// Name: reduce.h // Author: J. Michael Word // Date Written: 7/15/97 // Purpose: add hydrogens to a Protein Data Bank file and // writing a new Protein Data Bank file to standard output // // ************************************************************** // NOTICE: This is free software and the source code is freely // available. You are free to redistribute or modify under the // conditions that (1) this notice is not removed or modified // in any way and (2) any modified versions of the program are // also available for free. // ** Absolutely no Warranty ** // Copyright (C) 1999-2016 J. Michael Word // ************************************************************** #include #include #include "PDBrec.h" #include "CTab.h" #include "AtomPositions.h" struct SummaryStats { SummaryStats() : _H_found(0), _H_HET_found(0), _H_removed(0), _H_HET_removed(0), _H_added(0), _H_HET_added(0), _H_standardized(0), _H_HET_standardized(0), _num_atoms(0), _conect(0), _num_adj(0), _num_renamed(0) {} int _H_found, _H_HET_found; int _H_removed, _H_HET_removed; int _H_added, _H_HET_added; int _H_standardized, _H_HET_standardized; int _num_atoms, _conect; int _num_adj, _num_renamed; }; extern SummaryStats Tally; /// @brief Read the PDB records from the specified input stream. /// @param [in] s String with one PDB record per line. /// @return List (one entry per model) of PDB records found in the file. /// Each list contains all of the records that are outside of /// MODEL...ENDMDL records along with the records for the model /// that was read, with the first one being MODEL 1. extern std::list< std::list > inputModels(std::string s); /// @brief Drop hydrogens from a model in place. /// @param [in] RemoveATOMHydrogens Should we remove hydrogens in ATOM records? /// @param [in] RemoveOtherHydrogens Should we remove hydrogens in non_ATOM records? extern void dropHydrogens(std::list& records, bool RemoveATOMHydrogens, bool RemoveOtherHydrogens); /// @brief Optimize all of the records passed in in place. /// @return 0 on success, 1 on abandoned due to too many permutations. extern int optimize(AtomPositions &xyz, std::vector &adjNotes); //SJ 08/03/2015 for printing all models together extern void outputRecords_all(std::ostream& os, const std::list >& all_records); /// @brief Check the list of PDB records to see if we should use segment ID as chain /// @return TRUE if we should use the segment ID as the chain, FALSE if not extern bool checkSEGIDs(std::list& rlst); extern void scanAndGroupRecords(std::list& rlst, AtomPositions& xyz, std::list::iterator& startAtoms); extern void reduceList(CTab& db, std::list& records, AtomPositions& xyz, std::vector& fixNotes); /// Library-scoped global variables that are in the global name space. /// @todo Move these out of the global name space extern const char *versionString; extern const char *shortVersion; extern const char *referenceString; extern const char *electronicReference; extern bool Verbose; // do we write processing notes to stdout? extern bool KeepConnections; extern bool StandardizeRHBondLengths; extern bool ProcessConnHydOnHets; extern bool BuildHisHydrogens; extern bool SaveOHetcHydrogens; extern bool UseXplorNames; extern bool UseOldNames; extern bool BackBoneModel; extern bool DemandRotAllMethyls; extern bool RotExistingOH; extern bool NeutralTermini; extern bool DemandRotNH3; extern bool DemandRotExisting; extern bool DemandFlipAllHNQs; extern bool DoOnlyAltA; //jjh changed default 111118 extern bool OKProcessMetMe; //cjw changed default 160602 extern bool OKtoAdjust; extern bool ShowCliqueTicks; extern bool ShowOrientScore; extern bool StringInput; extern bool ShowCharges; extern bool UseNuclearDistances; //jjh 130111 extern bool UseSEGIDasChain; //jjh 130503 extern bool ProcessedFirstModel; //jjh 130718 extern bool RenameFlip; // SJ - 09/25/2015 - flag to specify if the final PDB file will have the coordinates according to //the rename atoms flip (is the flag is TRUE) or the new rot hinge dock flip (if the flag is FALSE, this is default). Can be set to true by the -renameflip flag in the commandline. extern bool GenerateFinalFlip; // SJ - 09/04/2015 to keep track of when scoring and decision of flips finishes and when the final PDB //coordinates are being generated. This is set to true after all the calculations are done, unless the RenameFlip flag is TRUE extern int MaxAromRingDih; // max dihedral angle in planarity check for aromatic rings 120724 - Aram extern int MinNTermResNo; // how high can a resno be for n-term? extern int NBondCutoff; // how many bonds away do we drop? extern int ExhaustiveLimit; //time limit, in seconds, to spend in brute force enumeration for a single clique extern float ProbeRadius; // how big is the probe in VDW calculations? extern float VdwDotDensity; // how many dots per sq Angstroms in VDW calculations? extern float OccupancyCutoff;// lowest occupancy considered when determining score extern float WaterBcutoff; // limit for water B values extern float WaterOCCcutoff;// limit for water occupancy extern float PenaltyMagnitude;// score bias towards original orientation (changed from 0.0 in 2.13.0) extern float MinRegHBgap; // Hbonds with greater gaps start to bump extern float MinChargedHBgap; // charged Hbonds start to bump at this point extern float BadBumpGapCut; // bump is bad if >= than this extern float NonMetalBumpBias;//bumps if H closer than atom radius, plus this extern float MetalBumpBias;// ditto, for metals extern float GapWidth; // half width for detecting chain breaks between residues // (center at 1.4; default allow 1.1-1.7 for accepting connected residues) extern std::string OFile; // if file exists, given orientations forced extern bool UseSEGIDtoChainMap; // if true, override some chain ids extern bool StopBeforeOptimizing; // If true, handle hydrogen drops/adds and then quit extern bool AddWaterHydrogens; // If true, add phantom hydrogens to waters extern bool AddOtherHydrogens; // If true, add hydrogens to non-water atoms extern bool RemoveATOMHydrogens; // If true, remove hydrogens from ATOM records extern bool RemoveOtherHydrogens;// If true, remove hydrogens from non-ATOM records