999987	0.0013	136
+112	A	141	MET	0.999987	0.0013	137
+113	A	59	THR	0.999988	0.0012	55
+114	A	153	VAL	0.999988	0.0012	149
+115	A	20	GLN	0.999988	0.0012	16
+116	A	81	THR	0.999988	0.0012	77
+117	A	106	ARG	0.999988	0.0012	102
+118	A	99	ASP	0.999988	0.0012	95
+119	A	74	LEU	0.999988	0.0012	70
+120	A	125	ILE	0.999989	0.0011	121
+121	A	42	GLU	0.999989	0.0011	38
+122	A	96	LEU	0.999989	0.0011	92
+123	A	5	GLU	0.999990	0.0010	1
+124	A	28	TYR	0.999990	0.0010	24
+125	A	23	ASN	0.999990	0.0010	19
+126	A	136	MET	0.999990	0.0010	132
+127	A	168	ALA	0.999990	0.0010	158
+128	A	56	MET	0.999990	0.0010	52
+129	A	93	GLN	0.999990	0.0010	89
+130	A	9	GLN	0.999990	0.0010	5
+131	A	127	ALA	0.999990	0.0010	123
+132	A	167	SER	0.999990	0.0010	157
+133	A	89	VAL	0.999990	0.0010	85
+134	A	137	ARG	0.999990	0.0010	133
+135	A	170	ARG	0.999990	0.0010	160
+136	A	95	ARG	0.999990	0.0010	91
+137	A	73	GLN	0.999990	0.0010	69
+138	A	6	VAL	0.999991	0.0009	2
+139	A	139	ARG	0.999991	0.0009	135
+140	A	150	ARG	0.999991	0.0009	146
+141	A	126	ARG	0.999991	0.0009	122
+142	A	41	GLU	0.999991	0.0009	37
+143	A	135	LYS	0.999992	0.0008	131
+144	A	27	ASP	0.999992	0.0008	23
+145	A	173	LEU	0.999992	0.0008	163
+146	A	152	ALA	0.999992	0.0008	148
+147	A	129	LEU	0.999993	0.0007	125
+148	A	100	MET	0.999993	0.0007	96
+149	A	55	LEU	0.999993	0.0007	51
+150	A	84	ARG	0.999994	0.0006	80
+151	A	25	PHE	0.999994	0.0006	21
+152	A	68	LYS	0.999994	0.0006	64
+153	A	43	LEU	0.999994	0.0006	39
+154	A	113	GLU	0.999994	0.0006	109
+155	A	107	LEU	0.999994	0.0006	103
+156	A	16	GLN	0.999994	0.0006	12
+157	A	13	GLN	0.999994	0.0006	9
+158	A	92	ALA	0.999994	0.0006	88
+159	A	101	GLU	0.999994	0.0006	97
+160	A	86	GLY	0.999995	0.0005	82
+161	A	31	TRP	0.999995	0.0005	27
+162	A	12	TRP	0.999996	0.0004	8
+163	A	69	GLU	0.999996	0.0004	65
+164	A	105	ASN	0.999996	0.0004	101
+165	A	138	LYS	0.999998	0.0002	134
+166	A	52	LEU	0.999998	0.0002	48
+167	A	147	LEU	0.999998	0.0002	143