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38 package ffx.xray.parsers;
39
40 import ffx.crystal.Crystal;
41 import ffx.crystal.HKL;
42 import ffx.crystal.ReflectionList;
43 import ffx.crystal.Resolution;
44 import ffx.crystal.SpaceGroupDefinitions;
45 import ffx.crystal.SpaceGroupInfo;
46 import ffx.xray.DiffractionRefinementData;
47 import org.apache.commons.configuration2.CompositeConfiguration;
48
49 import java.io.BufferedReader;
50 import java.io.File;
51 import java.io.FileReader;
52 import java.io.IOException;
53 import java.util.logging.Level;
54 import java.util.logging.Logger;
55
56 import static ffx.crystal.SpaceGroupInfo.spaceGroupNames;
57 import static java.lang.Double.parseDouble;
58 import static java.lang.Integer.parseInt;
59 import static java.lang.String.format;
60 import static org.apache.commons.math3.util.FastMath.min;
61
62
63
64
65
66
67
68 public class CNSFilter implements DiffractionFileFilter {
69
70 private static final Logger logger = Logger.getLogger(CNSFilter.class.getName());
71
72 private final double[] cell = {-1.0, -1.0, -1.0, -1.0, -1.0, -1.0};
73 private double resHigh = -1.0;
74 private String spaceGroupName = null;
75 private int spaceGroupNum = -1;
76
77
78 public CNSFilter() {
79 }
80
81
82 @Override
83 public ReflectionList getReflectionList(File cnsFile) {
84 return getReflectionList(cnsFile, null);
85 }
86
87
88 @Override
89 public ReflectionList getReflectionList(File cnsFile, CompositeConfiguration properties) {
90 try (BufferedReader br = new BufferedReader(new FileReader(cnsFile))) {
91 String string;
92 while ((string = br.readLine()) != null) {
93 String[] strArray = string.split("\\s+");
94 if (strArray[0].equalsIgnoreCase("{")) {
95 if (strArray[1].toLowerCase().startsWith("sg=")) {
96 spaceGroupName = strArray[1].substring(3);
97 cell[0] = parseDouble(strArray[2].substring(2));
98 cell[1] = parseDouble(strArray[3].substring(2));
99 cell[2] = parseDouble(strArray[4].substring(2));
100 cell[3] = parseDouble(strArray[5].substring(6));
101 cell[4] = parseDouble(strArray[6].substring(5));
102 cell[5] = parseDouble(strArray[7].substring(6));
103 }
104 } else if (strArray[0].equalsIgnoreCase("CRYST1")) {
105 cell[0] = parseDouble(strArray[1]);
106 cell[1] = parseDouble(strArray[2]);
107 cell[2] = parseDouble(strArray[3]);
108 cell[3] = parseDouble(strArray[4]);
109 cell[4] = parseDouble(strArray[5]);
110 cell[5] = parseDouble(strArray[6]);
111 spaceGroupName = SpaceGroupInfo.pdb2ShortName(string.substring(55, 65));
112 } else if (strArray[0].toLowerCase().startsWith("inde")) {
113 break;
114 }
115 }
116 } catch (IOException e) {
117 String message = " CNS IO Exception.";
118 logger.log(Level.WARNING, message, e);
119 return null;
120 }
121
122 Resolution resolution = null;
123 if (properties != null) {
124 resolution = Resolution.checkProperties(properties, false, -1.0);
125 resHigh = resolution.resolution;
126 }
127
128 if (spaceGroupName != null) {
129 spaceGroupNum = SpaceGroupDefinitions.spaceGroupNumber(spaceGroupName);
130 }
131
132 if (spaceGroupNum < 0 || cell[0] < 0 || resolution == null) {
133 logger.info(" The CNS file contains insufficient information to generate the reflection list.");
134 return null;
135 }
136
137 if (logger.isLoggable(Level.INFO)) {
138 StringBuilder sb = new StringBuilder();
139 sb.append(format("\n Opening %s\n", cnsFile.getName()));
140 sb.append(" Setting up Reflection List based on CNS:\n");
141 sb.append(format(" Spacegroup #: %d (name: %s)\n",
142 spaceGroupNum, spaceGroupNames[spaceGroupNum - 1]));
143 sb.append(format(" Resolution: %8.3f\n", resHigh));
144 sb.append(format(" Cell: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n",
145 cell[0], cell[1], cell[2], cell[3], cell[4], cell[5]));
146 logger.info(sb.toString());
147 }
148
149 Crystal crystal = new Crystal(cell[0], cell[1], cell[2],
150 cell[3], cell[4], cell[5], spaceGroupNames[spaceGroupNum - 1]);
151
152 return new ReflectionList(crystal, resolution, properties);
153 }
154
155
156 @Override
157 public double getResolution(File cnsFile, Crystal crystal) {
158 double res = Double.POSITIVE_INFINITY;
159
160 try (BufferedReader br = new BufferedReader(new FileReader(cnsFile))) {
161 HKL hkl = new HKL();
162 String string;
163 while ((string = br.readLine()) != null) {
164 String[] strArray = string.split("\\s+");
165 for (int i = 0; i < strArray.length; i++) {
166 if (strArray[i].toLowerCase().startsWith("inde")) {
167 if (i < strArray.length - 3) {
168 int ih = parseInt(strArray[i + 1]);
169 int ik = parseInt(strArray[i + 2]);
170 int il = parseInt(strArray[i + 3]);
171 hkl.setH(ih);
172 hkl.setK(ik);
173 hkl.setL(il);
174 res = min(res, crystal.res(hkl));
175 }
176 }
177 }
178 }
179 } catch (IOException e) {
180 String message = " CNS IO Exception.";
181 logger.log(Level.WARNING, message, e);
182 return -1.0;
183 }
184
185 return res;
186 }
187
188
189 @Override
190 public boolean readFile(
191 File cnsFile,
192 ReflectionList reflectionList,
193 DiffractionRefinementData refinementData,
194 CompositeConfiguration properties) {
195
196 int nRead, nRes, nIgnore, nFriedel, nCut;
197 boolean transpose = false;
198
199 StringBuilder sb = new StringBuilder();
200 sb.append(format("\n Opening %s\n", cnsFile.getName()));
201
202 if (refinementData.rFreeFlag < 0) {
203 refinementData.setFreeRFlag(1);
204 sb.append(format(" Setting R free flag to CNS default: %d\n", refinementData.rFreeFlag));
205 }
206
207
208 String foString = null;
209 String sigFoString = null;
210 String rFreeString = null;
211 int ih, ik, il, free;
212 double fo, sigFo;
213
214 try (BufferedReader br = new BufferedReader(new FileReader(cnsFile))) {
215 ih = ik = il = free = -1;
216 fo = sigFo = -1.0;
217
218
219 HKL mate = new HKL();
220 int nPosIgnore = 0;
221 int nTransIgnore = 0;
222
223 String string;
224 while ((string = br.readLine()) != null) {
225 String[] strArray = string.split("\\s+");
226
227 for (int i = 0; i < strArray.length; i++) {
228 if (strArray[i].toLowerCase().startsWith("inde")) {
229 if (i < strArray.length - 3) {
230 ih = parseInt(strArray[i + 1]);
231 ik = parseInt(strArray[i + 2]);
232 il = parseInt(strArray[i + 3]);
233 reflectionList.findSymHKL(ih, ik, il, mate, false);
234 HKL hklpos = reflectionList.getHKL(mate);
235 if (hklpos == null) {
236 nPosIgnore++;
237 }
238
239 reflectionList.findSymHKL(ih, ik, il, mate, true);
240 HKL hkltrans = reflectionList.getHKL(mate);
241 if (hkltrans == null) {
242 nTransIgnore++;
243 }
244 }
245 }
246 }
247 }
248 if (nPosIgnore > nTransIgnore) {
249 transpose = true;
250 }
251
252 if (properties != null) {
253 foString = properties.getString("fostring", null);
254 sigFoString = properties.getString("sigfostring", null);
255 rFreeString = properties.getString("rfreestring", null);
256 }
257 } catch (IOException e) {
258 String message = "CNS IO Exception.";
259 logger.log(Level.WARNING, message, e);
260 return false;
261 }
262
263 boolean hasHKL, hasFo, hasSigFo, hasFree;
264 hasHKL = hasFo = hasSigFo = hasFree = false;
265
266
267 try (BufferedReader br = new BufferedReader(new FileReader(cnsFile))) {
268
269
270 double[][] anofSigF = new double[refinementData.n][4];
271 for (int i = 0; i < refinementData.n; i++) {
272 anofSigF[i][0] = anofSigF[i][1] = anofSigF[i][2] = anofSigF[i][3] = Double.NaN;
273 }
274 nRead = nRes = nIgnore = nFriedel = nCut = 0;
275
276 String string;
277 HKL mate = new HKL();
278 while ((string = br.readLine()) != null) {
279 String[] strArray = string.split("\\s+");
280 for (int i = 0; i < strArray.length; i++) {
281 if (strArray[i].toLowerCase().startsWith("inde")) {
282 if (hasHKL && hasFo && hasSigFo && hasFree) {
283 boolean friedel = reflectionList.findSymHKL(ih, ik, il, mate, transpose);
284 HKL hkl = reflectionList.getHKL(mate);
285 if (hkl != null) {
286 if (refinementData.fSigFCutoff > 0.0 && (fo / sigFo) < refinementData.fSigFCutoff) {
287 nCut++;
288 } else if (friedel) {
289 anofSigF[hkl.getIndex()][2] = fo;
290 anofSigF[hkl.getIndex()][3] = sigFo;
291 nFriedel++;
292 } else {
293 anofSigF[hkl.getIndex()][0] = fo;
294 anofSigF[hkl.getIndex()][1] = sigFo;
295 }
296 refinementData.setFreeR(hkl.getIndex(), free);
297 nRead++;
298 } else {
299 HKL tmp = new HKL(ih, ik, il);
300 if (!reflectionList.resolution.inInverseResSqRange(
301 reflectionList.crystal.invressq(tmp))) {
302 nRes++;
303 } else {
304 nIgnore++;
305 }
306 }
307 }
308 hasHKL = false;
309 hasFo = false;
310 hasSigFo = false;
311 hasFree = false;
312 if (i < strArray.length - 3) {
313 ih = parseInt(strArray[i + 1]);
314 ik = parseInt(strArray[i + 2]);
315 il = parseInt(strArray[i + 3]);
316 hasHKL = true;
317 }
318 }
319 if (strArray[i].toLowerCase().startsWith("fobs=")
320 || strArray[i].equalsIgnoreCase(foString + "=")) {
321 fo = parseDouble(strArray[i + 1]);
322 hasFo = true;
323 }
324 if (strArray[i].toLowerCase().startsWith("sigma=")
325 || strArray[i].equalsIgnoreCase(sigFoString + "=")) {
326 sigFo = parseDouble(strArray[i + 1]);
327 hasSigFo = true;
328 }
329 if (strArray[i].toLowerCase().startsWith("test=")
330 || strArray[i].equalsIgnoreCase(rFreeString + "=")) {
331 free = parseInt(strArray[i + 1]);
332 hasFree = true;
333 }
334 }
335 }
336
337 refinementData.generateFsigFfromAnomalousFsigF(anofSigF);
338 } catch (IOException e) {
339 String message = "CNS IO Exception.";
340 logger.log(Level.WARNING, message, e);
341 return false;
342 }
343
344 if (logger.isLoggable(Level.INFO)) {
345 sb.append(format(" HKL read in: %d\n", nRead));
346 sb.append(format(" HKL read as friedel mates: %d\n", nFriedel));
347 sb.append(format(" HKL not read in (too high resolution): %d\n", nRes));
348 sb.append(format(" HKL not read in (not in internal list?): %d\n", nIgnore));
349 sb.append(format(" HKL not read in (F/sigF cutoff): %d\n", nCut));
350 sb.append(
351 format(" HKL in internal list: %d\n", reflectionList.hklList.size()));
352 logger.info(sb.toString());
353 }
354
355 return true;
356 }
357 }