OpenStructure: stage/include/ost/mol/alg/filter

00001 //------------------------------------------------------------------------------
00002 // This file is part of the OpenStructure project <www.openstructure.org>
00003 //
00004 // Copyright (C) 2008-2011 by the OpenStructure authors
00005 //
00006 // This library is free software; you can redistribute it and/or modify it under
00007 // the terms of the GNU Lesser General Public License as published by the Free
00008 // Software Foundation; either version 3.0 of the License, or (at your option)
00009 // any later version.
00010 // This library is distributed in the hope that it will be useful, but WITHOUT
00011 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
00012 // FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
00013 // details.
00014 //
00015 // You should have received a copy of the GNU Lesser General Public License
00016 // along with this library; if not, write to the Free Software Foundation, Inc.,
00017 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
00018 //------------------------------------------------------------------------------
00019 #ifndef OST_MOL_ALG_FILTER_CLASHES_HH
00020 #define OST_MOL_ALG_FILTER_CLASHES_HH
00021 
00022 #include <ost/mol/entity_view.hh>
00023 #include <ost/mol/alg/module_config.hh>
00024 #include <ost/mol/alg/distance_test_common.hh>
00025 namespace ost { namespace mol { namespace alg {
00026 
00027 class DLLEXPORT_OST_MOL_ALG BondLengthInfo
00028 {
00029 public:
00030   BondLengthInfo(): avg_length_(0),avg_zscore_(0),count_(0) {}
00031   BondLengthInfo(Real avg_length,Real avg_zscore, int count):
00032     avg_length_(avg_length),
00033     avg_zscore_(avg_zscore),
00034     count_(count){}
00035   Real GetAvgLength() {return avg_length_;}
00036   Real GetAvgZscore() {return avg_zscore_;}
00037   int GetCount() {return count_;}
00038 
00039 private:
00040   Real avg_length_;
00041   Real avg_zscore_;
00042   int count_;
00043 };
00044 
00045 class DLLEXPORT_OST_MOL_ALG ClashEvent
00046 {
00047 public:
00048   ClashEvent(): atom1_(UniqueAtomIdentifier()),atom2_(UniqueAtomIdentifier()),mdl_dist_(0.0),adjusted_ref_dist_(0.0) {}
00049   ClashEvent(const UniqueAtomIdentifier& atom1,const UniqueAtomIdentifier& atom2, Real mdl_dist, Real adjusted_ref_dist ):
00050     atom1_(atom1),atom2_(atom2),mdl_dist_(mdl_dist),adjusted_ref_dist_(adjusted_ref_dist) {}
00051   UniqueAtomIdentifier GetFirstAtom() const { return atom1_; }
00052   UniqueAtomIdentifier GetSecondAtom() const { return atom2_; }
00053   Real GetModelDistance() const { return mdl_dist_; }
00054   Real GetAdjustedReferenceDistance() const { return adjusted_ref_dist_; }
00055 private:
00056   UniqueAtomIdentifier atom1_;
00057   UniqueAtomIdentifier atom2_;
00058   Real mdl_dist_;
00059   Real adjusted_ref_dist_;
00060 };
00061 
00062 class DLLEXPORT_OST_MOL_ALG ClashingInfo
00063 {
00064 
00065 public:
00066   ClashingInfo(): clash_count_(0), average_offset_ (0), clash_list_(std::vector<ClashEvent>()) {}
00067   ClashingInfo (int clash_count, Real average_offset, const std::vector<ClashEvent>& clash_list):
00068     clash_count_(clash_count), average_offset_ (average_offset),clash_list_(clash_list) {}
00069   int GetClashCount() const {return clash_count_/2.0;}
00070   Real GetAverageOffset() const {return average_offset_;}
00071   std::vector<ClashEvent> GetClashList() const;
00072 
00073 private:
00074   int clash_count_;
00075   Real average_offset_;
00076   std::vector<ClashEvent> clash_list_;
00077 };
00078 
00079 class DLLEXPORT_OST_MOL_ALG StereoChemicalBondViolation
00080 {
00081 public:
00082   StereoChemicalBondViolation():
00083     atom1_(UniqueAtomIdentifier()),atom2_(UniqueAtomIdentifier()),mdl_value_(0.0),allowed_range_(std::pair<Real,Real>(0.0,0.0)) {}
00084   StereoChemicalBondViolation(const UniqueAtomIdentifier& atom1,
00085                               const UniqueAtomIdentifier& atom2,
00086                               Real mdl_value, std::pair<Real,Real> allowed_range ):
00087     atom1_(atom1),atom2_(atom2),mdl_value_(mdl_value),allowed_range_(allowed_range) {}
00088   UniqueAtomIdentifier GetFirstAtom() const { return atom1_; }
00089   UniqueAtomIdentifier GetSecondAtom() const { return atom2_; }
00090   Real GetBondLength() const { return mdl_value_; }
00091   std::pair<Real,Real> GetAllowedRange() const { return allowed_range_; }
00092 private:
00093   UniqueAtomIdentifier atom1_;
00094   UniqueAtomIdentifier atom2_;
00095   Real mdl_value_;
00096   std::pair<Real,Real> allowed_range_;
00097 };
00098 
00099 class DLLEXPORT_OST_MOL_ALG StereoChemicalAngleViolation
00100 {
00101 public:
00102   StereoChemicalAngleViolation():
00103     atom1_(UniqueAtomIdentifier()),atom2_(UniqueAtomIdentifier()),atom3_(UniqueAtomIdentifier()),mdl_value_(0.0),allowed_range_(std::pair<Real,Real>(0.0,0.0)) {}
00104   StereoChemicalAngleViolation(const UniqueAtomIdentifier& atom1,
00105                                const UniqueAtomIdentifier& atom2,
00106                                const UniqueAtomIdentifier& atom3,
00107                                Real mdl_value, std::pair<Real,Real> allowed_range ):
00108     atom1_(atom1),atom2_(atom2),atom3_(atom3),mdl_value_(mdl_value),allowed_range_(allowed_range) {}
00109   UniqueAtomIdentifier GetFirstAtom() const { return atom1_; }
00110   UniqueAtomIdentifier GetSecondAtom() const { return atom2_; }
00111   UniqueAtomIdentifier GetThirdAtom() const { return atom3_; }
00112   Real GetAngleWidth() const { return mdl_value_; }
00113   std::pair<Real,Real> GetAllowedRange() const { return allowed_range_; }
00114 private:
00115   UniqueAtomIdentifier atom1_;
00116   UniqueAtomIdentifier atom2_;
00117   UniqueAtomIdentifier atom3_;
00118   Real mdl_value_;
00119   std::pair<Real,Real> allowed_range_;
00120 };
00121 
00122 class DLLEXPORT_OST_MOL_ALG StereoChemistryInfo
00123 {
00124 public:
00125   StereoChemistryInfo():
00126      avg_zscore_bonds_(0),
00127      bad_bond_count_(0),
00128      bond_count_(0),
00129      avg_zscore_angles_(0),
00130      bad_angle_count_(0),
00131      angle_count_(0),
00132      avg_bond_length_info_(std::map<String,BondLengthInfo>()),
00133      bond_violation_list_(std::vector<StereoChemicalBondViolation>()),
00134      angle_violation_list_(std::vector<StereoChemicalAngleViolation>()) {}
00135   StereoChemistryInfo(Real avg_zscore_bonds, int bad_bond_count, int bond_count,
00136                       Real avg_zscore_angles, int bad_angle_count, int angle_count,
00137                       const std::map<String,BondLengthInfo>& avg_bond_length_info,
00138                       const std::vector<StereoChemicalBondViolation>& bond_violation_list,
00139                       const std::vector<StereoChemicalAngleViolation>& angle_violation_list):
00140     avg_zscore_bonds_(avg_zscore_bonds),
00141     bad_bond_count_(bad_bond_count),
00142     bond_count_(bond_count),
00143     avg_zscore_angles_(avg_zscore_angles),
00144     bad_angle_count_(bad_angle_count),
00145     angle_count_(angle_count),
00146     avg_bond_length_info_(avg_bond_length_info),
00147     bond_violation_list_(bond_violation_list),
00148     angle_violation_list_(angle_violation_list) {}
00149   Real GetAvgZscoreBonds() const {return avg_zscore_bonds_;}
00150   int GetBadBondCount() const {return bad_bond_count_;}
00151   int GetBondCount() const {return bond_count_;}
00152   Real GetAvgZscoreAngles() const {return avg_zscore_angles_;}
00153   int GetBadAngleCount() const {return bad_angle_count_;}
00154   int GetAngleCount() const {return angle_count_;}
00155   std::map<String,BondLengthInfo> GetAvgBondLengthInfo() {return avg_bond_length_info_;}
00156   std::vector<StereoChemicalBondViolation> GetBondViolationList() { return bond_violation_list_; }
00157   std::vector<StereoChemicalAngleViolation> GetAngleViolationList() { return angle_violation_list_; }
00158 
00159 
00160 private:
00161   Real avg_zscore_bonds_;
00162   int bad_bond_count_;
00163   int bond_count_;
00164   Real avg_zscore_angles_;
00165   int bad_angle_count_;
00166   int angle_count_;
00167   std::map<String,BondLengthInfo> avg_bond_length_info_;
00168   std::vector<StereoChemicalBondViolation> bond_violation_list_;
00169   std::vector<StereoChemicalAngleViolation> angle_violation_list_;
00170 };
00171 
00172 
00174 class DLLEXPORT_OST_MOL_ALG ClashingDistances
00175 {
00176 
00177 public:
00179   ClashingDistances(): valid_flag_(true) {}
00180 
00184   void SetClashingDistance(const String& ele1,const String& ele2, Real min_distance, Real tolerance);
00185 
00187   std::pair<Real,Real> GetClashingDistance(const String& ele1,const String& ele2) const;
00188 
00190   Real GetAdjustedClashingDistance(const String& ele1,const String& ele2) const;
00191 
00193   Real GetMaxAdjustedDistance() const;
00194 
00196   bool IsEmpty() const;
00197   
00199   void PrintAllDistances() const;
00200   
00201 private:
00202 
00203   std::map <String,std::pair<Real,Real> > min_distance_;
00204   Real default_min_distance_;
00205   Real default_min_distance_tolerance_;
00206   bool valid_flag_;
00207   
00208 };
00209 
00213 class DLLEXPORT_OST_MOL_ALG StereoChemicalParams
00214 {
00215 
00216 public:
00218   void SetParam(const String& param, const String& residue, Real value, Real st_dev);
00219 
00223   std::pair<Real,Real> GetParam(const String& element,const String& residue) const;
00224 
00228   bool ContainsParam(const String& param,const String& residue) const;
00229 
00233   bool IsEmpty() const;
00234   
00236   void PrintAllParameters() const;
00237   
00238 private:
00239 
00240   std::map<std::pair<String,String>,std::pair<Real,Real> >  params_;
00241  
00242 };
00243 
00247 ClashingDistances DLLEXPORT_OST_MOL_ALG FillClashingDistances(std::vector<String>& stereo_chemical_props_file);
00248 
00253 StereoChemicalParams DLLEXPORT_OST_MOL_ALG FillStereoChemicalParams(const String& header, std::vector<String>& stereo_chemical_props_file);  
00254 
00262 std::pair<EntityView,ClashingInfo> DLLEXPORT_OST_MOL_ALG FilterClashes(const EntityView& ent,
00263                                                const ClashingDistances& min_distances, bool always_remove_bb=false);
00264 
00272 std::pair<EntityView,ClashingInfo> DLLEXPORT_OST_MOL_ALG FilterClashes(const EntityHandle& ent,
00273                                                const ClashingDistances& min_distances, bool always_remove_bb=false);
00274 
00282 std::pair<EntityView,StereoChemistryInfo> DLLEXPORT_OST_MOL_ALG CheckStereoChemistry(const EntityView& ent,
00283                                                       const StereoChemicalParams& bond_table, 
00284                                                       const StereoChemicalParams& angle_table,
00285                                                       Real bond_tolerance,
00286                                                       Real angle_tolerance,
00287                                                       bool always_remove_bb=false);
00288 
00296 std::pair<EntityView,StereoChemistryInfo> DLLEXPORT_OST_MOL_ALG CheckStereoChemistry(const EntityHandle& ent,
00297                                                       const StereoChemicalParams& bond_table, 
00298                                                       const StereoChemicalParams& angle_table,
00299                                                       Real bond_tolerance,
00300                                                       Real angle_tolerance,
00301                                                       bool always_remove_bb=false);
00302 
00303 
00304 }}}
00305 
00306 
00307 #endif
stage/include/ost/mol/alg/filter_clashes.hh
