Guess j pro.m - Revision history

Kuprov: Update function See also links and function index membership

2026-06-06T18:37:22Z

Update function See also links and function index membership

2026-06-05T17:49:24Z

Rename Arguments section heading to Parameters

2026-04-25T11:25:43Z

Normalise sequential blank lines

2026-04-05T14:48:52Z

Restore pre-bulk-edit wiki content

2026-04-05T14:05:42Z

Sync syntax/arguments/outputs with current Spinach source

2020-10-21T15:46:23Z

‎See also

2020-10-21T15:45:46Z

2016-08-11T12:33:01Z

‎Notes

2016-08-10T16:32:59Z

‎Examples

2016-08-10T16:21:19Z

‎Syntax

@@ Line 45: / Line 45: @@
 ==See also==
-[[Spin_system_specification#Protein_and_nucleic_acid_import|Protein and nucleic acid import]]
+[[read_pdb_pro.m]], [[protein.m]], [[awg_interface.m]], [[bootstrap.m]], [[gslice.m]], [[guess_csa_pro.m]], [[guess_j_nuc.m]], [[py_run.m]], [[retrieve_file.m]], [[spinach2hiper.m]], [[Import,_export,_and_visualisation]], [[Spin_system_specification]]
 ''Version 2.5, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]]''

@@ Line 12: / Line 12: @@
       jmatrix=guess_j_pro(aa_num,aa_typ,pdb_id,coords)
-==Arguments==
+==Parameters==
       aa_num  - nspins x 1 vector giving the number of the amino acid to which each spin belongs

← Older revision		Revision as of 11:25, 25 April 2026
Line 48:		Line 48:

	[[Spin_system_specification#Spin-spin_interactions\|Spin system specification - Spin-spin interactions]]		[[Spin_system_specification#Spin-spin_interactions\|Spin system specification - Spin-spin interactions]]
−

	''Version 2.5, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]]''		''Version 2.5, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]]''

@@ Line 1: / Line 1: @@
 {{DISPLAYTITLE:guess_j_pro.m}} __NOTOC__
 A reasonable attempt at a function that guesses and assigns all J-couplings in a protein. This function assigns J-couplings in proteins from atomic coordinates using semiempirical estimates. It is a graph-theoretical estimator with the following stages:
@@ Line 11: / Line 10: @@
 ==Syntax==
-jmatrix=guess_j_pro(aa_num,aa_typ,pdb_id,coords)
+     jmatrix=guess_j_pro(aa_num,aa_typ,pdb_id,coords)
 ==Arguments==
-aa_num  - nspins x 1 vector giving the number of the amino acid to which each spin belongs
+     aa_num  - nspins x 1 vector giving the number of the amino acid to which each spin belongs
       aa_typ  - nspins x 1 cell array of strings giving the PDB identifier of the amino acid to
@@ Line 27: / Line 26: @@
 ==Outputs==
-jmatrix  - a matrix of J-couplings
+     jmatrix - nspins x nspins sparse matrix of J-couplings in Hz
 ==Examples==
 The function accepts, for example, the output of [[read_pdb_pro.m]]:
@@ Line 60: / Line 38: @@
 ==Notes==
 # You can add or modify the J-coupling database by editing the function text.
 # Atoms in the subgraph descriptors are listed alphabetically to make the descriptors unique.
@@ Line 68: / Line 45: @@
 ==See also==
 [[Spin_system_specification#Protein_and_nucleic_acid_import|Protein and nucleic acid import]]

@@ Line 1: / Line 1: @@
 {{DISPLAYTITLE:guess_j_pro.m}} __NOTOC__
 A reasonable attempt at a function that guesses and assigns all J-couplings in a protein. This function assigns J-couplings in proteins from atomic coordinates using semiempirical estimates. It is a graph-theoretical estimator with the following stages:
@@ Line 10: / Line 11: @@
 ==Syntax==
-     jmatrix=guess_j_pro(aa_num,aa_typ,pdb_id,coords)
+jmatrix=guess_j_pro(aa_num,aa_typ,pdb_id,coords)
 ==Arguments==
-     aa_num  - nspins x 1 vector giving the number of the amino acid to which each spin belongs
+aa_num  - nspins x 1 vector giving the number of the amino acid to which each spin belongs
       aa_typ  - nspins x 1 cell array of strings giving the PDB identifier of the amino acid to
@@ Line 26: / Line 27: @@
 ==Outputs==
-     jmatrix - nspins x nspins sparse matrix of J-couplings in Hz
+jmatrix  - a matrix of J-couplings
 ==Examples==
 The function accepts, for example, the output of [[read_pdb_pro.m]]:
@@ Line 38: / Line 60: @@
 ==Notes==
 # You can add or modify the J-coupling database by editing the function text.
 # Atoms in the subgraph descriptors are listed alphabetically to make the descriptors unique.
@@ Line 45: / Line 68: @@
 ==See also==
 [[Spin_system_specification#Protein_and_nucleic_acid_import|Protein and nucleic acid import]]

@@ Line 47: / Line 47: @@
 [[Spin_system_specification#Protein_and_nucleic_acid_import|Protein and nucleic acid import]]
-[[Spin_system_specification#Zeeman_interactions|Spin system specification - Zeeman interactions]]
+[[Spin_system_specification#Spin-spin_interactions|Spin system specification - Spin-spin interactions]]
 ''Version 2.5, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]]''

@@ Line 45: / Line 45: @@
 # J-couplings produced by this functions are rough estimates. For accurate protein work you must supply your own J-couplings.
 # This is an auxiliary function that is called by [[protein.m]]; direct calls are discouraged.
 ''Revision 3284, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]]''

@@ Line 37: / Line 37: @@
       % Guess the J-couplings
-      jmatrix=guess_j_pro(aa_num,aa_typ,pdb_id,coords)
+      jmatrix=guess_j_pro(pdb_aa_num,pdb_aa_typ,pdb_atom_id,pdb_coords);
 ==Notes==

@@ Line 3: / Line 3: @@
 ==Syntax==
-      jmatrix=guess_j_pro(resnums,resnames,labels,coords)
+      jmatrix=guess_j_pro(aa_num,aa_typ,pdb_id,coords)
 ==Description==