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| #svl | |
| // | |
| // db_SetAmide180.svl set the amide bond dihedral angle to 180 degrees | |
| // | |
| // 28-jan-2013 (exe) created | |
| // 12-feb-2013 (exe) added stand-alone function | |
| // 12-feb-2013 (exe) option to perform energy minimization after amide dihedral set to 180 | |
| // 12-feb-2013 (exe) returns number of amide dihedral angles that were changed | |
| // 12-feb-2013 (exe) energy minimization is turned off for the mdb version | |
| // 20-feb-2013 (exe) updated documentation | |
| // 04-mar-2013 (exe) updated documentation | |
| // 20-mar-2013 (exe) updated variable names and comments | |
| // 24-feb-2015 (exe) added checks for *amino residues | |
| // 24-feb-2015 (exe) made two distinct functions. CLI, single compound, with amino checking | |
| // and a MDB version that does not check for amino residue types | |
| // 24-feb-2015 (exe) removed the energy minimization option from the MDB version | |
| // | |
| // Copyright (C) 2008-2015 Emilio Xavier Esposito. All rights reserved. | |
| // | |
| // exeResearch LLC, East Lansing, Michigan 48823 USA | |
| // http://www.exeResearch.com | |
| // emilio AT exeResearch DOT com | |
| // emilio DOT esposito AT gmail DOT com | |
| // | |
| // This program is free software: you can redistribute it and/or modify | |
| // it under the terms of the GNU General Public License as published by | |
| // the Free Software Foundation, either version 3 of the License, or | |
| // (at your option) any later version. | |
| // | |
| // This program is distributed in the hope that it will be useful, | |
| // but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| // GNU General Public License for more details. | |
| // | |
| // You should have received a copy of the GNU General Public License | |
| // along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| // | |
| // http://www.gnu.org/licenses/gpl-3.0.html | |
| // | |
| // | |
| /* | |
| Description | |
| It is common for small drug-like compounds and peptides that are constructed | |
| from SMILES strings and even SDfiles to have amide bonds where the hydrogen of | |
| the nitrogen atom and the oxygen of the carboxyl group result in a dihedral | |
| angle of approximately 0 degrees. This function sets all amide dihedral angles | |
| to 180 degrees and provides the option for energy minimization (this | |
| functionality is not implemented in the MDB version because of the energy | |
| minimization function with the MDB framework). The interactive (3D window) | |
| version allows the user to select the amide bond of interest. | |
| The MDB version of this function provides the option to overwrite the original | |
| molecule or create a new column (field) for the compounds. The MDB version | |
| does indicate how many amide bonds were corrected. It is recommended that | |
| after changing the amide dihedral angle(s) within a database of compounds | |
| that the MDB energy minimization (MDB | Compute | Energy Minimize) function | |
| be performed using the desired molecular force field. | |
| Note: Amide groups within rings are not modified. | |
| The default values are: | |
| - No energy minimization for 3D window (nrgOpt:0) | |
| - Column (field) with molecule is 'mol' (molField:'mol') | |
| - Save corrected compound to a new column 'modMol' (newMolField:'modMol') | |
| - Maximum peptide length is set with 'maxPeptideLength' (maxPeptideLength:15) | |
| Instructions | |
| // load this function | |
| load '~/code/svl/utilities/db_SetAmide180.svl'; | |
| // for a compound in the MOE 3D window (either a single small-organic drug-like | |
| // compound or a selected molecule) | |
| SetAmide180[] | |
| // for a compound in the MOE 3D window with energy minimizatin of the new conformation | |
| SetAmide180[nrgOpt:1] | |
| // for a collection of compound in a MDB saving the new conformation to | |
| // the originating column of the compound | |
| db_SetAmide180['drugLike_compounds.mdb', [molField:'mol', newMolField:'']] | |
| */ | |
| #set title 'db_SetAmide180: Set the dihedral angle of an amide bond to ~180 as seen in a peptide backbone' | |
| #set class 'exeResearch:utilities' | |
| #set version 'february.24.2015' | |
| const DEFAULTS = [ | |
| nrgOpt:0, | |
| molField:'mol', | |
| newMolField:'modMol', | |
| maxPeptideLength:15 | |
| ]; | |
| function MM; | |
| function SetAmide180 opts | |
| opts = tagcat [opts, DEFAULTS]; | |
| //----- set the variables | |
| local cmpdAKs, cmpdRKs, amideAKs, completeSystem, resTypes; | |
| local origDihedralAngles, newDihedralAngles, diffDihedralAngles; | |
| local numChanged; | |
| //----- if there are selected atoms use them | |
| cmpdAKs = SelectedAtoms[]; | |
| cmpdRKs = uniq aResidue cmpdAKs; | |
| cmpdAKs = cat rAtoms uniq aResidue cmpdAKs; | |
| //----- if nothing is selected start with the complete system | |
| if length cmpdAKs == 0 then | |
| cmpdAKs = Atoms[]; | |
| //--- determine the type of residues (are they amino acid residues?) | |
| cmpdRKs = uniq aResidue cmpdAKs; | |
| resTypes = rType cmpdRKs; | |
| //--- keep residues that are assigned the 'none' type | |
| cmpdAKs = cat (rAtoms cmpdRKs | m_findmatch ['none', resTypes]); | |
| endif | |
| //----- drop atoms that are lone pair (LP) | |
| cmpdAKs = cmpdAKs | not m_findmatch['LP', aElement cmpdAKs]; | |
| //----- just use the complete system? | |
| if (length cmpdAKs == 0) and ((add m_findmatch ['*amino', resTypes]) <= opts.maxPeptideLength) then | |
| cmpdAKs = Atoms[]; | |
| endif | |
| //----- what if there are no cmpdAKs? | |
| if length cmpdAKs == 0 then | |
| Message[0, 'All residues in the system are type amino.\nNo amide bonds were changed.\n']; | |
| Message[0, 'If you are working with peptides, set maxPeptideLength to a value one greater\nthan the number of residues in you longest peptide.\n\n']; | |
| Message[0, 'There are NO molecules to modify.']; | |
| write['\nAll residues in the system are type amino.\nNo amide bonds were changed.\n']; | |
| write['If you are working with peptides, set maxPeptideLength to a value one greater\nthan the number of residues in you longest peptide.\n\n']; | |
| write['There are NO molecules to modify.\n\n']; | |
| sleep 2.5; | |
| endif | |
| //----- find the amides | |
| amideAKs = sm_MatchAtoms ['O=CN[#1]', cmpdAKs ]; | |
| amideAKs = amideAKs | not app isnull amideAKs; | |
| //----- get the original amide dihedral angles | |
| origDihedralAngles = app aDihedralCWDeg amideAKs; | |
| //----- set the amide dihedral angle to 180 | |
| apt aSetDihedralCWDeg [amideAKs, 180]; | |
| //----- energy minimize the system | |
| if opts.nrgOpt > 0 then | |
| (MM[]); | |
| endif | |
| //----- get the new amide dihedral angles | |
| newDihedralAngles = app aDihedralCWDeg amideAKs; | |
| //----- print the differences between original and new amide dihedral angles | |
| diffDihedralAngles = (abs origDihedralAngles) - (abs newDihedralAngles); | |
| //--- number of changed dihedral angles | |
| numChanged = add (abs diffDihedralAngles > 90); | |
| //----- return information to user | |
| write['Set {} amide bond(s) to 180degrees.\n', numChanged]; | |
| endfunction | |
| function db_SetAmide180 [mdbfile, opts] | |
| opts = tagcat [opts, DEFAULTS]; | |
| //--- disable the option for energy minimization | |
| opts = tagpoke [opts, 'nrgOpt', 0]; | |
| print opts; | |
| //----- close the current system | |
| Close[]; | |
| //----- get the mdb information | |
| local mdbkey; | |
| mdbkey = db_Open [mdbfile, 'read-write']; | |
| //----- add the needed columns to the database | |
| db_EnsureField [mdbkey, 'numDihedChanged', 'int']; | |
| //--- if the modified compound get put in to a new column, make the column | |
| if tok_length(opts.newMolField) > 0 then | |
| db_EnsureField [mdbkey, opts.newMolField, 'molecule']; | |
| opts.molWriteField = opts.newMolField; | |
| else | |
| opts.molWriteField = opts.molField; | |
| endif | |
| //----- set the variables within the loop | |
| local entry; | |
| local numChangedDihedrals; | |
| local origDihedralAngles, newDihedralAngles, diffDihedralAngles; | |
| local amideAKs; | |
| local cmpdCKs, cmpdAKs, cmpd_mol, cmpdDATA; | |
| //----- loop over the database... | |
| entry = 0; | |
| while entry = db_NextEntry [mdbkey, entry] loop | |
| //--- get the complex | |
| cmpdCKs = mol_Create first db_ReadFields [mdbkey, entry, opts.molField]; | |
| cmpdAKs = cat cAtoms cmpdCKs; | |
| //----- find the amides | |
| amideAKs = sm_MatchAtoms ['O=CN[#1]', cmpdAKs ]; | |
| amideAKs = amideAKs | not app isnull amideAKs; | |
| //----- get the original amide dihedral angles | |
| origDihedralAngles = app aDihedralCWDeg amideAKs; | |
| //----- set the amide dihedral angle to 180 | |
| apt aSetDihedralCWDeg [amideAKs, 180]; | |
| //----- get the new amide dihedral angles | |
| newDihedralAngles = app aDihedralCWDeg amideAKs; | |
| //----- get the differences between original and new amide dihedral angles | |
| diffDihedralAngles = (abs origDihedralAngles) - (abs newDihedralAngles); | |
| //--- number of changed dihedral angles | |
| numChangedDihedrals = add (abs diffDihedralAngles >= 90); | |
| //--- extract the molecular information | |
| cmpd_mol = mol_Extract cmpdAKs; | |
| cmpdDATA = tag [opts.molWriteField, nest cmpd_mol]; | |
| cmpdDATA = cat[cmpdDATA, tag ['numDihedChanged', numChangedDihedrals] ]; | |
| //--- write the data to the database | |
| db_Write [mdbkey, entry, cmpdDATA]; | |
| //--- remove (delete) the current compound (system) to get ready for the next complex | |
| oDestroy Chains[]; | |
| endloop | |
| //----- close the database | |
| db_Close mdbkey; | |
| endfunction | |
| #eof |