From bcc47b09eab8ab91e2a7c89a81f748c6015782bd Mon Sep 17 00:00:00 2001 From: josch Date: Wed, 18 Sep 2013 17:09:44 +0200 Subject: [PATCH] change license to MIT in accordance with Dr. Eisenhaber and Dr. Frishman --- README | 31 ++++++++++++++++++++ area.c | 23 +++++++++++++++ asngener.c | 23 +++++++++++++++ chk_atom.c | 23 +++++++++++++++ chk_res.c | 23 +++++++++++++++ chkchain.c | 23 +++++++++++++++ command.c | 23 +++++++++++++++ contact_map.c | 23 +++++++++++++++ contact_order.c | 23 +++++++++++++++ die.c | 23 +++++++++++++++ doc/stride.doc | 47 ++++++++++++----------------- dssp.c | 23 +++++++++++++++ elem.c | 23 +++++++++++++++ escape.c | 23 +++++++++++++++ filename.c | 23 +++++++++++++++ fillasn.c | 23 +++++++++++++++ geometry.c | 23 +++++++++++++++ hbenergy.c | 23 +++++++++++++++ helix.c | 23 +++++++++++++++ hydrbond.c | 23 +++++++++++++++ initchn.c | 23 +++++++++++++++ measure.c | 23 +++++++++++++++ memory.c | 23 +++++++++++++++ mergepat.c | 23 +++++++++++++++ molscr.c | 23 +++++++++++++++ nsc.c | 78 ++++++++++++------------------------------------- nsc.h | 78 ++++++++++++------------------------------------- one2thr.c | 23 +++++++++++++++ outseq.c | 23 +++++++++++++++ p_atom.c | 23 +++++++++++++++ p_compnd.c | 23 +++++++++++++++ p_endmdl.c | 23 +++++++++++++++ p_expdta.c | 23 +++++++++++++++ p_helix.c | 23 +++++++++++++++ p_jrnl.c | 23 +++++++++++++++ p_model.c | 23 +++++++++++++++ p_rem.c | 23 +++++++++++++++ p_sheet.c | 23 +++++++++++++++ p_ssbond.c | 23 +++++++++++++++ p_turn.c | 23 +++++++++++++++ pdbasn.c | 23 +++++++++++++++ phipsi.c | 23 +++++++++++++++ place_h.c | 23 +++++++++++++++ protot.h | 23 +++++++++++++++ rdmap.c | 23 +++++++++++++++ rdpdb.c | 23 +++++++++++++++ report.c | 23 +++++++++++++++ sheet.c | 23 +++++++++++++++ splitstr.c | 23 +++++++++++++++ ssbond.c | 23 +++++++++++++++ stred.c | 23 +++++++++++++++ stride.c | 23 +++++++++++++++ stride.h | 23 +++++++++++++++ strutil.c | 23 +++++++++++++++ thr2one.c | 23 +++++++++++++++ tolostr.c | 23 +++++++++++++++ turn.c | 23 +++++++++++++++ 57 files changed, 1306 insertions(+), 147 deletions(-) create mode 100644 README diff --git a/README b/README new file mode 100644 index 0000000..4d75395 --- /dev/null +++ b/README @@ -0,0 +1,31 @@ +This is the original implementation of the STRIDE algorithm by Dmitrij Frishman +as presented in: + + - Frishman D, Argos P. Knowledge-Based Protein Secondary Structure Assignment + Proteins: Structure, Function, and Genetics 23:566-579 (1995) + +From the abstract, STRIDE calculates "protein secondary structure assignments +form atomic coordinates based on the combined use of hydrogen bond energy and +statistically derived backbone torsional angle information" + +This program also exists as a webservice at + + http://webclu.bio.wzw.tum.de/stride/ + +This distribution also includes nsc by Frank Eisenhaber as presented in: + + - F.Eisenhaber, P.Lijnzaad, P.Argos, M.Scharf "The Double Cubic Lattice + Method: Efficient Approaches to Numerical Integration of Surface Area and + Volume and to Dot Surface Contouring of Molecular Assemblies" Journal of + Computational Chemistry (1994) submitted + + - F.Eisenhaber, P.Argos "Improved Strategy in Analytic Surface Calculation for + Molecular Systems: Handling of Singularities and Computational Efficiency" + Journal of Computational Chemistry (1993) v.14, N11, pp-1272-1280 + +The nsc component calculates residue solvent accessible areas. + +In 2013, the authors of STRIDE and nsc released the software under the terms of +the MIT licence. + +For more information on how to use stride, refer to doc/stride.doc diff --git a/area.c b/area.c index 8bfade7..ba09d3a 100644 --- a/area.c +++ b/area.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" void Area(CHAIN **Chain, int NChain, COMMAND *Cmd) diff --git a/asngener.c b/asngener.c index 589ebac..ac827f2 100644 --- a/asngener.c +++ b/asngener.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" /************************************************************************* diff --git a/chk_atom.c b/chk_atom.c index 899cc4e..7e1eeba 100644 --- a/chk_atom.c +++ b/chk_atom.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int CheckAtom(char *At) diff --git a/chk_res.c b/chk_res.c index d8c164a..471cd8c 100644 --- a/chk_res.c +++ b/chk_res.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int CheckRes(char *Res) diff --git a/chkchain.c b/chkchain.c index 33813fa..dcc900d 100644 --- a/chkchain.c +++ b/chkchain.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int CheckChain(CHAIN *Chain, COMMAND *Cmd) diff --git a/command.c b/command.c index 0a1df98..6bb0219 100644 --- a/command.c +++ b/command.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" FILE *efopen(char *file, char *mode, char *progname) /* fopen file, die if can't */ diff --git a/contact_map.c b/contact_map.c index 5a4cad5..85f9831 100644 --- a/contact_map.c +++ b/contact_map.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" void ContactMap(CHAIN **Chain, int NChain, COMMAND *Cmd ) diff --git a/contact_order.c b/contact_order.c index 265be19..4a52128 100644 --- a/contact_order.c +++ b/contact_order.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" #define CO_DIST 6.0 diff --git a/die.c b/die.c index 30495f4..86a89fe 100644 --- a/die.c +++ b/die.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include #include diff --git a/doc/stride.doc b/doc/stride.doc index e710d6a..b869aa9 100644 --- a/doc/stride.doc +++ b/doc/stride.doc @@ -58,40 +58,31 @@ 2. Copyright notice - - All rights reserved, whether the whole or part of the program is - concerned. Permission to use, copy, and modify this software and its - documentation is granted for academic use, provided that: - - - i. this copyright notice appears in all copies of the software and - related documentation; - - ii. the reference given below (Frishman and Argos, 1995) must be - cited in any publication of scientific results based in part or - completely on the use of the program; - - iii. bugs will be reported to the authors. - - The use of the software in commercial activities is not allowed - without a prior written commercial license agreement. - - WARNING: STRIDE is provided "as-is" and without warranty of any kind, - express, implied or otherwise, including without limitation any - warranty of merchantability or fitness for a particular purpose. In no - event will the authors be liable for any special, incidental, indirect - or consequential damages of any kind, or any damages whatsoever - resulting from loss of data or profits, whether or not advised of the - possibility of damage, and on any theory of liability, arising out of - or in connection with the use or performance of this software. + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. For calculation of the residue solvent accessible area the program NSC [3,4] is used and was kindly provided by Dr. F.Eisenhaber (EISENHABER@EMBL-HEIDELBERG.DE). Please direct to him all questions concerning specifically accessibility calculations. - - 3. Availability diff --git a/dssp.c b/dssp.c index db31797..2414ad4 100644 --- a/dssp.c +++ b/dssp.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int ReadDSSP(CHAIN **Chain, DSSP **Dssp, COMMAND *Cmd) diff --git a/elem.c b/elem.c index e87dcf8..e8eb29e 100644 --- a/elem.c +++ b/elem.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" /************************************************************************* diff --git a/escape.c b/escape.c index 1bad7d5..409bb95 100644 --- a/escape.c +++ b/escape.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include #include diff --git a/filename.c b/filename.c index 7ca7e91..28fa6bf 100644 --- a/filename.c +++ b/filename.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include #include diff --git a/fillasn.c b/fillasn.c index 210e874..2a88c6e 100644 --- a/fillasn.c +++ b/fillasn.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" void FillAsnAntiPar(char *Asn1, char *Asn2, CHAIN **Chain, int Cn1, int Cn2, diff --git a/geometry.c b/geometry.c index 4e8683f..b2ced1d 100644 --- a/geometry.c +++ b/geometry.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + /************************************************************************* ** ** ** Calculate torsion angle ** diff --git a/hbenergy.c b/hbenergy.c index f2a453c..f5bcbdc 100644 --- a/hbenergy.c +++ b/hbenergy.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" /************************************************* diff --git a/helix.c b/helix.c index 8a82714..4c11be6 100644 --- a/helix.c +++ b/helix.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" void Helix(CHAIN **Chain, int Cn, HBOND **HBond, COMMAND *Cmd, float **PhiPsiMap) diff --git a/hydrbond.c b/hydrbond.c index 47d5397..b0ef785 100644 --- a/hydrbond.c +++ b/hydrbond.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int FindDnr(CHAIN *Chain, DONOR **Dnr, int *NDnr, COMMAND *Cmd) diff --git a/initchn.c b/initchn.c index 3738a61..dd7fbd4 100644 --- a/initchn.c +++ b/initchn.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" diff --git a/measure.c b/measure.c index 832adb8..4512de4 100644 --- a/measure.c +++ b/measure.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" void Measure(CHAIN **Chain, int NChain, int El, COMMAND *Cmd, FILE *Out) diff --git a/memory.c b/memory.c index 429dd89..1a8a016 100644 --- a/memory.c +++ b/memory.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include #include #include diff --git a/mergepat.c b/mergepat.c index c3ed2ed..26e4cf2 100644 --- a/mergepat.c +++ b/mergepat.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" void MergePatternsAntiPar(PATTERN **Pat, int NPat) diff --git a/molscr.c b/molscr.c index 3b60591..31d419c 100644 --- a/molscr.c +++ b/molscr.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int MolScript(CHAIN **Chain, int NChain, COMMAND *Cmd) diff --git a/nsc.c b/nsc.c index 92b282c..1157000 100644 --- a/nsc.c +++ b/nsc.c @@ -1,65 +1,23 @@ /* - * - * program NSC - * version 1.0 (April 1994) - * - * Author: Frank Eisenhaber - * - * For user notes see file nsc.h !! - * - * Copyright Notice: - * All rights reserved, whether the whole or part of the program is - * concerned. The software may not be used without specific, prior - * written permission of the author. - * - * An academic licence agreement for the package ASC/GM or its parts - * is granted if you make the following commitments: - * 1) In using this software, the user will respect the interests of - * the author. - * 2) The use of the software in commercial activities is not allowed - * without a prior written commercial licence agreement. The program - * will not be used in classified research. - * 3) Other interested research groups will be redirected - * to the author. The user will not redistribute the code outside - * his immediate research group. - * 4) The copyright messages will not be modified or suppressed. - * 5) The reference given below will be cited in any publication - * of scientific results based in part or completely on use of the - * program. - * 6) Bugs will be reported to the author. - * - * Permission to use, copy, and modify this software and - * its documentation is hereby granted without fee for - * academic use, provided - * that the above copyright notices and this permission notice appear in - * all copies of the software and related documentation. - * - * THE SOFTWARE IS PROVIDED "AS-IS" AND WITHOUT WARRANTY OF - * ANY KIND, - * EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY - * WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. - * - * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - * ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, - * OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, - * WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF - * LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE - * OF THIS SOFTWARE. - * + * Copyright (C) 1994 Frank Eisenhaber * - * contact address : European Molecular Biology Laboratory - * Biocomputing Unit - * Meyerhofstr. 1 - * Postfach 10.2209 - * D-69012 Heidelberg - * Federal Republic of Germany - * - * - * - * E-mail : IN%"EISENHABER@EMBL-Heidelberg.DE" - * Please send your contact address to get information on updates and - * new features. Questions will be answered as soon as possible. - * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. * * references : * 1.F.Eisenhaber, P.Lijnzaad, P.Argos, M.Scharf diff --git a/nsc.h b/nsc.h index 4868814..04de2ce 100644 --- a/nsc.h +++ b/nsc.h @@ -1,63 +1,23 @@ /* - * - * program NSC - * version 1.0 (April 1994) - * - * Author: Frank Eisenhaber - * - * Copyright Notice: - * All rights reserved, whether the whole or part of the program is - * concerned. The software may not be used without specific, prior - * written permission of the author. - * - * An academic licence agreement for the package ASC/GM or its parts - * is granted if you make the following commitments: - * 1) In using this software, the user will respect the interests of - * the author. - * 2) The use of the software in commercial activities is not allowed - * without a prior written commercial licence agreement. The program - * will not be used in classified research. - * 3) Other interested research groups will be redirected - * to the author. The user will not redistribute the code outside - * his immediate research group. - * 4) The copyright messages will not be modified or suppressed. - * 5) The reference given below will be cited in any publication - * of scientific results based in part or completely on use of the - * program. - * 6) Bugs will be reported to the author. - * - * Permission to use, copy, and modify this software and - * its documentation is hereby granted without fee for - * academic use, provided - * that the above copyright notices and this permission notice appear in - * all copies of the software and related documentation. - * - * THE SOFTWARE IS PROVIDED "AS-IS" AND WITHOUT WARRANTY OF - * ANY KIND, - * EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY - * WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. - * - * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - * ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, - * OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, - * WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF - * LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE - * OF THIS SOFTWARE. - * - * - * contact address : European Molecular Biology Laboratory - * Biocomputing Unit - * Meyerhofstr. 1 - * Postfach 10.2209 - * D-69012 Heidelberg - * Federal Republic of Germany - * - * - * - * E-mail : IN%"EISENHABER@EMBL-Heidelberg.DE" - * Please send your contact address to get information on updates and - * new features. Questions will be answered as soon as possible. - * + * Copyright (C) 1994 Frank Eisenhaber + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. * * references : * 1.F.Eisenhaber, P.Lijnzaad, P.Argos, M.Scharf diff --git a/one2thr.c b/one2thr.c index aa79507..4095a69 100644 --- a/one2thr.c +++ b/one2thr.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include #include diff --git a/outseq.c b/outseq.c index f917660..23dde60 100644 --- a/outseq.c +++ b/outseq.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int OutSeq(CHAIN **Chain, int NChain, COMMAND *Cmd) diff --git a/p_atom.c b/p_atom.c index 2038c83..e3431b2 100644 --- a/p_atom.c +++ b/p_atom.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int Process_ATOM(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, diff --git a/p_compnd.c b/p_compnd.c index bcd82d5..d53e8c5 100644 --- a/p_compnd.c +++ b/p_compnd.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int Process_COMPND(BUFFER Buffer, enum METHOD *Method) diff --git a/p_endmdl.c b/p_endmdl.c index 392feb4..f74bd7d 100644 --- a/p_endmdl.c +++ b/p_endmdl.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int Process_ENDMDL(BUFFER Buffer, CHAIN **Chain, int *ChainNumber) diff --git a/p_expdta.c b/p_expdta.c index a1d422a..d9e7df0 100644 --- a/p_expdta.c +++ b/p_expdta.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int Process_EXPDTA(BUFFER Buffer, enum METHOD *Method) diff --git a/p_helix.c b/p_helix.c index 210cd5a..4095324 100644 --- a/p_helix.c +++ b/p_helix.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int Process_HELIX(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd) diff --git a/p_jrnl.c b/p_jrnl.c index c4b40ff..ac750e6 100644 --- a/p_jrnl.c +++ b/p_jrnl.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int Process_JRNL(BUFFER Buffer, BOOLEAN *Published) diff --git a/p_model.c b/p_model.c index db5eda8..8e72868 100644 --- a/p_model.c +++ b/p_model.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int Process_MODEL(enum METHOD *Method) diff --git a/p_rem.c b/p_rem.c index d9ade68..bc80f1f 100644 --- a/p_rem.c +++ b/p_rem.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int Process_REMARK(BUFFER Buffer, enum METHOD *Method, float *Resolution, BOOLEAN *DsspAssigned) diff --git a/p_sheet.c b/p_sheet.c index a8e151b..40955fd 100644 --- a/p_sheet.c +++ b/p_sheet.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int Process_SHEET(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd) diff --git a/p_ssbond.c b/p_ssbond.c index 03398b2..78ca3f4 100644 --- a/p_ssbond.c +++ b/p_ssbond.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int Process_SSBOND(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd) diff --git a/p_turn.c b/p_turn.c index 1d5be21..9a8c23c 100644 --- a/p_turn.c +++ b/p_turn.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int Process_TURN(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd) diff --git a/pdbasn.c b/pdbasn.c index 1c39766..a094ad9 100644 --- a/pdbasn.c +++ b/pdbasn.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" /************************************************************************* diff --git a/phipsi.c b/phipsi.c index c1ed710..7f46300 100644 --- a/phipsi.c +++ b/phipsi.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" void BackboneAngles(CHAIN **Chain, int NChain) diff --git a/place_h.c b/place_h.c index 3f64681..1194145 100644 --- a/place_h.c +++ b/place_h.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int PlaceHydrogens(CHAIN *Chain) diff --git a/protot.h b/protot.h index 3845e0e..39eca01 100644 --- a/protot.h +++ b/protot.h @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + BOOLEAN ChInStr(char *String, char Char); BOOLEAN ExistsSecStr(CHAIN **Chain, int NChain); BOOLEAN ExistSSBond(CHAIN **Chain,int NChain,int Cn1,int Cn2,char *Res1,char *Res2); diff --git a/rdmap.c b/rdmap.c index 2bc6d3b..bc16a10 100644 --- a/rdmap.c +++ b/rdmap.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int ReadPhiPsiMap(char *MapFile, float ***PhiPsiMap, COMMAND *Cmd) diff --git a/rdpdb.c b/rdpdb.c index 6a7f5da..a78a922 100644 --- a/rdpdb.c +++ b/rdpdb.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int ReadPDBFile(CHAIN **Chain, int *Cn, COMMAND *Cmd) diff --git a/report.c b/report.c index d8fcd27..84eebaf 100644 --- a/report.c +++ b/report.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" void Report(CHAIN **Chain, int NChain, HBOND **HBond, COMMAND *Cmd) diff --git a/sheet.c b/sheet.c index e843126..c9eb0f4 100644 --- a/sheet.c +++ b/sheet.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" diff --git a/splitstr.c b/splitstr.c index e69a2a9..f12ea67 100644 --- a/splitstr.c +++ b/splitstr.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + /* Split a char string into text fields */ #include "stride.h" diff --git a/ssbond.c b/ssbond.c index 772870d..688c045 100644 --- a/ssbond.c +++ b/ssbond.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" int SSBond(CHAIN **Chain, int NChain) diff --git a/stred.c b/stred.c index 4d40c33..ffbaa23 100644 --- a/stred.c +++ b/stred.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + int Replace(char *String, char From, char To) { diff --git a/stride.c b/stride.c index 5186d2b..ea6ef8d 100644 --- a/stride.c +++ b/stride.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" /* #include */ /* For Macintosh only, see readme.mac */ diff --git a/stride.h b/stride.h index 93929b0..c08e389 100644 --- a/stride.h +++ b/stride.h @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include #include #include diff --git a/strutil.c b/strutil.c index 93262b9..2c5a0bc 100644 --- a/strutil.c +++ b/strutil.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" /************************************************************************* diff --git a/thr2one.c b/thr2one.c index 2373e79..f1e0008 100644 --- a/thr2one.c +++ b/thr2one.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include #include diff --git a/tolostr.c b/tolostr.c index 4718b07..35578b0 100644 --- a/tolostr.c +++ b/tolostr.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include #include #include diff --git a/turn.c b/turn.c index d38f036..ee3c4ec 100644 --- a/turn.c +++ b/turn.c @@ -1,3 +1,26 @@ +/* + * Copyright (C) 1992-1994 Dmitrij Frishman + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + + #include "stride.h" void BetaTurn(CHAIN **Chain, int Cn)