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filter_clashes.hh
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1 //------------------------------------------------------------------------------
2 // This file is part of the OpenStructure project <www.openstructure.org>
3 //
4 // Copyright (C) 2008-2011 by the OpenStructure authors
5 //
6 // This library is free software; you can redistribute it and/or modify it under
7 // the terms of the GNU Lesser General Public License as published by the Free
8 // Software Foundation; either version 3.0 of the License, or (at your option)
9 // any later version.
10 // This library is distributed in the hope that it will be useful, but WITHOUT
11 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
12 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
13 // details.
14 //
15 // You should have received a copy of the GNU Lesser General Public License
16 // along with this library; if not, write to the Free Software Foundation, Inc.,
17 // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
18 //------------------------------------------------------------------------------
19 #ifndef OST_MOL_ALG_FILTER_CLASHES_HH
20 #define OST_MOL_ALG_FILTER_CLASHES_HH
21 
22 #include <ost/mol/entity_view.hh>
23 #include <ost/mol/alg/module_config.hh>
24 #include <ost/mol/alg/distance_test_common.hh>
25 namespace ost { namespace mol { namespace alg {
26 
27 class DLLEXPORT_OST_MOL_ALG BondLengthInfo
28 {
29 public:
30  BondLengthInfo(): avg_length_(0),avg_zscore_(0),count_(0) {}
31  BondLengthInfo(Real avg_length,Real avg_zscore, int count):
32  avg_length_(avg_length),
33  avg_zscore_(avg_zscore),
34  count_(count){}
35  Real GetAvgLength() {return avg_length_;}
36  Real GetAvgZscore() {return avg_zscore_;}
37  int GetCount() {return count_;}
38 
39 private:
40  Real avg_length_;
41  Real avg_zscore_;
42  int count_;
43 };
44 
45 class DLLEXPORT_OST_MOL_ALG ClashEvent
46 {
47 public:
48  ClashEvent(): atom1_(UniqueAtomIdentifier()),atom2_(UniqueAtomIdentifier()),mdl_dist_(0.0),adjusted_ref_dist_(0.0) {}
49  ClashEvent(const UniqueAtomIdentifier& atom1,const UniqueAtomIdentifier& atom2, Real mdl_dist, Real adjusted_ref_dist ):
50  atom1_(atom1),atom2_(atom2),mdl_dist_(mdl_dist),adjusted_ref_dist_(adjusted_ref_dist) {}
51  UniqueAtomIdentifier GetFirstAtom() const { return atom1_; }
52  UniqueAtomIdentifier GetSecondAtom() const { return atom2_; }
53  Real GetModelDistance() const { return mdl_dist_; }
54  Real GetAdjustedReferenceDistance() const { return adjusted_ref_dist_; }
55 private:
56  UniqueAtomIdentifier atom1_;
57  UniqueAtomIdentifier atom2_;
58  Real mdl_dist_;
59  Real adjusted_ref_dist_;
60 };
61 
62 class DLLEXPORT_OST_MOL_ALG ClashingInfo
63 {
64 
65 public:
66  ClashingInfo(): clash_count_(0), average_offset_ (0), clash_list_(std::vector<ClashEvent>()) {}
67  ClashingInfo (int clash_count, Real average_offset, const std::vector<ClashEvent>& clash_list):
68  clash_count_(clash_count), average_offset_ (average_offset),clash_list_(clash_list) {}
69  int GetClashCount() const {return clash_count_/2.0;}
70  Real GetAverageOffset() const {return average_offset_;}
71  std::vector<ClashEvent> GetClashList() const;
72 
73 private:
74  int clash_count_;
75  Real average_offset_;
76  std::vector<ClashEvent> clash_list_;
77 };
78 
79 class DLLEXPORT_OST_MOL_ALG StereoChemicalBondViolation
80 {
81 public:
82  StereoChemicalBondViolation():
83  atom1_(UniqueAtomIdentifier()),atom2_(UniqueAtomIdentifier()),mdl_value_(0.0),allowed_range_(std::pair<Real,Real>(0.0,0.0)) {}
84  StereoChemicalBondViolation(const UniqueAtomIdentifier& atom1,
85  const UniqueAtomIdentifier& atom2,
86  Real mdl_value, std::pair<Real,Real> allowed_range ):
87  atom1_(atom1),atom2_(atom2),mdl_value_(mdl_value),allowed_range_(allowed_range) {}
88  UniqueAtomIdentifier GetFirstAtom() const { return atom1_; }
89  UniqueAtomIdentifier GetSecondAtom() const { return atom2_; }
90  Real GetBondLength() const { return mdl_value_; }
91  std::pair<Real,Real> GetAllowedRange() const { return allowed_range_; }
92 private:
93  UniqueAtomIdentifier atom1_;
94  UniqueAtomIdentifier atom2_;
95  Real mdl_value_;
96  std::pair<Real,Real> allowed_range_;
97 };
98 
99 class DLLEXPORT_OST_MOL_ALG StereoChemicalAngleViolation
100 {
101 public:
102  StereoChemicalAngleViolation():
103  atom1_(UniqueAtomIdentifier()),atom2_(UniqueAtomIdentifier()),atom3_(UniqueAtomIdentifier()),mdl_value_(0.0),allowed_range_(std::pair<Real,Real>(0.0,0.0)) {}
104  StereoChemicalAngleViolation(const UniqueAtomIdentifier& atom1,
105  const UniqueAtomIdentifier& atom2,
106  const UniqueAtomIdentifier& atom3,
107  Real mdl_value, std::pair<Real,Real> allowed_range ):
108  atom1_(atom1),atom2_(atom2),atom3_(atom3),mdl_value_(mdl_value),allowed_range_(allowed_range) {}
109  UniqueAtomIdentifier GetFirstAtom() const { return atom1_; }
110  UniqueAtomIdentifier GetSecondAtom() const { return atom2_; }
111  UniqueAtomIdentifier GetThirdAtom() const { return atom3_; }
112  Real GetAngleWidth() const { return mdl_value_; }
113  std::pair<Real,Real> GetAllowedRange() const { return allowed_range_; }
114 private:
115  UniqueAtomIdentifier atom1_;
116  UniqueAtomIdentifier atom2_;
117  UniqueAtomIdentifier atom3_;
118  Real mdl_value_;
119  std::pair<Real,Real> allowed_range_;
120 };
121 
122 class DLLEXPORT_OST_MOL_ALG StereoChemistryInfo
123 {
124 public:
125  StereoChemistryInfo():
126  avg_zscore_bonds_(0),
127  bad_bond_count_(0),
128  bond_count_(0),
129  avg_zscore_angles_(0),
130  bad_angle_count_(0),
131  angle_count_(0),
132  avg_bond_length_info_(std::map<String,BondLengthInfo>()),
133  bond_violation_list_(std::vector<StereoChemicalBondViolation>()),
134  angle_violation_list_(std::vector<StereoChemicalAngleViolation>()) {}
135  StereoChemistryInfo(Real avg_zscore_bonds, int bad_bond_count, int bond_count,
136  Real avg_zscore_angles, int bad_angle_count, int angle_count,
137  const std::map<String,BondLengthInfo>& avg_bond_length_info,
138  const std::vector<StereoChemicalBondViolation>& bond_violation_list,
139  const std::vector<StereoChemicalAngleViolation>& angle_violation_list):
140  avg_zscore_bonds_(avg_zscore_bonds),
141  bad_bond_count_(bad_bond_count),
142  bond_count_(bond_count),
143  avg_zscore_angles_(avg_zscore_angles),
144  bad_angle_count_(bad_angle_count),
145  angle_count_(angle_count),
146  avg_bond_length_info_(avg_bond_length_info),
147  bond_violation_list_(bond_violation_list),
148  angle_violation_list_(angle_violation_list) {}
149  Real GetAvgZscoreBonds() const {return avg_zscore_bonds_;}
150  int GetBadBondCount() const {return bad_bond_count_;}
151  int GetBondCount() const {return bond_count_;}
152  Real GetAvgZscoreAngles() const {return avg_zscore_angles_;}
153  int GetBadAngleCount() const {return bad_angle_count_;}
154  int GetAngleCount() const {return angle_count_;}
155  std::map<String,BondLengthInfo> GetAvgBondLengthInfo() {return avg_bond_length_info_;}
156  std::vector<StereoChemicalBondViolation> GetBondViolationList() { return bond_violation_list_; }
157  std::vector<StereoChemicalAngleViolation> GetAngleViolationList() { return angle_violation_list_; }
158 
159 
160 private:
161  Real avg_zscore_bonds_;
162  int bad_bond_count_;
163  int bond_count_;
164  Real avg_zscore_angles_;
165  int bad_angle_count_;
166  int angle_count_;
167  std::map<String,BondLengthInfo> avg_bond_length_info_;
168  std::vector<StereoChemicalBondViolation> bond_violation_list_;
169  std::vector<StereoChemicalAngleViolation> angle_violation_list_;
170 };
171 
172 
174 class DLLEXPORT_OST_MOL_ALG ClashingDistances
175 {
176 
177 public:
179  ClashingDistances(): valid_flag_(true) {}
180 
184  void SetClashingDistance(const String& ele1,const String& ele2, Real min_distance, Real tolerance);
185 
187  std::pair<Real,Real> GetClashingDistance(const String& ele1,const String& ele2) const;
188 
190  Real GetAdjustedClashingDistance(const String& ele1,const String& ele2) const;
191 
193  Real GetMaxAdjustedDistance() const;
194 
196  bool IsEmpty() const;
197 
199  void PrintAllDistances() const;
200 
201 private:
202 
203  std::map <String,std::pair<Real,Real> > min_distance_;
204  Real default_min_distance_;
205  Real default_min_distance_tolerance_;
206  bool valid_flag_;
207 
208 };
209 
213 class DLLEXPORT_OST_MOL_ALG StereoChemicalParams
214 {
215 
216 public:
218  void SetParam(const String& param, const String& residue, Real value, Real st_dev);
219 
223  std::pair<Real,Real> GetParam(const String& element,const String& residue) const;
224 
228  bool ContainsParam(const String& param,const String& residue) const;
229 
233  bool IsEmpty() const;
234 
236  void PrintAllParameters() const;
237 
238 private:
239 
240  std::map<std::pair<String,String>,std::pair<Real,Real> > params_;
241 
242 };
243 
247 ClashingDistances DLLEXPORT_OST_MOL_ALG FillClashingDistances(std::vector<String>& stereo_chemical_props_file);
248 
253 StereoChemicalParams DLLEXPORT_OST_MOL_ALG FillStereoChemicalParams(const String& header, std::vector<String>& stereo_chemical_props_file);
254 
262 std::pair<EntityView,ClashingInfo> DLLEXPORT_OST_MOL_ALG FilterClashes(const EntityView& ent,
263  const ClashingDistances& min_distances, bool always_remove_bb=false);
264 
272 std::pair<EntityView,ClashingInfo> DLLEXPORT_OST_MOL_ALG FilterClashes(const EntityHandle& ent,
273  const ClashingDistances& min_distances, bool always_remove_bb=false);
274 
282 std::pair<EntityView,StereoChemistryInfo> DLLEXPORT_OST_MOL_ALG CheckStereoChemistry(const EntityView& ent,
283  const StereoChemicalParams& bond_table,
284  const StereoChemicalParams& angle_table,
285  Real bond_tolerance,
286  Real angle_tolerance,
287  bool always_remove_bb=false);
288 
296 std::pair<EntityView,StereoChemistryInfo> DLLEXPORT_OST_MOL_ALG CheckStereoChemistry(const EntityHandle& ent,
297  const StereoChemicalParams& bond_table,
298  const StereoChemicalParams& angle_table,
299  Real bond_tolerance,
300  Real angle_tolerance,
301  bool always_remove_bb=false);
302 
303 
304 }}}
305 
306 
307 #endif
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